Daily Papers

Recent advances in stereo matching have achieved remarkable accuracy, but often rely on large models, heavy computation, or additional foundation-model priors, making them difficult to deploy on resource-constrained platforms. In contrast, efficient stereo models offer faster inference but are commonly considered less capable of strong zero-shot generalization. In this paper, we challenge this assumption by introducing Lite Any Stereo V2 (LAS2), an ultra-fast model series designed for efficient zero-shot stereo matching. LAS2 is developed from both architecture and training perspectives. Architecturally, we revisit efficient stereo design under practical deployment settings and propose a 2D-only cost aggregation framework, optimized for real inference latency rather than theoretical MACs alone. For training, we develop a three-stage strategy that combines synthetic supervision, self-distillation, and real-world knowledge distillation. To improve the reliability of real-world pseudo supervision, we further introduce pseudo-label filtering and an error-clamping operation, enabling smoother synthetic-to-real transfer. We instantiate LAS2 as a family of models, including feed-forward variants for different efficiency budgets and an iterative variant for higher accuracy. Extensive experiments show that LAS2 achieves state-of-the-art accuracy among efficient stereo methods while maintaining significantly lower latency. Specifically, LAS2-H achieves stronger overall zero-shot performance than the iterative method Fast-FoundationStereo, with 1.8x and 2.7x faster inference on H200 and Orin, respectively. The project page, demos, and code are available at https://tomtomtommi.github.io/LiteAnyStereoV2/.

This paper investigates the key role of Feed-Forward Networks (FFNs) in transformer models by utilizing the Parallel Attention and Feed-Forward Net Design (PAF) architecture, and comparing it to their Series Attention and Feed-Forward Net Design (SAF) counterparts. Central to the effectiveness of PAF are two main assumptions regarding the FFN block and the attention block within a layer: 1) the primary function of the FFN block is to maintain isotropy among token embeddings and prevent their degeneration, and 2) the residual norm computed in the attention block is substantially smaller than the input token embedding norm. To empirically validate these assumptions, we train PAF variants of two large language models (RoBERTa-large and bert-large-uncased). Our results demonstrate that both assumptions hold true in the PAF design. This study contributes to a deeper understanding of the roles and interactions between FFNs and self-attention mechanisms in transformer architectures.

Gated Linear Units (arXiv:1612.08083) consist of the component-wise product of two linear projections, one of which is first passed through a sigmoid function. Variations on GLU are possible, using different nonlinear (or even linear) functions in place of sigmoid. We test these variants in the feed-forward sublayers of the Transformer (arXiv:1706.03762) sequence-to-sequence model, and find that some of them yield quality improvements over the typically-used ReLU or GELU activations.

Multi-view image diffusion models have significantly advanced open-domain 3D object generation. However, most existing models rely on 2D network architectures that lack inherent 3D biases, resulting in compromised geometric consistency. To address this challenge, we introduce 3D-Adapter, a plug-in module designed to infuse 3D geometry awareness into pretrained image diffusion models. Central to our approach is the idea of 3D feedback augmentation: for each denoising step in the sampling loop, 3D-Adapter decodes intermediate multi-view features into a coherent 3D representation, then re-encodes the rendered RGBD views to augment the pretrained base model through feature addition. We study two variants of 3D-Adapter: a fast feed-forward version based on Gaussian splatting and a versatile training-free version utilizing neural fields and meshes. Our extensive experiments demonstrate that 3D-Adapter not only greatly enhances the geometry quality of text-to-multi-view models such as Instant3D and Zero123++, but also enables high-quality 3D generation using the plain text-to-image Stable Diffusion. Furthermore, we showcase the broad application potential of 3D-Adapter by presenting high quality results in text-to-3D, image-to-3D, text-to-texture, and text-to-avatar tasks.

Following the success of dot-product attention in Transformers, numerous approximations have been recently proposed to address its quadratic complexity with respect to the input length. While these variants are memory and compute efficient, it is not possible to directly use them with popular pre-trained language models trained using vanilla attention, without an expensive corrective pre-training stage. In this work, we propose a simple yet highly accurate approximation for vanilla attention. We process the queries in chunks, and for each query, compute the top-k scores with respect to the keys. Our approach offers several advantages: (a) its memory usage is linear in the input size, similar to linear attention variants, such as Performer and RFA (b) it is a drop-in replacement for vanilla attention that does not require any corrective pre-training, and (c) it can also lead to significant memory savings in the feed-forward layers after casting them into the familiar query-key-value framework. We evaluate the quality of top-k approximation for multi-head attention layers on the Long Range Arena Benchmark, and for feed-forward layers of T5 and UnifiedQA on multiple QA datasets. We show our approach leads to accuracy that is nearly-identical to vanilla attention in multiple setups including training from scratch, fine-tuning, and zero-shot inference.

We present the latest generation of MobileNets, known as MobileNetV4 (MNv4), featuring universally efficient architecture designs for mobile devices. At its core, we introduce the Universal Inverted Bottleneck (UIB) search block, a unified and flexible structure that merges Inverted Bottleneck (IB), ConvNext, Feed Forward Network (FFN), and a novel Extra Depthwise (ExtraDW) variant. Alongside UIB, we present Mobile MQA, an attention block tailored for mobile accelerators, delivering a significant 39% speedup. An optimized neural architecture search (NAS) recipe is also introduced which improves MNv4 search effectiveness. The integration of UIB, Mobile MQA and the refined NAS recipe results in a new suite of MNv4 models that are mostly Pareto optimal across mobile CPUs, DSPs, GPUs, as well as specialized accelerators like Apple Neural Engine and Google Pixel EdgeTPU - a characteristic not found in any other models tested. Finally, to further boost accuracy, we introduce a novel distillation technique. Enhanced by this technique, our MNv4-Hybrid-Large model delivers 87% ImageNet-1K accuracy, with a Pixel 8 EdgeTPU runtime of just 3.8ms.

"Forward-only" algorithms, which train neural networks while avoiding a backward pass, have recently gained attention as a way of solving the biologically unrealistic aspects of backpropagation. Here, we first address compelling challenges related to the "forward-only" rules, which include reducing the performance gap with backpropagation and providing an analytical understanding of their dynamics. To this end, we show that the forward-only algorithm with top-down feedback is well-approximated by an "adaptive-feedback-alignment" algorithm, and we analytically track its performance during learning in a prototype high-dimensional setting. Then, we compare different versions of forward-only algorithms, focusing on the Forward-Forward and PEPITA frameworks, and we show that they share the same learning principles. Overall, our work unveils the connections between three key neuro-inspired learning rules, providing a link between "forward-only" algorithms, i.e., Forward-Forward and PEPITA, and an approximation of backpropagation, i.e., Feedback Alignment.

Feedforward computation, such as evaluating a neural network or sampling from an autoregressive model, is ubiquitous in machine learning. The sequential nature of feedforward computation, however, requires a strict order of execution and cannot be easily accelerated with parallel computing. To enable parallelization, we frame the task of feedforward computation as solving a system of nonlinear equations. We then propose to find the solution using a Jacobi or Gauss-Seidel fixed-point iteration method, as well as hybrid methods of both. Crucially, Jacobi updates operate independently on each equation and can be executed in parallel. Our method is guaranteed to give exactly the same values as the original feedforward computation with a reduced (or equal) number of parallelizable iterations, and hence reduced time given sufficient parallel computing power. Experimentally, we demonstrate the effectiveness of our approach in accelerating (i) backpropagation of RNNs, (ii) evaluation of DenseNets, and (iii) autoregressive sampling of MADE and PixelCNN++, with speedup factors between 2.1 and 26 under various settings.

