Daily Papers

The relationship between computing systems and the brain has served as motivation for pioneering theoreticians since John von Neumann and Alan Turing. Uniform, scale-free biological networks, such as the brain, have powerful properties, including generalizing over time, which is the main barrier for Machine Learning on the path to Universal Reasoning Models. We introduce `Dragon Hatchling' (BDH), a new Large Language Model architecture based on a scale-free biologically inspired network of \n locally-interacting neuron particles. BDH couples strong theoretical foundations and inherent interpretability without sacrificing Transformer-like performance. BDH is a practical, performant state-of-the-art attention-based state space sequence learning architecture. In addition to being a graph model, BDH admits a GPU-friendly formulation. It exhibits Transformer-like scaling laws: empirically BDH rivals GPT2 performance on language and translation tasks, at the same number of parameters (10M to 1B), for the same training data. BDH can be represented as a brain model. The working memory of BDH during inference entirely relies on synaptic plasticity with Hebbian learning using spiking neurons. We confirm empirically that specific, individual synapses strengthen connection whenever BDH hears or reasons about a specific concept while processing language inputs. The neuron interaction network of BDH is a graph of high modularity with heavy-tailed degree distribution. The BDH model is biologically plausible, explaining one possible mechanism which human neurons could use to achieve speech. BDH is designed for interpretability. Activation vectors of BDH are sparse and positive. We demonstrate monosemanticity in BDH on language tasks. Interpretability of state, which goes beyond interpretability of neurons and model parameters, is an inherent feature of the BDH architecture.

Recent works on context and memory benchmarking have primarily focused on conversational instances but the need for evaluating memory in dynamic enterprise environments is crucial for its effective application. We introduce MEMTRACK, a benchmark designed to evaluate long-term memory and state tracking in multi-platform agent environments. MEMTRACK models realistic organizational workflows by integrating asynchronous events across multiple communication and productivity platforms such as Slack, Linear and Git. Each benchmark instance provides a chronologically platform-interleaved timeline, with noisy, conflicting, cross-referring information as well as potential codebase/file-system comprehension and exploration. Consequently, our benchmark tests memory capabilities such as acquistion, selection and conflict resolution. We curate the MEMTRACK dataset through both manual expert driven design and scalable agent based synthesis, generating ecologically valid scenarios grounded in real world software development processes. We introduce pertinent metrics for Correctness, Efficiency, and Redundancy that capture the effectiveness of memory mechanisms beyond simple QA performance. Experiments across SoTA LLMs and memory backends reveal challenges in utilizing memory across long horizons, handling cross-platform dependencies, and resolving contradictions. Notably, the best performing GPT-5 model only achieves a 60\% Correctness score on MEMTRACK. This work provides an extensible framework for advancing evaluation research for memory-augmented agents, beyond existing focus on conversational setups, and sets the stage for multi-agent, multi-platform memory benchmarking in complex organizational settings

Large language models (LLMs) excel in language tasks, especially with supervised fine-tuning after pre-training. However, their substantial memory and computational requirements hinder practical applications. Structural pruning, which reduces less significant weight dimensions, is one solution. Yet, traditional post-hoc pruning often leads to significant performance loss, with limited recovery from further fine-tuning due to reduced capacity. Since the model fine-tuning refines the general and chaotic knowledge in pre-trained models, we aim to incorporate structural pruning with the fine-tuning, and propose the Pruning-Aware Tuning (PAT) paradigm to eliminate model redundancy while preserving the model performance to the maximum extend. Specifically, we insert the innovative Hybrid Sparsification Modules (HSMs) between the Attention and FFN components to accordingly sparsify the upstream and downstream linear modules. The HSM comprises a lightweight operator and a globally shared trainable mask. The lightweight operator maintains a training overhead comparable to that of LoRA, while the trainable mask unifies the channels to be sparsified, ensuring structural pruning. Additionally, we propose the Identity Loss which decouples the transformation and scaling properties of the HSMs to enhance training robustness. Extensive experiments demonstrate that PAT excels in both performance and efficiency. For example, our Llama2-7b model with a 25\% pruning ratio achieves 1.33times speedup while outperforming the LoRA-finetuned model by up to 1.26\% in accuracy with a similar training cost. Code: https://github.com/kriskrisliu/PAT_Pruning-Aware-Tuning

Generative models such as StyleGAN2 and Stable Diffusion have achieved state-of-the-art performance in computer vision tasks such as image synthesis, inpainting, and de-noising. However, current generative models for face inpainting often fail to preserve fine facial details and the identity of the person, despite creating aesthetically convincing image structures and textures. In this work, we propose Person Aware Tuning (PAT) of Mask-Aware Transformer (MAT) for face inpainting, which addresses this issue. Our proposed method, PATMAT, effectively preserves identity by incorporating reference images of a subject and fine-tuning a MAT architecture trained on faces. By using ~40 reference images, PATMAT creates anchor points in MAT's style module, and tunes the model using the fixed anchors to adapt the model to a new face identity. Moreover, PATMAT's use of multiple images per anchor during training allows the model to use fewer reference images than competing methods. We demonstrate that PATMAT outperforms state-of-the-art models in terms of image quality, the preservation of person-specific details, and the identity of the subject. Our results suggest that PATMAT can be a promising approach for improving the quality of personalized face inpainting.

We introduce the Byte Latent Transformer (BLT), a new byte-level LLM architecture that, for the first time, matches tokenization-based LLM performance at scale with significant improvements in inference efficiency and robustness. BLT encodes bytes into dynamically sized patches, which serve as the primary units of computation. Patches are segmented based on the entropy of the next byte, allocating more compute and model capacity where increased data complexity demands it. We present the first FLOP controlled scaling study of byte-level models up to 8B parameters and 4T training bytes. Our results demonstrate the feasibility of scaling models trained on raw bytes without a fixed vocabulary. Both training and inference efficiency improve due to dynamically selecting long patches when data is predictable, along with qualitative improvements on reasoning and long tail generalization. Overall, for fixed inference costs, BLT shows significantly better scaling than tokenization-based models, by simultaneously growing both patch and model size.

Recent advances in image editing, driven by image diffusion models, have shown remarkable progress. However, significant challenges remain, as these models often struggle to follow complex edit instructions accurately and frequently compromise fidelity by altering key elements of the original image. Simultaneously, video generation has made remarkable strides, with models that effectively function as consistent and continuous world simulators. In this paper, we propose merging these two fields by utilizing image-to-video models for image editing. We reformulate image editing as a temporal process, using pretrained video models to create smooth transitions from the original image to the desired edit. This approach traverses the image manifold continuously, ensuring consistent edits while preserving the original image's key aspects. Our approach achieves state-of-the-art results on text-based image editing, demonstrating significant improvements in both edit accuracy and image preservation.

The ubiquitous and demonstrably suboptimal choice of resizing images to a fixed resolution before processing them with computer vision models has not yet been successfully challenged. However, models such as the Vision Transformer (ViT) offer flexible sequence-based modeling, and hence varying input sequence lengths. We take advantage of this with NaViT (Native Resolution ViT) which uses sequence packing during training to process inputs of arbitrary resolutions and aspect ratios. Alongside flexible model usage, we demonstrate improved training efficiency for large-scale supervised and contrastive image-text pretraining. NaViT can be efficiently transferred to standard tasks such as image and video classification, object detection, and semantic segmentation and leads to improved results on robustness and fairness benchmarks. At inference time, the input resolution flexibility can be used to smoothly navigate the test-time cost-performance trade-off. We believe that NaViT marks a departure from the standard, CNN-designed, input and modelling pipeline used by most computer vision models, and represents a promising direction for ViTs.

Inspecting the information encoded in hidden representations of large language models (LLMs) can explain models' behavior and verify their alignment with human values. Given the capabilities of LLMs in generating human-understandable text, we propose leveraging the model itself to explain its internal representations in natural language. We introduce a framework called Patchscopes and show how it can be used to answer a wide range of research questions about an LLM's computation. We show that prior interpretability methods based on projecting representations into the vocabulary space and intervening on the LLM computation, can be viewed as special instances of this framework. Moreover, several of their shortcomings such as failure in inspecting early layers or lack of expressivity can be mitigated by a Patchscope. Beyond unifying prior inspection techniques, Patchscopes also opens up new possibilities such as using a more capable model to explain the representations of a smaller model, and unlocks new applications such as self-correction in multi-hop reasoning.

As Large Language Models (LLMs) achieve remarkable progress in language understanding and generation, their training efficiency has become a critical concern. Traditionally, LLMs are trained to predict the next token in a sequence. Despite the success of token-level training, it suffers from considerable computational costs due to the need to process an extensive number of tokens. To mitigate this issue, this paper introduces patch-level training for LLMs, which reduces the sequence length by compressing multiple tokens into a single patch. During patch-level training, we feed the language model shorter sequences of patches and train it to predict the next patch, thereby processing the majority of the training data at a significantly reduced computational cost. Following this, the model continues token-level training on the remaining training data to align with the inference mode. Experiments on a diverse range of models (370M-2.7B parameters) demonstrate that patch-level training can reduce overall computational costs to 0.5times, without compromising the model performance compared to token-level training. Source code: https://github.com/shaochenze/PatchTrain.

With recent advancements in large language models, methods like chain-of-thought prompting to elicit reasoning chains have been shown to improve results on reasoning tasks. However, tasks that require multiple steps of reasoning still pose significant challenges to state-of-the-art models. Drawing inspiration from the beam search algorithm, we propose PathFinder, a tree-search-based reasoning path generation approach. It enhances diverse branching and multi-hop reasoning through the integration of dynamic decoding, enabled by varying sampling methods and parameters. Using constrained reasoning, PathFinder integrates novel quality constraints, pruning, and exploration methods to enhance the efficiency and the quality of generation. Moreover, it includes scoring and ranking features to improve candidate selection. Our approach outperforms competitive baselines on three complex arithmetic and commonsense reasoning tasks by 6% on average. Our model generalizes well to longer, unseen reasoning chains, reflecting similar complexities to beam search with large branching factors.

