Daily Papers

We are now witnessing significant progress of deep learning methods in a variety of tasks (or datasets) of proteins. However, there is a lack of a standard benchmark to evaluate the performance of different methods, which hinders the progress of deep learning in this field. In this paper, we propose such a benchmark called PEER, a comprehensive and multi-task benchmark for Protein sEquence undERstanding. PEER provides a set of diverse protein understanding tasks including protein function prediction, protein localization prediction, protein structure prediction, protein-protein interaction prediction, and protein-ligand interaction prediction. We evaluate different types of sequence-based methods for each task including traditional feature engineering approaches, different sequence encoding methods as well as large-scale pre-trained protein language models. In addition, we also investigate the performance of these methods under the multi-task learning setting. Experimental results show that large-scale pre-trained protein language models achieve the best performance for most individual tasks, and jointly training multiple tasks further boosts the performance. The datasets and source codes of this benchmark are all available at https://github.com/DeepGraphLearning/PEER_Benchmark

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid sequences and then finetune the models with some labeled data in downstream tasks. Despite the effectiveness of sequence-based approaches, the power of pretraining on known protein structures, which are available in smaller numbers only, has not been explored for protein property prediction, though protein structures are known to be determinants of protein function. In this paper, we propose to pretrain protein representations according to their 3D structures. We first present a simple yet effective encoder to learn the geometric features of a protein. We pretrain the protein graph encoder by leveraging multiview contrastive learning and different self-prediction tasks. Experimental results on both function prediction and fold classification tasks show that our proposed pretraining methods outperform or are on par with the state-of-the-art sequence-based methods, while using much less pretraining data. Our implementation is available at https://github.com/DeepGraphLearning/GearNet.

User event modeling plays a central role in many machine learning applications, with use cases spanning e-commerce, social media, finance, cybersecurity, and other domains. User events can be broadly categorized into personal events, which involve individual actions, and relational events, which involve interactions between two users. These two types of events are typically modeled separately, using sequence-based methods for personal events and graph-based methods for relational events. Despite the need to capture both event types in real-world systems, prior work has rarely considered them together. This is often due to the convenient simplification that user behavior can be adequately represented by a single formalization, either as a sequence or a graph. To address this gap, there is a need for public datasets and prediction tasks that explicitly incorporate both personal and relational events. In this work, we introduce a collection of such datasets, propose a unified formalization, and empirically show that models benefit from incorporating both event types. Our results also indicate that current methods leave a notable room for improvements. We release these resources to support further research in unified user event modeling and encourage progress in this direction.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge. In contrast, structure-based methods leverage 3D structural information with graph neural networks and geometric pre-training methods show potential in function prediction tasks, but still suffers from the limited number of available structures. To bridge this gap, our study undertakes a comprehensive exploration of joint protein representation learning by integrating a state-of-the-art PLM (ESM-2) with distinct structure encoders (GVP, GearNet, CDConv). We introduce three representation fusion strategies and explore different pre-training techniques. Our method achieves significant improvements over existing sequence- and structure-based methods, setting new state-of-the-art for function annotation. This study underscores several important design choices for fusing protein sequence and structure information. Our implementation is available at https://github.com/DeepGraphLearning/ESM-GearNet.

Advances in peptide identification are revolutionizing our ability to decipher protein functions and accelerate therapeutic discovery. We present PDeepPP, a deep learning framework that integrates pretrained protein language models with parallel transformer-CNN architectures, achieving state-of-the-art performance in peptide characterization tasks. The model's hybrid architecture demonstrates unique capabilities in capturing both local sequence motifs and global structural features, as evidenced by 29% improved cluster separation in UMAP visualizations compared to conventional approaches. Evaluated across 33 biological recognition tasks - including post-translational modification site prediction and bioactive peptide identification - PDeepPP outperformed existing methods in 25 tasks with average AUC improvements of 4.2%. Notably, it achieved 0.9726 accuracy with PR AUC 0.9977 in antimicrobial peptide detection while reducing false negatives by 37.5% in antimalarial recognition scenarios. This framework enables accurate large-scale peptide analysis, achieving 218* acceleration over sequence-alignment-based methods while maintaining 99.5% specificity in critical glycosylation site detection.PDeepPP establishes a new paradigm for computational peptide analysis through its synergistic architecture design, enabling rapid yet precise functional annotation that bridges molecular pattern recognition with translational biomedical applications.We have made our implementation, including code, data, and pretrained models, publicly available via GitHub (https://github.com/fondress/PDeepPP) and Hugging Face (https://huggingface.co/fondress/PDeppPP).

Protein representation learning (PRL) is crucial for understanding structure-function relationships, yet current sequence- and graph-based methods fail to capture the hierarchical organization inherent in protein structures. We introduce Topotein, a comprehensive framework that applies topological deep learning to PRL through the novel Protein Combinatorial Complex (PCC) and Topology-Complete Perceptron Network (TCPNet). Our PCC represents proteins at multiple hierarchical levels -- from residues to secondary structures to complete proteins -- while preserving geometric information at each level. TCPNet employs SE(3)-equivariant message passing across these hierarchical structures, enabling more effective capture of multi-scale structural patterns. Through extensive experiments on four PRL tasks, TCPNet consistently outperforms state-of-the-art geometric graph neural networks. Our approach demonstrates particular strength in tasks such as fold classification which require understanding of secondary structure arrangements, validating the importance of hierarchical topological features for protein analysis.

Recently, sequence learning methods have been applied to the problem of off-policy Reinforcement Learning, including the seminal work on Decision Transformers, which employs transformers for this task. Since transformers are parameter-heavy, cannot benefit from history longer than a fixed window size, and are not computed using recurrence, we set out to investigate the suitability of the S4 family of models, which are based on state-space layers and have been shown to outperform transformers, especially in modeling long-range dependencies. In this work we present two main algorithms: (i) an off-policy training procedure that works with trajectories, while still maintaining the training efficiency of the S4 model. (ii) An on-policy training procedure that is trained in a recurrent manner, benefits from long-range dependencies, and is based on a novel stable actor-critic mechanism. Our results indicate that our method outperforms multiple variants of decision transformers, as well as the other baseline methods on most tasks, while reducing the latency, number of parameters, and training time by several orders of magnitude, making our approach more suitable for real-world RL.

In robotics, Visual Place Recognition is a continuous process that receives as input a video stream to produce a hypothesis of the robot's current position within a map of known places. This task requires robust, scalable, and efficient techniques for real applications. This work proposes a detailed taxonomy of techniques using sequential descriptors, highlighting different mechanism to fuse the information from the individual images. This categorization is supported by a complete benchmark of experimental results that provides evidence on the strengths and weaknesses of these different architectural choices. In comparison to existing sequential descriptors methods, we further investigate the viability of Transformers instead of CNN backbones, and we propose a new ad-hoc sequence-level aggregator called SeqVLAD, which outperforms prior state of the art on different datasets. The code is available at https://github.com/vandal-vpr/vg-transformers.

Visual Place Recognition (VPR) is the task of matching current visual imagery from a camera to images stored in a reference map of the environment. While initial VPR systems used simple direct image methods or hand-crafted visual features, recent work has focused on learning more powerful visual features and further improving performance through either some form of sequential matcher / filter or a hierarchical matching process. In both cases the performance of the initial single-image based system is still far from perfect, putting significant pressure on the sequence matching or (in the case of hierarchical systems) pose refinement stages. In this paper we present a novel hybrid system that creates a high performance initial match hypothesis generator using short learnt sequential descriptors, which enable selective control sequential score aggregation using single image learnt descriptors. Sequential descriptors are generated using a temporal convolutional network dubbed SeqNet, encoding short image sequences using 1-D convolutions, which are then matched against the corresponding temporal descriptors from the reference dataset to provide an ordered list of place match hypotheses. We then perform selective sequential score aggregation using shortlisted single image learnt descriptors from a separate pipeline to produce an overall place match hypothesis. Comprehensive experiments on challenging benchmark datasets demonstrate the proposed method outperforming recent state-of-the-art methods using the same amount of sequential information. Source code and supplementary material can be found at https://github.com/oravus/seqNet.

Handwriting recognition has seen significant success with the use of deep learning. However, a persistent shortcoming of neural networks is that they are not well-equipped to deal with shifting data distributions. In the field of handwritten text recognition (HTR), this shows itself in poor recognition accuracy for writers that are not similar to those seen during training. An ideal HTR model should be adaptive to new writing styles in order to handle the vast amount of possible writing styles. In this paper, we explore how HTR models can be made writer adaptive by using only a handful of examples from a new writer (e.g., 16 examples) for adaptation. Two HTR architectures are used as base models, using a ResNet backbone along with either an LSTM or Transformer sequence decoder. Using these base models, two methods are considered to make them writer adaptive: 1) model-agnostic meta-learning (MAML), an algorithm commonly used for tasks such as few-shot classification, and 2) writer codes, an idea originating from automatic speech recognition. Results show that an HTR-specific version of MAML known as MetaHTR improves performance compared to the baseline with a 1.4 to 2.0 improvement in word error rate (WER). The improvement due to writer adaptation is between 0.2 and 0.7 WER, where a deeper model seems to lend itself better to adaptation using MetaHTR than a shallower model. However, applying MetaHTR to larger HTR models or sentence-level HTR may become prohibitive due to its high computational and memory requirements. Lastly, writer codes based on learned features or Hinge statistical features did not lead to improved recognition performance.

Video recordings of user activities, particularly desktop recordings, offer a rich source of data for understanding user behaviors and automating processes. However, despite advancements in Vision-Language Models (VLMs) and their increasing use in video analysis, extracting user actions from desktop recordings remains an underexplored area. This paper addresses this gap by proposing two novel VLM-based methods for user action extraction: the Direct Frame-Based Approach (DF), which inputs sampled frames directly into VLMs, and the Differential Frame-Based Approach (DiffF), which incorporates explicit frame differences detected via computer vision techniques. We evaluate these methods using a basic self-curated dataset and an advanced benchmark adapted from prior work. Our results show that the DF approach achieves an accuracy of 70% to 80% in identifying user actions, with the extracted action sequences being re-playable though Robotic Process Automation. We find that while VLMs show potential, incorporating explicit UI changes can degrade performance, making the DF approach more reliable. This work represents the first application of VLMs for extracting user action sequences from desktop recordings, contributing new methods, benchmarks, and insights for future research.

Prompt-based methods have been successfully applied to multilingual pretrained language models for zero-shot cross-lingual understanding. However, most previous studies primarily focused on sentence-level classification tasks, and only a few considered token-level labeling tasks such as Named Entity Recognition (NER) and Part-of-Speech (POS) tagging. In this paper, we propose Token-Level Prompt Decomposition (ToPro), which facilitates the prompt-based method for token-level sequence labeling tasks. The ToPro method decomposes an input sentence into single tokens and applies one prompt template to each token. Our experiments on multilingual NER and POS tagging datasets demonstrate that ToPro-based fine-tuning outperforms Vanilla fine-tuning and Prompt-Tuning in zero-shot cross-lingual transfer, especially for languages that are typologically different from the source language English. Our method also attains state-of-the-art performance when employed with the mT5 model. Besides, our exploratory study in multilingual large language models shows that ToPro performs much better than the current in-context learning method. Overall, the performance improvements show that ToPro could potentially serve as a novel and simple benchmarking method for sequence labeling tasks.

Pathogen identification is pivotal in diagnosing, treating, and preventing diseases, crucial for controlling infections and safeguarding public health. Traditional alignment-based methods, though widely used, are computationally intense and reliant on extensive reference databases, often failing to detect novel pathogens due to their low sensitivity and specificity. Similarly, conventional machine learning techniques, while promising, require large annotated datasets and extensive feature engineering and are prone to overfitting. Addressing these challenges, we introduce PathoLM, a cutting-edge pathogen language model optimized for the identification of pathogenicity in bacterial and viral sequences. Leveraging the strengths of pre-trained DNA models such as the Nucleotide Transformer, PathoLM requires minimal data for fine-tuning, thereby enhancing pathogen detection capabilities. It effectively captures a broader genomic context, significantly improving the identification of novel and divergent pathogens. We developed a comprehensive data set comprising approximately 30 species of viruses and bacteria, including ESKAPEE pathogens, seven notably virulent bacterial strains resistant to antibiotics. Additionally, we curated a species classification dataset centered specifically on the ESKAPEE group. In comparative assessments, PathoLM dramatically outperforms existing models like DciPatho, demonstrating robust zero-shot and few-shot capabilities. Furthermore, we expanded PathoLM-Sp for ESKAPEE species classification, where it showed superior performance compared to other advanced deep learning methods, despite the complexities of the task.

Classification is one of the most widespread tasks in AI applications, serving often as the first step in filtering, sorting, and categorizing data. Since modern AI systems must handle large volumes of input data and early pipeline stages can propagate errors downstream, achieving high efficiency and accuracy is critical. Moreover, classification requirements can change dynamically based on user needs, necessitating models with strong zero-shot capabilities. While generative LLMs have become mainstream for zero-shot classification due to their versatility, they suffer from inconsistent instruction following and computational inefficiency. Cross-encoders, commonly used as rerankers in RAG pipelines, face a different bottleneck: they must process text-label pairs sequentially, significantly reducing efficiency with large label sets. Embedding-based approaches offer good efficiency but struggle with complex scenarios involving logical and semantic constraints. We propose GLiClass, a novel method that adapts the GLiNER architecture for sequence classification tasks. Our approach achieves strong accuracy and efficiency comparable to embedding-based methods, while maintaining the flexibility needed for zero-shot and few-shot learning scenarios. Additionally, we adapted proximal policy optimization (PPO) for multi-label text classification, enabling training classifiers in data-sparse conditions or from human feedback.

Many real-world systems exhibit temporal, dynamic behaviors, which are captured as time series of complex agent interactions. To perform temporal reasoning, current methods primarily encode temporal dynamics through simple sequence-based models. However, in general these models fail to efficiently capture the full spectrum of rich dynamics in the input, since the dynamics is not uniformly distributed. In particular, relevant information might be harder to extract and computing power is wasted for processing all individual timesteps, even if they contain no significant changes or no new information. Here we propose TimeGraphs, a novel approach that characterizes dynamic interactions as a hierarchical temporal graph, diverging from traditional sequential representations. Our approach models the interactions using a compact graph-based representation, enabling adaptive reasoning across diverse time scales. Adopting a self-supervised method, TimeGraphs constructs a multi-level event hierarchy from a temporal input, which is then used to efficiently reason about the unevenly distributed dynamics. This construction process is scalable and incremental to accommodate streaming data. We evaluate TimeGraphs on multiple datasets with complex, dynamic agent interactions, including a football simulator, the Resistance game, and the MOMA human activity dataset. The results demonstrate both robustness and efficiency of TimeGraphs on a range of temporal reasoning tasks. Our approach obtains state-of-the-art performance and leads to a performance increase of up to 12.2% on event prediction and recognition tasks over current approaches. Our experiments further demonstrate a wide array of capabilities including zero-shot generalization, robustness in case of data sparsity, and adaptability to streaming data flow.

De novo peptide sequencing is a critical task in proteomics. However, the performance of current deep learning-based methods is limited by the inherent complexity of mass spectrometry data and the heterogeneous distribution of noise signals, leading to data-specific biases. We present RankNovo, the first deep reranking framework that enhances de novo peptide sequencing by leveraging the complementary strengths of multiple sequencing models. RankNovo employs a list-wise reranking approach, modeling candidate peptides as multiple sequence alignments and utilizing axial attention to extract informative features across candidates. Additionally, we introduce two new metrics, PMD (Peptide Mass Deviation) and RMD (residual Mass Deviation), which offer delicate supervision by quantifying mass differences between peptides at both the sequence and residue levels. Extensive experiments demonstrate that RankNovo not only surpasses its base models used to generate training candidates for reranking pre-training, but also sets a new state-of-the-art benchmark. Moreover, RankNovo exhibits strong zero-shot generalization to unseen models whose generations were not exposed during training, highlighting its robustness and potential as a universal reranking framework for peptide sequencing. Our work presents a novel reranking strategy that fundamentally challenges existing single-model paradigms and advances the frontier of accurate de novo sequencing. Our source code is provided on GitHub.

We propose Long-LRM, a generalizable 3D Gaussian reconstruction model that is capable of reconstructing a large scene from a long sequence of input images. Specifically, our model can process 32 source images at 960x540 resolution within only 1.3 seconds on a single A100 80G GPU. Our architecture features a mixture of the recent Mamba2 blocks and the classical transformer blocks which allowed many more tokens to be processed than prior work, enhanced by efficient token merging and Gaussian pruning steps that balance between quality and efficiency. Unlike previous feed-forward models that are limited to processing 1~4 input images and can only reconstruct a small portion of a large scene, Long-LRM reconstructs the entire scene in a single feed-forward step. On large-scale scene datasets such as DL3DV-140 and Tanks and Temples, our method achieves performance comparable to optimization-based approaches while being two orders of magnitude more efficient. Project page: https://arthurhero.github.io/projects/llrm

We propose a method for in-hand 3D scanning of an unknown object with a monocular camera. Our method relies on a neural implicit surface representation that captures both the geometry and the appearance of the object, however, by contrast with most NeRF-based methods, we do not assume that the camera-object relative poses are known. Instead, we simultaneously optimize both the object shape and the pose trajectory. As direct optimization over all shape and pose parameters is prone to fail without coarse-level initialization, we propose an incremental approach that starts by splitting the sequence into carefully selected overlapping segments within which the optimization is likely to succeed. We reconstruct the object shape and track its poses independently within each segment, then merge all the segments before performing a global optimization. We show that our method is able to reconstruct the shape and color of both textured and challenging texture-less objects, outperforms classical methods that rely only on appearance features, and that its performance is close to recent methods that assume known camera poses.

Keyphrase Generation (KPG) is a longstanding task in NLP with widespread applications. The advent of sequence-to-sequence (seq2seq) pre-trained language models (PLMs) has ushered in a transformative era for KPG, yielding promising performance improvements. However, many design decisions remain unexplored and are often made arbitrarily. This paper undertakes a systematic analysis of the influence of model selection and decoding strategies on PLM-based KPG. We begin by elucidating why seq2seq PLMs are apt for KPG, anchored by an attention-driven hypothesis. We then establish that conventional wisdom for selecting seq2seq PLMs lacks depth: (1) merely increasing model size or performing task-specific adaptation is not parameter-efficient; (2) although combining in-domain pre-training with task adaptation benefits KPG, it does partially hinder generalization. Regarding decoding, we demonstrate that while greedy search achieves strong F1 scores, it lags in recall compared with sampling-based methods. Based on these insights, we propose DeSel, a likelihood-based decode-select algorithm for seq2seq PLMs. DeSel improves greedy search by an average of 4.7% semantic F1 across five datasets. Our collective findings pave the way for deeper future investigations into PLM-based KPG.

Motivation: Proteins are of great significance in living organisms. However, understanding their functions encounters numerous challenges, such as insufficient integration of multimodal information, a large number of training parameters, limited flexibility of classification-based methods, and the lack of systematic evaluation metrics for protein Q&A systems. To tackle these issues, we propose the Prot2Chat framework. Results: We modified ProteinMPNN to encode protein sequence and structural information in a unified way. We used a large language model (LLM) to encode questions into vectors and developed a protein-text adapter to compress protein information into virtual tokens based on these vectors, achieving the early fusion of text and protein information. Finally, the same LLM reads the virtual tokens and the questions to generate answers. To optimize training efficiency, we froze the encoder and employed Low-Rank Adaptation (LoRA) techniques for the LLM. Experiments on two datasets show that both automated metrics and expert evaluations demonstrate the superior performance of our model, and zero-shot prediction results highlight its generalization ability. The models and codes are available at https://github.com/ wangzc1233/Prot2Chat. Contact: [email protected] or [email protected] Key words: Protein Q&A, Early-Fusion, LLM

Scaling artist-designed meshes to high triangle numbers remains challenging for autoregressive generative models. Existing transformer-based methods suffer from long-sequence bottlenecks and limited quantization resolution, primarily due to the large number of tokens required and constrained quantization granularity. These issues prevent faithful reproduction of fine geometric details and structured density patterns. We introduce MeshMosaic, a novel local-to-global framework for artist mesh generation that scales to over 100K triangles--substantially surpassing prior methods, which typically handle only around 8K faces. MeshMosaic first segments shapes into patches, generating each patch autoregressively and leveraging shared boundary conditions to promote coherence, symmetry, and seamless connectivity between neighboring regions. This strategy enhances scalability to high-resolution meshes by quantizing patches individually, resulting in more symmetrical and organized mesh density and structure. Extensive experiments across multiple public datasets demonstrate that MeshMosaic significantly outperforms state-of-the-art methods in both geometric fidelity and user preference, supporting superior detail representation and practical mesh generation for real-world applications.