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

We propose a scalable Forward-Forward (FF) algorithm that eliminates the need for backpropagation by training each layer separately. Unlike backpropagation, FF avoids backward gradients and can be more modular and memory efficient, making it appealing for large networks. We extend FF to modern convolutional architectures, such as MobileNetV3 and ResNet18, by introducing a new way to compute losses for convolutional layers. Experiments show that our method achieves performance comparable to standard backpropagation. Furthermore, when we divide the network into blocks, such as the residual blocks in ResNet, and apply backpropagation only within each block, but not across blocks, our hybrid design tends to outperform backpropagation baselines while maintaining a similar training speed. Finally, we present experiments on small datasets and transfer learning that confirm the adaptability of our method.

Feed-forward layers constitute two-thirds of a transformer model's parameters, yet their role in the network remains under-explored. We show that feed-forward layers in transformer-based language models operate as key-value memories, where each key correlates with textual patterns in the training examples, and each value induces a distribution over the output vocabulary. Our experiments show that the learned patterns are human-interpretable, and that lower layers tend to capture shallow patterns, while upper layers learn more semantic ones. The values complement the keys' input patterns by inducing output distributions that concentrate probability mass on tokens likely to appear immediately after each pattern, particularly in the upper layers. Finally, we demonstrate that the output of a feed-forward layer is a composition of its memories, which is subsequently refined throughout the model's layers via residual connections to produce the final output distribution.

Graph neural networks (GNNs) have achieved remarkable success across a wide range of applications, such as recommendation, drug discovery, and question answering. Behind the success of GNNs lies the backpropagation (BP) algorithm, which is the de facto standard for training deep neural networks (NNs). However, despite its effectiveness, BP imposes several constraints, which are not only biologically implausible, but also limit the scalability, parallelism, and flexibility in learning NNs. Examples of such constraints include storage of neural activities computed in the forward pass for use in the subsequent backward pass, and the dependence of parameter updates on non-local signals. To address these limitations, the forward-forward algorithm (FF) was recently proposed as an alternative to BP in the image classification domain, which trains NNs by performing two forward passes over positive and negative data. Inspired by this advance, we propose ForwardGNN in this work, a new forward learning procedure for GNNs, which avoids the constraints imposed by BP via an effective layer-wise local forward training. ForwardGNN extends the original FF to deal with graph data and GNNs, and makes it possible to operate without generating negative inputs (hence no longer forward-forward). Further, ForwardGNN enables each layer to learn from both the bottom-up and top-down signals without relying on the backpropagation of errors. Extensive experiments on real-world datasets show the effectiveness and generality of the proposed forward graph learning framework. We release our code at https://github.com/facebookresearch/forwardgnn.

Recently, extensive deep learning architectures and pretraining strategies have been explored to support downstream protein applications. Additionally, domain-specific models incorporating biological knowledge have been developed to enhance performance in specialized tasks. In this work, we introduce Protap, a comprehensive benchmark that systematically compares backbone architectures, pretraining strategies, and domain-specific models across diverse and realistic downstream protein applications. Specifically, Protap covers five applications: three general tasks and two novel specialized tasks, i.e., enzyme-catalyzed protein cleavage site prediction and targeted protein degradation, which are industrially relevant yet missing from existing benchmarks. For each application, Protap compares various domain-specific models and general architectures under multiple pretraining settings. Our empirical studies imply that: (i) Though large-scale pretraining encoders achieve great results, they often underperform supervised encoders trained on small downstream training sets. (ii) Incorporating structural information during downstream fine-tuning can match or even outperform protein language models pretrained on large-scale sequence corpora. (iii) Domain-specific biological priors can enhance performance on specialized downstream tasks. Code and datasets are publicly available at https://github.com/Trust-App-AI-Lab/protap.

Backpropagation, which uses the chain rule, is the de-facto standard algorithm for optimizing neural networks nowadays. Recently, Hinton (2022) proposed the forward-forward algorithm, a promising alternative that optimizes neural nets layer-by-layer, without propagating gradients throughout the network. Although such an approach has several advantages over back-propagation and shows promising results, the fact that each layer is being trained independently limits the optimization process. Specifically, it prevents the network's layers from collaborating to learn complex and rich features. In this work, we study layer collaboration in the forward-forward algorithm. We show that the current version of the forward-forward algorithm is suboptimal when considering information flow in the network, resulting in a lack of collaboration between layers of the network. We propose an improved version that supports layer collaboration to better utilize the network structure, while not requiring any additional assumptions or computations. We empirically demonstrate the efficacy of the proposed version when considering both information flow and objective metrics. Additionally, we provide a theoretical motivation for the proposed method, inspired by functional entropy theory.

Visual Auto-Regressive (VAR) models significantly reduce inference steps through the "next-scale" prediction paradigm. However, progressive multi-scale generation incurs substantial memory overhead due to cumulative KV caching, limiting practical deployment. We observe a scale-depth asymmetric dependency in VAR: early scales exhibit extreme sensitivity to network depth, while later scales remain robust to depth reduction. Inspired by this, we propose VARiant: by equidistant sampling, we select multiple subnets ranging from 16 to 2 layers from the original 30-layer VAR-d30 network. Early scales are processed by the full network, while later scales utilize subnet. Subnet and the full network share weights, enabling flexible depth adjustment within a single model. However, weight sharing between subnet and the entire network can lead to optimization conflicts. To address this, we propose a progressive training strategy that breaks through the Pareto frontier of generation quality for both subnets and the full network under fixed-ratio training, achieving joint optimality. Experiments on ImageNet demonstrate that, compared to the pretrained VAR-d30 (FID 1.95), VARiant-d16 and VARiant-d8 achieve nearly equivalent quality (FID 2.05/2.12) while reducing memory consumption by 40-65%. VARiant-d2 achieves 3.5 times speedup and 80% memory reduction at moderate quality cost (FID 2.97). In terms of deployment, VARiant's single-model architecture supports zero-cost runtime depth switching and provides flexible deployment options from high quality to extreme efficiency, catering to diverse application scenarios.

Backpropagation is the standard method for achieving state-of-the-art accuracy in neural network training, but it often imposes high memory costs and lacks biological plausibility. In this paper, we introduce the Mono-Forward algorithm, a purely local layerwise learning method inspired by Hinton's Forward-Forward framework. Unlike backpropagation, Mono-Forward optimizes each layer solely with locally available information, eliminating the reliance on global error signals. We evaluated Mono-Forward on multi-layer perceptrons and convolutional neural networks across multiple benchmarks, including MNIST, Fashion-MNIST, CIFAR-10, and CIFAR-100. The test results show that Mono-Forward consistently matches or surpasses the accuracy of backpropagation across all tasks, with significantly reduced and more even memory usage, better parallelizability, and a comparable convergence rate.

In this work we introduce RITA: a suite of autoregressive generative models for protein sequences, with up to 1.2 billion parameters, trained on over 280 million protein sequences belonging to the UniRef-100 database. Such generative models hold the promise of greatly accelerating protein design. We conduct the first systematic study of how capabilities evolve with model size for autoregressive transformers in the protein domain: we evaluate RITA models in next amino acid prediction, zero-shot fitness, and enzyme function prediction, showing benefits from increased scale. We release the RITA models openly, to the benefit of the research community.

Feedforward neural networks are widely used as universal predictive models to fit data distribution. Common gradient-based learning, however, suffers from many drawbacks making the training process ineffective and time-consuming. Alternative randomized learning does not use gradients but selects hidden node parameters randomly. This makes the training process extremely fast. However, the problem in randomized learning is how to determine the random parameters. A recently proposed method uses autoencoders for unsupervised parameter learning. This method showed superior performance on classification tasks. In this work, we apply this method to regression problems, and, finding that it has some drawbacks, we show how to improve it. We propose a learning method of autoencoders that controls the produced random weights. We also propose how to determine the biases of hidden nodes. We empirically compare autoencoder based learning with other randomized learning methods proposed recently for regression and find that despite the proposed improvement of the autoencoder based learning, it does not outperform its competitors in fitting accuracy. Moreover, the method is much more complex than its competitors.