Pathology, the microscopic examination of diseased tissue, is critical for diagnosing various medical conditions, particularly cancers. Traditional methods are labor-intensive and prone to human error. Digital pathology, which converts glass slides into high-resolution digital images for analysis by computer algorithms, revolutionizes the field by enhancing diagnostic accuracy, consistency, and efficiency through automated image analysis and large-scale data processing. Foundational transformer pretraining is crucial for developing robust, generalizable models as it enables learning from vast amounts of unannotated data. This paper introduces the Hibou family of foundational vision transformers for pathology, leveraging the DINOv2 framework to pretrain two model variants, Hibou-B and Hibou-L, on a proprietary dataset of over 1 million whole slide images (WSIs) representing diverse tissue types and staining techniques. Our pretrained models demonstrate superior performance on both patch-level and slide-level benchmarks, surpassing existing state-of-the-art methods. Notably, Hibou-L achieves the highest average accuracy across multiple benchmark datasets. To support further research and application in the field, we have open-sourced the Hibou-B model, which can be accessed at https://github.com/HistAI/hibou

Vision transformers (ViTs) have significantly changed the computer vision landscape and have periodically exhibited superior performance in vision tasks compared to convolutional neural networks (CNNs). Although the jury is still out on which model type is superior, each has unique inductive biases that shape their learning and generalization performance. For example, ViTs have interesting properties with respect to early layer non-local feature dependence, as well as self-attention mechanisms which enhance learning flexibility, enabling them to ignore out-of-context image information more effectively. We hypothesize that this power to ignore out-of-context information (which we name patch selectivity), while integrating in-context information in a non-local manner in early layers, allows ViTs to more easily handle occlusion. In this study, our aim is to see whether we can have CNNs simulate this ability of patch selectivity by effectively hardwiring this inductive bias using Patch Mixing data augmentation, which consists of inserting patches from another image onto a training image and interpolating labels between the two image classes. Specifically, we use Patch Mixing to train state-of-the-art ViTs and CNNs, assessing its impact on their ability to ignore out-of-context patches and handle natural occlusions. We find that ViTs do not improve nor degrade when trained using Patch Mixing, but CNNs acquire new capabilities to ignore out-of-context information and improve on occlusion benchmarks, leaving us to conclude that this training method is a way of simulating in CNNs the abilities that ViTs already possess. We will release our Patch Mixing implementation and proposed datasets for public use. Project page: https://arielnlee.github.io/PatchMixing/

Recent advancements in the field of large language models, particularly through the Chain of Thought (CoT) approach, have demonstrated significant improvements in solving complex problems. However, existing models either tend to sacrifice detailed reasoning for brevity due to user preferences, or require extensive and expensive training data to learn complicated reasoning ability, limiting their potential in solving complex tasks. To bridge this gap, following the concept of scaling test-time, we propose a simple method by encouraging models to adopt a more patient reasoning style without the need of introducing new knowledge or skills. To employ a preference optimization approach, we generate detailed reasoning processes as positive examples and simple answers as negative examples, thereby training the model to favor thoroughness in its responses. Our results demonstrate a performance increase of up to 6.7% on GSM8k with training just on a lightweight dataset.

The growing volume of high-resolution Whole Slide Images in digital histopathology poses significant storage, transmission, and computational efficiency challenges. Standard compression methods, such as JPEG, reduce file sizes but often fail to preserve fine-grained phenotypic details critical for downstream tasks. In this work, we repurpose autoencoders (AEs) designed for Latent Diffusion Models as an efficient learned compression framework for pathology images. We systematically benchmark three AE models with varying compression levels and evaluate their reconstruction ability using pathology foundation models. We introduce a fine-tuning strategy to further enhance reconstruction fidelity that optimizes a pathology-specific learned perceptual metric. We validate our approach on downstream tasks, including segmentation, patch classification, and multiple instance learning, showing that replacing images with AE-compressed reconstructions leads to minimal performance degradation. Additionally, we propose a K-means clustering-based quantization method for AE latents, improving storage efficiency while maintaining reconstruction quality. We provide the weights of the fine-tuned autoencoders at https://huggingface.co/collections/StonyBrook-CVLab/pathology-fine-tuned-aes-67d45f223a659ff2e3402dd0.

Breast cancer survival prediction in computational pathology presents a remarkable challenge due to tumor heterogeneity. For instance, different regions of the same tumor in the pathology image can show distinct morphological and molecular characteristics. This makes it difficult to extract representative features from whole slide images (WSIs) that truly reflect the tumor's aggressive potential and likely survival outcomes. In this paper, we present PathoHR, a novel pipeline for accurate breast cancer survival prediction that enhances any size of pathological images to enable more effective feature learning. Our approach entails (1) the incorporation of a plug-and-play high-resolution Vision Transformer (ViT) to enhance patch-wise WSI representation, enabling more detailed and comprehensive feature extraction, (2) the systematic evaluation of multiple advanced similarity metrics for comparing WSI-extracted features, optimizing the representation learning process to better capture tumor characteristics, (3) the demonstration that smaller image patches enhanced follow the proposed pipeline can achieve equivalent or superior prediction accuracy compared to raw larger patches, while significantly reducing computational overhead. Experimental findings valid that PathoHR provides the potential way of integrating enhanced image resolution with optimized feature learning to advance computational pathology, offering a promising direction for more accurate and efficient breast cancer survival prediction. Code will be available at https://github.com/AIGeeksGroup/PathoHR.

The exponential growth of astronomical literature poses significant challenges for researchers navigating and synthesizing general insights or even domain-specific knowledge. We present Pathfinder, a machine learning framework designed to enable literature review and knowledge discovery in astronomy, focusing on semantic searching with natural language instead of syntactic searches with keywords. Utilizing state-of-the-art large language models (LLMs) and a corpus of 350,000 peer-reviewed papers from the Astrophysics Data System (ADS), Pathfinder offers an innovative approach to scientific inquiry and literature exploration. Our framework couples advanced retrieval techniques with LLM-based synthesis to search astronomical literature by semantic context as a complement to currently existing methods that use keywords or citation graphs. It addresses complexities of jargon, named entities, and temporal aspects through time-based and citation-based weighting schemes. We demonstrate the tool's versatility through case studies, showcasing its application in various research scenarios. The system's performance is evaluated using custom benchmarks, including single-paper and multi-paper tasks. Beyond literature review, Pathfinder offers unique capabilities for reformatting answers in ways that are accessible to various audiences (e.g. in a different language or as simplified text), visualizing research landscapes, and tracking the impact of observatories and methodologies. This tool represents a significant advancement in applying AI to astronomical research, aiding researchers at all career stages in navigating modern astronomy literature.

Pathology Foundation Models (FMs) hold great promise for healthcare. Before they can be used in clinical practice, it is essential to ensure they are robust to variations between medical centers. We measure whether pathology FMs focus on biological features like tissue and cancer type, or on the well known confounding medical center signatures introduced by staining procedure and other differences. We introduce the Robustness Index. This novel robustness metric reflects to what degree biological features dominate confounding features. Ten current publicly available pathology FMs are evaluated. We find that all current pathology foundation models evaluated represent the medical center to a strong degree. Significant differences in the robustness index are observed. Only one model so far has a robustness index greater than one, meaning biological features dominate confounding features, but only slightly. A quantitative approach to measure the influence of medical center differences on FM-based prediction performance is described. We analyze the impact of unrobustness on classification performance of downstream models, and find that cancer-type classification errors are not random, but specifically attributable to same-center confounders: images of other classes from the same medical center. We visualize FM embedding spaces, and find these are more strongly organized by medical centers than by biological factors. As a consequence, the medical center of origin is predicted more accurately than the tissue source and cancer type. The robustness index introduced here is provided with the aim of advancing progress towards clinical adoption of robust and reliable pathology FMs.

As the capabilities of Large Language Models (LLMs) continue to advance, the field of patent processing has garnered increased attention within the natural language processing community. However, the majority of research has been concentrated on classification tasks, such as patent categorization and examination, or on short text generation tasks like patent summarization and patent quizzes. In this paper, we introduce a novel and practical task known as Draft2Patent, along with its corresponding D2P benchmark, which challenges LLMs to generate full-length patents averaging 17K tokens based on initial drafts. Patents present a significant challenge to LLMs due to their specialized nature, standardized terminology, and extensive length. We propose a multi-agent framework called AutoPatent which leverages the LLM-based planner agent, writer agents, and examiner agent with PGTree and RRAG to generate lengthy, intricate, and high-quality complete patent documents. The experimental results demonstrate that our AutoPatent framework significantly enhances the ability to generate comprehensive patents across various LLMs. Furthermore, we have discovered that patents generated solely with the AutoPatent framework based on the Qwen2.5-7B model outperform those produced by larger and more powerful LLMs, such as GPT-4o, Qwen2.5-72B, and LLAMA3.1-70B, in both objective metrics and human evaluations. We will make the data and code available upon acceptance at https://github.com/QiYao-Wang/AutoPatent.

Logical reasoning task has attracted great interest since it was proposed. Faced with such a task, current competitive models, even large language models (e.g., ChatGPT and PaLM 2), still perform badly. Previous promising LMs struggle in logical consistency modeling and logical structure perception. To this end, we model the logical reasoning task by transforming each logical sample into reasoning paths and propose an architecture PathReasoner. It addresses the task from the views of both data and model. To expand the diversity of the logical samples, we propose an atom extension strategy supported by equivalent logical formulas, to form new reasoning paths. From the model perspective, we design a stack of transformer-style blocks. In particular, we propose a path-attention module to joint model in-atom and cross-atom relations with the high-order diffusion strategy. Experiments show that PathReasoner achieves competitive performances on two logical reasoning benchmarks and great generalization abilities.

The emergence of large multimodal models has unlocked remarkable potential in AI, particularly in pathology. However, the lack of specialized, high-quality benchmark impeded their development and precise evaluation. To address this, we introduce PathMMU, the largest and highest-quality expert-validated pathology benchmark for LMMs. It comprises 33,573 multimodal multi-choice questions and 21,599 images from various sources, and an explanation for the correct answer accompanies each question. The construction of PathMMU capitalizes on the robust capabilities of GPT-4V, utilizing approximately 30,000 gathered image-caption pairs to generate Q\&As. Significantly, to maximize PathMMU's authority, we invite six pathologists to scrutinize each question under strict standards in PathMMU's validation and test sets, while simultaneously setting an expert-level performance benchmark for PathMMU. We conduct extensive evaluations, including zero-shot assessments of 14 open-sourced and three closed-sourced LMMs and their robustness to image corruption. We also fine-tune representative LMMs to assess their adaptability to PathMMU. The empirical findings indicate that advanced LMMs struggle with the challenging PathMMU benchmark, with the top-performing LMM, GPT-4V, achieving only a 51.7\% zero-shot performance, significantly lower than the 71.4\% demonstrated by human pathologists. After fine-tuning, even open-sourced LMMs can surpass GPT-4V with a performance of over 60\%, but still fall short of the expertise shown by pathologists. We hope that the PathMMU will offer valuable insights and foster the development of more specialized, next-generation LLMs for pathology.