In the realm of multimodal research, numerous studies leverage substantial image-text pairs to conduct modal alignment learning, transforming Large Language Models (LLMs) into Multimodal LLMs and excelling in a variety of visual-language tasks. The prevailing methodologies primarily fall into two categories: self-attention-based and cross-attention-based methods. While self-attention-based methods offer superior data efficiency due to their simple MLP architecture, they often suffer from lower computational efficiency due to concatenating visual and textual tokens as input for LLM. Conversely, cross-attention-based methods, although less data-efficient due to additional learnable parameters, exhibit higher computational efficiency by avoiding long sequence input for LLM. To address these trade-offs, we introduce the Data-Efficient and Compute-Efficient Multimodal Large Language Model (EE-MLLM). Without introducing additional modules or learnable parameters, EE-MLLM achieves both data and compute efficiency. Specifically, we modify the original self-attention mechanism in MLLM to a composite attention mechanism. This mechanism has two key characteristics: 1) Eliminating the computational overhead of self-attention within visual tokens to achieve compute efficiency, and 2) Reusing the weights on each layer of LLM to facilitate effective modality alignment between vision and language for data efficiency. Experimental results demonstrate the effectiveness of EE-MLLM across a range of benchmarks, including general-purpose datasets like MMBench and SeedBench, as well as fine-grained tasks such as TextVQA and DocVQA.

Various tasks in data science are modeled utilizing the variational regularization approach, where manually selecting regularization parameters presents a challenge. The difficulty gets exacerbated when employing regularizers involving a large number of hyperparameters. To overcome this challenge, bilevel learning can be employed to learn such parameters from data. However, neither exact function values nor exact gradients with respect to the hyperparameters are attainable, necessitating methods that only rely on inexact evaluation of such quantities. State-of-the-art inexact gradient-based methods a priori select a sequence of the required accuracies and cannot identify an appropriate step size since the Lipschitz constant of the hypergradient is unknown. In this work, we propose an algorithm with backtracking line search that only relies on inexact function evaluations and hypergradients and show convergence to a stationary point. Furthermore, the proposed algorithm determines the required accuracy dynamically rather than manually selected before running it. Our numerical experiments demonstrate the efficiency and feasibility of our approach for hyperparameter estimation on a range of relevant problems in imaging and data science such as total variation and field of experts denoising and multinomial logistic regression. Particularly, the results show that the algorithm is robust to its own hyperparameters such as the initial accuracies and step size.

Manga is a fashionable Japanese-style comic form that is composed of black-and-white strokes and is generally displayed as raster images on digital devices. Typical mangas have simple textures, wide lines, and few color gradients, which are vectorizable natures to enjoy the merits of vector graphics, e.g., adaptive resolutions and small file sizes. In this paper, we propose MARVEL (MAnga's Raster to VEctor Learning), a primitive-wise approach for vectorizing raster mangas by Deep Reinforcement Learning (DRL). Unlike previous learning-based methods which predict vector parameters for an entire image, MARVEL introduces a new perspective that regards an entire manga as a collection of basic primitives\textemdash stroke lines, and designs a DRL model to decompose the target image into a primitive sequence for achieving accurate vectorization. To improve vectorization accuracies and decrease file sizes, we further propose a stroke accuracy reward to predict accurate stroke lines, and a pruning mechanism to avoid generating erroneous and repeated strokes. Extensive subjective and objective experiments show that our MARVEL can generate impressive results and reaches the state-of-the-art level. Our code is open-source at: https://github.com/SwordHolderSH/Mang2Vec.

We present VAPO, Value-based Augmented Proximal Policy Optimization framework for reasoning models., a novel framework tailored for reasoning models within the value-based paradigm. Benchmarked the AIME 2024 dataset, VAPO, built on the Qwen 32B pre-trained model, attains a state-of-the-art score of 60.4. In direct comparison under identical experimental settings, VAPO outperforms the previously reported results of DeepSeek-R1-Zero-Qwen-32B and DAPO by more than 10 points. The training process of VAPO stands out for its stability and efficiency. It reaches state-of-the-art performance within a mere 5,000 steps. Moreover, across multiple independent runs, no training crashes occur, underscoring its reliability. This research delves into long chain-of-thought (long-CoT) reasoning using a value-based reinforcement learning framework. We pinpoint three key challenges that plague value-based methods: value model bias, the presence of heterogeneous sequence lengths, and the sparsity of reward signals. Through systematic design, VAPO offers an integrated solution that effectively alleviates these challenges, enabling enhanced performance in long-CoT reasoning tasks.

We introduce MeshGPT, a new approach for generating triangle meshes that reflects the compactness typical of artist-created meshes, in contrast to dense triangle meshes extracted by iso-surfacing methods from neural fields. Inspired by recent advances in powerful large language models, we adopt a sequence-based approach to autoregressively generate triangle meshes as sequences of triangles. We first learn a vocabulary of latent quantized embeddings, using graph convolutions, which inform these embeddings of the local mesh geometry and topology. These embeddings are sequenced and decoded into triangles by a decoder, ensuring that they can effectively reconstruct the mesh. A transformer is then trained on this learned vocabulary to predict the index of the next embedding given previous embeddings. Once trained, our model can be autoregressively sampled to generate new triangle meshes, directly generating compact meshes with sharp edges, more closely imitating the efficient triangulation patterns of human-crafted meshes. MeshGPT demonstrates a notable improvement over state of the art mesh generation methods, with a 9% increase in shape coverage and a 30-point enhancement in FID scores across various categories.

The increasing prevalence of lumbar spinal canal stenosis has resulted in a surge of MRI (Magnetic Resonance Imaging), leading to labor-intensive interpretation and significant inter-reader variability, even among expert radiologists. This paper introduces a novel and efficient deep-learning framework that fully automates the grading of lumbar spinal canal stenosis. We demonstrate state-of-the-art performance in grading spinal canal stenosis on a dataset of 1,975 unique studies, each containing three distinct types of 3D cross-sectional spine images: Axial T2, Sagittal T1, and Sagittal T2/STIR. Employing a distinctive training strategy, our proposed multistage approach effectively integrates sagittal and axial images. This strategy employs a multi-view model with a sequence-based architecture, optimizing feature extraction and cross-view alignment to achieve an AUROC (Area Under the Receiver Operating Characteristic Curve) of 0.971 in spinal canal stenosis grading surpassing other state-of-the-art methods.

Retrosynthesis planning poses a formidable challenge in the organic chemical industry, particularly in pharmaceuticals. Single-step retrosynthesis prediction, a crucial step in the planning process, has witnessed a surge in interest in recent years due to advancements in AI for science. Various deep learning-based methods have been proposed for this task in recent years, incorporating diverse levels of additional chemical knowledge dependency. This paper introduces UAlign, a template-free graph-to-sequence pipeline for retrosynthesis prediction. By combining graph neural networks and Transformers, our method can more effectively leverage the inherent graph structure of molecules. Based on the fact that the majority of molecule structures remain unchanged during a chemical reaction, we propose a simple yet effective SMILES alignment technique to facilitate the reuse of unchanged structures for reactant generation. Extensive experiments show that our method substantially outperforms state-of-the-art template-free and semi-template-based approaches. Importantly, Our template-free method achieves effectiveness comparable to, or even surpasses, established powerful template-based methods. Scientific contribution: We present a novel graph-to-sequence template-free retrosynthesis prediction pipeline that overcomes the limitations of Transformer-based methods in molecular representation learning and insufficient utilization of chemical information. We propose an unsupervised learning mechanism for establishing product-atom correspondence with reactant SMILES tokens, achieving even better results than supervised SMILES alignment methods. Extensive experiments demonstrate that UAlign significantly outperforms state-of-the-art template-free methods and rivals or surpasses template-based approaches, with up to 5\% (top-5) and 5.4\% (top-10) increased accuracy over the strongest baseline.

Generating talking person portraits with arbitrary speech audio is a crucial problem in the field of digital human and metaverse. A modern talking face generation method is expected to achieve the goals of generalized audio-lip synchronization, good video quality, and high system efficiency. Recently, neural radiance field (NeRF) has become a popular rendering technique in this field since it could achieve high-fidelity and 3D-consistent talking face generation with a few-minute-long training video. However, there still exist several challenges for NeRF-based methods: 1) as for the lip synchronization, it is hard to generate a long facial motion sequence of high temporal consistency and audio-lip accuracy; 2) as for the video quality, due to the limited data used to train the renderer, it is vulnerable to out-of-domain input condition and produce bad rendering results occasionally; 3) as for the system efficiency, the slow training and inference speed of the vanilla NeRF severely obstruct its usage in real-world applications. In this paper, we propose GeneFace++ to handle these challenges by 1) utilizing the pitch contour as an auxiliary feature and introducing a temporal loss in the facial motion prediction process; 2) proposing a landmark locally linear embedding method to regulate the outliers in the predicted motion sequence to avoid robustness issues; 3) designing a computationally efficient NeRF-based motion-to-video renderer to achieves fast training and real-time inference. With these settings, GeneFace++ becomes the first NeRF-based method that achieves stable and real-time talking face generation with generalized audio-lip synchronization. Extensive experiments show that our method outperforms state-of-the-art baselines in terms of subjective and objective evaluation. Video samples are available at https://genefaceplusplus.github.io .

Transformers have recently been popular for learning and inference in the spatial-temporal domain. However, their performance relies on storing and applying attention to the feature tensor of each frame in video. Hence, their space and time complexity increase linearly as the length of video grows, which could be very costly for long videos. We propose a novel visual memory network architecture for the learning and inference problem in the spatial-temporal domain. We maintain a fixed set of memory slots in our memory network and propose an algorithm based on Gumbel-Softmax to learn an adaptive strategy to update this memory. Finally, this architecture is benchmarked on the video object segmentation (VOS) and video prediction problems. We demonstrate that our memory architecture achieves state-of-the-art results, outperforming transformer-based methods on VOS and other recent methods on video prediction while maintaining constant memory capacity independent of the sequence length.

Identifying drug-target interactions is essential for developing effective therapeutics. Binding affinity quantifies these interactions, and traditional approaches rely on computationally intensive 3D structural data. In contrast, language models can efficiently process sequential data, offering an alternative approach to molecular representation. In the current study, we introduce BAPULM, an innovative sequence-based framework that leverages the chemical latent representations of proteins via ProtT5-XL-U50 and ligands through MolFormer, eliminating reliance on complex 3D configurations. Our approach was validated extensively on benchmark datasets, achieving scoring power (R) values of 0.925 pm 0.043, 0.914 pm 0.004, and 0.8132 pm 0.001 on benchmark1k2101, Test2016_290, and CSAR-HiQ_36, respectively. These findings indicate the robustness and accuracy of BAPULM across diverse datasets and underscore the potential of sequence-based models in-silico drug discovery, offering a scalable alternative to 3D-centric methods for screening potential ligands.

The Yunshan Cup 2020 track focused on creating a framework for evaluating different methods of part-of-speech (POS). There were two tasks for this track: (1) POS tagging for the Indonesian language, and (2) POS tagging for the Lao tagging. The Indonesian dataset is comprised of 10000 sentences from Indonesian news within 29 tags. And the Lao dataset consists of 8000 sentences within 27 tags. 25 teams registered for the task. The methods of participants ranged from feature-based to neural networks using either classical machine learning techniques or ensemble methods. The best performing results achieve an accuracy of 95.82% for Indonesian and 93.03%, showing that neural sequence labeling models significantly outperform classic feature-based methods and rule-based methods.

Although the problem of hallucinations in neural machine translation (NMT) has received some attention, research on this highly pathological phenomenon lacks solid ground. Previous work has been limited in several ways: it often resorts to artificial settings where the problem is amplified, it disregards some (common) types of hallucinations, and it does not validate adequacy of detection heuristics. In this paper, we set foundations for the study of NMT hallucinations. First, we work in a natural setting, i.e., in-domain data without artificial noise neither in training nor in inference. Next, we annotate a dataset of over 3.4k sentences indicating different kinds of critical errors and hallucinations. Then, we turn to detection methods and both revisit methods used previously and propose using glass-box uncertainty-based detectors. Overall, we show that for preventive settings, (i) previously used methods are largely inadequate, (ii) sequence log-probability works best and performs on par with reference-based methods. Finally, we propose DeHallucinator, a simple method for alleviating hallucinations at test time that significantly reduces the hallucinatory rate. To ease future research, we release our annotated dataset for WMT18 German-English data, along with the model, training data, and code.

Designing sequences that satisfy multiple, often conflicting, objectives is a central challenge in therapeutic and biomolecular engineering. Existing generative frameworks largely operate in continuous spaces with single-objective guidance, while discrete approaches lack guarantees for multi-objective Pareto optimality. We introduce AReUReDi (Annealed Rectified Updates for Refining Discrete Flows), a discrete optimization algorithm with theoretical guarantees of convergence to the Pareto front. Building on Rectified Discrete Flows (ReDi), AReUReDi combines Tchebycheff scalarization, locally balanced proposals, and annealed Metropolis-Hastings updates to bias sampling toward Pareto-optimal states while preserving distributional invariance. Applied to peptide and SMILES sequence design, AReUReDi simultaneously optimizes up to five therapeutic properties (including affinity, solubility, hemolysis, half-life, and non-fouling) and outperforms both evolutionary and diffusion-based baselines. These results establish AReUReDi as a powerful, sequence-based framework for multi-property biomolecule generation.

We present significant extensions to diffusion-based sequence generation models, blurring the line with autoregressive language models. We introduce hyperschedules, which assign distinct noise schedules to individual token positions, generalizing both autoregressive models (e.g., GPT) and conventional diffusion models (e.g., SEDD, MDLM) as special cases. Second, we propose two hybrid token-wise noising processes that interpolate between absorbing and uniform processes, enabling the model to fix past mistakes, and we introduce a novel inference algorithm that leverages this new feature in a simplified context inspired from MDLM. To support efficient training and inference, we design attention masks compatible with KV-caching. Our methods achieve state-of-the-art perplexity and generate diverse, high-quality sequences across standard benchmarks, suggesting a promising path for autoregressive diffusion-based sequence generation.

Classifying genome sequences based on metadata has been an active area of research in comparative genomics for decades with many important applications across the life sciences. Established methods for classifying genomes can be broadly grouped into sequence alignment-based and alignment-free models. Conventional alignment-based models rely on genome similarity measures calculated based on local sequence alignments or consistent ordering among sequences. However, such methods are computationally expensive when dealing with large ensembles of even moderately sized genomes. In contrast, alignment-free (AF) approaches measure genome similarity based on summary statistics in an unsupervised setting and are efficient enough to analyze large datasets. However, both alignment-based and AF methods typically assume fixed scoring rubrics that lack the flexibility to assign varying importance to different parts of the sequences based on prior knowledge. In this study, we integrate AI and network science approaches to develop a comparative genomic analysis framework that addresses these limitations. Our approach, termed the Genome Misclassification Network Analysis (GMNA), simultaneously leverages misclassified instances, a learned scoring rubric, and label information to classify genomes based on associated metadata and better understand potential drivers of misclassification. We evaluate the utility of the GMNA using Naive Bayes and convolutional neural network models, supplemented by additional experiments with transformer-based models, to construct SARS-CoV-2 sampling location classifiers using over 500,000 viral genome sequences and study the resulting network of misclassifications. We demonstrate the global health potential of the GMNA by leveraging the SARS-CoV-2 genome misclassification networks to investigate the role human mobility played in structuring geographic clustering of SARS-CoV-2.

Question-Options Generation (QOG) is a task that involves generating a set of question-options pairs given context. This task has various applications, including fine-tuning large models, information retrieval, and automated multiple-choice question generation for education. In this paper, we develop QOG models using three different methods based on fine-tuning sequence-to-sequence language models (LMs). Experiments demonstrate that the end-to-end QOG model is computationally efficient and stable during both training and inference, outperforming other methods. Furthermore, our analysis indicates that our QOG models are competitive on the QOG task compared to the large language model Llama 3-8B.

Deep state-space models (SSMs), like recent Mamba architectures, are emerging as a promising alternative to CNN and Transformer networks. Existing Mamba-based restoration methods process visual data by leveraging a flatten-and-scan strategy that converts image patches into a 1D sequence before scanning. However, this scanning paradigm ignores local pixel dependencies and introduces spatial misalignment by positioning distant pixels incorrectly adjacent, which reduces local noise-awareness and degrades image sharpness in low-level vision tasks. To overcome these issues, we propose a novel slice-and-scan strategy that alternates scanning along intra- and inter-slices. We further design a new Vision State Space Module (VSSM) for image deblurring, and tackle the inefficiency challenges of the current Mamba-based vision module. Building upon this, we develop XYScanNet, an SSM architecture integrated with a lightweight feature fusion module for enhanced image deblurring. XYScanNet, maintains competitive distortion metrics and significantly improves perceptual performance. Experimental results show that XYScanNet enhances KID by 17% compared to the nearest competitor.

Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence alignments, such as MSA Transformer and the EvoFormer module of AlphaFold. We formulate the problem of pairing interacting partners among the paralogs of two protein families in a differentiable way. We introduce a method called DiffPALM that solves it by exploiting the ability of MSA Transformer to fill in masked amino acids in multiple sequence alignments using the surrounding context. MSA Transformer encodes coevolution between functionally or structurally coupled amino acids. We show that it captures inter-chain coevolution, while it was trained on single-chain data, which means that it can be used out-of-distribution. Relying on MSA Transformer without fine-tuning, DiffPALM outperforms existing coevolution-based pairing methods on difficult benchmarks of shallow multiple sequence alignments extracted from ubiquitous prokaryotic protein datasets. It also outperforms an alternative method based on a state-of-the-art protein language model trained on single sequences. Paired alignments of interacting protein sequences are a crucial ingredient of supervised deep learning methods to predict the three-dimensional structure of protein complexes. DiffPALM substantially improves the structure prediction of some eukaryotic protein complexes by AlphaFold-Multimer, without significantly deteriorating any of those we tested. It also achieves competitive performance with using orthology-based pairing.

Skeleton sequence representation learning has shown great advantages for action recognition due to its promising ability to model human joints and topology. However, the current methods usually require sufficient labeled data for training computationally expensive models, which is labor-intensive and time-consuming. Moreover, these methods ignore how to utilize the fine-grained dependencies among different skeleton joints to pre-train an efficient skeleton sequence learning model that can generalize well across different datasets. In this paper, we propose an efficient skeleton sequence learning framework, named Skeleton Sequence Learning (SSL). To comprehensively capture the human pose and obtain discriminative skeleton sequence representation, we build an asymmetric graph-based encoder-decoder pre-training architecture named SkeletonMAE, which embeds skeleton joint sequence into Graph Convolutional Network (GCN) and reconstructs the masked skeleton joints and edges based on the prior human topology knowledge. Then, the pre-trained SkeletonMAE encoder is integrated with the Spatial-Temporal Representation Learning (STRL) module to build the SSL framework. Extensive experimental results show that our SSL generalizes well across different datasets and outperforms the state-of-the-art self-supervised skeleton-based action recognition methods on FineGym, Diving48, NTU 60 and NTU 120 datasets. Additionally, we obtain comparable performance to some fully supervised methods. The code is avaliable at https://github.com/HongYan1123/SkeletonMAE.

Self-attention is an attention mechanism that learns a representation by relating different positions in the sequence. The transformer, which is a sequence model solely based on self-attention, and its variants achieved state-of-the-art results in many natural language processing tasks. Since music composes its semantics based on the relations between components in sparse positions, adopting the self-attention mechanism to solve music information retrieval (MIR) problems can be beneficial. Hence, we propose a self-attention based deep sequence model for music tagging. The proposed architecture consists of shallow convolutional layers followed by stacked Transformer encoders. Compared to conventional approaches using fully convolutional or recurrent neural networks, our model is more interpretable while reporting competitive results. We validate the performance of our model with the MagnaTagATune and the Million Song Dataset. In addition, we demonstrate the interpretability of the proposed architecture with a heat map visualization.

This paper describes our study on using mutilingual BERT embeddings and some new neural models for improving sequence tagging tasks for the Vietnamese language. We propose new model architectures and evaluate them extensively on two named entity recognition datasets of VLSP 2016 and VLSP 2018, and on two part-of-speech tagging datasets of VLSP 2010 and VLSP 2013. Our proposed models outperform existing methods and achieve new state-of-the-art results. In particular, we have pushed the accuracy of part-of-speech tagging to 95.40% on the VLSP 2010 corpus, to 96.77% on the VLSP 2013 corpus; and the F1 score of named entity recognition to 94.07% on the VLSP 2016 corpus, to 90.31% on the VLSP 2018 corpus. Our code and pre-trained models viBERT and vELECTRA are released as open source to facilitate adoption and further research.

World models represent a promising approach for training reinforcement learning agents with significantly improved sample efficiency. While most world model methods primarily rely on sequences of discrete latent variables to model environment dynamics, this compression often neglects critical visual details essential for reinforcement learning. Recent diffusion-based world models condition generation on a fixed context length of frames to predict the next observation, using separate recurrent neural networks to model rewards and termination signals. Although this architecture effectively enhances visual fidelity, the fixed context length approach inherently limits memory capacity. In this paper, we introduce EDELINE, a unified world model architecture that integrates state space models with diffusion models. Our approach outperforms existing baselines across visually challenging Atari 100k tasks, memory-demanding Crafter benchmark, and 3D first-person ViZDoom environments, demonstrating superior performance in all these diverse challenges.