The ability to accurately model the fitness landscape of protein sequences is critical to a wide range of applications, from quantifying the effects of human variants on disease likelihood, to predicting immune-escape mutations in viruses and designing novel biotherapeutic proteins. Deep generative models of protein sequences trained on multiple sequence alignments have been the most successful approaches so far to address these tasks. The performance of these methods is however contingent on the availability of sufficiently deep and diverse alignments for reliable training. Their potential scope is thus limited by the fact many protein families are hard, if not impossible, to align. Large language models trained on massive quantities of non-aligned protein sequences from diverse families address these problems and show potential to eventually bridge the performance gap. We introduce Tranception, a novel transformer architecture leveraging autoregressive predictions and retrieval of homologous sequences at inference to achieve state-of-the-art fitness prediction performance. Given its markedly higher performance on multiple mutants, robustness to shallow alignments and ability to score indels, our approach offers significant gain of scope over existing approaches. To enable more rigorous model testing across a broader range of protein families, we develop ProteinGym -- an extensive set of multiplexed assays of variant effects, substantially increasing both the number and diversity of assays compared to existing benchmarks.

Instruction-following is a fundamental capability of language models, requiring the model to recognize even the most subtle requirements in the instructions and accurately reflect them in its output. Such an ability is well-suited for and often optimized by preference learning. However, existing methods often directly sample multiple independent responses from the model when creating preference pairs. Such practice can introduce content variations irrelevant to whether the instruction is precisely followed (e.g., different expressions about the same semantic), interfering with the goal of teaching models to recognize the key differences that lead to improved instruction following. In light of this, we introduce SPaR, a self-play framework integrating tree-search self-refinement to yield valid and comparable preference pairs free from distractions. By playing against itself, an LLM employs a tree-search strategy to refine its previous responses with respect to the instruction while minimizing unnecessary variations. Our experiments show that a LLaMA3-8B model, trained over three iterations guided by SPaR, surpasses GPT-4-Turbo on the IFEval benchmark without losing general capabilities. Furthermore, SPaR demonstrates promising scalability and transferability, greatly enhancing models like GLM-4-9B and LLaMA3-70B. We also identify how inference scaling in tree search would impact model performance. Our code and data are publicly available at https://github.com/thu-coai/SPaR.

Language models (LMs) are often adapted through supervised fine-tuning (SFT) to specialize their capabilities for downstream tasks. However, in typical scenarios where the fine-tuning data is limited, e.g., compared to pre-training, SFT can lead LMs to overfit, causing them to rely on spurious patterns within the target task or to compromise other broadly useful capabilities as a side effect of narrow specialization. In this paper, we propose Learning-from-the-Undesirable (LfU), a simple yet effective regularization scheme for SFT to mitigate overfitting issues when fine-tuning LMs with limited data. Specifically, we aim to regularize the fine-tuning process to favor solutions that are resilient to "undesirable" model updates, e.g., gradient ascent steps that steer the model toward undesirable behaviors. To this end, we propose a novel form of consistency regularization that directly aligns internal representations of the model with those after an undesirable update. By leveraging representation-level data augmentation through undesirable updates, LfU effectively promotes generalization under limited data. Our experiments on diverse LM downstream tasks show that LfU serves as an effective prior that enhances adaptability while preserving pretrained knowledge. For example, our LM from LfU achieves a 16.8% average improvement on math tasks compared to vanilla SFT on the same dataset, where the latter even leads to degraded performance on those tasks. Furthermore, LfU exhibits improved robustness to prompt variations, e.g., yielding a 92.1% lower standard deviation in output performances compared to SFT, highlighting its versatile effects.

Autoregressive (AR) language modeling is the dominant paradigm for text generation, yet its sequential token-by-token decoding makes inference memory-bound and inefficient. Existing acceleration approaches, such as speculative decoding and diffusion language models, can yield speedups under certain conditions but do not directly address high-load batch serving--the scenario most critical for industrial-scale deployment. We introduce K-Forcing, a push-forward language modeling paradigm for joint next-k-token decoding. K-Forcing distills an existing AR model into a conditional push-forward mapping--one that transforms independent uniform noise variables into a joint sample of multiple future tokens in a single forward pass. This design preserves fixed-length outputs, reuses the AR teacher backbone, and remains compatible with standard AR serving infrastructure. We train this mapping via progressive self-forcing distillation, which gradually expands the prediction window while enabling the student to closely match the sequence distribution of the AR teacher. We evaluate K-Forcing on LM1B and OpenWebText using a standard causal Transformer backbone. When aggressively configured to generate k = 4 tokens per forward pass, K-Forcing delivers approximately 2.4-3.5x speedup across different batch sizes, while incurring modest quality degradation relative to its AR teacher. As inference increasingly dominates the lifetime compute cost of modern LLMs, K-Forcing offers a promising route toward accelerating AR generation under real-world high-load deployment.

Protein Language Models (PLMs) have emerged as performant and scalable tools for predicting the functional impact and clinical significance of protein-coding variants, but they still lag experimental accuracy. Here, we present a novel fine-tuning approach to improve the performance of PLMs with experimental maps of variant effects from Deep Mutational Scanning (DMS) assays using a Normalised Log-odds Ratio (NLR) head. We find consistent improvements in a held-out protein test set, and on independent DMS and clinical variant annotation benchmarks from ProteinGym and ClinVar. These findings demonstrate that DMS is a promising source of sequence diversity and supervised training data for improving the performance of PLMs for variant effect prediction.

Foundation models are redefining how AI systems are built. Practitioners now follow a standard procedure to build their machine learning solutions: from a pre-trained foundation model, they fine-tune the weights on the target task of interest. So, the Internet is swarmed by a handful of foundation models fine-tuned on many diverse tasks: these individual fine-tunings exist in isolation without benefiting from each other. In our opinion, this is a missed opportunity, as these specialized models contain rich and diverse features. In this paper, we thus propose model ratatouille, a new strategy to recycle the multiple fine-tunings of the same foundation model on diverse auxiliary tasks. Specifically, we repurpose these auxiliary weights as initializations for multiple parallel fine-tunings on the target task; then, we average all fine-tuned weights to obtain the final model. This recycling strategy aims at maximizing the diversity in weights by leveraging the diversity in auxiliary tasks. Empirically, it improves the state of the art on the reference DomainBed benchmark for out-of-distribution generalization. Looking forward, this work contributes to the emerging paradigm of updatable machine learning where, akin to open-source software development, the community collaborates to reliably update machine learning models.

Recent advances have shown that sequential fine-tuning (SeqFT) of pre-trained vision transformers (ViTs), followed by classifier refinement using approximate distributions of class features, can be an effective strategy for class-incremental learning (CIL). However, this approach is susceptible to distribution drift, caused by the sequential optimization of shared backbone parameters. This results in a mismatch between the distributions of the previously learned classes and that of the updater model, ultimately degrading the effectiveness of classifier performance over time. To address this issue, we introduce a latent space transition operator and propose Sequential Learning with Drift Compensation (SLDC). SLDC aims to align feature distributions across tasks to mitigate the impact of drift. First, we present a linear variant of SLDC, which learns a linear operator by solving a regularized least-squares problem that maps features before and after fine-tuning. Next, we extend this with a weakly nonlinear SLDC variant, which assumes that the ideal transition operator lies between purely linear and fully nonlinear transformations. This is implemented using learnable, weakly nonlinear mappings that balance flexibility and generalization. To further reduce representation drift, we apply knowledge distillation (KD) in both algorithmic variants. Extensive experiments on standard CIL benchmarks demonstrate that SLDC significantly improves the performance of SeqFT. Notably, by combining KD to address representation drift with SLDC to compensate distribution drift, SeqFT achieves performance comparable to joint training across all evaluated datasets. Code: https://github.com/raoxuan98-hash/sldc.git.