Single image depth estimation is a foundational task in computer vision and generative modeling. However, prevailing depth estimation models grapple with accommodating the increasing resolutions commonplace in today's consumer cameras and devices. Existing high-resolution strategies show promise, but they often face limitations, ranging from error propagation to the loss of high-frequency details. We present PatchFusion, a novel tile-based framework with three key components to improve the current state of the art: (1) A patch-wise fusion network that fuses a globally-consistent coarse prediction with finer, inconsistent tiled predictions via high-level feature guidance, (2) A Global-to-Local (G2L) module that adds vital context to the fusion network, discarding the need for patch selection heuristics, and (3) A Consistency-Aware Training (CAT) and Inference (CAI) approach, emphasizing patch overlap consistency and thereby eradicating the necessity for post-processing. Experiments on UnrealStereo4K, MVS-Synth, and Middleburry 2014 demonstrate that our framework can generate high-resolution depth maps with intricate details. PatchFusion is independent of the base model for depth estimation. Notably, our framework built on top of SOTA ZoeDepth brings improvements for a total of 17.3% and 29.4% in terms of the root mean squared error (RMSE) on UnrealStereo4K and MVS-Synth, respectively.

Pathology diagnosis based on EEG signals and decoding brain activity holds immense importance in understanding neurological disorders. With the advancement of artificial intelligence methods and machine learning techniques, the potential for accurate data-driven diagnoses and effective treatments has grown significantly. However, applying machine learning algorithms to real-world datasets presents diverse challenges at multiple levels. The scarcity of labelled data, especially in low regime scenarios with limited availability of real patient cohorts due to high costs of recruitment, underscores the vital deployment of scaling and transfer learning techniques. In this study, we explore a real-world pathology classification task to highlight the effectiveness of data and model scaling and cross-dataset knowledge transfer. As such, we observe varying performance improvements through data scaling, indicating the need for careful evaluation and labelling. Additionally, we identify the challenges of possible negative transfer and emphasize the significance of some key components to overcome distribution shifts and potential spurious correlations and achieve positive transfer. We see improvement in the performance of the target model on the target (NMT) datasets by using the knowledge from the source dataset (TUAB) when a low amount of labelled data was available. Our findings indicate a small and generic model (e.g. ShallowNet) performs well on a single dataset, however, a larger model (e.g. TCN) performs better on transfer and learning from a larger and diverse dataset.

In deep learning, mixture-of-experts (MoE) activates one or few experts (sub-networks) on a per-sample or per-token basis, resulting in significant computation reduction. The recently proposed patch-level routing in MoE (pMoE) divides each input into n patches (or tokens) and sends l patches (lll n) to each expert through prioritized routing. pMoE has demonstrated great empirical success in reducing training and inference costs while maintaining test accuracy. However, the theoretical explanation of pMoE and the general MoE remains elusive. Focusing on a supervised classification task using a mixture of two-layer convolutional neural networks (CNNs), we show for the first time that pMoE provably reduces the required number of training samples to achieve desirable generalization (referred to as the sample complexity) by a factor in the polynomial order of n/l, and outperforms its single-expert counterpart of the same or even larger capacity. The advantage results from the discriminative routing property, which is justified in both theory and practice that pMoE routers can filter label-irrelevant patches and route similar class-discriminative patches to the same expert. Our experimental results on MNIST, CIFAR-10, and CelebA support our theoretical findings on pMoE's generalization and show that pMoE can avoid learning spurious correlations.

We present the design of a new large scale orchestration layer for accelerators. Our system, Pathways, is explicitly designed to enable exploration of new systems and ML research ideas, while retaining state of the art performance for current models. Pathways uses a sharded dataflow graph of asynchronous operators that consume and produce futures, and efficiently gang-schedules heterogeneous parallel computations on thousands of accelerators while coordinating data transfers over their dedicated interconnects. Pathways makes use of a novel asynchronous distributed dataflow design that lets the control plane execute in parallel despite dependencies in the data plane. This design, with careful engineering, allows Pathways to adopt a single-controller model that makes it easier to express complex new parallelism patterns. We demonstrate that Pathways can achieve performance parity (~100% accelerator utilization) with state-of-the-art systems when running SPMD computations over 2048 TPUs, while also delivering throughput comparable to the SPMD case for Transformer models that are pipelined across 16 stages, or sharded across two islands of accelerators connected over a data center network.

The growing popularity of wearable sensors has generated large quantities of temporal physiological and activity data. Ability to analyze this data offers new opportunities for real-time health monitoring and forecasting. However, temporal physiological data presents many analytic challenges: the data is noisy, contains many missing values, and each series has a different length. Most methods proposed for time series analysis and classification do not handle datasets with these characteristics nor do they offer interpretability and explainability, a critical requirement in the health domain. We propose an unsupervised method for learning representations of time series based on common patterns identified within them. The patterns are, interpretable, variable in length, and extracted using Byte Pair Encoding compression technique. In this way the method can capture both long-term and short-term dependencies present in the data. We show that this method applies to both univariate and multivariate time series and beats state-of-the-art approaches on a real world dataset collected from wearable sensors.

Retrieval-augmented generation (RAG) improves the response quality of large language models (LLMs) by retrieving knowledge from external databases. Typical RAG approaches split the text database into chunks, organizing them in a flat structure for efficient searches. To better capture the inherent dependencies and structured relationships across the text database, researchers propose to organize textual information into an indexing graph, known asgraph-based RAG. However, we argue that the limitation of current graph-based RAG methods lies in the redundancy of the retrieved information, rather than its insufficiency. Moreover, previous methods use a flat structure to organize retrieved information within the prompts, leading to suboptimal performance. To overcome these limitations, we propose PathRAG, which retrieves key relational paths from the indexing graph, and converts these paths into textual form for prompting LLMs. Specifically, PathRAG effectively reduces redundant information with flow-based pruning, while guiding LLMs to generate more logical and coherent responses with path-based prompting. Experimental results show that PathRAG consistently outperforms state-of-the-art baselines across six datasets and five evaluation dimensions. The code is available at the following link: https://github.com/BUPT-GAMMA/PathRAG

Automated drug discovery offers significant potential for accelerating the development of novel therapeutics by substituting labor-intensive human workflows with machine-driven processes. However, molecules generated by artificial intelligence may unintentionally infringe on existing patents, posing legal and financial risks that impede the full automation of drug discovery pipelines. This paper introduces PatentFinder, a novel multi-agent and tool-enhanced intelligence system that can accurately and comprehensively evaluate small molecules for patent infringement. PatentFinder features five specialized agents that collaboratively analyze patent claims and molecular structures with heuristic and model-based tools, generating interpretable infringement reports. To support systematic evaluation, we curate MolPatent-240, a benchmark dataset tailored for patent infringement assessment algorithms. On this benchmark, PatentFinder outperforms baseline methods that rely solely on large language models or specialized chemical tools, achieving a 13.8% improvement in F1-score and a 12% increase in accuracy. Additionally, PatentFinder autonomously generates detailed and interpretable patent infringement reports, showcasing enhanced accuracy and improved interpretability. The high accuracy and interpretability of PatentFinder make it a valuable and reliable tool for automating patent infringement assessments, offering a practical solution for integrating patent protection analysis into the drug discovery pipeline.

This paper introduces Patched MOA (Mixture of Agents), an inference optimization technique that significantly enhances the performance of large language models (LLMs) across diverse software development tasks. We evaluate three inference optimization algorithms - Best of N, Mixture of Agents, and Monte Carlo Tree Search and demonstrate that Patched MOA can boost the performance of smaller models to surpass that of larger, more expensive models. Notably, our approach improves the gpt-4o-mini model's performance on the Arena-Hard-Auto benchmark by 15.52%, outperforming gpt-4-turbo at a fraction of the cost. We also apply Patched MOA to various software development workflows, showing consistent improvements in task completion rates. Our method is model-agnostic, transparent to end-users, and can be easily integrated into existing LLM pipelines. This work contributes to the growing field of LLM optimization, offering a cost-effective solution for enhancing model performance without the need for fine-tuning or larger models.

This paper introduces Patched Round-Trip Correctness (Patched RTC), a novel evaluation technique for Large Language Models (LLMs) applied to diverse software development tasks, particularly focusing on "outer loop" activities such as bug fixing, code review, and documentation updates. Patched RTC extends the original Round-Trip Correctness method to work with any LLM and downstream task, offering a self-evaluating framework that measures consistency and robustness of model responses without human intervention. The study demonstrates a correlation between Patched RTC scores and task-specific accuracy metrics, presenting it as an alternative to the LLM-as-Judge paradigm for open-domain task evaluation. We implement Patched RTC in an open-source framework called patchwork, allowing for transparent evaluation during inference across various patchflows. Experiments comparing GPT-3.5 and GPT-4 models across different software development tasks reveal that Patched RTC effectively distinguishes model performance and task difficulty. The paper also explores the impact of consistency prompts on improving model accuracy, suggesting that Patched RTC can guide prompt refinement and model selection for complex software development workflows.

Pathology is the study of microscopic inspection of tissue, and a pathology diagnosis is often the medical gold standard to diagnose disease. Pathology images provide a unique challenge for computer-vision-based analysis: a single pathology Whole Slide Image (WSI) is gigapixel-sized and often contains hundreds of thousands to millions of objects of interest across multiple resolutions. In this work, we propose PathoLogy Universal TransfOrmer (PLUTO): a light-weight pathology FM that is pre-trained on a diverse dataset of 195 million image tiles collected from multiple sites and extracts meaningful representations across multiple WSI scales that enable a large variety of downstream pathology tasks. In particular, we design task-specific adaptation heads that utilize PLUTO's output embeddings for tasks which span pathology scales ranging from subcellular to slide-scale, including instance segmentation, tile classification, and slide-level prediction. We compare PLUTO's performance to other state-of-the-art methods on a diverse set of external and internal benchmarks covering multiple biologically relevant tasks, tissue types, resolutions, stains, and scanners. We find that PLUTO matches or outperforms existing task-specific baselines and pathology-specific foundation models, some of which use orders-of-magnitude larger datasets and model sizes when compared to PLUTO. Our findings present a path towards a universal embedding to power pathology image analysis, and motivate further exploration around pathology foundation models in terms of data diversity, architectural improvements, sample efficiency, and practical deployability in real-world applications.

The objective of Entity Alignment (EA) is to identify equivalent entity pairs from multiple Knowledge Graphs (KGs) and create a more comprehensive and unified KG. The majority of EA methods have primarily focused on the structural modality of KGs, lacking exploration of multi-modal information. A few multi-modal EA methods have made good attempts in this field. Still, they have two shortcomings: (1) inconsistent and inefficient modality modeling that designs complex and distinct models for each modality; (2) ineffective modality fusion due to the heterogeneous nature of modalities in EA. To tackle these challenges, we propose PathFusion, consisting of two main components: (1) MSP, a unified modeling approach that simplifies the alignment process by constructing paths connecting entities and modality nodes to represent multiple modalities; (2) IRF, an iterative fusion method that effectively combines information from different modalities using the path as an information carrier. Experimental results on real-world datasets demonstrate the superiority of PathFusion over state-of-the-art methods, with 22.4%-28.9% absolute improvement on Hits@1, and 0.194-0.245 absolute improvement on MRR.