The PI-CAI (Prostate Imaging: Cancer AI) challenge led to expert-level diagnostic algorithms for clinically significant prostate cancer detection. The algorithms receive biparametric MRI scans as input, which consist of T2-weighted and diffusion-weighted scans. These scans can be misaligned due to multiple factors in the scanning process. Image registration can alleviate this issue by predicting the deformation between the sequences. We investigate the effect of image registration on the diagnostic performance of AI-based prostate cancer diagnosis. First, the image registration algorithm, developed in MeVisLab, is analyzed using a dataset with paired lesion annotations. Second, the effect on diagnosis is evaluated by comparing case-level cancer diagnosis performance between using the original dataset, rigidly aligned diffusion-weighted scans, or deformably aligned diffusion-weighted scans. Rigid registration showed no improvement. Deformable registration demonstrated a substantial improvement in lesion overlap (+10% median Dice score) and a positive yet non-significant improvement in diagnostic performance (+0.3% AUROC, p=0.18). Our investigation shows that a substantial improvement in lesion alignment does not directly lead to a significant improvement in diagnostic performance. Qualitative analysis indicated that jointly developing image registration methods and diagnostic AI algorithms could enhance diagnostic accuracy and patient outcomes.

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the high-throughput analysis of protein composition in biological tissues. Many deep learning methods have been developed for de novo peptide sequencing task, i.e., predicting the peptide sequence for the observed mass spectrum. However, two key challenges seriously hinder the further advancement of this important task. Firstly, since there is no consensus for the evaluation datasets, the empirical results in different research papers are often not comparable, leading to unfair comparison. Secondly, the current methods are usually limited to amino acid-level or peptide-level precision and recall metrics. In this work, we present the first unified benchmark NovoBench for de novo peptide sequencing, which comprises diverse mass spectrum data, integrated models, and comprehensive evaluation metrics. Recent impressive methods, including DeepNovo, PointNovo, Casanovo, InstaNovo, AdaNovo and pi-HelixNovo are integrated into our framework. In addition to amino acid-level and peptide-level precision and recall, we evaluate the models' performance in terms of identifying post-tranlational modifications (PTMs), efficiency and robustness to peptide length, noise peaks and missing fragment ratio, which are important influencing factors while seldom be considered. Leveraging this benchmark, we conduct a large-scale study of current methods, report many insightful findings that open up new possibilities for future development.

Applying Reinforcement Learning (RL) to sequence generation models enables the direct optimization of long-term rewards (e.g., BLEU and human feedback), but typically requires large-scale sampling over a space of action sequences. This is a computational challenge as presented by the practice of sequence generation problems, such as machine translation, where we often deal with a large action space (e.g., a vocabulary) and a long action sequence (e.g., a translation). In this work, we introduce two-stage sampling and dynamic sampling approaches to improve the sampling efficiency during training sequence generation models via RL. We experiment with our approaches on the traditional sequence generation tasks, including machine translation and abstractive summarization. Furthermore, we evaluate our approaches in RL from human feedback (RLHF) through training a large language model using the reward model. Experimental results show that the efficient sampling-based RL, referred to as ESRL, can outperform all baselines in terms of both training efficiency and memory consumption. Notably, ESRL yields consistent performance gains over the strong REINFORCE, minimum risk training, and proximal policy optimization methods.

We introduce the Autoregressive Block-Based Iterative Encoder (AbbIE), a novel recursive generalization of the encoder-only Transformer architecture, which achieves better perplexity than a standard Transformer and allows for the dynamic scaling of compute resources at test time. This simple, recursive approach is a complement to scaling large language model (LLM) performance through parameter and token counts. AbbIE performs its iterations in latent space, but unlike latent reasoning models, does not require a specialized dataset or training protocol. We show that AbbIE upward generalizes (ability to generalize to arbitrary iteration lengths) at test time by only using 2 iterations during train time, far outperforming alternative iterative methods. AbbIE's ability to scale its computational expenditure based on the complexity of the task gives it an up to 12\% improvement in zero-shot in-context learning tasks versus other iterative and standard methods and up to 5\% improvement in language perplexity. The results from this study open a new avenue to Transformer performance scaling. We perform all of our evaluations on model sizes up to 350M parameters.

Sequence modeling is a crucial area across various domains, including Natural Language Processing (NLP), speech recognition, time series forecasting, music generation, and bioinformatics. Recurrent Neural Networks (RNNs) and Long Short Term Memory Networks (LSTMs) have historically dominated sequence modeling tasks like Machine Translation, Named Entity Recognition (NER), etc. However, the advancement of transformers has led to a shift in this paradigm, given their superior performance. Yet, transformers suffer from O(N^2) attention complexity and challenges in handling inductive bias. Several variations have been proposed to address these issues which use spectral networks or convolutions and have performed well on a range of tasks. However, they still have difficulty in dealing with long sequences. State Space Models(SSMs) have emerged as promising alternatives for sequence modeling paradigms in this context, especially with the advent of S4 and its variants, such as S4nd, Hippo, Hyena, Diagnol State Spaces (DSS), Gated State Spaces (GSS), Linear Recurrent Unit (LRU), Liquid-S4, Mamba, etc. In this survey, we categorize the foundational SSMs based on three paradigms namely, Gating architectures, Structural architectures, and Recurrent architectures. This survey also highlights diverse applications of SSMs across domains such as vision, video, audio, speech, language (especially long sequence modeling), medical (including genomics), chemical (like drug design), recommendation systems, and time series analysis, including tabular data. Moreover, we consolidate the performance of SSMs on benchmark datasets like Long Range Arena (LRA), WikiText, Glue, Pile, ImageNet, Kinetics-400, sstv2, as well as video datasets such as Breakfast, COIN, LVU, and various time series datasets. The project page for Mamba-360 work is available on this webpage.https://github.com/badripatro/mamba360.

Language models have recently been shown capable of performing regression tasks wherein numeric predictions are represented as decoded strings. In this work, we provide theoretical grounds for this capability and furthermore investigate the utility of causal auto-regressive sequence models when they are applied to any feature representation. We find that, despite being trained in the usual way - for next-token prediction via cross-entropy loss - decoding-based regression is as performant as traditional approaches for tabular regression tasks, while being flexible enough to capture arbitrary distributions, such as in the task of density estimation.

Scene text recognition has attracted a great many researches due to its importance to various applications. Existing methods mainly adopt recurrence or convolution based networks. Though have obtained good performance, these methods still suffer from two limitations: slow training speed due to the internal recurrence of RNNs, and high complexity due to stacked convolutional layers for long-term feature extraction. This paper, for the first time, proposes a no-recurrence sequence-to-sequence text recognizer, named NRTR, that dispenses with recurrences and convolutions entirely. NRTR follows the encoder-decoder paradigm, where the encoder uses stacked self-attention to extract image features, and the decoder applies stacked self-attention to recognize texts based on encoder output. NRTR relies solely on self-attention mechanism thus could be trained with more parallelization and less complexity. Considering scene image has large variation in text and background, we further design a modality-transform block to effectively transform 2D input images to 1D sequences, combined with the encoder to extract more discriminative features. NRTR achieves state-of-the-art or highly competitive performance on both regular and irregular benchmarks, while requires only a small fraction of training time compared to the best model from the literature (at least 8 times faster).

Directly learning to model 4D content, including shape, color and motion, is challenging. Existing methods depend on skeleton-based motion control and offer limited continuity in detail. To address this, we propose a novel framework that generates coherent 4D sequences with animation of 3D shapes under given conditions with dynamic evolution of shape and color over time through integrative latent mapping. We first employ an integrative latent unified representation to encode shape and color information of each detailed 3D geometry frame. The proposed skeleton-free latent 4D sequence joint representation allows us to leverage diffusion models in a low-dimensional space to control the generation of 4D sequences. Finally, temporally coherent 4D sequences are generated conforming well to the input images and text prompts. Extensive experiments on the ShapeNet, 3DBiCar and DeformingThings4D datasets for several tasks demonstrate that our method effectively learns to generate quality 3D shapes with color and 4D mesh animations, improving over the current state-of-the-art. Source code will be released.

Building huge and highly capable language models has been a trend in the past years. Despite their great performance, they incur high computational cost. A common solution is to apply model compression or choose light-weight architectures, which often need a separate fixed-size model for each desirable computational budget, and may lose performance in case of heavy compression. This paper proposes an effective dynamic inference approach, called E-LANG, which distributes the inference between large accurate Super-models and light-weight Swift models. To this end, a decision making module routes the inputs to Super or Swift models based on the energy characteristics of the representations in the latent space. This method is easily adoptable and architecture agnostic. As such, it can be applied to black-box pre-trained models without a need for architectural manipulations, reassembling of modules, or re-training. Unlike existing methods that are only applicable to encoder-only backbones and classification tasks, our method also works for encoder-decoder structures and sequence-to-sequence tasks such as translation. The E-LANG performance is verified through a set of experiments with T5 and BERT backbones on GLUE, SuperGLUE, and WMT. In particular, we outperform T5-11B with an average computations speed-up of 3.3times on GLUE and 2.9times on SuperGLUE. We also achieve BERT-based SOTA on GLUE with 3.2times less computations. Code and demo are available in the supplementary materials.

Diffusion models have become a cornerstone in image editing, offering flexibility with language prompts and source images. However, a key challenge is attribute leakage, where unintended modifications occur in non-target regions or within target regions due to attribute interference. Existing methods often suffer from leakage due to naive text embeddings and inadequate handling of End-of-Sequence (EOS) token embeddings. To address this, we propose ALE-Edit (Attribute-leakage-free editing), a novel framework to minimize attribute leakage with three components: (1) Object-Restricted Embeddings (ORE) to localize object-specific attributes in text embeddings, (2) Region-Guided Blending for Cross-Attention Masking (RGB-CAM) to align attention with target regions, and (3) Background Blending (BB) to preserve non-edited regions. Additionally, we introduce ALE-Bench, a benchmark for evaluating attribute leakage with new metrics for target-external and target-internal leakage. Experiments demonstrate that our framework significantly reduces attribute leakage while maintaining high editing quality, providing an efficient and tuning-free solution for multi-object image editing.

Recent studies in DNA sequence classification have leveraged sophisticated machine learning techniques, achieving notable accuracy in categorizing complex genomic data. Among these, methods such as k-mer counting have proven effective in distinguishing sequences from varied species like chimpanzees, dogs, and humans, becoming a staple in contemporary genomic research. However, these approaches often demand extensive computational resources, posing a challenge in terms of scalability and efficiency. Addressing this issue, our study introduces a novel adaptation of Jiang et al.'s compressor-based, parameter-free classification method, specifically tailored for DNA sequence analysis. This innovative approach utilizes a variety of compression algorithms, such as Gzip, Brotli, and LZMA, to efficiently process and classify genomic sequences. Not only does this method align with the current state-of-the-art in terms of accuracy, but it also offers a more resource-efficient alternative to traditional machine learning methods. Our comprehensive evaluation demonstrates the proposed method's effectiveness in accurately classifying DNA sequences from multiple species. We present a detailed analysis of the performance of each algorithm used, highlighting the strengths and limitations of our approach in various genomic contexts. Furthermore, we discuss the broader implications of our findings for bioinformatics, particularly in genomic data processing and analysis. The results of our study pave the way for more efficient and scalable DNA sequence classification methods, offering significant potential for advancements in genomic research and applications.

Dynamic Music Emotion Recognition (DMER) aims to predict the emotion of different moments in music, playing a crucial role in music information retrieval. The existing DMER methods struggle to capture long-term dependencies when dealing with sequence data, which limits their performance. Furthermore, these methods often overlook the influence of individual differences on emotion perception, even though everyone has their own personalized emotional perception in the real world. Motivated by these issues, we explore more effective sequence processing methods and introduce the Personalized DMER (PDMER) problem, which requires models to predict emotions that align with personalized perception. Specifically, we propose a Dual-Scale Attention-Based Meta-Learning (DSAML) method. This method fuses features from a dual-scale feature extractor and captures both short and long-term dependencies using a dual-scale attention transformer, improving the performance in traditional DMER. To achieve PDMER, we design a novel task construction strategy that divides tasks by annotators. Samples in a task are annotated by the same annotator, ensuring consistent perception. Leveraging this strategy alongside meta-learning, DSAML can predict personalized perception of emotions with just one personalized annotation sample. Our objective and subjective experiments demonstrate that our method can achieve state-of-the-art performance in both traditional DMER and PDMER.

Zero-resource cross-lingual transfer approaches aim to apply supervised models from a source language to unlabelled target languages. In this paper we perform an in-depth study of the two main techniques employed so far for cross-lingual zero-resource sequence labelling, based either on data or model transfer. Although previous research has proposed translation and annotation projection (data-based cross-lingual transfer) as an effective technique for cross-lingual sequence labelling, in this paper we experimentally demonstrate that high capacity multilingual language models applied in a zero-shot (model-based cross-lingual transfer) setting consistently outperform data-based cross-lingual transfer approaches. A detailed analysis of our results suggests that this might be due to important differences in language use. More specifically, machine translation often generates a textual signal which is different to what the models are exposed to when using gold standard data, which affects both the fine-tuning and evaluation processes. Our results also indicate that data-based cross-lingual transfer approaches remain a competitive option when high-capacity multilingual language models are not available.

Due to reasons of convenience and lack of tech literacy, transliteration (i.e., Romanizing native scripts instead of using localization tools) is eminently prevalent in the context of low-resource languages such as Sinhala, which have their own writing script. In this study, our focus is on Romanized Sinhala transliteration. We propose two methods to address this problem: Our baseline is a rule-based method, which is then compared against our second method where we approach the transliteration problem as a sequence-to-sequence task akin to the established Neural Machine Translation (NMT) task. For the latter, we propose a Transformer-based Encode-Decoder solution. We witnessed that the Transformer-based method could grab many ad-hoc patterns within the Romanized scripts compared to the rule-based method. The code base associated with this paper is available on GitHub - https://github.com/kasunw22/Sinhala-Transliterator/

Transformers have emerged as a powerful tool for a broad range of natural language processing tasks. A key component that drives the impressive performance of Transformers is the self-attention mechanism that encodes the influence or dependence of other tokens on each specific token. While beneficial, the quadratic complexity of self-attention on the input sequence length has limited its application to longer sequences -- a topic being actively studied in the community. To address this limitation, we propose Nystr\"{o}mformer -- a model that exhibits favorable scalability as a function of sequence length. Our idea is based on adapting the Nystr\"{o}m method to approximate standard self-attention with O(n) complexity. The scalability of Nystr\"{o}mformer enables application to longer sequences with thousands of tokens. We perform evaluations on multiple downstream tasks on the GLUE benchmark and IMDB reviews with standard sequence length, and find that our Nystr\"{o}mformer performs comparably, or in a few cases, even slightly better, than standard self-attention. On longer sequence tasks in the Long Range Arena (LRA) benchmark, Nystr\"{o}mformer performs favorably relative to other efficient self-attention methods. Our code is available at https://github.com/mlpen/Nystromformer.

Query rewrite, which aims to generate more efficient queries by altering a SQL query's structure without changing the query result, has been an important research problem. In order to maintain equivalence between the rewritten query and the original one during rewriting, traditional query rewrite methods always rewrite the queries following certain rewrite rules. However, some problems still remain. Firstly, existing methods of finding the optimal choice or sequence of rewrite rules are still limited and the process always costs a lot of resources. Methods involving discovering new rewrite rules typically require complicated proofs of structural logic or extensive user interactions. Secondly, current query rewrite methods usually rely highly on DBMS cost estimators which are often not accurate. In this paper, we address these problems by proposing a novel method of query rewrite named LLM-R2, adopting a large language model (LLM) to propose possible rewrite rules for a database rewrite system. To further improve the inference ability of LLM in recommending rewrite rules, we train a contrastive model by curriculum to learn query representations and select effective query demonstrations for the LLM. Experimental results have shown that our method can significantly improve the query execution efficiency and outperform the baseline methods. In addition, our method enjoys high robustness across different datasets.

Watch time prediction (WTP) has emerged as a pivotal task in short video recommendation systems, designed to quantify user engagement through continuous interaction modeling. Predicting users' watch times on videos often encounters fundamental challenges, including wide value ranges and imbalanced data distributions, which can lead to significant estimation bias when directly applying regression techniques. Recent studies have attempted to address these issues by converting the continuous watch time estimation into an ordinal regression task. While these methods demonstrate partial effectiveness, they exhibit notable limitations: (1) the discretization process frequently relies on bucket partitioning, inherently reducing prediction flexibility and accuracy and (2) the interdependencies among different partition intervals remain underutilized, missing opportunities for effective error correction. Inspired by language modeling paradigms, we propose a novel Generative Regression (GR) framework that reformulates WTP as a sequence generation task. Our approach employs structural discretization to enable nearly lossless value reconstruction while maintaining prediction fidelity. Through carefully designed vocabulary construction and label encoding schemes, each watch time is bijectively mapped to a token sequence. To mitigate the training-inference discrepancy caused by teacher-forcing, we introduce a curriculum learning with embedding mixup strategy that gradually transitions from guided to free-generation modes. We evaluate our method against state-of-the-art approaches on two public datasets and one industrial dataset. We also perform online A/B testing on the Kuaishou App to confirm the real-world effectiveness. The results conclusively show that GR outperforms existing techniques significantly.

Sequence Parallel (SP) serves as a prevalent strategy to handle long sequences that exceed the memory limit of a single GPU. However, existing SP methods do not take advantage of linear attention features, resulting in sub-optimal parallelism efficiency and usability for linear attention-based language models. In this paper, we introduce Linear Attention Sequence Parallel (LASP), an efficient SP method tailored to linear attention-based language models. Specifically, we design an efficient point-to-point communication mechanism to leverage the right-product kernel trick of linear attention, which sharply decreases the communication overhead of SP. We also enhance the practical efficiency of LASP by performing kernel fusion and intermediate state caching, making the implementation of LASP hardware-friendly on GPU clusters. Furthermore, we meticulously ensure the compatibility of sequence-level LASP with all types of batch-level data parallel methods, which is vital for distributed training on large clusters with long sequences and large batches. We conduct extensive experiments on two linear attention-based models with varying sequence lengths and GPU cluster sizes. LASP scales sequence length up to 4096K using 128 A100 80G GPUs on 1B models, which is 8 times longer than existing SP methods while being significantly faster. The code is available at https://github.com/OpenNLPLab/LASP.

Extraction of building footprint polygons from remotely sensed data is essential for several urban understanding tasks such as reconstruction, navigation, and mapping. Despite significant progress in the area, extracting accurate polygonal building footprints remains an open problem. In this paper, we introduce Pix2Poly, an attention-based end-to-end trainable and differentiable deep neural network capable of directly generating explicit high-quality building footprints in a ring graph format. Pix2Poly employs a generative encoder-decoder transformer to produce a sequence of graph vertex tokens whose connectivity information is learned by an optimal matching network. Compared to previous graph learning methods, ours is a truly end-to-end trainable approach that extracts high-quality building footprints and road networks without requiring complicated, computationally intensive raster loss functions and intricate training pipelines. Upon evaluating Pix2Poly on several complex and challenging datasets, we report that Pix2Poly outperforms state-of-the-art methods in several vector shape quality metrics while being an entirely explicit method. Our code is available at https://github.com/yeshwanth95/Pix2Poly.

Despite seemingly performant web agents on the task-completion benchmarks, most existing methods evaluate the agents based on a presupposition: the web navigation task consists of linear sequence of actions with an end state that marks task completion. In contrast, our work focuses on web navigation for information aggregation, wherein the agent must explore different websites to gather information for a complex query. We consider web information aggregation from two different perspectives: (i) Direct API-driven Access relies on a text-only view of the Web, leveraging external tools such as Google Search API to navigate the web and a scraper to extract website contents. (ii) Interactive Visual Access uses screenshots of the webpages and requires interaction with the browser to navigate and access information. Motivated by these diverse information access settings, we introduce Infogent, a novel modular framework for web information aggregation involving three distinct components: Navigator, Extractor and Aggregator. Experiments on different information access settings demonstrate Infogent beats an existing SOTA multi-agent search framework by 7% under Direct API-Driven Access on FRAMES, and improves over an existing information-seeking web agent by 4.3% under Interactive Visual Access on AssistantBench.