The aim of this paper is to introduce a new learning procedure for neural networks and to demonstrate that it works well enough on a few small problems to be worth further investigation. The Forward-Forward algorithm replaces the forward and backward passes of backpropagation by two forward passes, one with positive (i.e. real) data and the other with negative data which could be generated by the network itself. Each layer has its own objective function which is simply to have high goodness for positive data and low goodness for negative data. The sum of the squared activities in a layer can be used as the goodness but there are many other possibilities, including minus the sum of the squared activities. If the positive and negative passes could be separated in time, the negative passes could be done offline, which would make the learning much simpler in the positive pass and allow video to be pipelined through the network without ever storing activities or stopping to propagate derivatives.

Given the variety of the visual world there is not one true scale for recognition: objects may appear at drastically different sizes across the visual field. Rather than enumerate variations across filter channels or pyramid levels, dynamic models locally predict scale and adapt receptive fields accordingly. The degree of variation and diversity of inputs makes this a difficult task. Existing methods either learn a feedforward predictor, which is not itself totally immune to the scale variation it is meant to counter, or select scales by a fixed algorithm, which cannot learn from the given task and data. We extend dynamic scale inference from feedforward prediction to iterative optimization for further adaptivity. We propose a novel entropy minimization objective for inference and optimize over task and structure parameters to tune the model to each input. Optimization during inference improves semantic segmentation accuracy and generalizes better to extreme scale variations that cause feedforward dynamic inference to falter.

In many domains, autoregressive models can attain high likelihood on the task of predicting the next observation. However, this maximum-likelihood (MLE) objective does not necessarily match a downstream use-case of autoregressively generating high-quality sequences. The MLE objective weights sequences proportionally to their frequency under the data distribution, with no guidance for the model's behaviour out of distribution (OOD): leading to compounding error during autoregressive generation. In order to address this compounding error problem, we formulate sequence generation as an imitation learning (IL) problem. This allows us to minimize a variety of divergences between the distribution of sequences generated by an autoregressive model and sequences from a dataset, including divergences with weight on OOD generated sequences. The IL framework also allows us to incorporate backtracking by introducing a backspace action into the generation process. This further mitigates the compounding error problem by allowing the model to revert a sampled token if it takes the sequence OOD. Our resulting method, SequenceMatch, can be implemented without adversarial training or major architectural changes. We identify the SequenceMatch-chi^2 divergence as a more suitable training objective for autoregressive models which are used for generation. We show that empirically, SequenceMatch training leads to improvements over MLE on text generation with language models.

Fast feedforward networks (FFFs) are a class of neural networks that exploit the observation that different regions of the input space activate distinct subsets of neurons in wide networks. FFFs partition the input space into separate sections using a differentiable binary tree of neurons and during inference descend the binary tree in order to improve computational efficiency. Inspired by Mixture of Experts (MoE) research, we propose the incorporation of load balancing and Master Leaf techniques into the FFF architecture to improve performance and simplify the training process. We reproduce experiments found in literature and present results on FFF models enhanced using these techniques. The proposed architecture and training recipe achieves up to 16.3% and 3% absolute classification accuracy increase in training and test accuracy, respectively, compared to the original FFF architecture. Additionally, we observe a smaller variance in the results compared to those reported in prior research. These findings demonstrate the potential of integrating MoE-inspired techniques into FFFs for developing more accurate and efficient models.

Supervised fine-tuning (SFT) provides the standard approach for teaching LLMs new behaviors from offline expert demonstrations. However, standard SFT uniformly fits all samples -- including those with low likelihood under the base model -- which can disproportionately drive training updates toward overfitting specific samples rather than learning the target behavior. Moreover, adapting to these unlikely samples induces substantial policy shifts that degrade prior capabilities. Existing methods mitigate this by filtering, regenerating, or down-weighting low-likelihood data. In doing so, they often suppress precisely the novel behaviors the base model has yet to learn. We propose InfoSFT, a principled weighting scheme for the SFT objective that concentrates learning signals on maximally informative, medium-confidence tokens -- those neither overly familiar to the base model nor too unlikely to cause instability. Requiring only a one-line modification to the standard token-wise loss, InfoSFT demonstrably improves generalization over vanilla SFT and likelihood-weighted baselines across math, code, and chain-of-thought tasks with diverse model families, while better preserving pre-existing capabilities.

Zero-shot reinforcement learning (RL) promises to provide agents that can perform any task in an environment after an offline pre-training phase. Forward-backward (FB) representations represent remarkable progress towards this ideal, achieving 85% of the performance of task-specific agents in this setting. However, such performance is contingent on access to large and diverse datasets for pre-training, which cannot be expected for most real problems. Here, we explore how FB performance degrades when trained on small datasets that lack diversity, and mitigate it with conservatism, a well-established feature of performant offline RL algorithms. We evaluate our family of methods across various datasets, domains and tasks, reaching 150% of vanilla FB performance in aggregate. Somewhat surprisingly, conservative FB algorithms also outperform the task-specific baseline, despite lacking access to reward labels and being required to maintain policies for all tasks. Conservative FB algorithms perform no worse than FB on full datasets, and so present little downside over their predecessor. Our code is available open-source via https://enjeeneer.io/projects/conservative-world-models/.

Recent research has demonstrated that Feed-Forward Networks (FFNs) in Large Language Models (LLMs) play a pivotal role in storing diverse linguistic and factual knowledge. Conventional methods frequently face challenges due to knowledge confusion stemming from their monolithic and redundant architectures, which calls for more efficient solutions with minimal computational overhead, particularly for LLMs. In this paper, we explore the FFN computation paradigm in LLMs and introduce FactorLLM, a novel approach that decomposes well-trained dense FFNs into sparse sub-networks without requiring any further modifications, while maintaining the same level of performance. Furthermore, we embed a router from the Mixture-of-Experts (MoE), combined with our devised Prior-Approximate (PA) loss term that facilitates the dynamic activation of experts and knowledge adaptation, thereby accelerating computational processes and enhancing performance using minimal training data and fine-tuning steps. FactorLLM thus enables efficient knowledge factorization and activates select groups of experts specifically tailored to designated tasks, emulating the interactive functional segmentation of the human brain. Extensive experiments across various benchmarks demonstrate the effectiveness of our proposed FactorLLM which achieves comparable performance to the source model securing up to 85% model performance while obtaining over a 30% increase in inference speed. Code: https://github.com/zhenwuweihe/FactorLLM.

Sequential dependencies present a fundamental bottleneck in deploying large-scale autoregressive models, particularly for real-time applications. While traditional optimization approaches like pruning and quantization often compromise model quality, recent advances in generation-refinement frameworks demonstrate that this trade-off can be significantly mitigated. This survey presents a comprehensive taxonomy of generation-refinement frameworks, analyzing methods across autoregressive sequence tasks. We categorize methods based on their generation strategies (from simple n-gram prediction to sophisticated draft models) and refinement mechanisms (including single-pass verification and iterative approaches). Through systematic analysis of both algorithmic innovations and system-level implementations, we examine deployment strategies across computing environments and explore applications spanning text, images, and speech generation. This systematic examination of both theoretical frameworks and practical implementations provides a foundation for future research in efficient autoregressive decoding.

Recurrent neural networks (RNNs) are a cornerstone of sequence modeling across various scientific and industrial applications. Owing to their versatility, numerous RNN variants have been proposed over the past decade, aiming to improve the modeling of long-term dependencies and to address challenges such as vanishing and exploding gradients. However, no central library is available to test these variations, and reimplementing diverse architectures can be time-consuming and error-prone, limiting reproducibility and exploration. Here, we introduce three open-source libraries in Julia and Python that centralize numerous recurrent cell implementations and higher-level recurrent architectures. torchrecurrent, RecurrentLayers.jl, and LuxRecurrentLayers.jl offer a consistent framework for constructing and extending RNN models, providing built-in mechanisms for customization and experimentation. All packages are available under the MIT license and actively maintained on GitHub.