Vision Transformers have achieved great success in computer visions, delivering exceptional performance across various tasks. However, their inherent reliance on sequential input enforces the manual partitioning of images into patch sequences, which disrupts the image's inherent structural and semantic continuity. To handle this, we propose a novel Pattern Transformer (Patternformer) to adaptively convert images to pattern sequences for Transformer input. Specifically, we employ the Convolutional Neural Network to extract various patterns from the input image, with each channel representing a unique pattern that is fed into the succeeding Transformer as a visual token. By enabling the network to optimize these patterns, each pattern concentrates on its local region of interest, thereby preserving its intrinsic structural and semantic information. Only employing the vanilla ResNet and Transformer, we have accomplished state-of-the-art performance on CIFAR-10 and CIFAR-100, and have achieved competitive results on ImageNet.

Patient recruitment is challenging for clinical trials. We introduce TrialGPT, an end-to-end framework for zero-shot patient-to-trial matching with large language models. TrialGPT comprises three modules: it first performs large-scale filtering to retrieve candidate trials (TrialGPT-Retrieval); then predicts criterion-level patient eligibility (TrialGPT-Matching); and finally generates trial-level scores (TrialGPT-Ranking). We evaluate TrialGPT on three cohorts of 183 synthetic patients with over 75,000 trial annotations. TrialGPT-Retrieval can recall over 90% of relevant trials using less than 6% of the initial collection. Manual evaluations on 1,015 patient-criterion pairs show that TrialGPT-Matching achieves an accuracy of 87.3% with faithful explanations, close to the expert performance. The TrialGPT-Ranking scores are highly correlated with human judgments and outperform the best-competing models by 43.8% in ranking and excluding trials. Furthermore, our user study reveals that TrialGPT can reduce the screening time by 42.6% in patient recruitment. Overall, these results have demonstrated promising opportunities for patient-to-trial matching with TrialGPT.

Graph neural networks (GNNs) have recently become the standard approach for learning with graph-structured data. Prior work has shed light into their potential, but also their limitations. Unfortunately, it was shown that standard GNNs are limited in their expressive power. These models are no more powerful than the 1-dimensional Weisfeiler-Leman (1-WL) algorithm in terms of distinguishing non-isomorphic graphs. In this paper, we propose Path Neural Networks (PathNNs), a model that updates node representations by aggregating paths emanating from nodes. We derive three different variants of the PathNN model that aggregate single shortest paths, all shortest paths and all simple paths of length up to K. We prove that two of these variants are strictly more powerful than the 1-WL algorithm, and we experimentally validate our theoretical results. We find that PathNNs can distinguish pairs of non-isomorphic graphs that are indistinguishable by 1-WL, while our most expressive PathNN variant can even distinguish between 3-WL indistinguishable graphs. The different PathNN variants are also evaluated on graph classification and graph regression datasets, where in most cases, they outperform the baseline methods.

We target a 3D generative model for general natural scenes that are typically unique and intricate. Lacking the necessary volumes of training data, along with the difficulties of having ad hoc designs in presence of varying scene characteristics, renders existing setups intractable. Inspired by classical patch-based image models, we advocate for synthesizing 3D scenes at the patch level, given a single example. At the core of this work lies important algorithmic designs w.r.t the scene representation and generative patch nearest-neighbor module, that address unique challenges arising from lifting classical 2D patch-based framework to 3D generation. These design choices, on a collective level, contribute to a robust, effective, and efficient model that can generate high-quality general natural scenes with both realistic geometric structure and visual appearance, in large quantities and varieties, as demonstrated upon a variety of exemplar scenes.

Objective: We investigate whether deep learning techniques for natural language processing (NLP) can be used efficiently for patient phenotyping. Patient phenotyping is a classification task for determining whether a patient has a medical condition, and is a crucial part of secondary analysis of healthcare data. We assess the performance of deep learning algorithms and compare them with classical NLP approaches. Materials and Methods: We compare convolutional neural networks (CNNs), n-gram models, and approaches based on cTAKES that extract pre-defined medical concepts from clinical notes and use them to predict patient phenotypes. The performance is tested on 10 different phenotyping tasks using 1,610 discharge summaries extracted from the MIMIC-III database. Results: CNNs outperform other phenotyping algorithms in all 10 tasks. The average F1-score of our model is 76 (PPV of 83, and sensitivity of 71) with our model having an F1-score up to 37 points higher than alternative approaches. We additionally assess the interpretability of our model by presenting a method that extracts the most salient phrases for a particular prediction. Conclusion: We show that NLP methods based on deep learning improve the performance of patient phenotyping. Our CNN-based algorithm automatically learns the phrases associated with each patient phenotype. As such, it reduces the annotation complexity for clinical domain experts, who are normally required to develop task-specific annotation rules and identify relevant phrases. Our method performs well in terms of both performance and interpretability, which indicates that deep learning is an effective approach to patient phenotyping based on clinicians' notes.

Patient notes contain a wealth of information of potentially great interest to medical investigators. However, to protect patients' privacy, Protected Health Information (PHI) must be removed from the patient notes before they can be legally released, a process known as patient note de-identification. The main objective for a de-identification system is to have the highest possible recall. Recently, the first neural-network-based de-identification system has been proposed, yielding state-of-the-art results. Unlike other systems, it does not rely on human-engineered features, which allows it to be quickly deployed, but does not leverage knowledge from human experts or from electronic health records (EHRs). In this work, we explore a method to incorporate human-engineered features as well as features derived from EHRs to a neural-network-based de-identification system. Our results show that the addition of features, especially the EHR-derived features, further improves the state-of-the-art in patient note de-identification, including for some of the most sensitive PHI types such as patient names. Since in a real-life setting patient notes typically come with EHRs, we recommend developers of de-identification systems to leverage the information EHRs contain.

Dichotomous Image Segmentation (DIS) is a high-precision object segmentation task for high-resolution natural images. The current mainstream methods focus on the optimization of local details but overlook the fundamental challenge of modeling the integrity of objects. We have found that the depth integrity-prior implicit in the the pseudo-depth maps generated by Depth Anything Model v2 and the local detail features of image patches can jointly address the above dilemmas. Based on the above findings, we have designed a novel Patch-Depth Fusion Network (PDFNet) for high-precision dichotomous image segmentation. The core of PDFNet consists of three aspects. Firstly, the object perception is enhanced through multi-modal input fusion. By utilizing the patch fine-grained strategy, coupled with patch selection and enhancement, the sensitivity to details is improved. Secondly, by leveraging the depth integrity-prior distributed in the depth maps, we propose an integrity-prior loss to enhance the uniformity of the segmentation results in the depth maps. Finally, we utilize the features of the shared encoder and, through a simple depth refinement decoder, improve the ability of the shared encoder to capture subtle depth-related information in the images. Experiments on the DIS-5K dataset show that PDFNet significantly outperforms state-of-the-art non-diffusion methods. Due to the incorporation of the depth integrity-prior, PDFNet achieves or even surpassing the performance of the latest diffusion-based methods while using less than 11% of the parameters of diffusion-based methods. The source code at https://github.com/Tennine2077/PDFNet.

With the rapid development of computational pathology, many AI-assisted diagnostic tasks have emerged. Cellular nuclei segmentation can segment various types of cells for downstream analysis, but it relies on predefined categories and lacks flexibility. Moreover, pathology visual question answering can perform image-level understanding but lacks region-level detection capability. To address this, we propose a new benchmark called Pathology Visual Grounding (PathVG), which aims to detect regions based on expressions with different attributes. To evaluate PathVG, we create a new dataset named RefPath which contains 27,610 images with 33,500 language-grounded boxes. Compared to visual grounding in other domains, PathVG presents pathological images at multi-scale and contains expressions with pathological knowledge. In the experimental study, we found that the biggest challenge was the implicit information underlying the pathological expressions. Based on this, we proposed Pathology Knowledge-enhanced Network (PKNet) as the baseline model for PathVG. PKNet leverages the knowledge-enhancement capabilities of Large Language Models (LLMs) to convert pathological terms with implicit information into explicit visual features, and fuses knowledge features with expression features through the designed Knowledge Fusion Module (KFM). The proposed method achieves state-of-the-art performance on the PathVG benchmark.

We apply a Gaussian process method to the extreme gamma-ray flares of 3C 454.3 and 3C 279 to discover the variable patterns and then to investigate the physical origins of the giant flares. The kernels of stochastically driven damped simple harmonic oscillator (SHO), the damped random-walk (DRW), and Matrm ern-3/2 are respectively used to describe the adaptive-binning gamma-ray light curves of the two flares. Our findings show that both the extreme gamma-ray flares of 3C 454.3 and 3C 279 clearly prefer the SHO kernel in the over-damped mode and the Matrm ern-3/2 kernel over the DRW kernel. The resulted SHO and Matrm ern-3/2 power spectral densities (PSDs) are the same for each object, with the index changing from -4 at high frequencies to 0 at low frequencies. The patterns of the two flares are both approaching the critical damping mode with the quality factor Q approx 0.4 (i.e., the damping ratio eta approx 1.25), but with slightly different damping timescales. The characteristic timescale (corresponding to the broken frequency in the PSD) for 3C 454.3 is 2-3 days and 3-5 days for 3C 279. The variable patterns found here suggest that once the system responds to the energy injection disturbance, the release of the energy in the system is finished abruptly. The obtained timescale provides a constraint on the size of energy dissipation region for each source.

Predicting disease trajectories from electronic health records (EHRs) is a complex task due to major challenges such as data non-stationarity, high granularity of medical codes, and integration of multimodal data. EHRs contain both structured data, such as diagnostic codes, and unstructured data, such as clinical notes, which hold essential information often overlooked. Current models, primarily based on structured data, struggle to capture the complete medical context of patients, resulting in a loss of valuable information. To address this issue, we propose an approach that integrates unstructured clinical notes into transformer-based deep learning models for sequential disease prediction. This integration enriches the representation of patients' medical histories, thereby improving the accuracy of diagnosis predictions. Experiments on MIMIC-IV datasets demonstrate that the proposed approach outperforms traditional models relying solely on structured data.