A hallmark of human intelligence is the ability to create complex artifacts through structured multi-step processes. Generating procedural tutorials with AI is a longstanding but challenging goal, facing three key obstacles: (1) scarcity of multi-task procedural datasets, (2) maintaining logical continuity and visual consistency between steps, and (3) generalizing across multiple domains. To address these challenges, we propose a multi-domain dataset covering 21 tasks with over 24,000 procedural sequences. Building upon this foundation, we introduce MakeAnything, a framework based on the diffusion transformer (DIT), which leverages fine-tuning to activate the in-context capabilities of DIT for generating consistent procedural sequences. We introduce asymmetric low-rank adaptation (LoRA) for image generation, which balances generalization capabilities and task-specific performance by freezing encoder parameters while adaptively tuning decoder layers. Additionally, our ReCraft model enables image-to-process generation through spatiotemporal consistency constraints, allowing static images to be decomposed into plausible creation sequences. Extensive experiments demonstrate that MakeAnything surpasses existing methods, setting new performance benchmarks for procedural generation tasks.

Background. Fully automatic analysis of myocardial perfusion MRI datasets enables rapid and objective reporting of stress/rest studies in patients with suspected ischemic heart disease. Developing deep learning techniques that can analyze multi-center datasets despite limited training data and variations in software and hardware is an ongoing challenge. Methods. Datasets from 3 medical centers acquired at 3T (n = 150 subjects) were included: an internal dataset (inD; n = 95) and two external datasets (exDs; n = 55) used for evaluating the robustness of the trained deep neural network (DNN) models against differences in pulse sequence (exD-1) and scanner vendor (exD-2). A subset of inD (n = 85) was used for training/validation of a pool of DNNs for segmentation, all using the same spatiotemporal U-Net architecture and hyperparameters but with different parameter initializations. We employed a space-time sliding-patch analysis approach that automatically yields a pixel-wise "uncertainty map" as a byproduct of the segmentation process. In our approach, a given test case is segmented by all members of the DNN pool and the resulting uncertainty maps are leveraged to automatically select the "best" one among the pool of solutions. Results. The proposed DAUGS analysis approach performed similarly to the established approach on the internal dataset (p = n.s.) whereas it significantly outperformed on the external datasets (p < 0.005 for exD-1 and exD-2). Moreover, the number of image series with "failed" segmentation was significantly lower for the proposed vs. the established approach (4.3% vs. 17.1%, p < 0.0005). Conclusions. The proposed DAUGS analysis approach has the potential to improve the robustness of deep learning methods for segmentation of multi-center stress perfusion datasets with variations in the choice of pulse sequence, site location or scanner vendor.

The language model (LM) approach based on acoustic and linguistic prompts, such as VALL-E, has achieved remarkable progress in the field of zero-shot audio generation. However, existing methods still have some limitations: 1) repetitions, transpositions, and omissions in the output synthesized speech due to limited alignment constraints between audio and phoneme tokens; 2) challenges of fine-grained control over the synthesized speech with autoregressive (AR) language model; 3) infinite silence generation due to the nature of AR-based decoding, especially under the greedy strategy. To alleviate these issues, we propose ELLA-V, a simple but efficient LM-based zero-shot text-to-speech (TTS) framework, which enables fine-grained control over synthesized audio at the phoneme level. The key to ELLA-V is interleaving sequences of acoustic and phoneme tokens, where phoneme tokens appear ahead of the corresponding acoustic tokens. The experimental findings reveal that our model outperforms VALL-E in terms of accuracy and delivers more stable results using both greedy and sampling-based decoding strategies. The code of ELLA-V will be open-sourced after cleanups. Audio samples are available at https://ereboas.github.io/ELLAV/.

This work aims to predict channels in wireless communication systems based on noisy observations, utilizing sequence-to-sequence models with attention (Seq2Seq-attn) and transformer models. Both models are adapted from natural language processing to tackle the complex challenge of channel prediction. Additionally, a new technique called reverse positional encoding is introduced in the transformer model to improve the robustness of the model against varying sequence lengths. Similarly, the encoder outputs of the Seq2Seq-attn model are reversed before applying attention. Simulation results demonstrate that the proposed ordering techniques allow the models to better capture the relationships between the channel snapshots within the sequence, irrespective of the sequence length, as opposed to existing methods.

We propose a novel method called Long Expressive Memory (LEM) for learning long-term sequential dependencies. LEM is gradient-based, it can efficiently process sequential tasks with very long-term dependencies, and it is sufficiently expressive to be able to learn complicated input-output maps. To derive LEM, we consider a system of multiscale ordinary differential equations, as well as a suitable time-discretization of this system. For LEM, we derive rigorous bounds to show the mitigation of the exploding and vanishing gradients problem, a well-known challenge for gradient-based recurrent sequential learning methods. We also prove that LEM can approximate a large class of dynamical systems to high accuracy. Our empirical results, ranging from image and time-series classification through dynamical systems prediction to speech recognition and language modeling, demonstrate that LEM outperforms state-of-the-art recurrent neural networks, gated recurrent units, and long short-term memory models.

By computing the rank correlation between attention weights and feature-additive explanation methods, previous analyses either invalidate or support the role of attention-based explanations as a faithful and plausible measure of salience. To investigate whether this approach is appropriate, we compare LIME, Integrated Gradients, DeepLIFT, Grad-SHAP, Deep-SHAP, and attention-based explanations, applied to two neural architectures trained on single- and pair-sequence language tasks. In most cases, we find that none of our chosen methods agree. Based on our empirical observations and theoretical objections, we conclude that rank correlation does not measure the quality of feature-additive methods. Practitioners should instead use the numerous and rigorous diagnostic methods proposed by the community.

Electronic Theses and Dissertations (ETDs) contain domain knowledge that can be used for many digital library tasks, such as analyzing citation networks and predicting research trends. Automatic metadata extraction is important to build scalable digital library search engines. Most existing methods are designed for born-digital documents, so they often fail to extract metadata from scanned documents such as for ETDs. Traditional sequence tagging methods mainly rely on text-based features. In this paper, we propose a conditional random field (CRF) model that combines text-based and visual features. To verify the robustness of our model, we extended an existing corpus and created a new ground truth corpus consisting of 500 ETD cover pages with human validated metadata. Our experiments show that CRF with visual features outperformed both a heuristic and a CRF model with only text-based features. The proposed model achieved 81.3%-96% F1 measure on seven metadata fields. The data and source code are publicly available on Google Drive (https://tinyurl.com/y8kxzwrp) and a GitHub repository (https://github.com/lamps-lab/ETDMiner/tree/master/etd_crf), respectively.

Learning skills in open-world environments is essential for developing agents capable of handling a variety of tasks by combining basic skills. Online demonstration videos are typically long but unsegmented, making them difficult to segment and label with skill identifiers. Unlike existing methods that rely on sequence sampling or human labeling, we have developed a self-supervised learning-based approach to segment these long videos into a series of semantic-aware and skill-consistent segments. Drawing inspiration from human cognitive event segmentation theory, we introduce Skill Boundary Detection (SBD), an annotation-free temporal video segmentation algorithm. SBD detects skill boundaries in a video by leveraging prediction errors from a pretrained unconditional action-prediction model. This approach is based on the assumption that a significant increase in prediction error indicates a shift in the skill being executed. We evaluated our method in Minecraft, a rich open-world simulator with extensive gameplay videos available online. Our SBD-generated segments improved the average performance of conditioned policies by 63.7% and 52.1% on short-term atomic skill tasks, and their corresponding hierarchical agents by 11.3% and 20.8% on long-horizon tasks. Our method can leverage the diverse YouTube videos to train instruction-following agents. The project page can be found in https://craftjarvis.github.io/SkillDiscovery.

How can we design protein sequences folding into the desired structures effectively and efficiently? AI methods for structure-based protein design have attracted increasing attention in recent years; however, few methods can simultaneously improve the accuracy and efficiency due to the lack of expressive features and autoregressive sequence decoder. To address these issues, we propose PiFold, which contains a novel residue featurizer and PiGNN layers to generate protein sequences in a one-shot way with improved recovery. Experiments show that PiFold could achieve 51.66\% recovery on CATH 4.2, while the inference speed is 70 times faster than the autoregressive competitors. In addition, PiFold achieves 58.72\% and 60.42\% recovery scores on TS50 and TS500, respectively. We conduct comprehensive ablation studies to reveal the role of different types of protein features and model designs, inspiring further simplification and improvement. The PyTorch code is available at https://github.com/A4Bio/PiFold{GitHub}.

In this paper, we present CAD2Program, a new method for reconstructing 3D parametric models from 2D CAD drawings. Our proposed method is inspired by recent successes in vision-language models (VLMs), and departs from traditional methods which rely on task-specific data representations and/or algorithms. Specifically, on the input side, we simply treat the 2D CAD drawing as a raster image, regardless of its original format, and encode the image with a standard ViT model. We show that such an encoding scheme achieves competitive performance against existing methods that operate on vector-graphics inputs, while imposing substantially fewer restrictions on the 2D drawings. On the output side, our method auto-regressively predicts a general-purpose language describing 3D parametric models in text form. Compared to other sequence modeling methods for CAD which use domain-specific sequence representations with fixed-size slots, our text-based representation is more flexible, and can be easily extended to arbitrary geometric entities and semantic or functional properties. Experimental results on a large-scale dataset of cabinet models demonstrate the effectiveness of our method.

State-of-the-art end-to-end Optical Music Recognition (OMR) has, to date, primarily been carried out using monophonic transcription techniques to handle complex score layouts, such as polyphony, often by resorting to simplifications or specific adaptations. Despite their efficacy, these approaches imply challenges related to scalability and limitations. This paper presents the Sheet Music Transformer, the first end-to-end OMR model designed to transcribe complex musical scores without relying solely on monophonic strategies. Our model employs a Transformer-based image-to-sequence framework that predicts score transcriptions in a standard digital music encoding format from input images. Our model has been tested on two polyphonic music datasets and has proven capable of handling these intricate music structures effectively. The experimental outcomes not only indicate the competence of the model, but also show that it is better than the state-of-the-art methods, thus contributing to advancements in end-to-end OMR transcription.

Attention-based models such as Transformers and recurrent models like state space models (SSMs) have emerged as successful methods for autoregressive sequence modeling. Although both enable parallel training, none enable parallel generation due to their autoregressiveness. We propose the variational SSM (VSSM), a variational autoencoder (VAE) where both the encoder and decoder are SSMs. Since sampling the latent variables and decoding them with the SSM can be parallelized, both training and generation can be conducted in parallel. Moreover, the decoder recurrence allows generation to be resumed without reprocessing the whole sequence. Finally, we propose the autoregressive VSSM that can be conditioned on a partial realization of the sequence, as is common in language generation tasks. Interestingly, the autoregressive VSSM still enables parallel generation. We highlight on toy problems (MNIST, CIFAR) the empirical gains in speed-up and show that it competes with traditional models in terms of generation quality (Transformer, Mamba SSM).

This paper studies Chinese Spelling Correction (CSC), which aims to detect and correct the potential spelling errors in a given sentence. Current state-of-the-art methods regard CSC as a sequence tagging task and fine-tune BERT-based models on sentence pairs. However, we note a critical flaw in the process of tagging one character to another, that the correction is excessively conditioned on the error. This is opposite from human mindset, where individuals rephrase the complete sentence based on its semantics, rather than solely on the error patterns memorized before. Such a counter-intuitive learning process results in the bottleneck of generalizability and transferability of machine spelling correction. To address this, we propose Rephrasing Language Model (ReLM), where the model is trained to rephrase the entire sentence by infilling additional slots, instead of character-to-character tagging. This novel training paradigm achieves the new state-of-the-art results across fine-tuned and zero-shot CSC benchmarks, outperforming previous counterparts by a large margin. Our method also learns transferable language representation when CSC is jointly trained with other tasks.

Large-scale transformer models have become the de-facto architectures for various machine learning applications, e.g., CV and NLP. However, those large models also introduce prohibitive training costs. To mitigate this issue, we propose a novel random and layerwise token dropping method (random-LTD), which skips the computation of a subset of the input tokens at all middle layers. Particularly, random-LTD achieves considerable speedups and comparable accuracy as the standard training baseline. Compared to other token dropping methods, random-LTD does not require (1) any importance score-based metrics, (2) any special token treatment (e.g., [CLS]), and (3) many layers in full sequence length training except the first and the last layers. Besides, a new LayerToken learning rate schedule is proposed for pretraining problems that resolve the heavy tuning requirement for our proposed training mechanism. Finally, we demonstrate that random-LTD can be applied to broader applications, including GPT and BERT pretraining as well as ViT and GPT finetuning tasks. Our results show that random-LTD can save about 33.3% theoretical compute cost and 25.6% wall-clock training time while achieving similar zero-shot evaluations on GPT-31.3B as compared to baseline.

Although great progress has been made by previous table understanding methods including recent approaches based on large language models (LLMs), they rely heavily on the premise that given tables must be converted into a certain text sequence (such as Markdown or HTML) to serve as model input. However, it is difficult to access such high-quality textual table representations in some real-world scenarios, and table images are much more accessible. Therefore, how to directly understand tables using intuitive visual information is a crucial and urgent challenge for developing more practical applications. In this paper, we propose a new problem, multimodal table understanding, where the model needs to generate correct responses to various table-related requests based on the given table image. To facilitate both the model training and evaluation, we construct a large-scale dataset named MMTab, which covers a wide spectrum of table images, instructions and tasks. On this basis, we develop Table-LLaVA, a generalist tabular multimodal large language model (MLLM), which significantly outperforms recent open-source MLLM baselines on 23 benchmarks under held-in and held-out settings. The code and data is available at this https://github.com/SpursGoZmy/Table-LLaVA

When handling complicated text images (e.g., irregular structures, low resolution, heavy occlusion, and uneven illumination), existing supervised text recognition methods are data-hungry. Although these methods employ large-scale synthetic text images to reduce the dependence on annotated real images, the domain gap still limits the recognition performance. Therefore, exploring the robust text feature representations on unlabeled real images by self-supervised learning is a good solution. However, existing self-supervised text recognition methods conduct sequence-to-sequence representation learning by roughly splitting the visual features along the horizontal axis, which limits the flexibility of the augmentations, as large geometric-based augmentations may lead to sequence-to-sequence feature inconsistency. Motivated by this, we propose a novel self-supervised Character-to-Character Distillation method, CCD, which enables versatile augmentations to facilitate general text representation learning. Specifically, we delineate the character structures of unlabeled real images by designing a self-supervised character segmentation module. Following this, CCD easily enriches the diversity of local characters while keeping their pairwise alignment under flexible augmentations, using the transformation matrix between two augmented views from images. Experiments demonstrate that CCD achieves state-of-the-art results, with average performance gains of 1.38% in text recognition, 1.7% in text segmentation, 0.24 dB (PSNR) and 0.0321 (SSIM) in text super-resolution. Code is available at https://github.com/TongkunGuan/CCD.

Neural end-to-end TTS can generate very high-quality synthesized speech, and even close to human recording within similar domain text. However, it performs unsatisfactory when scaling it to challenging test sets. One concern is that the encoder-decoder with attention-based network adopts autoregressive generative sequence model with the limitation of "exposure bias" To address this issue, we propose two novel methods, which learn to predict future by improving agreement between forward and backward decoding sequence. The first one is achieved by introducing divergence regularization terms into model training objective to reduce the mismatch between two directional models, namely L2R and R2L (which generates targets from left-to-right and right-to-left, respectively). While the second one operates on decoder-level and exploits the future information during decoding. In addition, we employ a joint training strategy to allow forward and backward decoding to improve each other in an interactive process. Experimental results show our proposed methods especially the second one (bidirectional decoder regularization), leads a significantly improvement on both robustness and overall naturalness, as outperforming baseline (the revised version of Tacotron2) with a MOS gap of 0.14 in a challenging test, and achieving close to human quality (4.42 vs. 4.49 in MOS) on general test.

Synthesizing SQL queries from natural language is a long-standing open problem and has been attracting considerable interest recently. Toward solving the problem, the de facto approach is to employ a sequence-to-sequence-style model. Such an approach will necessarily require the SQL queries to be serialized. Since the same SQL query may have multiple equivalent serializations, training a sequence-to-sequence-style model is sensitive to the choice from one of them. This phenomenon is documented as the "order-matters" problem. Existing state-of-the-art approaches rely on reinforcement learning to reward the decoder when it generates any of the equivalent serializations. However, we observe that the improvement from reinforcement learning is limited. In this paper, we propose a novel approach, i.e., SQLNet, to fundamentally solve this problem by avoiding the sequence-to-sequence structure when the order does not matter. In particular, we employ a sketch-based approach where the sketch contains a dependency graph so that one prediction can be done by taking into consideration only the previous predictions that it depends on. In addition, we propose a sequence-to-set model as well as the column attention mechanism to synthesize the query based on the sketch. By combining all these novel techniques, we show that SQLNet can outperform the prior art by 9% to 13% on the WikiSQL task.

Efficient quantum compiling tactics greatly enhance the capability of quantum computers to execute complicated quantum algorithms. Due to its fundamental importance, a plethora of quantum compilers has been designed in past years. However, there are several caveats to current protocols, which are low optimality, high inference time, limited scalability, and lack of universality. To compensate for these defects, here we devise an efficient and practical quantum compiler assisted by advanced deep reinforcement learning (RL) techniques, i.e., data generation, deep Q-learning, and AQ* search. In this way, our protocol is compatible with various quantum machines and can be used to compile multi-qubit operators. We systematically evaluate the performance of our proposal in compiling quantum operators with both inverse-closed and inverse-free universal basis sets. In the task of single-qubit operator compiling, our proposal outperforms other RL-based quantum compilers in the measure of compiling sequence length and inference time. Meanwhile, the output solution is near-optimal, guaranteed by the Solovay-Kitaev theorem. Notably, for the inverse-free universal basis set, the achieved sequence length complexity is comparable with the inverse-based setting and dramatically advances previous methods. These empirical results contribute to improving the inverse-free Solovay-Kitaev theorem. In addition, for the first time, we demonstrate how to leverage RL-based quantum compilers to accomplish two-qubit operator compiling. The achieved results open an avenue for integrating RL with quantum compiling to unify efficiency and practicality and thus facilitate the exploration of quantum advantages.

The reproduction of state-of-the-art multimodal LLM pre-training faces barriers at every stage of the pipeline, including high-quality data filtering, multimodal data mixture strategies, sequence packing techniques, and training frameworks. We introduce Open-Qwen2VL, a fully open-source 2B-parameter Multimodal Large Language Model pre-trained efficiently on 29M image-text pairs using only 442 A100-40G GPU hours. Our approach employs low-to-high dynamic image resolution and multimodal sequence packing to significantly enhance pre-training efficiency. The training dataset was carefully curated using both MLLM-based filtering techniques (e.g., MLM-Filter) and conventional CLIP-based filtering methods, substantially improving data quality and training efficiency. The Open-Qwen2VL pre-training is conducted on academic level 8xA100-40G GPUs at UCSB on 5B packed multimodal tokens, which is 0.36\% of 1.4T multimodal pre-training tokens of Qwen2-VL. The final instruction-tuned Open-Qwen2VL outperforms partially-open state-of-the-art MLLM Qwen2-VL-2B on various multimodal benchmarks of MMBench, SEEDBench, MMstar, and MathVista, indicating the remarkable training efficiency of Open-Qwen2VL. We open-source all aspects of our work, including compute-efficient and data-efficient training details, data filtering methods, sequence packing scripts, pre-training data in WebDataset format, FSDP-based training codebase, and both base and instruction-tuned model checkpoints. We redefine "fully open" for multimodal LLMs as the complete release of: 1) the training codebase, 2) detailed data filtering techniques, and 3) all pre-training and supervised fine-tuning data used to develop the model.

Vectorized high-definition map online construction has garnered considerable attention in the field of autonomous driving research. Most existing approaches model changeable map elements using a fixed number of points, or predict local maps in a two-stage autoregressive manner, which may miss essential details and lead to error accumulation. Towards precise map element learning, we propose a simple yet effective architecture named PivotNet, which adopts unified pivot-based map representations and is formulated as a direct set prediction paradigm. Concretely, we first propose a novel point-to-line mask module to encode both the subordinate and geometrical point-line priors in the network. Then, a well-designed pivot dynamic matching module is proposed to model the topology in dynamic point sequences by introducing the concept of sequence matching. Furthermore, to supervise the position and topology of the vectorized point predictions, we propose a dynamic vectorized sequence loss. Extensive experiments and ablations show that PivotNet is remarkably superior to other SOTAs by 5.9 mAP at least. The code will be available soon.

The last few years have seen the development of numerous deep learning-based protein-ligand docking methods. They offer huge promise in terms of speed and accuracy. However, despite claims of state-of-the-art performance in terms of crystallographic root-mean-square deviation (RMSD), upon closer inspection, it has become apparent that they often produce physically implausible molecular structures. It is therefore not sufficient to evaluate these methods solely by RMSD to a native binding mode. It is vital, particularly for deep learning-based methods, that they are also evaluated on steric and energetic criteria. We present PoseBusters, a Python package that performs a series of standard quality checks using the well-established cheminformatics toolkit RDKit. Only methods that both pass these checks and predict native-like binding modes should be classed as having "state-of-the-art" performance. We use PoseBusters to compare five deep learning-based docking methods (DeepDock, DiffDock, EquiBind, TankBind, and Uni-Mol) and two well-established standard docking methods (AutoDock Vina and CCDC Gold) with and without an additional post-prediction energy minimisation step using a molecular mechanics force field. We show that both in terms of physical plausibility and the ability to generalise to examples that are distinct from the training data, no deep learning-based method yet outperforms classical docking tools. In addition, we find that molecular mechanics force fields contain docking-relevant physics missing from deep-learning methods. PoseBusters allows practitioners to assess docking and molecular generation methods and may inspire new inductive biases still required to improve deep learning-based methods, which will help drive the development of more accurate and more realistic predictions.