Genomic language models (gLMs) have shown mostly modest success in identifying evolutionarily constrained elements in mammalian genomes. To address this issue, we introduce a novel framework for training gLMs that explicitly models nucleotide evolution on phylogenetic trees using multispecies whole-genome alignments. Our approach integrates an alignment into the loss function during training but does not require it for making predictions, thereby enhancing the model's applicability. We applied this framework to train PhyloGPN, a model that excels at predicting functionally disruptive variants from a single sequence alone and demonstrates strong transfer learning capabilities.

While tabular classification has traditionally relied on from-scratch training, a recent breakthrough called prior-data fitted networks (PFNs) challenges this approach. Similar to large language models, PFNs make use of pretraining and in-context learning to achieve strong performance on new tasks in a single forward pass. However, current PFNs have limitations that prohibit their widespread adoption. Notably, TabPFN achieves very strong performance on small tabular datasets but is not designed to make predictions for datasets of size larger than 1000. In this work, we overcome these limitations and substantially improve the performance of PFNs via context optimization. We introduce TuneTables, a parameter-efficient fine-tuning strategy for PFNs that compresses large datasets into a smaller learned context. We conduct extensive experiments on 19 algorithms over 98 datasets and find that TuneTables achieves the best performance on average, outperforming boosted trees such as CatBoost, while optimizing fewer than 5% of TabPFN's parameters. Furthermore, we show that TuneTables can be used as an interpretability tool and can even be used to mitigate biases by optimizing a fairness objective. We open-source our code and raw results at https://github.com/penfever/TuneTables.

The recent surge in large-scale foundation models has spurred the development of efficient methods for adapting these models to various downstream tasks. Low-rank adaptation methods, such as LoRA, have gained significant attention due to their outstanding parameter efficiency and no additional inference latency. This paper investigates a more general form of adapter module based on the analysis that parallel and sequential adaptation branches learn novel and general features during fine-tuning, respectively. The proposed method, named Hydra, due to its multi-head computational branches, combines parallel and sequential branch to integrate capabilities, which is more expressive than existing single branch methods and enables the exploration of a broader range of optimal points in the fine-tuning process. In addition, the proposed adaptation method explicitly leverages the pre-trained weights by performing a linear combination of the pre-trained features. It allows the learned features to have better generalization performance across diverse downstream tasks. Furthermore, we perform a comprehensive analysis of the characteristics of each adaptation branch with empirical evidence. Through an extensive range of experiments, encompassing comparisons and ablation studies, we substantiate the efficiency and demonstrate the superior performance of Hydra. This comprehensive evaluation underscores the potential impact and effectiveness of Hydra in a variety of applications. Our code is available on https://github.com/extremebird/Hydra

Many have observed that the development and deployment of generative machine learning (ML) and artificial intelligence (AI) models follow a distinctive pattern in which pre-trained models are adapted and fine-tuned for specific downstream tasks. However, there is limited empirical work that examines the structure of these interactions. This paper analyzes 1.86 million models on Hugging Face, a leading peer production platform for model development. Our study of model family trees -- networks that connect fine-tuned models to their base or parent -- reveals sprawling fine-tuning lineages that vary widely in size and structure. Using an evolutionary biology lens to study ML models, we use model metadata and model cards to measure the genetic similarity and mutation of traits over model families. We find that models tend to exhibit a family resemblance, meaning their genetic markers and traits exhibit more overlap when they belong to the same model family. However, these similarities depart in certain ways from standard models of asexual reproduction, because mutations are fast and directed, such that two `sibling' models tend to exhibit more similarity than parent/child pairs. Further analysis of the directional drifts of these mutations reveals qualitative insights about the open machine learning ecosystem: Licenses counter-intuitively drift from restrictive, commercial licenses towards permissive or copyleft licenses, often in violation of upstream license's terms; models evolve from multi-lingual compatibility towards english-only compatibility; and model cards reduce in length and standardize by turning, more often, to templates and automatically generated text. Overall, this work takes a step toward an empirically grounded understanding of model fine-tuning and suggests that ecological models and methods can yield novel scientific insights.

Attention-based models trained on protein sequences have demonstrated incredible success at classification and generation tasks relevant for artificial intelligence-driven protein design. However, we lack a sufficient understanding of how very large-scale models and data play a role in effective protein model development. We introduce a suite of protein language models, named ProGen2, that are scaled up to 6.4B parameters and trained on different sequence datasets drawn from over a billion proteins from genomic, metagenomic, and immune repertoire databases. ProGen2 models show state-of-the-art performance in capturing the distribution of observed evolutionary sequences, generating novel viable sequences, and predicting protein fitness without additional finetuning. As large model sizes and raw numbers of protein sequences continue to become more widely accessible, our results suggest that a growing emphasis needs to be placed on the data distribution provided to a protein sequence model. We release the ProGen2 models and code at https://github.com/salesforce/progen.

Recurrent neural networks (RNNs) sequentially process data by updating their state with each new data point, and have long been the de facto choice for sequence modeling tasks. However, their inherently sequential computation makes them slow to train. Feed-forward and convolutional architectures have recently been shown to achieve superior results on some sequence modeling tasks such as machine translation, with the added advantage that they concurrently process all inputs in the sequence, leading to easy parallelization and faster training times. Despite these successes, however, popular feed-forward sequence models like the Transformer fail to generalize in many simple tasks that recurrent models handle with ease, e.g. copying strings or even simple logical inference when the string or formula lengths exceed those observed at training time. We propose the Universal Transformer (UT), a parallel-in-time self-attentive recurrent sequence model which can be cast as a generalization of the Transformer model and which addresses these issues. UTs combine the parallelizability and global receptive field of feed-forward sequence models like the Transformer with the recurrent inductive bias of RNNs. We also add a dynamic per-position halting mechanism and find that it improves accuracy on several tasks. In contrast to the standard Transformer, under certain assumptions, UTs can be shown to be Turing-complete. Our experiments show that UTs outperform standard Transformers on a wide range of algorithmic and language understanding tasks, including the challenging LAMBADA language modeling task where UTs achieve a new state of the art, and machine translation where UTs achieve a 0.9 BLEU improvement over Transformers on the WMT14 En-De dataset.

Common deep learning approaches for antibody engineering focus on modeling the marginal distribution of sequences. By treating sequences as independent samples, however, these methods overlook affinity maturation as a rich and largely untapped source of information about the evolutionary process by which antibodies explore the underlying fitness landscape. In contrast, classical phylogenetic models explicitly represent evolutionary dynamics but lack the expressivity to capture complex epistatic interactions. We bridge this gap with CoSiNE, a continuous-time Markov chain parameterized by a deep neural network. Mathematically, we prove that CoSiNE provides a first-order approximation to the intractable sequential point mutation process, capturing epistatic effects with an error bound that is quadratic in branch length. Empirically, CoSiNE outperforms state-of-the-art language models in zero-shot variant effect prediction by explicitly disentangling selection from context-dependent somatic hypermutation. Finally, we introduce Guided Gillespie, a classifier-guided sampling scheme that steers CoSiNE at inference time, enabling efficient optimization of antibody binding affinity toward specific antigens.

Large pre-trained, zero-shot capable models have shown considerable success both for standard transfer and adaptation tasks, with particular robustness towards distribution shifts. In addition, subsequent fine-tuning can considerably improve performance on a selected downstream task. However, through naive fine-tuning, these zero-shot models lose their generalizability and robustness towards distribution shifts. This is a particular problem for tasks such as Continual Learning (CL), where continuous adaptation has to be performed as new task distributions are introduced sequentially. In this work, we showcase that where fine-tuning falls short to adapt such zero-shot capable models, simple momentum-based weight interpolation can provide consistent improvements for CL tasks in both memory-free and memory-based settings. In particular, we find improvements of over +4% on standard CL benchmarks, while reducing the error to the upper limit of jointly training on all tasks at once in parts by more than half, allowing the continual learner to inch closer to the joint training limits.