Pathology plays a critical role in diagnosing a wide range of diseases, yet existing approaches often rely heavily on task-specific models trained on extensive, well-labeled datasets. These methods face sustainability challenges due to the diversity of pathologies and the labor-intensive nature of data collection. To address these limitations, we highlight the need for universal multimodal embeddings that can support multiple downstream tasks. Previous approaches often involve fine-tuning CLIP-based models, which handle images and text separately, limiting their ability to capture complex multimodal relationships. Additionally, these models are evaluated across diverse datasets without a unified benchmark for assessing multimodal embeddings in pathology. To address these challenges, we propose MLLM4PUE, a novel framework that leverages Multimodal Large Language Models (MLLMs) to generate Pathology Universal Embeddings. The MLLM4PUE framework not only facilitates robust integration of images and text but also enhances understanding and fusion capabilities across various tasks. We further introduce the Pathology Multimodal Embedding Benchmark (PMEB), a comprehensive benchmark designed to assess the quality of pathology multimodal embeddings. PMEB comprises 15 original tasks drawn from 14 datasets, organized into three meta-tasks: retrieval, classification, and composed retrieval. Experimental results demonstrate the superiority of MLLM4PUE, illustrating MLLM-based models can effectively support a wide range of downstream tasks and unify the research direction for foundation models in pathology.

Writing comprehensive and accurate descriptions of technical drawings in patent documents is crucial to effective knowledge sharing and enabling the replication and protection of intellectual property. However, automation of this task has been largely overlooked by the research community. To this end, we introduce PatentDesc-355K, a novel large-scale dataset containing ~355K patent figures along with their brief and detailed textual descriptions extracted from more than 60K US patent documents. In addition, we propose PatentLMM - a novel multimodal large language model specifically tailored to generate high-quality descriptions of patent figures. Our proposed PatentLMM comprises two key components: (i) PatentMME, a specialized multimodal vision encoder that captures the unique structural elements of patent figures, and (ii) PatentLLaMA, a domain-adapted version of LLaMA fine-tuned on a large collection of patents. Extensive experiments demonstrate that training a vision encoder specifically designed for patent figures significantly boosts the performance, generating coherent descriptions compared to fine-tuning similar-sized off-the-shelf multimodal models. PatentDesc-355K and PatentLMM pave the way for automating the understanding of patent figures, enabling efficient knowledge sharing and faster drafting of patent documents. We make the code and data publicly available.

While current high-resolution depth estimation methods achieve strong results, they often suffer from computational inefficiencies due to reliance on heavyweight models and multiple inference steps, increasing inference time. To address this, we introduce PatchRefiner V2 (PRV2), which replaces heavy refiner models with lightweight encoders. This reduces model size and inference time but introduces noisy features. To overcome this, we propose a Coarse-to-Fine (C2F) module with a Guided Denoising Unit for refining and denoising the refiner features and a Noisy Pretraining strategy to pretrain the refiner branch to fully exploit the potential of the lightweight refiner branch. Additionally, we introduce a Scale-and-Shift Invariant Gradient Matching (SSIGM) loss to enhance synthetic-to-real domain transfer. PRV2 outperforms state-of-the-art depth estimation methods on UnrealStereo4K in both accuracy and speed, using fewer parameters and faster inference. It also shows improved depth boundary delineation on real-world datasets like CityScape, ScanNet++, and KITTI, demonstrating its versatility across domains.

This paper presents Patent-CR, the first dataset created for the patent claim revision task in English. It includes both initial patent applications rejected by patent examiners and the final granted versions. Unlike normal text revision tasks that predominantly focus on enhancing sentence quality, such as grammar correction and coherence improvement, patent claim revision aims at ensuring the claims meet stringent legal criteria. These criteria are beyond novelty and inventiveness, including clarity of scope, technical accuracy, language precision, and legal robustness. We assess various large language models (LLMs) through professional human evaluation, including general LLMs with different sizes and architectures, text revision models, and domain-specific models. Our results indicate that LLMs often bring ineffective edits that deviate from the target revisions. In addition, domain-specific models and the method of fine-tuning show promising results. Notably, GPT-4 outperforms other tested LLMs, but further revisions are still necessary to reach the examination standard. Furthermore, we demonstrate the inconsistency between automated and human evaluation results, suggesting that GPT-4-based automated evaluation has the highest correlation with human judgment. This dataset, along with our preliminary empirical research, offers invaluable insights for further exploration in patent claim revision.

A patent must be deemed novel and non-obvious in order to be granted by the US Patent Office (USPTO). If it is not, a US patent examiner will cite the prior work, or prior art, that invalidates the novelty and issue a non-final rejection. Predicting what claims of the invention should change given the prior art is an essential and crucial step in securing invention rights, yet has not been studied before as a learnable task. In this work we introduce the PatentEdits dataset, which contains 105K examples of successful revisions that overcome objections to novelty. We design algorithms to label edits sentence by sentence, then establish how well these edits can be predicted with large language models (LLMs). We demonstrate that evaluating textual entailment between cited references and draft sentences is especially effective in predicting which inventive claims remained unchanged or are novel in relation to prior art.

Disclaimer: Samples in this paper may be harmful and cause discomfort! Patronizing and condescending language (PCL) is a form of speech directed at vulnerable groups. As an essential branch of toxic language, this type of language exacerbates conflicts and confrontations among Internet communities and detrimentally impacts disadvantaged groups. Traditional pre-trained language models (PLMs) perform poorly in detecting PCL due to its implicit toxicity traits like hypocrisy and false sympathy. With the rise of large language models (LLMs), we can harness their rich emotional semantics to establish a paradigm for exploring implicit toxicity. In this paper, we introduce PclGPT, a comprehensive LLM benchmark designed specifically for PCL. We collect, annotate, and integrate the Pcl-PT/SFT dataset, and then develop a bilingual PclGPT-EN/CN model group through a comprehensive pre-training and supervised fine-tuning staircase process to facilitate implicit toxic detection. Group detection results and fine-grained detection from PclGPT and other models reveal significant variations in the degree of bias in PCL towards different vulnerable groups, necessitating increased societal attention to protect them.

Pathological diagnosis remains the definitive standard for identifying tumors. The rise of multimodal large models has simplified the process of integrating image analysis with textual descriptions. Despite this advancement, the substantial costs associated with training and deploying these complex multimodal models, together with a scarcity of high-quality training datasets, create a significant divide between cutting-edge technology and its application in the clinical setting. We had meticulously compiled a dataset of approximately 45,000 cases, covering over 6 different tasks, including the classification of organ tissues, generating pathology report descriptions, and addressing pathology-related questions and answers. We have fine-tuned multimodal large models, specifically LLaVA, Qwen-VL, InternLM, with this dataset to enhance instruction-based performance. We conducted a qualitative assessment of the capabilities of the base model and the fine-tuned model in performing image captioning and classification tasks on the specific dataset. The evaluation results demonstrate that the fine-tuned model exhibits proficiency in addressing typical pathological questions. We hope that by making both our models and datasets publicly available, they can be valuable to the medical and research communities.

Recently, large language models (LLMs) have been gaining a lot of interest due to their adaptability and extensibility in emerging applications, including communication networks. It is anticipated that ZSM networks will be able to support LLMs as a service, as they provide ultra reliable low-latency communications and closed loop massive connectivity. However, LLMs are vulnerable to data and model privacy issues that affect the trustworthiness of LLMs to be deployed for user-based services. In this paper, we explore the security vulnerabilities associated with fine-tuning LLMs in ZSM networks, in particular the membership inference attack. We define the characteristics of an attack network that can perform a membership inference attack if the attacker has access to the fine-tuned model for the downstream task. We show that the membership inference attacks are effective for any downstream task, which can lead to a personal data breach when using LLM as a service. The experimental results show that the attack success rate of maximum 92% can be achieved on named entity recognition task. Based on the experimental analysis, we discuss possible defense mechanisms and present possible research directions to make the LLMs more trustworthy in the context of ZSM networks.

Graph databases are gaining momentum thanks to the flexibility and expressiveness of their data models and query languages. A standardization activity driven by the ISO/IEC standardization body is also ongoing and has already conducted to the specification of the first versions of two standard graph query languages, namely SQL/PGQ and GQL, respectively in 2023 and 2024. Apart from the standards, there exists a panoply of concrete graph query languages provided by current graph database systems, each offering different query features. A common limitation of current graph query engines is the absence of an algebraic approach for evaluating path queries. To address this, we introduce an abstract algebra for evaluating path queries, allowing paths to be treated as first-class entities within the query processing pipeline. We demonstrate that our algebra can express a core fragment of path queries defined in GQL and SQL/PGQ, thereby serving as a formal framework for studying both standards and supporting their implementation in current graph database systems. We also show that evaluation trees for path algebra expressions can function as logical plans for evaluating path queries and enable the application of query optimization techniques. Our algebraic framework has the potential to act as a lingua franca for path query evaluation, enabling different implementations to be expressed and compared.

Vision Language Models (VLMs) like CLIP have attracted substantial attention in pathology, serving as backbones for applications such as zero-shot image classification and Whole Slide Image (WSI) analysis. Additionally, they can function as vision encoders when combined with large language models (LLMs) to support broader capabilities. Current efforts to train pathology VLMs rely on pathology image-text pairs from platforms like PubMed, YouTube, and Twitter, which provide limited, unscalable data with generally suboptimal image quality. In this work, we leverage large-scale WSI datasets like TCGA to extract numerous high-quality image patches. We then train a large multimodal model to generate captions for these images, creating PathGen-1.6M, a dataset containing 1.6 million high-quality image-caption pairs. Our approach involves multiple agent models collaborating to extract representative WSI patches, generating and refining captions to obtain high-quality image-text pairs. Extensive experiments show that integrating these generated pairs with existing datasets to train a pathology-specific CLIP model, PathGen-CLIP, significantly enhances its ability to analyze pathological images, with substantial improvements across nine pathology-related zero-shot image classification tasks and three whole-slide image tasks. Furthermore, we construct 200K instruction-tuning data based on PathGen-1.6M and integrate PathGen-CLIP with the Vicuna LLM to create more powerful multimodal models through instruction tuning. Overall, we provide a scalable pathway for high-quality data generation in pathology, paving the way for next-generation general pathology models.

Complex Logical Query Answering (CLQA) over incomplete knowledge graphs is a challenging task. Recently, Query Embedding (QE) methods are proposed to solve CLQA by performing multi-hop logical reasoning. However, most of them only consider historical query context information while ignoring future information, which leads to their failure to capture the complex dependencies behind the elements of a query. In recent years, the transformer architecture has shown a strong ability to model long-range dependencies between words. The bidirectional attention mechanism proposed by the transformer can solve the limitation of these QE methods regarding query context. Still, as a sequence model, it is difficult for the transformer to model complex logical queries with branch structure computation graphs directly. To this end, we propose a neural one-point embedding method called Pathformer based on the tree-like computation graph, i.e., query computation tree. Specifically, Pathformer decomposes the query computation tree into path query sequences by branches and then uses the transformer encoder to recursively encode these path query sequences to obtain the final query embedding. This allows Pathformer to fully utilize future context information to explicitly model the complex interactions between various parts of the path query. Experimental results show that Pathformer outperforms existing competitive neural QE methods, and we found that Pathformer has the potential to be applied to non-one-point embedding space.