In e-commerce industry, user behavior sequence data has been widely used in many business units such as search and merchandising to improve their products. However, it is rarely used in financial services not only due to its 3V characteristics - i.e. Volume, Velocity and Variety - but also due to its unstructured nature. In this paper, we propose a Financial Service scenario Deep learning based Behavior data representation method for Clustering (FinDeepBehaviorCluster) to detect fraudulent transactions. To utilize the behavior sequence data, we treat click stream data as event sequence, use time attention based Bi-LSTM to learn the sequence embedding in an unsupervised fashion, and combine them with intuitive features generated by risk experts to form a hybrid feature representation. We also propose a GPU powered HDBSCAN (pHDBSCAN) algorithm, which is an engineering optimization for the original HDBSCAN algorithm based on FAISS project, so that clustering can be carried out on hundreds of millions of transactions within a few minutes. The computation efficiency of the algorithm has increased 500 times compared with the original implementation, which makes flash fraud pattern detection feasible. Our experimental results show that the proposed FinDeepBehaviorCluster framework is able to catch missed fraudulent transactions with considerable business values. In addition, rule extraction method is applied to extract patterns from risky clusters using intuitive features, so that narrative descriptions can be attached to the risky clusters for case investigation, and unknown risk patterns can be mined for real-time fraud detection. In summary, FinDeepBehaviorCluster as a complementary risk management strategy to the existing real-time fraud detection engine, can further increase our fraud detection and proactive risk defense capabilities.

Human motion generation stands as a significant pursuit in generative computer vision, while achieving long-sequence and efficient motion generation remains challenging. Recent advancements in state space models (SSMs), notably Mamba, have showcased considerable promise in long sequence modeling with an efficient hardware-aware design, which appears to be a promising direction to build motion generation model upon it. Nevertheless, adapting SSMs to motion generation faces hurdles since the lack of a specialized design architecture to model motion sequence. To address these challenges, we propose Motion Mamba, a simple and efficient approach that presents the pioneering motion generation model utilized SSMs. Specifically, we design a Hierarchical Temporal Mamba (HTM) block to process temporal data by ensemble varying numbers of isolated SSM modules across a symmetric U-Net architecture aimed at preserving motion consistency between frames. We also design a Bidirectional Spatial Mamba (BSM) block to bidirectionally process latent poses, to enhance accurate motion generation within a temporal frame. Our proposed method achieves up to 50% FID improvement and up to 4 times faster on the HumanML3D and KIT-ML datasets compared to the previous best diffusion-based method, which demonstrates strong capabilities of high-quality long sequence motion modeling and real-time human motion generation. See project website https://steve-zeyu-zhang.github.io/MotionMamba/

In this paper, we present Neural Phrase-based Machine Translation (NPMT). Our method explicitly models the phrase structures in output sequences using Sleep-WAke Networks (SWAN), a recently proposed segmentation-based sequence modeling method. To mitigate the monotonic alignment requirement of SWAN, we introduce a new layer to perform (soft) local reordering of input sequences. Different from existing neural machine translation (NMT) approaches, NPMT does not use attention-based decoding mechanisms. Instead, it directly outputs phrases in a sequential order and can decode in linear time. Our experiments show that NPMT achieves superior performances on IWSLT 2014 German-English/English-German and IWSLT 2015 English-Vietnamese machine translation tasks compared with strong NMT baselines. We also observe that our method produces meaningful phrases in output languages.

Skeletal sequence data, as a widely employed representation of human actions, are crucial in Human Activity Recognition (HAR). Recently, adversarial attacks have been proposed in this area, which exposes potential security concerns, and more importantly provides a good tool for model robustness test. Within this research, transfer-based attack is an important tool as it mimics the real-world scenario where an attacker has no knowledge of the target model, but is under-explored in Skeleton-based HAR (S-HAR). Consequently, existing S-HAR attacks exhibit weak adversarial transferability and the reason remains largely unknown. In this paper, we investigate this phenomenon via the characterization of the loss function. We find that one prominent indicator of poor transferability is the low smoothness of the loss function. Led by this observation, we improve the transferability by properly smoothening the loss when computing the adversarial examples. This leads to the first Transfer-based Attack on Skeletal Action Recognition, TASAR. TASAR explores the smoothened model posterior of pre-trained surrogates, which is achieved by a new post-train Dual Bayesian optimization strategy. Furthermore, unlike existing transfer-based methods which overlook the temporal coherence within sequences, TASAR incorporates motion dynamics into the Bayesian attack, effectively disrupting the spatial-temporal coherence of S-HARs. For exhaustive evaluation, we build the first large-scale robust S-HAR benchmark, comprising 7 S-HAR models, 10 attack methods, 3 S-HAR datasets and 2 defense models. Extensive results demonstrate the superiority of TASAR. Our benchmark enables easy comparisons for future studies, with the code available in the https://github.com/yunfengdiao/Skeleton-Robustness-Benchmark.

Recently, diffusion-based methods for monocular 3D human pose estimation have achieved state-of-the-art (SOTA) performance by directly regressing the 3D joint coordinates from the 2D pose sequence. Although some methods decompose the task into bone length and bone direction prediction based on the human anatomical skeleton to explicitly incorporate more human body prior constraints, the performance of these methods is significantly lower than that of the SOTA diffusion-based methods. This can be attributed to the tree structure of the human skeleton. Direct application of the disentangled method could amplify the accumulation of hierarchical errors, propagating through each hierarchy. Meanwhile, the hierarchical information has not been fully explored by the previous methods. To address these problems, a Disentangled Diffusion-based 3D Human Pose Estimation method with Hierarchical Spatial and Temporal Denoiser is proposed, termed DDHPose. In our approach: (1) We disentangle the 3D pose and diffuse the bone length and bone direction during the forward process of the diffusion model to effectively model the human pose prior. A disentanglement loss is proposed to supervise diffusion model learning. (2) For the reverse process, we propose Hierarchical Spatial and Temporal Denoiser (HSTDenoiser) to improve the hierarchical modeling of each joint. Our HSTDenoiser comprises two components: the Hierarchical-Related Spatial Transformer (HRST) and the Hierarchical-Related Temporal Transformer (HRTT). HRST exploits joint spatial information and the influence of the parent joint on each joint for spatial modeling, while HRTT utilizes information from both the joint and its hierarchical adjacent joints to explore the hierarchical temporal correlations among joints. Code and models are available at https://github.com/Andyen512/DDHPose

Symbolic regression (SR) is a challenging task in machine learning that involves finding a mathematical expression for a function based on its values. Recent advancements in SR have demonstrated the effectiveness of pretrained transformer-based models in generating equations as sequences, leveraging large-scale pretraining on synthetic datasets and offering notable advantages in terms of inference time over GP-based methods. However, these models primarily rely on supervised pretraining goals borrowed from text generation and overlook equation-specific objectives like accuracy and complexity. To address this, we propose TPSR, a Transformer-based Planning strategy for Symbolic Regression that incorporates Monte Carlo Tree Search into the transformer decoding process. Unlike conventional decoding strategies, TPSR enables the integration of non-differentiable feedback, such as fitting accuracy and complexity, as external sources of knowledge into the transformer-based equation generation process. Extensive experiments on various datasets show that our approach outperforms state-of-the-art methods, enhancing the model's fitting-complexity trade-off, extrapolation abilities, and robustness to noise

Lip-reading aims to infer the speech content from the lip movement sequence and can be seen as a typical sequence-to-sequence (seq2seq) problem which translates the input image sequence of lip movements to the text sequence of the speech content. However, the traditional learning process of seq2seq models always suffers from two problems: the exposure bias resulted from the strategy of "teacher-forcing", and the inconsistency between the discriminative optimization target (usually the cross-entropy loss) and the final evaluation metric (usually the character/word error rate). In this paper, we propose a novel pseudo-convolutional policy gradient (PCPG) based method to address these two problems. On the one hand, we introduce the evaluation metric (refers to the character error rate in this paper) as a form of reward to optimize the model together with the original discriminative target. On the other hand, inspired by the local perception property of convolutional operation, we perform a pseudo-convolutional operation on the reward and loss dimension, so as to take more context around each time step into account to generate a robust reward and loss for the whole optimization. Finally, we perform a thorough comparison and evaluation on both the word-level and sentence-level benchmarks. The results show a significant improvement over other related methods, and report either a new state-of-the-art performance or a competitive accuracy on all these challenging benchmarks, which clearly proves the advantages of our approach.

Most language model pre-training frameworks concatenate multiple documents into fixed-length sequences and use causal masking to compute the likelihood of each token given its context; this strategy is widely adopted due to its simplicity and efficiency. However, to this day, the influence of the pre-training sequence composition strategy on the generalisation properties of the model remains under-explored. In this work, we find that applying causal masking can lead to the inclusion of distracting information from previous documents during pre-training, which negatively impacts the performance of the models on language modelling and downstream tasks. In intra-document causal masking, the likelihood of each token is only conditioned on the previous tokens in the same document, eliminating potential distracting information from previous documents and significantly improving performance. Furthermore, we find that concatenating related documents can reduce some potential distractions during pre-training, and our proposed efficient retrieval-based sequence construction method, BM25Chunk, can improve in-context learning (+11.6\%), knowledge memorisation (+9.8\%), and context utilisation (+7.2\%) abilities of language models without sacrificing efficiency.

Visual Odometry (VO) is crucial for autonomous robotic navigation, especially in GPS-denied environments like planetary terrains. While standard RGB cameras struggle in low-light or high-speed motion, event-based cameras offer high dynamic range and low latency. However, seamlessly integrating asynchronous event data with synchronous frames remains challenging. We introduce RAMP-VO, the first end-to-end learned event- and image-based VO system. It leverages novel Recurrent, Asynchronous, and Massively Parallel (RAMP) encoders that are 8x faster and 20% more accurate than existing asynchronous encoders. RAMP-VO further employs a novel pose forecasting technique to predict future poses for initialization. Despite being trained only in simulation, RAMP-VO outperforms image- and event-based methods by 52% and 20%, respectively, on traditional, real-world benchmarks as well as newly introduced Apollo and Malapert landing sequences, paving the way for robust and asynchronous VO in space.

We present a flow-based approach to the optimal transport (OT) problem between two continuous distributions pi_0,pi_1 on R^d, of minimizing a transport cost E[c(X_1-X_0)] in the set of couplings (X_0,X_1) whose marginal distributions on X_0,X_1 equals pi_0,pi_1, respectively, where c is a cost function. Our method iteratively constructs a sequence of neural ordinary differentiable equations (ODE), each learned by solving a simple unconstrained regression problem, which monotonically reduce the transport cost while automatically preserving the marginal constraints. This yields a monotonic interior approach that traverses inside the set of valid couplings to decrease the transport cost, which distinguishes itself from most existing approaches that enforce the coupling constraints from the outside. The main idea of the method draws from rectified flow, a recent approach that simultaneously decreases the whole family of transport costs induced by convex functions c (and is hence multi-objective in nature), but is not tailored to minimize a specific transport cost. Our method is a single-object variant of rectified flow that guarantees to solve the OT problem for a fixed, user-specified convex cost function c.

The identification of bitter peptides is crucial in various domains, including food science, drug discovery, and biochemical research. These peptides not only contribute to the undesirable taste of hydrolyzed proteins but also play key roles in physiological and pharmacological processes. However, experimental methods for identifying bitter peptides are time-consuming and expensive. With the rapid expansion of peptide sequence databases in the post-genomic era, the demand for efficient computational approaches to distinguish bitter from non-bitter peptides has become increasingly significant. In this study, we propose a novel stacking-based ensemble learning framework aimed at enhancing the accuracy and reliability of bitter peptide classification. Our method integrates diverse sequence-based feature representations and leverages a broad set of machine learning classifiers. The first stacking layer comprises multiple base classifiers, each trained on distinct feature encoding schemes, while the second layer employs logistic regression to refine predictions using an eight-dimensional probability vector. Extensive evaluations on a carefully curated dataset demonstrate that our model significantly outperforms existing predictive methods, providing a robust and reliable computational tool for bitter peptide identification. Our approach achieves an accuracy of 96.09\% and a Matthews Correlation Coefficient (MCC) of 0.9220 on the independent test set, underscoring its effectiveness and generalizability. To facilitate real-time usage and broader accessibility, we have also developed a user-friendly web server based on the proposed method, which is freely accessible at https://ibitter-stack-webserver.streamlit.app/. This tool enables researchers and practitioners to conveniently screen peptide sequences for bitterness in real-time applications.

Deploying transformer models in practice is challenging due to their inference cost, which scales quadratically with input sequence length. To address this, we present a novel Learned Token Pruning (LTP) method which adaptively removes unimportant tokens as an input sequence passes through transformer layers. In particular, LTP prunes tokens with an attention score below a threshold value which is learned for each layer during training. Our threshold-based method allows the length of the pruned sequence to vary adaptively based on the input sequence, and avoids algorithmically expensive operations such as top-k token selection. We extensively test the performance of LTP on GLUE tasks and show that our method outperforms the prior state-of-the-art token pruning methods by up to ~2.5% higher accuracy with the same amount of FLOPs. In particular, LTP achieves up to 2.1x FLOPs reduction with less than 1% accuracy drop, which results in up to 1.9x and 2.0x throughput improvement on Intel Haswell CPUs and NVIDIA V100 GPUs, respectively. Furthermore, we demonstrate that LTP is more robust than prior methods to variations on input sentence lengths. Our code has been developed in PyTorch and has been open-sourced.

Deep learning-based methods have been widely researched in the areas of language and vision, demonstrating their capacity to understand long sequences of data and their usefulness in numerous helio-physics applications. Foundation models (FMs), which are pre-trained on a large-scale datasets, form the basis for a variety of downstream tasks. These models, especially those based on transformers in vision and language, show exceptional potential for adapting to a wide range of downstream applications. In this paper, we provide our perspective on the criteria for designing an FM for heliophysics and associated challenges and applications using the Solar Dynamics Observatory (SDO) dataset. We believe that this is the first study to design an FM in the domain of heliophysics.

Automated source code refactoring, particularly extract method refactoring, is a crucial and frequently employed technique during software development. Despite its importance and frequent use by practitioners, current automated techniques face significant limitations. These approaches often rely on developers to identify the precise bounds of refactoring opportunities in terms of source code statements. Also, they often do not capture the semantic context, resulting in offering no automated means to suggest meaningful method name, for instance. To address these challenges, we propose a novel reinforcement learning-based approach for fine-tuning and aligning code language models to perform automated, intelligent extract method refactoring on Java source code. Our approach fine-tunes sequence-to-sequence generative models and aligns them using the Proximal Policy Optimization (PPO) algorithm. We utilize code compilation and presence of the refactoring in the generated code as reward signals, providing a code-centric optimization process. Our experiments demonstrate that our approach significantly enhances the performance of large language models in code refactoring, as evidenced by both quantitative evaluation metrics such as BLEU, ROUGE, and CodeBLEU, and qualitative measures including syntactical and functional correctness. The supervised fine-tuned model, further aligned with PPO, surpasses traditional supervised fine-tuning by 11.96% and 16.45% in terms of BLEU and CodeBLEU scores, respectively. When subjected to a suite of 122 unit tests, the number of successful tests increased from 41 to 66 for the reinforcement learning aligned fine-tuned Code-T5 model, highlighting the effectiveness of our approach in producing functionally correct refactorings.

Facial Expression Recognition (FER) in the wild is extremely challenging due to occlusions, variant head poses, face deformation and motion blur under unconstrained conditions. Although substantial progresses have been made in automatic FER in the past few decades, previous studies were mainly designed for lab-controlled FER. Real-world occlusions, variant head poses and other issues definitely increase the difficulty of FER on account of these information-deficient regions and complex backgrounds. Different from previous pure CNNs based methods, we argue that it is feasible and practical to translate facial images into sequences of visual words and perform expression recognition from a global perspective. Therefore, we propose the Visual Transformers with Feature Fusion (VTFF) to tackle FER in the wild by two main steps. First, we propose the attentional selective fusion (ASF) for leveraging two kinds of feature maps generated by two-branch CNNs. The ASF captures discriminative information by fusing multiple features with the global-local attention. The fused feature maps are then flattened and projected into sequences of visual words. Second, inspired by the success of Transformers in natural language processing, we propose to model relationships between these visual words with the global self-attention. The proposed method is evaluated on three public in-the-wild facial expression datasets (RAF-DB, FERPlus and AffectNet). Under the same settings, extensive experiments demonstrate that our method shows superior performance over other methods, setting new state of the art on RAF-DB with 88.14%, FERPlus with 88.81% and AffectNet with 61.85%. The cross-dataset evaluation on CK+ shows the promising generalization capability of the proposed method.

Cryo-electron microscopy (cryo-EM) is a technique for reconstructing the 3-dimensional (3D) structure of biomolecules (especially large protein complexes and molecular assemblies). As the resolution increases to the near-atomic scale, building protein structures de novo from cryo-EM maps becomes possible. Recently, recognition-based de novo building methods have shown the potential to streamline this process. However, it cannot build a complete structure due to the low signal-to-noise ratio (SNR) problem. At the same time, AlphaFold has led to a great breakthrough in predicting protein structures. This has inspired us to combine fragment recognition and structure prediction methods to build a complete structure. In this paper, we propose a new method named FFF that bridges protein structure prediction and protein structure recognition with flexible fitting. First, a multi-level recognition network is used to capture various structural features from the input 3D cryo-EM map. Next, protein structural fragments are generated using pseudo peptide vectors and a protein sequence alignment method based on these extracted features. Finally, a complete structural model is constructed using the predicted protein fragments via flexible fitting. Based on our benchmark tests, FFF outperforms the baseline methods for building complete protein structures.

This paper tackles the challenge of real-time 3D trajectory prediction for UAVs, which is critical for applications such as aerial surveillance and defense. Existing prediction models that rely primarily on position data struggle with accuracy, especially when UAV movements fall outside the position domain used in training. Our research identifies a gap in utilizing velocity estimates, first-order dynamics, to better capture the dynamics and enhance prediction accuracy and generalizability in any position domain. To bridge this gap, we propose a new trajectory prediction method using Gated Recurrent Units (GRUs) within sequence-based neural networks. Unlike traditional methods that rely on RNNs or transformers, this approach forecasts future velocities and positions based on historical velocity data instead of positions. This is designed to enhance prediction accuracy and scalability, overcoming challenges faced by conventional models in handling complex UAV dynamics. The methodology employs both synthetic and real-world 3D UAV trajectory data, capturing a wide range of flight patterns, speeds, and agility. Synthetic data is generated using the Gazebo simulator and PX4 Autopilot, while real-world data comes from the UZH-FPV and Mid-Air drone racing datasets. The GRU-based models significantly outperform state-of-the-art RNN approaches, with a mean square error (MSE) as low as 2 x 10^-8. Overall, our findings confirm the effectiveness of incorporating velocity data in improving the accuracy of UAV trajectory predictions across both synthetic and real-world scenarios, in and out of position data distributions. Finally, we open-source our 5000 trajectories dataset and a ROS 2 package to facilitate the integration with existing ROS-based UAV systems.

Speculative decoding is an inference-acceleration method for large language models (LLMs) where a small language model generates a draft-token sequence which is further verified by the target LLM in parallel. Recent works have advanced this method by establishing a draft-token tree, achieving superior performance over a single-sequence speculative decoding. However, those works independently generate tokens at each level of the tree, not leveraging the tree's entire diversifiability. Besides, their empirical superiority has been shown for fixed length of sequences, implicitly granting more computational resource to LLM for the tree-based methods. None of the existing works has conducted empirical studies with fixed target computational budgets despite its importance to resource-bounded devices. We present Recursive Speculative Decoding (RSD), a novel tree-based method that samples draft tokens without replacement and maximizes the diversity of the tree. During RSD's drafting, the tree is built by either Gumbel-Top-k trick that draws tokens without replacement in parallel or Stochastic Beam Search that samples sequences without replacement while early-truncating unlikely draft sequences and reducing the computational cost of LLM. We empirically evaluate RSD with Llama 2 and OPT models, showing that RSD outperforms the baseline methods, consistently for fixed draft sequence length and in most cases for fixed computational budgets at LLM.