Despite being self-supervised, protein language models have shown remarkable performance in fundamental biological tasks such as predicting impact of genetic variation on protein structure and function. The effectiveness of these models on diverse set of tasks suggests that they learn meaningful representations of fitness landscape that can be useful for downstream clinical applications. Here, we interrogate the use of these language models in characterizing known pathogenic mutations in curated, medically actionable genes through an exhaustive search of putative compensatory mutations on each variant's genetic background. Systematic analysis of the predicted effects of these compensatory mutations reveal unappreciated structural features of proteins that are missed by other structure predictors like AlphaFold. While deep mutational scan experiments provide an unbiased estimate of the mutational landscape, we encourage the community to generate and curate rescue mutation experiments to inform the design of more sophisticated co-masking strategies and leverage large language models more effectively for downstream clinical prediction tasks.

Given that Transformers are ubiquitous in wide tasks, interpreting their internals is a pivotal issue. Still, their particular components, feed-forward (FF) blocks, have typically been less analyzed despite their substantial parameter amounts. We analyze the input contextualization effects of FF blocks by rendering them in the attention maps as a human-friendly visualization scheme. Our experiments with both masked- and causal-language models reveal that FF networks modify the input contextualization to emphasize specific types of linguistic compositions. In addition, FF and its surrounding components tend to cancel out each other's effects, suggesting potential redundancy in the processing of the Transformer layer.

Real-world large language model deployments (e.g., conversational AI systems, code generation assistants) naturally generate abundant implicit user dissatisfaction (DSAT) signals, as users iterate toward better answers through refinements, corrections, and expressed preferences, while explicit satisfaction (SAT) feedback is scarce. Existing preference learning approaches are poorly aligned with this data profile, as they rely on costly human annotations or assume plentiful positive responses. In this paper, we introduce DRIFT (Dissatisfaction-Refined Iterative preFerence Training), which anchors training on real-world DSAT signals and samples positives dynamically from the evolving policy. Empirically, DRIFT models trained on real-world WildFeedback datasets and synthetic UltraFeedback datasets achieve up to +6.23\% (7B) / +7.61\% (14B) on WildBench Task Score and up to +8.95\% (7B) / +12.29\% (14B) on AlpacaEval2 win rate over base models, outperforming strong baseline methods such as iterative DPO and SPIN. At larger scales, the improvements are particularly pronounced: 14B models trained with DRIFT surpass GPT-4o-mini on WildBench. Further analysis shows that DRIFT also preserves exploratory capacity, yielding more diverse high-reward solutions rather than collapsing to narrow subsets. Theoretically, we demonstrate that this design preserves preference margins and avoids the gradient degeneration. These results show that DRIFT is an effective and scalable recipe for real-world post-training that leverages the most abundant and informative signal. The code and data are available at https://github.com/cacayaya/DRIFT.git.

Smaller LLMs still face significant challenges even in medium-resourced languages, particularly when it comes to language-specific knowledge -- a problem not easily resolved with machine-translated data. In this case study on Icelandic, we aim to enhance the generation performance of an LLM by specialising it using unstructured text corpora. A key focus is on preventing interference with the models' capabilities of handling longer context during this adaptation. Through ablation studies using various parameter-efficient fine-tuning (PEFT) methods and setups, we find that increasing the number of trainable parameters leads to better and more robust language adaptation. LoRAs placed in the feed-forward layers and bottleneck adapters show promising results with sufficient parameters, while prefix tuning and (IA)3 are not suitable. Although improvements are consistent in 0-shot summarisation, some adapted models struggle with longer context lengths, an issue that can be mitigated by adapting only the final layers.

As large language models (LLMs) scale, the question is not only how large they become, but how much of their capacity is effectively utilized. Existing scaling laws relate model size to loss, yet overlook how components exploit their latent space. We study feed-forward networks (FFNs) and recast width selection as a spectral utilization problem. Using a lightweight diagnostic suite -- Hard Rank (participation ratio), Soft Rank (Shannon rank), Spectral Concentration, and the composite Spectral Utilization Index (SUI) -- we quantify how many latent directions are meaningfully activated across LLaMA, GPT-2, and nGPT families. Our key finding is an asymmetric spectral scaling law: soft rank follows an almost perfect power law with FFN width, while hard rank grows only sublinearly and with high variance. This asymmetry suggests that widening FFNs mostly adds low-energy tail directions, while dominant-mode subspaces saturate early. Moreover, at larger widths, variance further collapses into a narrow subspace, leaving much of the latent space under-utilized. These results recast FFN width selection as a principled trade-off between tail capacity and dominant-mode capacity, offering concrete guidance for inference-efficient LLM design.

Antibodies comprise the most versatile class of binding molecules, with numerous applications in biomedicine. Computational design of antibodies involves generating novel and diverse sequences, while maintaining structural consistency. Unique to antibodies, designing the complementarity-determining region (CDR), which determines the antigen binding affinity and specificity, creates its own unique challenges. Recent deep learning models have shown impressive results, however the limited number of known antibody sequence/structure pairs frequently leads to degraded performance, particularly lacking diversity in the generated sequences. In our work we address this challenge by leveraging Model Reprogramming (MR), which repurposes pretrained models on a source language to adapt to the tasks that are in a different language and have scarce data - where it may be difficult to train a high-performing model from scratch or effectively fine-tune an existing pre-trained model on the specific task. Specifically, we introduce ReprogBert in which a pretrained English language model is repurposed for protein sequence infilling - thus considers cross-language adaptation using less data. Results on antibody design benchmarks show that our model on low-resourced antibody sequence dataset provides highly diverse CDR sequences, up to more than a two-fold increase of diversity over the baselines, without losing structural integrity and naturalness. The generated sequences also demonstrate enhanced antigen binding specificity and virus neutralization ability. Code is available at https://github.com/IBM/ReprogBERT

Conditional neural text generation models generate high-quality outputs, but often concentrate around a mode when what we really want is a diverse set of options. We present a search algorithm to construct lattices encoding a massive number of generation options. First, we restructure decoding as a best-first search, which explores the space differently than beam search and improves efficiency by avoiding pruning paths. Second, we revisit the idea of hypothesis recombination: we can identify pairs of similar generation candidates during search and merge them as an approximation. On both summarization and machine translation, we show that our algorithm encodes thousands of diverse options that remain grammatical and high-quality into one lattice. This algorithm provides a foundation for building downstream generation applications on top of massive-scale diverse outputs.

Large Language Models (LLMs) are frequently updated due to data or architecture changes to improve their performance. When updating models, developers often focus on increasing overall performance metrics with less emphasis on being compatible with previous model versions. However, users often build a mental model of the functionality and capabilities of a particular machine learning model they are interacting with. They have to adapt their mental model with every update -- a draining task that can lead to user dissatisfaction. In practice, fine-tuned downstream task adapters rely on pretrained LLM base models. When these base models are updated, these user-facing downstream task models experience instance regression or negative flips -- previously correct instances are now predicted incorrectly. This happens even when the downstream task training procedures remain identical. Our work aims to provide seamless model updates to a user in two ways. First, we provide evaluation metrics for a notion of compatibility to prior model versions, specifically for generative tasks but also applicable for discriminative tasks. We observe regression and inconsistencies between different model versions on a diverse set of tasks and model updates. Second, we propose a training strategy to minimize the number of inconsistencies in model updates, involving training of a compatibility model that can enhance task fine-tuned language models. We reduce negative flips -- instances where a prior model version was correct, but a new model incorrect -- by up to 40% from Llama 1 to Llama 2.