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.

This paper introduces PatchRefiner, an advanced framework for metric single image depth estimation aimed at high-resolution real-domain inputs. While depth estimation is crucial for applications such as autonomous driving, 3D generative modeling, and 3D reconstruction, achieving accurate high-resolution depth in real-world scenarios is challenging due to the constraints of existing architectures and the scarcity of detailed real-world depth data. PatchRefiner adopts a tile-based methodology, reconceptualizing high-resolution depth estimation as a refinement process, which results in notable performance enhancements. Utilizing a pseudo-labeling strategy that leverages synthetic data, PatchRefiner incorporates a Detail and Scale Disentangling (DSD) loss to enhance detail capture while maintaining scale accuracy, thus facilitating the effective transfer of knowledge from synthetic to real-world data. Our extensive evaluations demonstrate PatchRefiner's superior performance, significantly outperforming existing benchmarks on the Unreal4KStereo dataset by 18.1% in terms of the root mean squared error (RMSE) and showing marked improvements in detail accuracy and consistent scale estimation on diverse real-world datasets like CityScape, ScanNet++, and ETH3D.

Mental illness remains one of the most critical public health issues. Despite its importance, many mental health professionals highlight a disconnect between their training and actual real-world patient practice. To help bridge this gap, we propose PATIENT-{\Psi}, a novel patient simulation framework for cognitive behavior therapy (CBT) training. To build PATIENT-{\Psi}, we construct diverse patient cognitive models based on CBT principles and use large language models (LLMs) programmed with these cognitive models to act as a simulated therapy patient. We propose an interactive training scheme, PATIENT-{\Psi}-TRAINER, for mental health trainees to practice a key skill in CBT -- formulating the cognitive model of the patient -- through role-playing a therapy session with PATIENT-{\Psi}. To evaluate PATIENT-{\Psi}, we conducted a comprehensive user study of 13 mental health trainees and 20 experts. The results demonstrate that practice using PATIENT-{\Psi}-TRAINER enhances the perceived skill acquisition and confidence of the trainees beyond existing forms of training such as textbooks, videos, and role-play with non-patients. Based on the experts' perceptions, PATIENT-{\Psi} is perceived to be closer to real patient interactions than GPT-4, and PATIENT-{\Psi}-TRAINER holds strong promise to improve trainee competencies. Our code and data are released at https://github.com/ruiyiw/patient-psi.

Evaluating anomaly detection algorithms in time series data is critical as inaccuracies can lead to flawed decision-making in various domains where real-time analytics and data-driven strategies are essential. Traditional performance metrics assume iid data and fail to capture the complex temporal dynamics and specific characteristics of time series anomalies, such as early and delayed detections. We introduce Proximity-Aware Time series anomaly Evaluation (PATE), a novel evaluation metric that incorporates the temporal relationship between prediction and anomaly intervals. PATE uses proximity-based weighting considering buffer zones around anomaly intervals, enabling a more detailed and informed assessment of a detection. Using these weights, PATE computes a weighted version of the area under the Precision and Recall curve. Our experiments with synthetic and real-world datasets show the superiority of PATE in providing more sensible and accurate evaluations than other evaluation metrics. We also tested several state-of-the-art anomaly detectors across various benchmark datasets using the PATE evaluation scheme. The results show that a common metric like Point-Adjusted F1 Score fails to characterize the detection performances well, and that PATE is able to provide a more fair model comparison. By introducing PATE, we redefine the understanding of model efficacy that steers future studies toward developing more effective and accurate detection models.

Patient data from real-world clinical practice often suffers from data scarcity and long-tail imbalances, leading to biased outcomes or algorithmic unfairness. This study addresses these challenges by generating lesion-containing image-segmentation pairs from lesion-free images. Previous efforts in medical imaging synthesis have struggled with separating lesion information from background, resulting in low-quality backgrounds and limited control over the synthetic output. Inspired by diffusion-based image inpainting, we propose LeFusion, a lesion-focused diffusion model. By redesigning the diffusion learning objectives to focus on lesion areas, we simplify the learning process and improve control over the output while preserving high-fidelity backgrounds by integrating forward-diffused background contexts into the reverse diffusion process. Additionally, we tackle two major challenges in lesion texture synthesis: 1) multi-peak and 2) multi-class lesions. We introduce two effective strategies: histogram-based texture control and multi-channel decomposition, enabling the controlled generation of high-quality lesions in difficult scenarios. Furthermore, we incorporate lesion mask diffusion, allowing control over lesion size, location, and boundary, thus increasing lesion diversity. Validated on 3D cardiac lesion MRI and lung nodule CT datasets, LeFusion-generated data significantly improves the performance of state-of-the-art segmentation models, including nnUNet and SwinUNETR. Code and model are available at https://github.com/M3DV/LeFusion.

The discharge summary is a one of critical documents in the patient journey, encompassing all events experienced during hospitalization, including multiple visits, medications, tests, surgery/procedures, and admissions/discharge. Providing a summary of the patient's progress is crucial, as it significantly influences future care and planning. Consequently, clinicians face the laborious and resource-intensive task of manually collecting, organizing, and combining all the necessary data for a discharge summary. Therefore, we propose "NOTE", which stands for "Notable generation Of patient Text summaries through an Efficient approach based on direct preference optimization". NOTE is based on Medical Information Mart for Intensive Care- III dataset and summarizes a single hospitalization of a patient. Patient events are sequentially combined and used to generate a discharge summary for each hospitalization. In the present circumstances, large language models' application programming interfaces (LLMs' APIs) are widely available, but importing and exporting medical data presents significant challenges due to privacy protection policies in healthcare institutions. Moreover, to ensure optimal performance, it is essential to implement a lightweight model for internal server or program within the hospital. Therefore, we utilized DPO and parameter efficient fine tuning (PEFT) techniques to apply a fine-tuning method that guarantees superior performance. To demonstrate the practical application of the developed NOTE, we provide a webpage-based demonstration software. In the future, we will aim to deploy the software available for actual use by clinicians in hospital. NOTE can be utilized to generate various summaries not only discharge summaries but also throughout a patient's journey, thereby alleviating the labor-intensive workload of clinicians and aiming for increased efficiency.

Transformers for time series forecasting mainly model time series from limited or fixed scales, making it challenging to capture different characteristics spanning various scales. We propose Pathformer, a multi-scale Transformer with adaptive pathways. It integrates both temporal resolution and temporal distance for multi-scale modeling. Multi-scale division divides the time series into different temporal resolutions using patches of various sizes. Based on the division of each scale, dual attention is performed over these patches to capture global correlations and local details as temporal dependencies. We further enrich the multi-scale Transformer with adaptive pathways, which adaptively adjust the multi-scale modeling process based on the varying temporal dynamics of the input, improving the accuracy and generalization of Pathformer. Extensive experiments on eleven real-world datasets demonstrate that Pathformer not only achieves state-of-the-art performance by surpassing all current models but also exhibits stronger generalization abilities under various transfer scenarios. The code is made available at https://github.com/decisionintelligence/pathformer.

Rigorousness and clarity are both essential for interpretations of DNNs to engender human trust. Path methods are commonly employed to generate rigorous attributions that satisfy three axioms. However, the meaning of attributions remains ambiguous due to distinct path choices. To address the ambiguity, we introduce Concentration Principle, which centrally allocates high attributions to indispensable features, thereby endowing aesthetic and sparsity. We then present SAMP, a model-agnostic interpreter, which efficiently searches the near-optimal path from a pre-defined set of manipulation paths. Moreover, we propose the infinitesimal constraint (IC) and momentum strategy (MS) to improve the rigorousness and optimality. Visualizations show that SAMP can precisely reveal DNNs by pinpointing salient image pixels. We also perform quantitative experiments and observe that our method significantly outperforms the counterparts. Code: https://github.com/zbr17/SAMP.

Recent generative models show impressive performance in generating photographic images. Humans can hardly distinguish such incredibly realistic-looking AI-generated images from real ones. AI-generated images may lead to ubiquitous disinformation dissemination. Therefore, it is of utmost urgency to develop a detector to identify AI generated images. Most existing detectors suffer from sharp performance drops over unseen generative models. In this paper, we propose a novel AI-generated image detector capable of identifying fake images created by a wide range of generative models. We observe that the texture patches of images tend to reveal more traces left by generative models compared to the global semantic information of the images. A novel Smash&Reconstruction preprocessing is proposed to erase the global semantic information and enhance texture patches. Furthermore, pixels in rich texture regions exhibit more significant fluctuations than those in poor texture regions. Synthesizing realistic rich texture regions proves to be more challenging for existing generative models. Based on this principle, we leverage the inter-pixel correlation contrast between rich and poor texture regions within an image to further boost the detection performance. In addition, we build a comprehensive AI-generated image detection benchmark, which includes 17 kinds of prevalent generative models, to evaluate the effectiveness of existing baselines and our approach. Our benchmark provides a leaderboard for follow-up studies. Extensive experimental results show that our approach outperforms state-of-the-art baselines by a significant margin. Our project: https://fdmas.github.io/AIGCDetect

This paper introduces Qatent PatFig, a novel large-scale patent figure dataset comprising 30,000+ patent figures from over 11,000 European patent applications. For each figure, this dataset provides short and long captions, reference numerals, their corresponding terms, and the minimal claim set that describes the interactions between the components of the image. To assess the usability of the dataset, we finetune an LVLM model on Qatent PatFig to generate short and long descriptions, and we investigate the effects of incorporating various text-based cues at the prediction stage of the patent figure captioning process.

We propose an effective denoising diffusion model for generating high-resolution images (e.g., 1024times512), trained on small-size image patches (e.g., 64times64). We name our algorithm Patch-DM, in which a new feature collage strategy is designed to avoid the boundary artifact when synthesizing large-size images. Feature collage systematically crops and combines partial features of the neighboring patches to predict the features of a shifted image patch, allowing the seamless generation of the entire image due to the overlap in the patch feature space. Patch-DM produces high-quality image synthesis results on our newly collected dataset of nature images (1024times512), as well as on standard benchmarks of smaller sizes (256times256), including LSUN-Bedroom, LSUN-Church, and FFHQ. We compare our method with previous patch-based generation methods and achieve state-of-the-art FID scores on all four datasets. Further, Patch-DM also reduces memory complexity compared to the classic diffusion models.