Proteins power a vast array of functional processes in living cells. The capability to create new proteins with designed structures and functions would thus enable the engineering of cellular behavior and development of protein-based therapeutics and materials. Structure-based protein design aims to find structures that are designable (can be realized by a protein sequence), novel (have dissimilar geometry from natural proteins), and diverse (span a wide range of geometries). While advances in protein structure prediction have made it possible to predict structures of novel protein sequences, the combinatorially large space of sequences and structures limits the practicality of search-based methods. Generative models provide a compelling alternative, by implicitly learning the low-dimensional structure of complex data distributions. Here, we leverage recent advances in denoising diffusion probabilistic models and equivariant neural networks to develop Genie, a generative model of protein structures that performs discrete-time diffusion using a cloud of oriented reference frames in 3D space. Through in silico evaluations, we demonstrate that Genie generates protein backbones that are more designable, novel, and diverse than existing models. This indicates that Genie is capturing key aspects of the distribution of protein structure space and facilitates protein design with high success rates. Code for generating new proteins and training new versions of Genie is available at https://github.com/aqlaboratory/genie.

Named entity recognition is a fundamental task in natural language processing, identifying the span and category of entities in unstructured texts. The traditional sequence labeling methodology ignores the nested entities, i.e. entities included in other entity mentions. Many approaches attempt to address this scenario, most of which rely on complex structures or have high computation complexity. The representation learning of the heterogeneous star graph containing text nodes and type nodes is investigated in this paper. In addition, we revise the graph attention mechanism into a hybrid form to address its unreasonableness in specific topologies. The model performs the type-supervised sequence labeling after updating nodes in the graph. The annotation scheme is an extension of the single-layer sequence labeling and is able to cope with the vast majority of nested entities. Extensive experiments on public NER datasets reveal the effectiveness of our model in extracting both flat and nested entities. The method achieved state-of-the-art performance on both flat and nested datasets. The significant improvement in accuracy reflects the superiority of the multi-layer labeling strategy.

Quantifying uncertainty in large language models (LLMs) is important for safety-critical applications because it helps spot incorrect answers, known as hallucinations. One major trend of uncertainty quantification methods is based on estimating the entropy of the distribution of the LLM's potential output sequences. This estimation is based on a set of output sequences and associated probabilities obtained by querying the LLM several times. In this paper, we advocate and experimentally show that the probability of unobserved sequences plays a crucial role, and we recommend future research to integrate it to enhance such LLM uncertainty quantification methods.

In multilingual settings, non-Latin scripts and low-resource languages are usually disadvantaged in terms of language models' utility, efficiency, and cost. Specifically, previous studies have reported multiple modeling biases that the current tokenization algorithms introduce to non-Latin script languages, the main one being over-segmentation. In this work, we propose MAGNET; multilingual adaptive gradient-based tokenization to reduce over-segmentation via adaptive gradient-based subword tokenization. MAGNET learns to predict segment boundaries between byte tokens in a sequence via sub-modules within the model, which act as internal boundary predictors (tokenizers). Previous gradient-based tokenization methods aimed for uniform compression across sequences by integrating a single boundary predictor during training and optimizing it end-to-end through stochastic reparameterization alongside the next token prediction objective. However, this approach still results in over-segmentation for non-Latin script languages in multilingual settings. In contrast, MAGNET offers a customizable architecture where byte-level sequences are routed through language-script-specific predictors, each optimized for its respective language script. This modularity enforces equitable segmentation granularity across different language scripts compared to previous methods. Through extensive experiments, we demonstrate that in addition to reducing segmentation disparities, MAGNET also enables faster language modelling and improves downstream utility.

We introduce HOIGPT, a token-based generative method that unifies 3D hand-object interactions (HOI) perception and generation, offering the first comprehensive solution for captioning and generating high-quality 3D HOI sequences from a diverse range of conditional signals (\eg text, objects, partial sequences). At its core, HOIGPT utilizes a large language model to predict the bidrectional transformation between HOI sequences and natural language descriptions. Given text inputs, HOIGPT generates a sequence of hand and object meshes; given (partial) HOI sequences, HOIGPT generates text descriptions and completes the sequences. To facilitate HOI understanding with a large language model, this paper introduces two key innovations: (1) a novel physically grounded HOI tokenizer, the hand-object decomposed VQ-VAE, for discretizing HOI sequences, and (2) a motion-aware language model trained to process and generate both text and HOI tokens. Extensive experiments demonstrate that HOIGPT sets new state-of-the-art performance on both text generation (+2.01% R Precision) and HOI generation (-2.56 FID) across multiple tasks and benchmarks.

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we developed k-mer embeddings that merge contextual and structural string information by enhancing De Bruijn graphs with structural similarity connections. Subsequently, we crafted a self-supervised method based on Contrastive Learning that employs a heterogeneous Graph Convolutional Network encoder and constructs positive pairs based on node similarities. Our embeddings consistently outperform prior techniques for Edit Distance Approximation and Closest String Retrieval tasks.

Context information in search sessions has proven to be useful for capturing user search intent. Existing studies explored user behavior sequences in sessions in different ways to enhance query suggestion or document ranking. However, a user behavior sequence has often been viewed as a definite and exact signal reflecting a user's behavior. In reality, it is highly variable: user's queries for the same intent can vary, and different documents can be clicked. To learn a more robust representation of the user behavior sequence, we propose a method based on contrastive learning, which takes into account the possible variations in user's behavior sequences. Specifically, we propose three data augmentation strategies to generate similar variants of user behavior sequences and contrast them with other sequences. In so doing, the model is forced to be more robust regarding the possible variations. The optimized sequence representation is incorporated into document ranking. Experiments on two real query log datasets show that our proposed model outperforms the state-of-the-art methods significantly, which demonstrates the effectiveness of our method for context-aware document ranking.

Flow matching in the continuous simplex has emerged as a promising strategy for DNA sequence design, but struggles to scale to higher simplex dimensions required for peptide and protein generation. We introduce Gumbel-Softmax Flow and Score Matching, a generative framework on the simplex based on a novel Gumbel-Softmax interpolant with a time-dependent temperature. Using this interpolant, we introduce Gumbel-Softmax Flow Matching by deriving a parameterized velocity field that transports from smooth categorical distributions to distributions concentrated at a single vertex of the simplex. We alternatively present Gumbel-Softmax Score Matching which learns to regress the gradient of the probability density. Our framework enables high-quality, diverse generation and scales efficiently to higher-dimensional simplices. To enable training-free guidance, we propose Straight-Through Guided Flows (STGFlow), a classifier-based guidance method that leverages straight-through estimators to steer the unconditional velocity field toward optimal vertices of the simplex. STGFlow enables efficient inference-time guidance using classifiers pre-trained on clean sequences, and can be used with any discrete flow method. Together, these components form a robust framework for controllable de novo sequence generation. We demonstrate state-of-the-art performance in conditional DNA promoter design, sequence-only protein generation, and target-binding peptide design for rare disease treatment.

Unsupervised constituency parsing focuses on identifying word sequences that form a syntactic unit (i.e., constituents) in target sentences. Linguists identify the constituent by evaluating a set of Predicate-Argument Structure (PAS) equivalent sentences where we find the constituent appears more frequently than non-constituents (i.e., the constituent corresponds to a frequent word sequence within the sentence set). However, such frequency information is unavailable in previous parsing methods that identify the constituent by observing sentences with diverse PAS. In this study, we empirically show that constituents correspond to frequent word sequences in the PAS-equivalent sentence set. We propose a frequency-based parser span-overlap that (1) computes the span-overlap score as the word sequence's frequency in the PAS-equivalent sentence set and (2) identifies the constituent structure by finding a constituent tree with the maximum span-overlap score. The parser achieves state-of-the-art level parsing accuracy, outperforming existing unsupervised parsers in eight out of ten languages. Additionally, we discover a multilingual phenomenon: participant-denoting constituents tend to have higher span-overlap scores than equal-length event-denoting constituents, meaning that the former tend to appear more frequently in the PAS-equivalent sentence set than the latter. The phenomenon indicates a statistical difference between the two constituent types, laying the foundation for future labeled unsupervised parsing research.

Despite significant popularity, Large-language Models (LLMs) require explicit, contextual facts to support domain-specific knowledge-intensive tasks in the design process. The applications built using LLMs should hence adopt Retrieval-Augmented Generation (RAG) to better suit the design process. In this article, we present a data-driven method to identify explicit facts from patent documents that provide standard descriptions of over 8 million artefacts. In our method, we train roBERTa Transformer-based sequence classification models using our dataset of 44,227 sentences and facts. Upon classifying tokens in a sentence as entities or relationships, our method uses another classifier to identify specific relationship tokens for a given pair of entities so that explicit facts of the form head entity :: relationship :: tail entity are identified. In the benchmark approaches for constructing facts, we use linear classifiers and Graph Neural Networks (GNNs) both incorporating BERT Transformer-based token embeddings to predict associations among the entities and relationships. We apply our method to 4,870 fan system related patents and populate a knowledge base of around 3 million facts. Upon retrieving the facts representing generalisable domain knowledge and the knowledge of specific subsystems and issues, we demonstrate how these facts contextualise LLMs for generating text that is more relevant to the design process.

Recent advancements in Mamba have shown promising results in image restoration. These methods typically flatten 2D images into multiple distinct 1D sequences along rows and columns, process each sequence independently using selective scan operation, and recombine them to form the outputs. However, such a paradigm overlooks two vital aspects: i) the local relationships and spatial continuity inherent in natural images, and ii) the discrepancies among sequences unfolded through totally different ways. To overcome the drawbacks, we explore two problems in Mamba-based restoration methods: i) how to design a scanning strategy preserving both locality and continuity while facilitating restoration, and ii) how to aggregate the distinct sequences unfolded in totally different ways. To address these problems, we propose a novel Mamba-based Image Restoration model (MaIR), which consists of Nested S-shaped Scanning strategy (NSS) and Sequence Shuffle Attention block (SSA). Specifically, NSS preserves locality and continuity of the input images through the stripe-based scanning region and the S-shaped scanning path, respectively. SSA aggregates sequences through calculating attention weights within the corresponding channels of different sequences. Thanks to NSS and SSA, MaIR surpasses 40 baselines across 14 challenging datasets, achieving state-of-the-art performance on the tasks of image super-resolution, denoising, deblurring and dehazing. The code is available at https://github.com/XLearning-SCU/2025-CVPR-MaIR.

The ionosphere electromagnetic activity is a major factor of the quality of satellite telecommunications, Global Navigation Satellite Systems (GNSS) and other vital space applications. Being able to forecast globally the Total Electron Content (TEC) would enable a better anticipation of potential performance degradations. A few studies have proposed models able to predict the TEC locally, but not worldwide for most of them. Thanks to a large record of past TEC maps publicly available, we propose a method based on Deep Neural Networks (DNN) to forecast a sequence of global TEC maps consecutive to an input sequence of TEC maps, without introducing any prior knowledge other than Earth rotation periodicity. By combining several state-of-the-art architectures, the proposed approach is competitive with previous works on TEC forecasting while predicting the TEC globally.

Recently, the state space model Mamba has demonstrated efficient long-sequence modeling capabilities, particularly for addressing long-sequence visual tasks in 3D medical imaging. However, existing generative self-supervised learning methods have not yet fully unleashed Mamba's potential for handling long-range dependencies because they overlook the inherent causal properties of state space sequences in masked modeling. To address this challenge, we propose a general-purpose pre-training framework called MambaMIM, a masked image modeling method based on a novel TOKen-Interpolation strategy (TOKI) for the selective structure state space sequence, which learns causal relationships of state space within the masked sequence. Further, MambaMIM introduces a bottom-up 3D hybrid masking strategy to maintain a masking consistency across different architectures and can be used on any single or hybrid Mamba architecture to enhance its multi-scale and long-range representation capability. We pre-train MambaMIM on a large-scale dataset of 6.8K CT scans and evaluate its performance across eight public medical segmentation benchmarks. Extensive downstream experiments reveal the feasibility and advancement of using Mamba for medical image pre-training. In particular, when we apply the MambaMIM to a customized architecture that hybridizes MedNeXt and Vision Mamba, we consistently obtain the state-of-the-art segmentation performance. The code is available at: https://github.com/FengheTan9/MambaMIM.

Offline model-based optimization aims to maximize a black-box objective function with a static dataset of designs and their scores. In this paper, we focus on biological sequence design to maximize some sequence score. A recent approach employs bidirectional learning, combining a forward mapping for exploitation and a backward mapping for constraint, and it relies on the neural tangent kernel (NTK) of an infinitely wide network to build a proxy model. Though effective, the NTK cannot learn features because of its parametrization, and its use prevents the incorporation of powerful pre-trained Language Models (LMs) that can capture the rich biophysical information in millions of biological sequences. We adopt an alternative proxy model, adding a linear head to a pre-trained LM, and propose a linearization scheme. This yields a closed-form loss and also takes into account the biophysical information in the pre-trained LM. In addition, the forward mapping and the backward mapping play different roles and thus deserve different weights during sequence optimization. To achieve this, we train an auxiliary model and leverage its weak supervision signal via a bi-level optimization framework to effectively learn how to balance the two mappings. Further, by extending the framework, we develop the first learning rate adaptation module Adaptive-eta, which is compatible with all gradient-based algorithms for offline model-based optimization. Experimental results on DNA/protein sequence design tasks verify the effectiveness of our algorithm. Our code is available~https://anonymous.4open.science/r/BIB-ICLR2023-Submission/README.md{here.}

We address the challenge of efficient auto-regressive generation in sequence prediction models by introducing FutureFill - a method for fast generation that applies to any sequence prediction algorithm based on convolutional operators. Our approach reduces the generation time requirement from quadratic to quasilinear relative to the context length. Additionally, FutureFill requires a prefill cache sized only by the number of tokens generated, which is smaller than the cache requirements for standard convolutional and attention-based models. We validate our theoretical findings with experimental evidence demonstrating correctness and efficiency gains in a synthetic generation task.

As the field of artificial intelligence progresses, assistive technologies are becoming more widely used across all industries. The healthcare industry is no different, with numerous studies being done to develop assistive tools for healthcare professionals. Automatic diagnostic systems are one such beneficial tool that can assist with a variety of tasks, including collecting patient information, analyzing test results, and diagnosing patients. However, the idea of developing systems that can provide a differential diagnosis has been largely overlooked in most of these research studies. In this study, we propose a transformer-based approach for providing differential diagnoses based on a patient's age, sex, medical history, and symptoms. We use the DDXPlus dataset, which provides differential diagnosis information for patients based on 49 disease types. Firstly, we propose a method to process the tabular patient data from the dataset and engineer them into patient reports to make them suitable for our research. In addition, we introduce two data modification modules to diversify the training data and consequently improve the robustness of the models. We approach the task as a multi-label classification problem and conduct extensive experiments using four transformer models. All the models displayed promising results by achieving over 97% F1 score on the held-out test set. Moreover, we design additional behavioral tests to get a broader understanding of the models. In particular, for one of our test cases, we prepared a custom test set of 100 samples with the assistance of a doctor. The results on the custom set showed that our proposed data modification modules improved the model's generalization capabilities. We hope our findings will provide future researchers with valuable insights and inspire them to develop reliable systems for automatic differential diagnosis.

We introduce Entropy-Guided Sequence Weighting (EGSW), a novel approach that enhances the exploration-exploitation tradeoff by dynamically assigning weights to generated outputs based on their advantage and entropy for Reinforcement Learning-based Large Language Model fine-tuning. EGSW integrates entropy regularization with advantage-based weighting to balance policy updates, enabling efficient exploration in high-dimensional state spaces. By employing temperature-scaled softmax weighting over sequences, EGSW prioritizing high-reward, high-uncertainty steps while maintaining training stability. Although originally developed to improve Group Relative Policy Optimization (GRPO) during large language model (LLM) fine-tuning, EGSW is generalizable to other reinforcement learning (RL) algorithms and can be implemented in both step-wise and trajectory-wise settings. Empirical evaluations demonstrate that EGSW enhances GRPO reasoning ability, yielding improvements in sample efficiency. Future work will explore the application of EGSW to advanced RL methodologies.

Recent advances in diffusion models have significantly improved conditional video generation, particularly in the pose-guided human image animation task. Although existing methods are capable of generating high-fidelity and time-consistent animation sequences in regular motions and static scenes, there are still obvious limitations when facing complex human body motions (Hypermotion) that contain highly dynamic, non-standard motions, and the lack of a high-quality benchmark for evaluation of complex human motion animations. To address this challenge, we introduce the Open-HyperMotionX Dataset and HyperMotionX Bench, which provide high-quality human pose annotations and curated video clips for evaluating and improving pose-guided human image animation models under complex human motion conditions. Furthermore, we propose a simple yet powerful DiT-based video generation baseline and design spatial low-frequency enhanced RoPE, a novel module that selectively enhances low-frequency spatial feature modeling by introducing learnable frequency scaling. Our method significantly improves structural stability and appearance consistency in highly dynamic human motion sequences. Extensive experiments demonstrate the effectiveness of our dataset and proposed approach in advancing the generation quality of complex human motion image animations. Code and dataset will be made publicly available.

Camera control is crucial for generating expressive and cinematic videos. Existing methods rely on explicit sequences of camera parameters as control conditions, which can be cumbersome for users to construct, particularly for intricate camera movements. To provide a more intuitive camera control method, we propose CamCloneMaster, a framework that enables users to replicate camera movements from reference videos without requiring camera parameters or test-time fine-tuning. CamCloneMaster seamlessly supports reference-based camera control for both Image-to-Video and Video-to-Video tasks within a unified framework. Furthermore, we present the Camera Clone Dataset, a large-scale synthetic dataset designed for camera clone learning, encompassing diverse scenes, subjects, and camera movements. Extensive experiments and user studies demonstrate that CamCloneMaster outperforms existing methods in terms of both camera controllability and visual quality.

Large language models have achieved notable success across various domains, yet efficient inference is still limited by the quadratic computation complexity of the attention mechanism. The inference consists of prefilling and decoding phases. Although several attempts have been made to accelerate decoding, the inefficiency of the prefilling phase, especially for long-context tasks, remains a challenge. In this paper, we observe a locality in query criticality during the prefilling phase of long-context processing: adjacent query tokens tend to focus on similar subsets of the past Key-Value (KV) cache. Based on this observation, we propose CritiPrefill, a criticality-based segment-wise prefilling method. This method partitions the input sequence's queries and KV cache into segments and blocks, utilizing a segment-wise algorithm to estimate the query criticality. By pruning non-critical computations between query segments and cache blocks in the self-attention mechanism, the prefilling process can be significantly accelerated. Extensive evaluations on multiple long-context datasets show up to 2.7x speedup on Llama3-8B and 3.0x speedup on Yi-9B for 128K context length on a single A100 GPU, with minimal quality degradation.

Transducer and Attention based Encoder-Decoder (AED) are two widely used frameworks for speech-to-text tasks. They are designed for different purposes and each has its own benefits and drawbacks for speech-to-text tasks. In order to leverage strengths of both modeling methods, we propose a solution by combining Transducer and Attention based Encoder-Decoder (TAED) for speech-to-text tasks. The new method leverages AED's strength in non-monotonic sequence to sequence learning while retaining Transducer's streaming property. In the proposed framework, Transducer and AED share the same speech encoder. The predictor in Transducer is replaced by the decoder in the AED model, and the outputs of the decoder are conditioned on the speech inputs instead of outputs from an unconditioned language model. The proposed solution ensures that the model is optimized by covering all possible read/write scenarios and creates a matched environment for streaming applications. We evaluate the proposed approach on the MuST-C dataset and the findings demonstrate that TAED performs significantly better than Transducer for offline automatic speech recognition (ASR) and speech-to-text translation (ST) tasks. In the streaming case, TAED outperforms Transducer in the ASR task and one ST direction while comparable results are achieved in another translation direction.

Cis-regulatory elements (CREs), such as promoters and enhancers, are relatively short DNA sequences that directly regulate gene expression. The fitness of CREs, measured by their ability to modulate gene expression, highly depends on the nucleotide sequences, especially specific motifs known as transcription factor binding sites (TFBSs). Designing high-fitness CREs is crucial for therapeutic and bioengineering applications. Current CRE design methods are limited by two major drawbacks: (1) they typically rely on iterative optimization strategies that modify existing sequences and are prone to local optima, and (2) they lack the guidance of biological prior knowledge in sequence optimization. In this paper, we address these limitations by proposing a generative approach that leverages reinforcement learning (RL) to fine-tune a pre-trained autoregressive (AR) model. Our method incorporates data-driven biological priors by deriving computational inference-based rewards that simulate the addition of activator TFBSs and removal of repressor TFBSs, which are then integrated into the RL process. We evaluate our method on promoter design tasks in two yeast media conditions and enhancer design tasks for three human cell types, demonstrating its ability to generate high-fitness CREs while maintaining sequence diversity. The code is available at https://github.com/yangzhao1230/TACO.