Modern LLMs struggle with efficient updates, as each new pretrained model version requires repeating expensive alignment processes. This challenge also applies to domain- or language-specific models, where fine-tuning on specialized data must be redone for every new base model release. In this paper, we explore the transfer of fine-tuning updates between model versions. Specifically, we derive the diff vector from one source model version, which represents the weight changes from fine-tuning, and apply it to the base model of a different target version. Through empirical evaluations on various open-weight model versions, we show that transferring diff vectors can significantly improve the target base model, often achieving performance comparable to its fine-tuned counterpart. For example, reusing the fine-tuning updates from Llama 3.0 8B leads to an absolute accuracy improvement of 10.7% on GPQA over the base Llama 3.1 8B without additional training, surpassing Llama 3.1 8B Instruct. In a multilingual model development setting, we show that this approach can significantly increase performance on target-language tasks without retraining, achieving an absolute improvement of 4.7% and 15.5% on Global MMLU for Malagasy and Turkish, respectively, compared to Llama 3.1 8B Instruct. Our controlled experiments reveal that fine-tuning transfer is most effective when the source and target models are linearly connected in the parameter space. Additionally, we demonstrate that fine-tuning transfer offers a stronger and more computationally efficient starting point for further fine-tuning. Finally, we propose an iterative recycling-then-finetuning approach for continuous model development, which improves both efficiency and effectiveness. Our findings suggest that fine-tuning transfer is a viable strategy to reduce training costs while maintaining model performance.

As machine learning has moved towards leveraging large models as priors for downstream tasks, the community has debated the right form of prior for solving reinforcement learning (RL) problems. If one were to try to prefetch as much computation as possible, they would attempt to learn a prior over the policies for some yet-to-be-determined reward function. Recent work (forward-backward (FB) representation learning) has tried this, arguing that an unsupervised representation learning procedure can enable optimal control over arbitrary rewards without further fine-tuning. However, FB's training objective and learning behavior remain mysterious. In this paper, we demystify FB by clarifying when such representations can exist, what its objective optimizes, and how it converges in practice. We draw connections with rank matching, fitted Q-evaluation, and contraction mapping. Our analysis suggests a simplified unsupervised pre-training method for RL that, instead of enabling optimal control, performs one step of policy improvement. We call our proposed method one-step forward-backward representation learning (one-step FB). Experiments in didactic settings, as well as in 10 state-based and image-based continuous control domains, demonstrate that one-step FB converges to errors 10^5 smaller and improves zero-shot performance by +24% on average. Our project website is available at https://chongyi-zheng.github.io/onestep-fb.

Strong inductive biases enable learning from little data and help generalization outside of the training distribution. Popular neural architectures such as Transformers lack strong structural inductive biases for seq2seq NLP tasks on their own. Consequently, they struggle with systematic generalization beyond the training distribution, e.g. with extrapolating to longer inputs, even when pre-trained on large amounts of text. We show how a structural inductive bias can be efficiently injected into a seq2seq model by pre-training it to simulate structural transformations on synthetic data. Specifically, we inject an inductive bias towards Finite State Transducers (FSTs) into a Transformer by pre-training it to simulate FSTs given their descriptions. Our experiments show that our method imparts the desired inductive bias, resulting in improved systematic generalization and better few-shot learning for FST-like tasks. Our analysis shows that fine-tuned models accurately capture the state dynamics of the unseen underlying FSTs, suggesting that the simulation process is internalized by the fine-tuned model.

This paper aims to improve the performance of large language models by addressing the variable computational demands in inference steps, where some tokens require more computational resources than others. We present HARP, a simple modification to "off-the-shelf" Transformer forward pass. Drawing from hesitation and the framing effect in decision-making, HARP selectively applies additional computation when the model encounters uncertainty during token generation. Our method mimics human cognitive processes by pausing at difficult decision points and reframing inputs for a different perspective. Unlike other approaches, HARP is model-agnostic, training-free, and easy to implement. We thoroughly evaluate our method across various downstream tasks and model sizes, demonstrating performance improvements up to +5.16%. Notably, HARP achieves these gains while maintaining inference times twice faster than beam search. Simple and yet with significant gains, HARP offers a practical solution for enhancing the performance of Transformer-based language models with minimal computational impact.

Continued pretraining offers a promising solution for adapting foundation models to a new target domain. However, in specialized domains, available datasets are often very small, limiting the applicability of SSL methods developed for large-scale pretraining and making hyperparameter search infeasible. In addition, pretrained models are usually released as backbone-weights only, lacking important information to continue pretraining. We propose to bridge this gap with DIET-CP, a simple continued pretraining strategy, where any strong foundation model can be steered towards the new data distribution of interest. DIET-CP relies on a very simple objective, requires no labels, and introduces no more hyperparameters than supervised finetuning. It is stable across data modalities and backbone choices, while providing a significant performance boost for state-of-the-art models such as DINOv3 using only 1000 images.

Parameter-efficient fine-tuning (PEFT) has become a common method for fine-tuning large language models, where a base model can serve multiple users through PEFT module switching. To enhance user experience, base models require periodic updates. However, once updated, PEFT modules fine-tuned on previous versions often suffer substantial performance degradation on newer versions. Re-tuning these numerous modules to restore performance would incur significant computational costs. Through a comprehensive analysis of the changes that occur during base model updates, we uncover an interesting phenomenon: continual training primarily affects task-specific knowledge stored in Feed-Forward Networks (FFN), while having less impact on the task-specific pattern in the Attention mechanism. Based on these findings, we introduce Trans-PEFT, a novel approach that enhances the PEFT module by focusing on the task-specific pattern while reducing its dependence on certain knowledge in the base model. Further theoretical analysis supports our approach. Extensive experiments across 7 base models and 12 datasets demonstrate that Trans-PEFT trained modules can maintain performance on updated base models without re-tuning, significantly reducing maintenance overhead in real-world applications.

This work presents an analysis of the effectiveness of using standard shallow feed-forward networks to mimic the behavior of the attention mechanism in the original Transformer model, a state-of-the-art architecture for sequence-to-sequence tasks. We substitute key elements of the attention mechanism in the Transformer with simple feed-forward networks, trained using the original components via knowledge distillation. Our experiments, conducted on the IWSLT2017 dataset, reveal the capacity of these "attentionless Transformers" to rival the performance of the original architecture. Through rigorous ablation studies, and experimenting with various replacement network types and sizes, we offer insights that support the viability of our approach. This not only sheds light on the adaptability of shallow feed-forward networks in emulating attention mechanisms but also underscores their potential to streamline complex architectures for sequence-to-sequence tasks.

We present specialized Large Language Models for theoretical High-Energy Physics, obtained as 20 fine-tuned variants of the 8-billion parameter Llama-3.1 model. Each variant was trained on arXiv abstracts (through August 2024) from different combinations of hep-th, hep-ph and gr-qc. For a comparative study, we also trained models on datasets that contained abstracts from disparate fields such as the q-bio and cs categories. All models were fine-tuned using two distinct Low-Rank Adaptation fine-tuning approaches and varying dataset sizes, and outperformed the base model on hep-th abstract completion tasks. We compare performance against leading commercial LLMs (ChatGPT, Claude, Gemini, DeepSeek) and derive insights for further developing specialized language models for High-Energy Theoretical Physics.

Large language models (LLMs) fine-tuned with reinforcement learning from human feedback (RLHF) have been used in some of the most widely deployed AI models to date, such as OpenAI's ChatGPT, Anthropic's Claude, or Meta's LLaMA-2. While there has been significant work developing these methods, our understanding of the benefits and downsides of each stage in RLHF is still limited. To fill this gap, we present an extensive analysis of how each stage of the process (i.e. supervised fine-tuning (SFT), reward modelling, and RLHF) affects two key properties: out-of-distribution (OOD) generalisation and output diversity. OOD generalisation is crucial given the wide range of real-world scenarios in which these models are being used, while output diversity refers to the model's ability to generate varied outputs and is important for a variety of use cases. We perform our analysis across two base models on both summarisation and instruction following tasks, the latter being highly relevant for current LLM use cases. We find that RLHF generalises better than SFT to new inputs, particularly as the distribution shift between train and test becomes larger. However, RLHF significantly reduces output diversity compared to SFT across a variety of measures, implying a tradeoff in current LLM fine-tuning methods between generalisation and diversity. Our results provide guidance on which fine-tuning method should be used depending on the application, and show that more research is needed to improve the trade-off between generalisation and diversity.