Multi-label image classification is a prediction task that aims to identify more than one label from a given image. This paper considers the semantic consistency of the latent space between the visual patch and linguistic label domains and introduces the conditional transport (CT) theory to bridge the acknowledged gap. While recent cross-modal attention-based studies have attempted to align such two representations and achieved impressive performance, they required carefully-designed alignment modules and extra complex operations in the attention computation. We find that by formulating the multi-label classification as a CT problem, we can exploit the interactions between the image and label efficiently by minimizing the bidirectional CT cost. Specifically, after feeding the images and textual labels into the modality-specific encoders, we view each image as a mixture of patch embeddings and a mixture of label embeddings, which capture the local region features and the class prototypes, respectively. CT is then employed to learn and align those two semantic sets by defining the forward and backward navigators. Importantly, the defined navigators in CT distance model the similarities between patches and labels, which provides an interpretable tool to visualize the learned prototypes. Extensive experiments on three public image benchmarks show that the proposed model consistently outperforms the previous methods.

As advances in large language models (LLMs) and multimodal techniques continue to mature, the development of general-purpose multimodal large language models (MLLMs) has surged, offering significant applications in interpreting natural images. However, the field of pathology has largely remained untapped, particularly in gathering high-quality data and designing comprehensive model frameworks. To bridge the gap in pathology MLLMs, we present PathAsst, a multimodal generative foundation AI assistant to revolutionize diagnostic and predictive analytics in pathology. The development of PathAsst involves three pivotal steps: data acquisition, CLIP model adaptation, and the training of PathAsst's multimodal generative capabilities. Firstly, we collect over 207K high-quality pathology image-text pairs from authoritative sources. Leveraging the advanced power of ChatGPT, we generate over 180K instruction-following samples. Furthermore, we devise additional instruction-following data specifically tailored for invoking eight pathology-specific sub-models we prepared, allowing the PathAsst to effectively collaborate with these models, enhancing its diagnostic ability. Secondly, by leveraging the collected data, we construct PathCLIP, a pathology-dedicated CLIP, to enhance PathAsst's capabilities in interpreting pathology images. Finally, we integrate PathCLIP with the Vicuna-13b and utilize pathology-specific instruction-tuning data to enhance the multimodal generation capacity of PathAsst and bolster its synergistic interactions with sub-models. The experimental results of PathAsst show the potential of harnessing AI-powered generative foundation model to improve pathology diagnosis and treatment processes.

Recently, self-supervised learning (SSL) was shown to be vulnerable to patch-based data poisoning backdoor attacks. It was shown that an adversary can poison a small part of the unlabeled data so that when a victim trains an SSL model on it, the final model will have a backdoor that the adversary can exploit. This work aims to defend self-supervised learning against such attacks. We use a three-step defense pipeline, where we first train a model on the poisoned data. In the second step, our proposed defense algorithm (PatchSearch) uses the trained model to search the training data for poisoned samples and removes them from the training set. In the third step, a final model is trained on the cleaned-up training set. Our results show that PatchSearch is an effective defense. As an example, it improves a model's accuracy on images containing the trigger from 38.2% to 63.7% which is very close to the clean model's accuracy, 64.6%. Moreover, we show that PatchSearch outperforms baselines and state-of-the-art defense approaches including those using additional clean, trusted data. Our code is available at https://github.com/UCDvision/PatchSearch

Keyphrase extraction is the process of automatically selecting a small set of most relevant phrases from a given text. Supervised keyphrase extraction approaches need large amounts of labeled training data and perform poorly outside the domain of the training data. In this paper, we present PatternRank, which leverages pretrained language models and part-of-speech for unsupervised keyphrase extraction from single documents. Our experiments show PatternRank achieves higher precision, recall and F1-scores than previous state-of-the-art approaches. In addition, we present the KeyphraseVectorizers package, which allows easy modification of part-of-speech patterns for candidate keyphrase selection, and hence adaptation of our approach to any domain.

Pathology text mining is a challenging task given the reporting variability and constant new findings in cancer sub-type definitions. However, successful text mining of a large pathology database can play a critical role to advance 'big data' cancer research like similarity-based treatment selection, case identification, prognostication, surveillance, clinical trial screening, risk stratification, and many others. While there is a growing interest in developing language models for more specific clinical domains, no pathology-specific language space exist to support the rapid data-mining development in pathology space. In literature, a few approaches fine-tuned general transformer models on specialized corpora while maintaining the original tokenizer, but in fields requiring specialized terminology, these models often fail to perform adequately. We propose PathologyBERT - a pre-trained masked language model which was trained on 347,173 histopathology specimen reports and publicly released in the Huggingface repository. Our comprehensive experiments demonstrate that pre-training of transformer model on pathology corpora yields performance improvements on Natural Language Understanding (NLU) and Breast Cancer Diagnose Classification when compared to nonspecific language models.

Image-level corruptions and perturbations degrade the performance of CNNs on different downstream vision tasks. Social media filters are one of the most common resources of various corruptions and perturbations for real-world visual analysis applications. The negative effects of these distractive factors can be alleviated by recovering the original images with their pure style for the inference of the downstream vision tasks. Assuming these filters substantially inject a piece of additional style information to the social media images, we can formulate the problem of recovering the original versions as a reverse style transfer problem. We introduce Contrastive Instagram Filter Removal Network (CIFR), which enhances this idea for Instagram filter removal by employing a novel multi-layer patch-wise contrastive style learning mechanism. Experiments show our proposed strategy produces better qualitative and quantitative results than the previous studies. Moreover, we present the results of our additional experiments for proposed architecture within different settings. Finally, we present the inference outputs and quantitative comparison of filtered and recovered images on localization and segmentation tasks to encourage the main motivation for this problem.

Objective: Data unavailability has been one of the biggest barriers in clinical natural language processing. This paper is aimed at providing a large-scale and publicly available patient note dataset, named PMC-Patients, with relevant articles and similar patients annotations. The ultimate goal of PMC-Patients is to facilitate the development of retrieval-based clinical decision support systems. Materials and Methods: To collect PMC-Patients, we extract patient notes from case reports in PubMed Central by recognizing certain section patterns. Patient-article relevance and patient-patient similarity are annotated by citation relationships in PubMed. In addition, we perform three tasks with PMC-Patients to demonstrate its utility in providing clinical decision support for a given patient, including (1) classifying whether another patient is similar, (2) retrieving similar patients in PMC-Patients, and (3) retrieving relevant articles in PubMed. Results: We collect and release PMC-Patients under the CC BY-NC-SA license, which becomes the largest publicly available patient note dataset so far. PMC-Patients contains 167k patient notes that are annotated with 3.1M relevant articles and 293k similar patients. Qualitative and quantitative analyses reveal the high quality and richness of our dataset. Experiments show that classifying the similarity of patient pairs is relatively easy, but it is hard to retrieve similar patients or relevant articles for a given patient from a large set of candidates. Conclusion: We present PMC-Patients, a large-scale dataset of patient notes with high quality, easy access, diverse conditions, and rich annotations. The proposed dataset can also serve as a hard benchmark for evaluating retrieval-based clinical decision support systems.

We propose a deep learning methodology for multivariate regression that is based on pattern recognition that triggers fast learning over sensor data. We used a conversion of sensors-to-image which enables us to take advantage of Computer Vision architectures and training processes. In addition to this data preparation methodology, we explore the use of state-of-the-art architectures to generate regression outputs to predict agricultural crop continuous yield information. Finally, we compare with some of the top models reported in MLCAS2021. We found that using a straightforward training process, we were able to accomplish an MAE of 4.394, RMSE of 5.945, and R^2 of 0.861.

Although convolutional networks have been the dominant architecture for vision tasks for many years, recent experiments have shown that Transformer-based models, most notably the Vision Transformer (ViT), may exceed their performance in some settings. However, due to the quadratic runtime of the self-attention layers in Transformers, ViTs require the use of patch embeddings, which group together small regions of the image into single input features, in order to be applied to larger image sizes. This raises a question: Is the performance of ViTs due to the inherently-more-powerful Transformer architecture, or is it at least partly due to using patches as the input representation? In this paper, we present some evidence for the latter: specifically, we propose the ConvMixer, an extremely simple model that is similar in spirit to the ViT and the even-more-basic MLP-Mixer in that it operates directly on patches as input, separates the mixing of spatial and channel dimensions, and maintains equal size and resolution throughout the network. In contrast, however, the ConvMixer uses only standard convolutions to achieve the mixing steps. Despite its simplicity, we show that the ConvMixer outperforms the ViT, MLP-Mixer, and some of their variants for similar parameter counts and data set sizes, in addition to outperforming classical vision models such as the ResNet. Our code is available at https://github.com/locuslab/convmixer.

Tiny deep learning on microcontroller units (MCUs) is challenging due to the limited memory size. We find that the memory bottleneck is due to the imbalanced memory distribution in convolutional neural network (CNN) designs: the first several blocks have an order of magnitude larger memory usage than the rest of the network. To alleviate this issue, we propose a generic patch-by-patch inference scheduling, which operates only on a small spatial region of the feature map and significantly cuts down the peak memory. However, naive implementation brings overlapping patches and computation overhead. We further propose network redistribution to shift the receptive field and FLOPs to the later stage and reduce the computation overhead. Manually redistributing the receptive field is difficult. We automate the process with neural architecture search to jointly optimize the neural architecture and inference scheduling, leading to MCUNetV2. Patch-based inference effectively reduces the peak memory usage of existing networks by 4-8x. Co-designed with neural networks, MCUNetV2 sets a record ImageNet accuracy on MCU (71.8%), and achieves >90% accuracy on the visual wake words dataset under only 32kB SRAM. MCUNetV2 also unblocks object detection on tiny devices, achieving 16.9% higher mAP on Pascal VOC compared to the state-of-the-art result. Our study largely addressed the memory bottleneck in tinyML and paved the way for various vision applications beyond image classification.

The pre-trained model (PTM) is revolutionizing Artificial Intelligence (AI) technology. However, the hardware requirement of PTM training is prohibitively high, making it a game for a small proportion of people. Therefore, we proposed PatrickStar system to lower the hardware requirements of PTMs and make them accessible to everyone. PatrickStar uses the CPU-GPU heterogeneous memory space to store the model data. Different from existing works, we organize the model data in memory chunks and dynamically distribute them in the heterogeneous memory. Guided by the runtime memory statistics collected in a warm-up iteration, chunks are orchestrated efficiently in heterogeneous memory and generate lower CPU-GPU data transmission volume and higher bandwidth utilization. Symbiosis with the Zero Redundancy Optimizer, PatrickStar scales to multiple GPUs on multiple nodes. % using data parallelism. The system can train tasks on bigger models and larger batch sizes, which cannot be accomplished by existing works. Experimental results show that PatrickStar extends model scales 2.27 and 2.5 times of DeepSpeed, and consistently exhibits significantly higher execution speed. PatricStar also successfully runs the 175B GPT3 training task on a 32 GPU cluster. Our code is publicly available at https://github.com/Tencent/PatrickStar.