Diffusion models have achieved state-of-the-art performance across multiple domains, with recent advancements extending their applicability to discrete data. However, aligning discrete diffusion models with task-specific preferences remains challenging, particularly in scenarios where explicit reward functions are unavailable. In this work, we introduce Discrete Diffusion DPO (D3PO), the first adaptation of Direct Preference Optimization (DPO) to discrete diffusion models formulated as continuous-time Markov chains. Our approach derives a novel loss function that directly fine-tunes the generative process using preference data while preserving fidelity to a reference distribution. We validate D3PO on a structured binary sequence generation task, demonstrating that the method effectively aligns model outputs with preferences while maintaining structural validity. Our results highlight that D3PO enables controlled fine-tuning without requiring explicit reward models, making it a practical alternative to reinforcement learning-based approaches. Future research will explore extending D3PO to more complex generative tasks, including language modeling and protein sequence generation, as well as investigating alternative noise schedules, such as uniform noising, to enhance flexibility across different applications.

Online inclusive financial services encounter significant financial risks due to their expansive user base and low default costs. By real-world practice, we reveal that utilizing longer-term user payment behaviors can enhance models' ability to forecast financial risks. However, learning long behavior sequences is non-trivial for deep sequential models. Additionally, the diverse fields of payment behaviors carry rich information, requiring thorough exploitation. These factors collectively complicate the task of long-term user behavior modeling. To tackle these challenges, we propose a Long-term Payment Behavior Sequence Folding method, referred to as LBSF. In LBSF, payment behavior sequences are folded based on merchants, using the merchant field as an intrinsic grouping criterion, which enables informative parallelism without reliance on external knowledge. Meanwhile, we maximize the utility of payment details through a multi-field behavior encoding mechanism. Subsequently, behavior aggregation at the merchant level followed by relational learning across merchants facilitates comprehensive user financial representation. We evaluate LBSF on the financial risk assessment task using a large-scale real-world dataset. The results demonstrate that folding long behavior sequences based on internal behavioral cues effectively models long-term patterns and changes, thereby generating more accurate user financial profiles for practical applications.

In this work, we propose sequence-level certainty as a common theme over hallucination in Knowledge Grounded Dialogue Generation (KGDG). We explore the correlation between the level of hallucination and two types of sequence-level certainty: probabilistic certainty and semantic certainty. Empirical results reveal that a higher level of both types of sequence-level certainty in model responses is correlated with a lower level of hallucination. We further propose Certainty-based Response Ranking (CRR), a decoding-time hallucination mitigation method that ranks response candidates based on their sequence-level certainty and outputs the answer with the highest certainty level. Aligning with our definitions of sequence-level certainty, we design 2 types of CRR approaches: Probabilistic CRR (P-CRR) and Semantic CRR (S-CRR). P-CRR ranks individually sampled model responses using the arithmetic mean log-probability of the entire sequence. S-CRR approaches certainty estimation from meaning-space, and ranks model response candidates based on their semantic certainty level as measured by an entailment-based Agreement Score (AS). Through extensive experiments across 3 KGDG datasets, 3 decoding methods, and 4 different models, we validate the effectiveness of the CRR methods in reducing model hallucination.

One of the predominant methods for training world models is autoregressive prediction in the output space of the next element of a sequence. In Natural Language Processing (NLP), this takes the form of Large Language Models (LLMs) predicting the next token; in Computer Vision (CV), this takes the form of autoregressive models predicting the next frame/token/pixel. However, this approach differs from human cognition in several respects. First, human predictions about the future actively influence internal cognitive processes. Second, humans naturally evaluate the plausibility of predictions regarding future states. Based on this capability, and third, by assessing when predictions are sufficient, humans allocate a dynamic amount of time to make a prediction. This adaptive process is analogous to System 2 thinking in psychology. All these capabilities are fundamental to the success of humans at high-level reasoning and planning. Therefore, to address the limitations of traditional autoregressive models lacking these human-like capabilities, we introduce Energy-Based World Models (EBWM). EBWM involves training an Energy-Based Model (EBM) to predict the compatibility of a given context and a predicted future state. In doing so, EBWM enables models to achieve all three facets of human cognition described. Moreover, we developed a variant of the traditional autoregressive transformer tailored for Energy-Based models, termed the Energy-Based Transformer (EBT). Our results demonstrate that EBWM scales better with data and GPU Hours than traditional autoregressive transformers in CV, and that EBWM offers promising early scaling in NLP. Consequently, this approach offers an exciting path toward training future models capable of System 2 thinking and intelligently searching across state spaces.

Compared to frame-based methods, computational neuromorphic imaging using event cameras offers significant advantages, such as minimal motion blur, enhanced temporal resolution, and high dynamic range. The multi-view consistency of Neural Radiance Fields combined with the unique benefits of event cameras, has spurred recent research into reconstructing NeRF from data captured by moving event cameras. While showing impressive performance, existing methods rely on ideal conditions with the availability of uniform and high-quality event sequences and accurate camera poses, and mainly focus on the object level reconstruction, thus limiting their practical applications. In this work, we propose AE-NeRF to address the challenges of learning event-based NeRF from non-ideal conditions, including non-uniform event sequences, noisy poses, and various scales of scenes. Our method exploits the density of event streams and jointly learn a pose correction module with an event-based NeRF (e-NeRF) framework for robust 3D reconstruction from inaccurate camera poses. To generalize to larger scenes, we propose hierarchical event distillation with a proposal e-NeRF network and a vanilla e-NeRF network to resample and refine the reconstruction process. We further propose an event reconstruction loss and a temporal loss to improve the view consistency of the reconstructed scene. We established a comprehensive benchmark that includes large-scale scenes to simulate practical non-ideal conditions, incorporating both synthetic and challenging real-world event datasets. The experimental results show that our method achieves a new state-of-the-art in event-based 3D reconstruction.

Encoder layer fusion (EncoderFusion) is a technique to fuse all the encoder layers (instead of the uppermost layer) for sequence-to-sequence (Seq2Seq) models, which has proven effective on various NLP tasks. However, it is still not entirely clear why and when EncoderFusion should work. In this paper, our main contribution is to take a step further in understanding EncoderFusion. Many of previous studies believe that the success of EncoderFusion comes from exploiting surface and syntactic information embedded in lower encoder layers. Unlike them, we find that the encoder embedding layer is more important than other intermediate encoder layers. In addition, the uppermost decoder layer consistently pays more attention to the encoder embedding layer across NLP tasks. Based on this observation, we propose a simple fusion method, SurfaceFusion, by fusing only the encoder embedding layer for the softmax layer. Experimental results show that SurfaceFusion outperforms EncoderFusion on several NLP benchmarks, including machine translation, text summarization, and grammatical error correction. It obtains the state-of-the-art performance on WMT16 Romanian-English and WMT14 English-French translation tasks. Extensive analyses reveal that SurfaceFusion learns more expressive bilingual word embeddings by building a closer relationship between relevant source and target embedding. Source code is freely available at https://github.com/SunbowLiu/SurfaceFusion.

One limitation of existing Transformer-based models is that they cannot handle very long sequences as input since their self-attention operations exhibit quadratic time and space complexity. This problem becomes especially acute when Transformers are deployed on hardware platforms equipped only with CPUs. To address this issue, we propose a novel method for accelerating self-attention at inference time that works with pretrained Transformer models out-of-the-box without requiring retraining. We experiment using our method to accelerate various long-sequence Transformers, including a leading LLaMA 2-based LLM, on various benchmarks and demonstrate a greater speedup of 2.73x - 7.63x while retaining 98.6% - 99.6% of the accuracy of the original pretrained models. The code is available on our project website at https://yuzhenmao.github.io/IceFormer/.

Token-based text-to-speech (TTS) models have emerged as a promising avenue for generating natural and realistic speech, yet they grapple with low pronunciation accuracy, speaking style and timbre inconsistency, and a substantial need for diverse training data. In response, we introduce a novel hierarchical acoustic modeling approach complemented by a tailored data augmentation strategy and train it on the combination of real and synthetic data, scaling the data size up to 650k hours, leading to the zero-shot TTS model with 0.8B parameters. Specifically, our method incorporates a latent variable sequence containing supplementary acoustic information based on refined self-supervised learning (SSL) discrete units into the TTS model by a predictor. This significantly mitigates pronunciation errors and style mutations in synthesized speech. During training, we strategically replace and duplicate segments of the data to enhance timbre uniformity. Moreover, a pretrained few-shot voice conversion model is utilized to generate a plethora of voices with identical content yet varied timbres. This facilitates the explicit learning of utterance-level one-to-many mappings, enriching speech diversity and also ensuring consistency in timbre. Comparative experiments (Demo page: https://anonymous.4open.science/w/ham-tts/)demonstrate our model's superiority over VALL-E in pronunciation precision and maintaining speaking style, as well as timbre continuity.

Effectively training language models on long inputs poses many technical challenges. As a cost consideration, languages models are pretrained on a fixed sequence length before being adapted to longer sequences. We explore various methods for adapting models to longer inputs by training on segmented sequences and an interpolation-based method for extending absolute positional embeddings. We develop a training procedure to extend the input context size of pretrained models with no architectural changes and no additional memory costs than training on the original input lengths. By sub-sampling segments from long inputs while maintaining their original position the model is able to learn new positional interactions. Our method benefits both models trained with absolute positional embeddings, by extending their input contexts, as well as popular relative positional embedding methods showing a reduced perplexity on sequences longer than they were trained on. We demonstrate our method can extend input contexts by a factor of 4x while improving perplexity.

Smart-parking solutions use sensors, cameras, and data analysis to improve parking efficiency and reduce traffic congestion. Computer vision-based methods have been used extensively in recent years to tackle the problem of parking lot management, but most of the works assume that the parking spots are manually labeled, impacting the cost and feasibility of deployment. To fill this gap, this work presents an automatic parking space detection method, which receives a sequence of images of a parking lot and returns a list of coordinates identifying the detected parking spaces. The proposed method employs instance segmentation to identify cars and, using vehicle occurrence, generate a heat map of parking spaces. The results using twelve different subsets from the PKLot and CNRPark-EXT parking lot datasets show that the method achieved an AP25 score up to 95.60\% and AP50 score up to 79.90\%.

Computer vision models suffer from a phenomenon known as catastrophic forgetting when learning novel concepts from continuously shifting training data. Typical solutions for this continual learning problem require extensive rehearsal of previously seen data, which increases memory costs and may violate data privacy. Recently, the emergence of large-scale pre-trained vision transformer models has enabled prompting approaches as an alternative to data-rehearsal. These approaches rely on a key-query mechanism to generate prompts and have been found to be highly resistant to catastrophic forgetting in the well-established rehearsal-free continual learning setting. However, the key mechanism of these methods is not trained end-to-end with the task sequence. Our experiments show that this leads to a reduction in their plasticity, hence sacrificing new task accuracy, and inability to benefit from expanded parameter capacity. We instead propose to learn a set of prompt components which are assembled with input-conditioned weights to produce input-conditioned prompts, resulting in a novel attention-based end-to-end key-query scheme. Our experiments show that we outperform the current SOTA method DualPrompt on established benchmarks by as much as 4.5% in average final accuracy. We also outperform the state of art by as much as 4.4% accuracy on a continual learning benchmark which contains both class-incremental and domain-incremental task shifts, corresponding to many practical settings. Our code is available at https://github.com/GT-RIPL/CODA-Prompt

Motivated by the success of Transformers when applied to sequences of discrete symbols, token-based world models (TBWMs) were recently proposed as sample-efficient methods. In TBWMs, the world model consumes agent experience as a language-like sequence of tokens, where each observation constitutes a sub-sequence. However, during imagination, the sequential token-by-token generation of next observations results in a severe bottleneck, leading to long training times, poor GPU utilization, and limited representations. To resolve this bottleneck, we devise a novel Parallel Observation Prediction (POP) mechanism. POP augments a Retentive Network (RetNet) with a novel forward mode tailored to our reinforcement learning setting. We incorporate POP in a novel TBWM agent named REM (Retentive Environment Model), showcasing a 15.4x faster imagination compared to prior TBWMs. REM attains superhuman performance on 12 out of 26 games of the Atari 100K benchmark, while training in less than 12 hours. Our code is available at https://github.com/leor-c/REM.

Inspired by the great success of Masked Language Modeling (MLM) in the natural language domain, the paradigm of self-supervised pre-training and fine-tuning has also achieved remarkable progress in the field of DNA sequence modeling. However, previous methods often relied on massive pre-training data or large-scale base models with huge parameters, imposing a significant computational burden. To address this, many works attempted to use more compact models to achieve similar outcomes but still fell short by a considerable margin. In this work, we propose a Hybrid Architecture Distillation (HAD) approach, leveraging both distillation and reconstruction tasks for more efficient and effective pre-training. Specifically, we employ the NTv2-500M as the teacher model and devise a grouping masking strategy to align the feature embeddings of visible tokens while concurrently reconstructing the invisible tokens during MLM pre-training. To validate the effectiveness of our proposed method, we conducted comprehensive experiments on the Nucleotide Transformer Benchmark and Genomic Benchmark. Compared to models with similar parameters, our model achieved excellent performance. More surprisingly, it even surpassed the distillation ceiling-teacher model on some sub-tasks, which is more than 500 times larger. Lastly, we utilize t-SNE for more intuitive visualization, which shows that our model can gain a sophisticated understanding of the intrinsic representation pattern in genomic sequences.

Relation linking is essential to enable question answering over knowledge bases. Although there are various efforts to improve relation linking performance, the current state-of-the-art methods do not achieve optimal results, therefore, negatively impacting the overall end-to-end question answering performance. In this work, we propose a novel approach for relation linking framing it as a generative problem facilitating the use of pre-trained sequence-to-sequence models. We extend such sequence-to-sequence models with the idea of infusing structured data from the target knowledge base, primarily to enable these models to handle the nuances of the knowledge base. Moreover, we train the model with the aim to generate a structured output consisting of a list of argument-relation pairs, enabling a knowledge validation step. We compared our method against the existing relation linking systems on four different datasets derived from DBpedia and Wikidata. Our method reports large improvements over the state-of-the-art while using a much simpler model that can be easily adapted to different knowledge bases.

Effective planning in model-based reinforcement learning (MBRL) and model-predictive control (MPC) relies on the accuracy of the learned dynamics model. In many instances of MBRL and MPC, this model is assumed to be stationary and is periodically re-trained from scratch on state transition experience collected from the beginning of environment interactions. This implies that the time required to train the dynamics model - and the pause required between plan executions - grows linearly with the size of the collected experience. We argue that this is too slow for lifelong robot learning and propose HyperCRL, a method that continually learns the encountered dynamics in a sequence of tasks using task-conditional hypernetworks. Our method has three main attributes: first, it includes dynamics learning sessions that do not revisit training data from previous tasks, so it only needs to store the most recent fixed-size portion of the state transition experience; second, it uses fixed-capacity hypernetworks to represent non-stationary and task-aware dynamics; third, it outperforms existing continual learning alternatives that rely on fixed-capacity networks, and does competitively with baselines that remember an ever increasing coreset of past experience. We show that HyperCRL is effective in continual model-based reinforcement learning in robot locomotion and manipulation scenarios, such as tasks involving pushing and door opening. Our project website with videos is at this link https://rvl.cs.toronto.edu/blog/2020/hypercrl

Large Language Models (LLMs) have recently emerged as promising tools for recommendation thanks to their advanced textual understanding ability and context-awareness. Despite the current practice of training and evaluating LLM-based recommendation (LLM4Rec) models under a sequential recommendation scenario, we found that whether these models understand the sequential information inherent in users' item interaction sequences has been largely overlooked. In this paper, we first demonstrate through a series of experiments that existing LLM4Rec models do not fully capture sequential information both during training and inference. Then, we propose a simple yet effective LLM-based sequential recommender, called LLM-SRec, a method that enhances the integration of sequential information into LLMs by distilling the user representations extracted from a pre-trained CF-SRec model into LLMs. Our extensive experiments show that LLM-SRec enhances LLMs' ability to understand users' item interaction sequences, ultimately leading to improved recommendation performance. Furthermore, unlike existing LLM4Rec models that require fine-tuning of LLMs, LLM-SRec achieves state-of-the-art performance by training only a few lightweight MLPs, highlighting its practicality in real-world applications. Our code is available at https://github.com/Sein-Kim/LLM-SRec.

Vision in adverse weather conditions, whether it be snow, rain, or fog is challenging. In these scenarios, scattering and attenuation severly degrades image quality. Handling such inclement weather conditions, however, is essential to operate autonomous vehicles, drones and robotic applications where human performance is impeded the most. A large body of work explores removing weather-induced image degradations with dehazing methods. Most methods rely on single images as input and struggle to generalize from synthetic fully-supervised training approaches or to generate high fidelity results from unpaired real-world datasets. With data as bottleneck and most of today's training data relying on good weather conditions with inclement weather as outlier, we rely on an inverse rendering approach to reconstruct the scene content. We introduce ScatterNeRF, a neural rendering method which adequately renders foggy scenes and decomposes the fog-free background from the participating media-exploiting the multiple views from a short automotive sequence without the need for a large training data corpus. Instead, the rendering approach is optimized on the multi-view scene itself, which can be typically captured by an autonomous vehicle, robot or drone during operation. Specifically, we propose a disentangled representation for the scattering volume and the scene objects, and learn the scene reconstruction with physics-inspired losses. We validate our method by capturing multi-view In-the-Wild data and controlled captures in a large-scale fog chamber.

Long Short Term Memory LSTM-based structures have demonstrated their efficiency for daily living recognition activities in smart homes by capturing the order of sensor activations and their temporal dependencies. Nevertheless, they still fail in dealing with the semantics and the context of the sensors. More than isolated id and their ordered activation values, sensors also carry meaning. Indeed, their nature and type of activation can translate various activities. Their logs are correlated with each other, creating a global context. We propose to use and compare two Natural Language Processing embedding methods to enhance LSTM-based structures in activity-sequences classification tasks: Word2Vec, a static semantic embedding, and ELMo, a contextualized embedding. Results, on real smart homes datasets, indicate that this approach provides useful information, such as a sensor organization map, and makes less confusion between daily activity classes. It helps to better perform on datasets with competing activities of other residents or pets. Our tests show also that the embeddings can be pretrained on different datasets than the target one, enabling transfer learning. We thus demonstrate that taking into account the context of the sensors and their semantics increases the classification performances and enables transfer learning.

This analysis explores the temporal sequencing of objects in a movie trailer. Temporal sequencing of objects in a movie trailer (e.g., a long shot of an object vs intermittent short shots) can convey information about the type of movie, plot of the movie, role of the main characters, and the filmmakers cinematographic choices. When combined with historical customer data, sequencing analysis can be used to improve predictions of customer behavior. E.g., a customer buys tickets to a new movie and maybe the customer has seen movies in the past that contained similar sequences. To explore object sequencing in movie trailers, we propose a video convolutional network to capture actions and scenes that are predictive of customers' preferences. The model learns the specific nature of sequences for different types of objects (e.g., cars vs faces), and the role of sequences in predicting customer future behavior. We show how such a temporal-aware model outperforms simple feature pooling methods proposed in our previous works and, importantly, demonstrate the additional model explain-ability allowed by such a model.

Protein design, a grand challenge of the day, involves optimization on a fitness landscape, and leading methods adopt a model-based approach where a model is trained on a training set (protein sequences and fitness) and proposes candidates to explore next. These methods are challenged by sparsity of high-fitness samples in the training set, a problem that has been in the literature. A less recognized but equally important problem stems from the distribution of training samples in the design space: leading methods are not designed for scenarios where the desired optimum is in a region that is not only poorly represented in training data, but also relatively far from the highly represented low-fitness regions. We show that this problem of "separation" in the design space is a significant bottleneck in existing model-based optimization tools and propose a new approach that uses a novel VAE as its search model to overcome the problem. We demonstrate its advantage over prior methods in robustly finding improved samples, regardless of the imbalance and separation between low- and high-fitness training samples. Our comprehensive benchmark on real and semi-synthetic protein datasets as well as solution design for physics-informed neural networks, showcases the generality of our approach in discrete and continuous design spaces. Our implementation is available at https://github.com/sabagh1994/PGVAE.

Conversational passage retrieval is challenging as it often requires the resolution of references to previous utterances and needs to deal with the complexities of natural language, such as coreference and ellipsis. To address these challenges, pre-trained sequence-to-sequence neural query rewriters are commonly used to generate a single de-contextualized query based on conversation history. Previous research shows that combining multiple query rewrites for the same user utterance has a positive effect on retrieval performance. We propose the use of a neural query rewriter to generate multiple queries and show how to integrate those queries in the passage retrieval pipeline efficiently. The main strength of our approach lies in its simplicity: it leverages how the beam search algorithm works and can produce multiple query rewrites at no additional cost. Our contributions further include devising ways to utilize multi-query rewrites in both sparse and dense first-pass retrieval. We demonstrate that applying our approach on top of a standard passage retrieval pipeline delivers state-of-the-art performance without sacrificing efficiency.