This study provides an efficient approach for using text data to calculate patent-to-patent (p2p) technological similarity, and presents a hybrid framework for leveraging the resulting p2p similarity for applications such as semantic search and automated patent classification. We create embeddings using Sentence-BERT (SBERT) based on patent claims. We leverage SBERTs efficiency in creating embedding distance measures to map p2p similarity in large sets of patent data. We deploy our framework for classification with a simple Nearest Neighbors (KNN) model that predicts Cooperative Patent Classification (CPC) of a patent based on the class assignment of the K patents with the highest p2p similarity. We thereby validate that the p2p similarity captures their technological features in terms of CPC overlap, and at the same demonstrate the usefulness of this approach for automatic patent classification based on text data. Furthermore, the presented classification framework is simple and the results easy to interpret and evaluate by end-users. In the out-of-sample model validation, we are able to perform a multi-label prediction of all assigned CPC classes on the subclass (663) level on 1,492,294 patents with an accuracy of 54% and F1 score > 66%, which suggests that our model outperforms the current state-of-the-art in text-based multi-label and multi-class patent classification. We furthermore discuss the applicability of the presented framework for semantic IP search, patent landscaping, and technology intelligence. We finally point towards a future research agenda for leveraging multi-source patent embeddings, their appropriateness across applications, as well as to improve and validate patent embeddings by creating domain-expert curated Semantic Textual Similarity (STS) benchmark datasets.

Patent examiners need to solve a complex information retrieval task when they assess the novelty and inventive step of claims made in a patent application. Given a claim, they search for prior art, which comprises all relevant publicly available information. This time-consuming task requires a deep understanding of the respective technical domain and the patent-domain-specific language. For these reasons, we address the computer-assisted search for prior art by creating a training dataset for supervised machine learning called PatentMatch. It contains pairs of claims from patent applications and semantically corresponding text passages of different degrees from cited patent documents. Each pair has been labeled by technically-skilled patent examiners from the European Patent Office. Accordingly, the label indicates the degree of semantic correspondence (matching), i.e., whether the text passage is prejudicial to the novelty of the claimed invention or not. Preliminary experiments using a baseline system show that PatentMatch can indeed be used for training a binary text pair classifier on this challenging information retrieval task. The dataset is available online: https://hpi.de/naumann/s/patentmatch.

We present PatchmatchNet, a novel and learnable cascade formulation of Patchmatch for high-resolution multi-view stereo. With high computation speed and low memory requirement, PatchmatchNet can process higher resolution imagery and is more suited to run on resource limited devices than competitors that employ 3D cost volume regularization. For the first time we introduce an iterative multi-scale Patchmatch in an end-to-end trainable architecture and improve the Patchmatch core algorithm with a novel and learned adaptive propagation and evaluation scheme for each iteration. Extensive experiments show a very competitive performance and generalization for our method on DTU, Tanks & Temples and ETH3D, but at a significantly higher efficiency than all existing top-performing models: at least two and a half times faster than state-of-the-art methods with twice less memory usage.

Switchbacks are discrete angular deflections in the solar wind magnetic field that have been observed throughout the heliosphere. Recent observations by Parker Solar Probe (PSP) have revealed the presence of patches of switchbacks on the scale of hours to days, separated by 'quieter' radial fields. We aim to further diagnose the origin of these patches using measurements of proton temperature anisotropy that can illuminate possible links to formation processes in the solar corona. We fitted 3D bi-Maxwellian functions to the core of proton velocity distributions measured by the SPAN-Ai instrument onboard PSP to obtain the proton parallel, T_{p,|}, and perpendicular, T_{p,perp}, temperature. We show that the presence of patches is highlighted by a transverse deflection in the flow and magnetic field away from the radial direction. These deflections are correlated with enhancements in T_{p,|}, while T_{p,perp} remains relatively constant. Patches sometimes exhibit small proton and electron density enhancements. We interpret that patches are not simply a group of switchbacks, but rather switchbacks are embedded within a larger-scale structure identified by enhanced T_{p,|} that is distinct from the surrounding solar wind. We suggest that these observations are consistent with formation by reconnection-associated mechanisms in the corona.

Is it possible to develop an "AI Pathologist" to pass the board-certified examination of the American Board of Pathology? To achieve this goal, the first step is to create a visual question answering (VQA) dataset where the AI agent is presented with a pathology image together with a question and is asked to give the correct answer. Our work makes the first attempt to build such a dataset. Different from creating general-domain VQA datasets where the images are widely accessible and there are many crowdsourcing workers available and capable of generating question-answer pairs, developing a medical VQA dataset is much more challenging. First, due to privacy concerns, pathology images are usually not publicly available. Second, only well-trained pathologists can understand pathology images, but they barely have time to help create datasets for AI research. To address these challenges, we resort to pathology textbooks and online digital libraries. We develop a semi-automated pipeline to extract pathology images and captions from textbooks and generate question-answer pairs from captions using natural language processing. We collect 32,799 open-ended questions from 4,998 pathology images where each question is manually checked to ensure correctness. To our best knowledge, this is the first dataset for pathology VQA. Our dataset will be released publicly to promote research in medical VQA.

In this work we focus on fine-tuning a pre-trained BERT model and applying it to patent classification. When applied to large datasets of over two millions patents, our approach outperforms the state of the art by an approach using CNN with word embeddings. In addition, we focus on patent claims without other parts in patent documents. Our contributions include: (1) a new state-of-the-art method based on pre-trained BERT model and fine-tuning for patent classification, (2) a large dataset USPTO-3M at the CPC subclass level with SQL statements that can be used by future researchers, (3) showing that patent claims alone are sufficient for classification task, in contrast to conventional wisdom.

Extraction of relevant pathological terms from radiology reports is important for correct image label generation and disease population studies. In this letter, we compare the performance of some known application program interface (APIs) for the task of thoracic abnormality extraction from radiology reports. We explored several medical domain specific annotation tools like Medical Text Indexer(MTI) with Non-MEDLINE and Mesh On Demand(MOD) options and generic Natural Language Understanding (NLU) API provided by the IBM cloud. Our results show that although MTI and MOD are intended for extracting medical terms, their performance is worst compared to generic extraction API like IBM NLU. Finally, we trained a DNN-based Named Entity Recognition (NER) model to extract the key concept words from radiology reports. Our model outperforms the medical specific and generic API performance by a large margin. Our results demonstrate the inadequacy of generic APIs for pathology extraction task and establish the importance of domain specific model training for improved results. We hope that these results motivate the research community to release larger de-identified radiology reports corpus for building high accuracy machine learning models for the important task of pathology extraction.

We introduce a new function-preserving transformation for efficient neural architecture search. This network transformation allows reusing previously trained networks and existing successful architectures that improves sample efficiency. We aim to address the limitation of current network transformation operations that can only perform layer-level architecture modifications, such as adding (pruning) filters or inserting (removing) a layer, which fails to change the topology of connection paths. Our proposed path-level transformation operations enable the meta-controller to modify the path topology of the given network while keeping the merits of reusing weights, and thus allow efficiently designing effective structures with complex path topologies like Inception models. We further propose a bidirectional tree-structured reinforcement learning meta-controller to explore a simple yet highly expressive tree-structured architecture space that can be viewed as a generalization of multi-branch architectures. We experimented on the image classification datasets with limited computational resources (about 200 GPU-hours), where we observed improved parameter efficiency and better test results (97.70% test accuracy on CIFAR-10 with 14.3M parameters and 74.6% top-1 accuracy on ImageNet in the mobile setting), demonstrating the effectiveness and transferability of our designed architectures.

The way that information propagates in neural networks is of great importance. In this paper, we propose Path Aggregation Network (PANet) aiming at boosting information flow in proposal-based instance segmentation framework. Specifically, we enhance the entire feature hierarchy with accurate localization signals in lower layers by bottom-up path augmentation, which shortens the information path between lower layers and topmost feature. We present adaptive feature pooling, which links feature grid and all feature levels to make useful information in each feature level propagate directly to following proposal subnetworks. A complementary branch capturing different views for each proposal is created to further improve mask prediction. These improvements are simple to implement, with subtle extra computational overhead. Our PANet reaches the 1st place in the COCO 2017 Challenge Instance Segmentation task and the 2nd place in Object Detection task without large-batch training. It is also state-of-the-art on MVD and Cityscapes. Code is available at https://github.com/ShuLiu1993/PANet

In rapid release development processes, patches that fix critical issues, or implement high-value features are often promoted directly from the development channel to a stabilization channel, potentially skipping one or more stabilization channels. This practice is called patch uplift. Patch uplift is risky, because patches that are rushed through the stabilization phase can end up introducing regressions in the code. This paper examines patch uplift operations at Mozilla, with the aim to identify the characteristics of uplifted patches that introduce regressions. Through statistical and manual analyses, we quantitatively and qualitatively investigate the reasons behind patch uplift decisions and the characteristics of uplifted patches that introduced regressions. Additionally, we interviewed three Mozilla release managers to understand organizational factors that affect patch uplift decisions and outcomes. Results show that most patches are uplifted because of a wrong functionality or a crash. Uplifted patches that lead to faults tend to have larger patch size, and most of the faults are due to semantic or memory errors in the patches. Also, release managers are more inclined to accept patch uplift requests that concern certain specific components, and-or that are submitted by certain specific developers.

Visual patterns represent the discernible regularity in the visual world. They capture the essential nature of visual objects or scenes. Understanding and modeling visual patterns is a fundamental problem in visual recognition that has wide ranging applications. In this paper, we study the problem of visual pattern mining and propose a novel deep neural network architecture called PatternNet for discovering these patterns that are both discriminative and representative. The proposed PatternNet leverages the filters in the last convolution layer of a convolutional neural network to find locally consistent visual patches, and by combining these filters we can effectively discover unique visual patterns. In addition, PatternNet can discover visual patterns efficiently without performing expensive image patch sampling, and this advantage provides an order of magnitude speedup compared to most other approaches. We evaluate the proposed PatternNet subjectively by showing randomly selected visual patterns which are discovered by our method and quantitatively by performing image classification with the identified visual patterns and comparing our performance with the current state-of-the-art. We also directly evaluate the quality of the discovered visual patterns by leveraging the identified patterns as proposed objects in an image and compare with other relevant methods. Our proposed network and procedure, PatterNet, is able to outperform competing methods for the tasks described.