In line with recent advances in neural drug design and sensitivity prediction, we propose a novel architecture for interpretable prediction of anticancer compound sensitivity using a multimodal attention-based convolutional encoder. Our model is based on the three key pillars of drug sensitivity: compounds' structure in the form of a SMILES sequence, gene expression profiles of tumors and prior knowledge on intracellular interactions from protein-protein interaction networks. We demonstrate that our multiscale convolutional attention-based (MCA) encoder significantly outperforms a baseline model trained on Morgan fingerprints, a selection of encoders based on SMILES as well as previously reported state of the art for multimodal drug sensitivity prediction (R2 = 0.86 and RMSE = 0.89). Moreover, the explainability of our approach is demonstrated by a thorough analysis of the attention weights. We show that the attended genes significantly enrich apoptotic processes and that the drug attention is strongly correlated with a standard chemical structure similarity index. Finally, we report a case study of two receptor tyrosine kinase (RTK) inhibitors acting on a leukemia cell line, showcasing the ability of the model to focus on informative genes and submolecular regions of the two compounds. The demonstrated generalizability and the interpretability of our model testify its potential for in-silico prediction of anticancer compound efficacy on unseen cancer cells, positioning it as a valid solution for the development of personalized therapies as well as for the evaluation of candidate compounds in de novo drug design.

While deep learning has revolutionized the prediction of rigid protein structures, modelling the conformational ensembles of Intrinsically Disordered Proteins (IDPs) remains a key frontier. Current AI paradigms present a trade-off: Protein Language Models (PLMs) capture evolutionary statistics but lack explicit physical grounding, while generative models trained to model full ensembles are computationally expensive. In this work we critically assess these limits and propose a path forward. We introduce GeoGraph, a simulation-informed surrogate trained to predict ensemble-averaged statistics of residue-residue contact-map topology directly from sequence. By featurizing coarse-grained molecular dynamics simulations into residue- and sequence-level graph descriptors, we create a robust and information-rich learning target. Our evaluation demonstrates that this approach yields representations that are more predictive of key biophysical properties than existing methods.

Coronaviruses are membrane-enveloped, non-segmented positive-strand RNA viruses belonging to the Coronaviridae family. Various animal species, mainly mammalian and avian, are severely infected by various coronaviruses, causing serious concerns like the recent pandemic (COVID-19). Therefore, building a deeper understanding of these viruses is essential to devise prevention and mitigation mechanisms. In the Coronavirus genome, an essential structural region is the spike region, and it's responsible for attaching the virus to the host cell membrane. Therefore, the usage of only the spike protein, instead of the full genome, provides most of the essential information for performing analyses such as host classification. In this paper, we propose a novel method for predicting the host specificity of coronaviruses by analyzing spike protein sequences from different viral subgenera and species. Our method involves using the Poisson correction distance to generate a distance matrix, followed by using a radial basis function (RBF) kernel and kernel principal component analysis (PCA) to generate a low-dimensional embedding. Finally, we apply classification algorithms to the low-dimensional embedding to generate the resulting predictions of the host specificity of coronaviruses. We provide theoretical proofs for the non-negativity, symmetry, and triangle inequality properties of the Poisson correction distance metric, which are important properties in a machine-learning setting. By encoding the spike protein structure and sequences using this comprehensive approach, we aim to uncover hidden patterns in the biological sequences to make accurate predictions about host specificity. Finally, our classification results illustrate that our method can achieve higher predictive accuracy and improve performance over existing baselines.

This paper introduces the Masked Voxel Jigsaw and Reconstruction (MV-JAR) method for LiDAR-based self-supervised pre-training and a carefully designed data-efficient 3D object detection benchmark on the Waymo dataset. Inspired by the scene-voxel-point hierarchy in downstream 3D object detectors, we design masking and reconstruction strategies accounting for voxel distributions in the scene and local point distributions within the voxel. We employ a Reversed-Furthest-Voxel-Sampling strategy to address the uneven distribution of LiDAR points and propose MV-JAR, which combines two techniques for modeling the aforementioned distributions, resulting in superior performance. Our experiments reveal limitations in previous data-efficient experiments, which uniformly sample fine-tuning splits with varying data proportions from each LiDAR sequence, leading to similar data diversity across splits. To address this, we propose a new benchmark that samples scene sequences for diverse fine-tuning splits, ensuring adequate model convergence and providing a more accurate evaluation of pre-training methods. Experiments on our Waymo benchmark and the KITTI dataset demonstrate that MV-JAR consistently and significantly improves 3D detection performance across various data scales, achieving up to a 6.3% increase in mAPH compared to training from scratch. Codes and the benchmark will be available at https://github.com/SmartBot-PJLab/MV-JAR .

3D object localisation based on a sequence of camera measurements is essential for safety-critical surveillance tasks, such as drone-based wildfire monitoring. Localisation of objects detected with a camera can typically be solved with dense depth estimation or 3D scene reconstruction. However, in the context of distant objects or tasks limited by the amount of available computational resources, neither solution is feasible. In this paper, we show that the task can be solved using particle filters for both single and multiple target scenarios. The method was studied using a 3D simulation and a drone-based image segmentation sequence with global navigation satellite system (GNSS)-based camera pose estimates. The results showed that a particle filter can be used to solve practical localisation tasks based on camera poses and image segments in these situations where other solutions fail. The particle filter is independent of the detection method, making it flexible for new tasks. The study also demonstrates that drone-based wildfire monitoring can be conducted using the proposed method paired with a pre-existing image segmentation model.

During times of increasing antibiotic resistance and the spread of infectious diseases like COVID-19, it is important to classify genes related to antibiotic resistance. As natural language processing has advanced with transformer-based language models, many language models that learn characteristics of nucleotide sequences have also emerged. These models show good performance in classifying various features of nucleotide sequences. When classifying nucleotide sequences, not only the sequence itself, but also various background knowledge is utilized. In this study, we use not only a nucleotide sequence-based language model but also a text language model based on PubMed articles to reflect more biological background knowledge in the model. We propose a method to fine-tune the nucleotide sequence language model and the text language model based on various databases of antibiotic resistance genes. We also propose an LLM-based augmentation technique to supplement the data and an ensemble method to effectively combine the two models. We also propose a benchmark for evaluating the model. Our method achieved better performance than the nucleotide sequence language model in the drug resistance class prediction.

This paper investigates robot manipulation based on human instruction with ambiguous requests. The intent is to compensate for imperfect natural language via visual observations. Early symbolic methods, based on manually defined symbols, built modular framework consist of semantic parsing and task planning for producing sequences of actions from natural language requests. Modern connectionist methods employ deep neural networks to automatically learn visual and linguistic features and map to a sequence of low-level actions, in an endto-end fashion. These two approaches are blended to create a hybrid, modular framework: it formulates instruction following as symbolic goal learning via deep neural networks followed by task planning via symbolic planners. Connectionist and symbolic modules are bridged with Planning Domain Definition Language. The vision-and-language learning network predicts its goal representation, which is sent to a planner for producing a task-completing action sequence. For improving the flexibility of natural language, we further incorporate implicit human intents with explicit human instructions. To learn generic features for vision and language, we propose to separately pretrain vision and language encoders on scene graph parsing and semantic textual similarity tasks. Benchmarking evaluates the impacts of different components of, or options for, the vision-and-language learning model and shows the effectiveness of pretraining strategies. Manipulation experiments conducted in the simulator AI2THOR show the robustness of the framework to novel scenarios.

3D reconstruction of dynamic scenes is a long-standing problem in computer graphics and increasingly difficult the less information is available. Shape-from-Template (SfT) methods aim to reconstruct a template-based geometry from RGB images or video sequences, often leveraging just a single monocular camera without depth information, such as regular smartphone recordings. Unfortunately, existing reconstruction methods are either unphysical and noisy or slow in optimization. To solve this problem, we propose a novel SfT reconstruction algorithm for cloth using a pre-trained neural surrogate model that is fast to evaluate, stable, and produces smooth reconstructions due to a regularizing physics simulation. Differentiable rendering of the simulated mesh enables pixel-wise comparisons between the reconstruction and a target video sequence that can be used for a gradient-based optimization procedure to extract not only shape information but also physical parameters such as stretching, shearing, or bending stiffness of the cloth. This allows to retain a precise, stable, and smooth reconstructed geometry while reducing the runtime by a factor of 400-500 compared to phi-SfT, a state-of-the-art physics-based SfT approach.

Incrementally recovering real-sized 3D geometry from a pose-free RGB stream is a challenging task in 3D reconstruction, requiring minimal assumptions on input data. Existing methods can be broadly categorized into end-to-end and visual SLAM-based approaches, both of which either struggle with long sequences or depend on slow test-time optimization and depth sensors. To address this, we first integrate a depth estimator into an RGB-D SLAM system, but this approach is hindered by inaccurate geometric details in predicted depth. Through further investigation, we find that 3D Gaussian mapping can effectively solve this problem. Building on this, we propose an online 3D reconstruction method using 3D Gaussian-based SLAM, combined with a feed-forward recurrent prediction module to directly infer camera pose from optical flow. This approach replaces slow test-time optimization with fast network inference, significantly improving tracking speed. Additionally, we introduce a local graph rendering technique to enhance robustness in feed-forward pose prediction. Experimental results on the Replica and TUM-RGBD datasets, along with a real-world deployment demonstration, show that our method achieves performance on par with the state-of-the-art SplaTAM, while reducing tracking time by more than 90\%.

Music-driven choreography is a challenging problem with a wide variety of industrial applications. Recently, many methods have been proposed to synthesize dance motions from music for a single dancer. However, generating dance motion for a group remains an open problem. In this paper, we present rm AIOZ-GDANCE, a new large-scale dataset for music-driven group dance generation. Unlike existing datasets that only support single dance, our new dataset contains group dance videos, hence supporting the study of group choreography. We propose a semi-autonomous labeling method with humans in the loop to obtain the 3D ground truth for our dataset. The proposed dataset consists of 16.7 hours of paired music and 3D motion from in-the-wild videos, covering 7 dance styles and 16 music genres. We show that naively applying single dance generation technique to creating group dance motion may lead to unsatisfactory results, such as inconsistent movements and collisions between dancers. Based on our new dataset, we propose a new method that takes an input music sequence and a set of 3D positions of dancers to efficiently produce multiple group-coherent choreographies. We propose new evaluation metrics for measuring group dance quality and perform intensive experiments to demonstrate the effectiveness of our method. Our project facilitates future research on group dance generation and is available at: https://aioz-ai.github.io/AIOZ-GDANCE/

Modern language models mostly take sub-words as input, a design that balances the trade-off between vocabulary size, number of parameters, and performance. However, sub-word tokenization still has disadvantages like not being robust to noise and difficult to generalize to new languages. Also, the current trend of scaling up models reveals that larger models require larger embeddings but that makes parallelization hard. Previous work on image classification proves splitting raw input into a sequence of chucks is a strong, model-agnostic inductive bias. Based on this observation, we rethink the existing character-aware method that takes character-level inputs but makes word-level sequence modeling and prediction. We overhaul this method by introducing a cross-attention network that builds word-level representation directly from bytes, and a sub-word level prediction based on word-level hidden states to avoid the time and space requirement of word-level prediction. With these two improvements combined, we have a token free model with slim input embeddings for downstream tasks. We name our method Byte2Word and perform evaluations on language modeling and text classification. Experiments show that Byte2Word is on par with the strong sub-word baseline BERT but only takes up 10\% of embedding size. We further test our method on synthetic noise and cross-lingual transfer and find it competitive to baseline methods on both settings.

Based on the BioBricks standard, restriction synthesis is a novel catabolic iterative DNA synthesis method that utilizes endonucleases to synthesize a query sequence from a reference sequence. In this work, the reference sequence is built from shorter subsequences by classifying them as applicable or inapplicable for the synthesis method using three different machine learning methods: Support Vector Machines (SVMs), random forest, and Convolution Neural Networks (CNNs). Before applying these methods to the data, a series of feature selection, curation, and reduction steps are applied to create an accurate and representative feature space. Following these preprocessing steps, three different pipelines are proposed to classify subsequences based on their nucleotide sequence and other relevant features corresponding to the restriction sites of over 200 endonucleases. The sensitivity using SVMs, random forest, and CNNs are 94.9%, 92.7%, 91.4%, respectively. Moreover, each method scores lower in specificity with SVMs, random forest, and CNNs resulting in 77.4%, 85.7%, and 82.4%, respectively. In addition to analyzing these results, the misclassifications in SVMs and CNNs are investigated. Across these two models, different features with a derived nucleotide specificity visually contribute more to classification compared to other features. This observation is an important factor when considering new nucleotide sensitivity features for future studies.

The ability of large language models (LLMs) to perform zero-shot classification makes them viable solutions for data annotation in rapidly evolving domains where quality labeled data is often scarce and costly to obtain. However, the large-scale deployment of LLMs can be prohibitively expensive. This paper introduces an LLM chain ensemble methodology that aligns multiple LLMs in a sequence, routing data subsets to subsequent models based on classification uncertainty. This approach leverages the strengths of individual LLMs within a broader system, allowing each model to handle data points where it exhibits the highest confidence, while forwarding more complex cases to potentially more robust models. Our results show that the chain ensemble method often exceeds the performance of the best individual model in the chain and achieves substantial cost savings, making LLM chain ensembles a practical and efficient solution for large-scale data annotation challenges.

We introduce SceneScript, a method that directly produces full scene models as a sequence of structured language commands using an autoregressive, token-based approach. Our proposed scene representation is inspired by recent successes in transformers & LLMs, and departs from more traditional methods which commonly describe scenes as meshes, voxel grids, point clouds or radiance fields. Our method infers the set of structured language commands directly from encoded visual data using a scene language encoder-decoder architecture. To train SceneScript, we generate and release a large-scale synthetic dataset called Aria Synthetic Environments consisting of 100k high-quality in-door scenes, with photorealistic and ground-truth annotated renders of egocentric scene walkthroughs. Our method gives state-of-the art results in architectural layout estimation, and competitive results in 3D object detection. Lastly, we explore an advantage for SceneScript, which is the ability to readily adapt to new commands via simple additions to the structured language, which we illustrate for tasks such as coarse 3D object part reconstruction.

Recent advances in deep learning have relied heavily on the use of large Transformers due to their ability to learn at scale. However, the core building block of Transformers, the attention operator, exhibits quadratic cost in sequence length, limiting the amount of context accessible. Existing subquadratic methods based on low-rank and sparse approximations need to be combined with dense attention layers to match Transformers, indicating a gap in capability. In this work, we propose Hyena, a subquadratic drop-in replacement for attention constructed by interleaving implicitly parametrized long convolutions and data-controlled gating. In recall and reasoning tasks on sequences of thousands to hundreds of thousands of tokens, Hyena improves accuracy by more than 50 points over operators relying on state-spaces and other implicit and explicit methods, matching attention-based models. We set a new state-of-the-art for dense-attention-free architectures on language modeling in standard datasets (WikiText103 and The Pile), reaching Transformer quality with a 20% reduction in training compute required at sequence length 2K. Hyena operators are twice as fast as highly optimized attention at sequence length 8K, and 100x faster at sequence length 64K.

Large Language Models (LLMs) excel in text-based natural language processing tasks but remain constrained by their reliance on textual inputs and outputs. To enable more natural human-LLM interaction, recent progress have focused on deriving a spoken language model (SLM) that can not only listen but also generate speech. To achieve this, a promising direction is to conduct speech-text joint modeling. However, recent SLM still lag behind text LLM due to the modality mismatch. One significant mismatch can be the sequence lengths between speech and text tokens. To address this, we introduce Text-Aligned Speech Tokenization and Embedding (TASTE), a method that directly addresses the modality gap by aligning speech token with the corresponding text transcription during the tokenization stage. We propose a method that can achieve this through the special aggregation mechanism and with speech reconstruction as the training objective. We conduct extensive experiments and show that TASTE can preserve essential paralinguistic information while dramatically reducing the token sequence length. Furthermore, by leveraging TASTE, we can adapt text-based LLMs into effective SLMs with parameter-efficient fine-tuning techniques such as Low-Rank Adaptation (LoRA). Experimental results on benchmark tasks, including SALMON and StoryCloze, demonstrate that TASTE-based SLMs perform similarly to previous full-finetuning methods. To our knowledge, TASTE is the first end-to-end approach that utilizes a reconstruction objective to automatically learn a text-aligned speech tokenization and embedding suitable for spoken language modeling. Our demo, code, and models are publicly available at https://github.com/mtkresearch/TASTE-SpokenLM.

While score-based generative models are the model of choice across diverse domains, there are limited tools available for controlling inference-time behavior in a principled manner, e.g. for composing multiple pretrained models. Existing classifier-free guidance methods use a simple heuristic to mix conditional and unconditional scores to approximately sample from conditional distributions. However, such methods do not approximate the intermediate distributions, necessitating additional 'corrector' steps. In this work, we provide an efficient and principled method for sampling from a sequence of annealed, geometric-averaged, or product distributions derived from pretrained score-based models. We derive a weighted simulation scheme which we call Feynman-Kac Correctors (FKCs) based on the celebrated Feynman-Kac formula by carefully accounting for terms in the appropriate partial differential equations (PDEs). To simulate these PDEs, we propose Sequential Monte Carlo (SMC) resampling algorithms that leverage inference-time scaling to improve sampling quality. We empirically demonstrate the utility of our methods by proposing amortized sampling via inference-time temperature annealing, improving multi-objective molecule generation using pretrained models, and improving classifier-free guidance for text-to-image generation. Our code is available at https://github.com/martaskrt/fkc-diffusion.

Sequential recommendation aims to model user preferences based on historical behavior sequences, which is crucial for various online platforms. Data sparsity remains a significant challenge in this area as most users have limited interactions and many items receive little attention. To mitigate this issue, contrastive learning has been widely adopted. By constructing positive sample pairs from the data itself and maximizing their agreement in the embedding space,it can leverage available data more effectively. Constructing reasonable positive sample pairs is crucial for the success of contrastive learning. However, current approaches struggle to generate reliable positive pairs as they either rely on representations learned from inherently sparse collaborative signals or use random perturbations which introduce significant uncertainty. To address these limitations, we propose a novel approach named Semantic Retrieval Augmented Contrastive Learning (SRA-CL), which leverages semantic information to improve the reliability of contrastive samples. SRA-CL comprises two main components: (1) Cross-Sequence Contrastive Learning via User Semantic Retrieval, which utilizes large language models (LLMs) to understand diverse user preferences and retrieve semantically similar users to form reliable positive samples through a learnable sample synthesis method; and (2) Intra-Sequence Contrastive Learning via Item Semantic Retrieval, which employs LLMs to comprehend items and retrieve similar items to perform semantic-based item substitution, thereby creating semantically consistent augmented views for contrastive learning. SRA-CL is plug-and-play and can be integrated into standard sequential recommendation models. Extensive experiments on four public datasets demonstrate the effectiveness and generalizability of the proposed approach.

We present a debiased dataset for the Person-centric Visual Grounding (PCVG) task first proposed by Cui et al. (2021) in the Who's Waldo dataset. Given an image and a caption, PCVG requires pairing up a person's name mentioned in a caption with a bounding box that points to the person in the image. We find that the original Who's Waldo dataset compiled for this task contains a large number of biased samples that are solvable simply by heuristic methods; for instance, in many cases the first name in the sentence corresponds to the largest bounding box, or the sequence of names in the sentence corresponds to an exact left-to-right order in the image. Naturally, models trained on these biased data lead to over-estimation of performance on the benchmark. To enforce models being correct for the correct reasons, we design automated tools to filter and debias the original dataset by ruling out all examples of insufficient context, such as those with no verb or with a long chain of conjunct names in their captions. Our experiments show that our new sub-sampled dataset contains less bias with much lowered heuristic performances and widened gaps between heuristic and supervised methods. We also demonstrate the same benchmark model trained on our debiased training set outperforms that trained on the original biased (and larger) training set on our debiased test set. We argue our debiased dataset offers the PCVG task a more practical baseline for reliable benchmarking and future improvements.

Comprehending how humans process visual information in dynamic settings is crucial for psychology and designing user-centered interactions. While mobile eye-tracking systems combining egocentric video and gaze signals can offer valuable insights, manual analysis of these recordings is time-intensive. In this work, we present a novel human-centered learning algorithm designed for automated object recognition within mobile eye-tracking settings. Our approach seamlessly integrates an object detector with a spatial relation-aware inductive message-passing network (I-MPN), harnessing node profile information and capturing object correlations. Such mechanisms enable us to learn embedding functions capable of generalizing to new object angle views, facilitating rapid adaptation and efficient reasoning in dynamic contexts as users navigate their environment. Through experiments conducted on three distinct video sequences, our interactive-based method showcases significant performance improvements over fixed training/testing algorithms, even when trained on considerably smaller annotated samples collected through user feedback. Furthermore, we demonstrate exceptional efficiency in data annotation processes and surpass prior interactive methods that use complete object detectors, combine detectors with convolutional networks, or employ interactive video segmentation.