Speculative decoding accelerates large language model inference by pairing a target model with a lightweight draft model whose proposed tokens are verified in parallel. A common way to build draft models, like EAGLE3 or DFlash is supervised fine-tuning (SFT) on target-generated trajectories. However, we observe that SFT quickly plateaus: the draft model's acceptance length on test data stops improving. The reason is an offline-to-inference mismatch: In SFT, the drafter learns from fixed target-generated trajectories, whereas during speculative decoding it is evaluated on blocks proposed under its own policy. This motivates on-policy distillation (OPD), where the target model supervises the drafter on draft-induced states. Yet OPD remains difficult for draft models, as they cannot reliably roll out complete sequences independently, whereas target-assisted generation makes the collected sequences follow the target distribution and thus eliminates the on-policy signal. We therefore propose Draft-OPD, which uses target-assisted rollout for stable continuations and replays drafting from the verification-exposed error positions. This allows the drafter to learn from target feedback on both accepted and rejected proposals, focusing training on the draft-induced errors that limit speculative acceptance. Experiments show that Draft-OPD achieves over 5times lossless acceleration for thinking models across diverse tasks, improving over EAGLE-3 and DFlash by 23\% and 13\%.

As opposed to scaling-up protein language models (PLMs), we seek improving performance via protein-specific optimization. Although the proportionality between the language model size and the richness of its learned representations is validated, we prioritize accessibility and pursue a path of data-efficient, cost-reduced, and knowledge-guided optimization. Through over twenty experiments ranging from masking, architecture, and pre-training data, we derive insights from protein-specific experimentation into building a model that interprets the language of life, optimally. We present Ankh, the first general-purpose PLM trained on Google's TPU-v4 surpassing the state-of-the-art performance with fewer parameters (<10% for pre-training, <7% for inference, and <30% for the embedding dimension). We provide a representative range of structure and function benchmarks where Ankh excels. We further provide a protein variant generation analysis on High-N and One-N input data scales where Ankh succeeds in learning protein evolutionary conservation-mutation trends and introducing functional diversity while retaining key structural-functional characteristics. We dedicate our work to promoting accessibility to research innovation via attainable resources.

This paper introduces the counter-intuitive generalization results of overfitting pre-trained large language models (LLMs) on very small datasets. In the setting of open-ended text generation, it is well-documented that LLMs tend to generate repetitive and dull sequences, a phenomenon that is especially apparent when generating using greedy decoding. This issue persists even with state-of-the-art LLMs containing billions of parameters, trained via next-token prediction on large datasets. We find that by further fine-tuning these models to achieve a near-zero training loss on a small set of samples -- a process we refer to as hyperfitting -- the long-sequence generative capabilities are greatly enhanced. Greedy decoding with these Hyperfitted models even outperform Top-P sampling over long-sequences, both in terms of diversity and human preferences. This phenomenon extends to LLMs of various sizes, different domains, and even autoregressive image generation. We further find this phenomena to be distinctly different from that of Grokking and double descent. Surprisingly, our experiments indicate that hyperfitted models rarely fall into repeating sequences they were trained on, and even explicitly blocking these sequences results in high-quality output. All hyperfitted models produce extremely low-entropy predictions, often allocating nearly all probability to a single token.

We introduce FFN Fusion, an architectural optimization technique that reduces sequential computation in large language models by identifying and exploiting natural opportunities for parallelization. Our key insight is that sequences of Feed-Forward Network (FFN) layers, particularly those remaining after the removal of specific attention layers, can often be parallelized with minimal accuracy impact. We develop a principled methodology for identifying and fusing such sequences, transforming them into parallel operations that significantly reduce inference latency while preserving model behavior. Applying these techniques to Llama-3.1-405B-Instruct, we create Llama-Nemotron-Ultra-253B-Base (Ultra-253B-Base), an efficient and soon-to-be publicly available model that achieves a 1.71X speedup in inference latency and 35X lower per-token cost while maintaining strong performance across benchmarks. Through extensive experiments on models from 49B to 253B parameters, we demonstrate that FFN Fusion becomes increasingly effective at larger scales and can complement existing optimization techniques like quantization and pruning. Most intriguingly, we find that even full transformer blocks containing both attention and FFN layers can sometimes be parallelized, suggesting new directions for neural architecture design.

Autoregressive Large Language Models (e.g., LLaMa, GPTs) are omnipresent achieving remarkable success in language understanding and generation. However, such impressive capability typically comes with a substantial model size, which presents significant challenges for autoregressive token-by-token generation. To mitigate computation overload incurred during generation, several early-exit and layer-dropping strategies have been proposed. Despite some promising success due to the redundancy across LLMs layers on metrics like Rough-L/BLUE, our careful knowledge-intensive evaluation unveils issues such as generation collapse, hallucination of wrong facts, and noticeable performance drop even at the trivial exit ratio of 10-15% of layers. We attribute these errors primarily to ineffective handling of the KV cache through state copying during early-exit. In this work, we observed the saturation of computationally expensive feed-forward blocks of LLM layers and proposed FFN-SkipLLM, which is a novel fine-grained skip strategy of autoregressive LLMs. More specifically, FFN-SkipLLM is an input-adaptive feed-forward skipping strategy that can skip 25-30% of FFN blocks of LLMs with marginal change in performance on knowledge-intensive generation tasks without any requirement to handle KV cache. Our extensive experiments and ablation across benchmarks like MT-Bench, Factoid-QA, and variable-length text summarization illustrate how our simple and ease-at-use method can facilitate faster autoregressive decoding.

Speculative decoding is widely adopted to reduce latency in large language model (LLM) inference by leveraging smaller draft models capable of handling diverse user tasks. However, emerging AI applications, such as LLM-based agents, present unique workload characteristics: instead of diverse independent requests, agentic frameworks typically submit repetitive inference requests, such as multi-agent pipelines performing similar subtasks or self-refinement loops iteratively enhancing outputs. These workloads result in long and highly predictable sequences, which current speculative decoding methods do not effectively exploit. To address this gap, we introduce SuffixDecoding, a novel method that utilizes efficient suffix trees to cache long token sequences from prompts and previous outputs. By adaptively speculating more tokens when acceptance likelihood is high and fewer when it is low, SuffixDecoding effectively exploits opportunities for longer speculations while conserving computation when those opportunities are limited. Evaluations on agentic benchmarks, including SWE-Bench and Text-to-SQL, demonstrate that SuffixDecoding achieves speedups of up to 5.3times, outperforming state-of-the-art methods -- 2.8times faster than model-based approaches like EAGLE-2/3 and 1.9times faster than model-free approaches such as Token Recycling. SuffixDecoding is open-sourced at https://github.com/snowflakedb/ArcticInference

This thesis provides methods and analysis of models which make progress on this goal. The techniques outlined are task agnostic, and should provide benefit when used with nearly any transformer LM. We introduce two new finetuning methods which add new capabilities to the models they are used on. The first adds a recurrence mechanism, which removes the fixed-window sized constraint and improves the efficiency of a transformer decoder. The second allows masked language models (MLMs) to be used for initialization of both the encoder and decoder of a non-autoregressive sequence-to-sequence transformer, opening up generative applications of models which were previously only used for natural language understanding tasks. We also introduce two new techniques for improving the quality of predictions of any transformer decoder without additional finetuning. One, hidden state optimization, can be applied to any transformer decoder to improve the quality of predictions at inference time, especially for few-shot classification. The other, conditional beam search, allows practitioners to search for natural language generation (NLG) model outputs with high likelihood while conditioning on the event that the output is not degenerate (e.g. empty, repetitive, etc.). Finally, we provide theoretical and empirical insights on the divergence of model-likelihood and output quality which has widely been observed in prior work. These insights apply to any model which represents a distribution over text, and apply to language models which are not transformers or even autoregressive. We argue that the NLP community has, to some extent, misunderstood the implications of these findings, and encourage a point of view which has more nuance.

We incorporate discrete and continuous time Markov processes as building blocks into probabilistic graphical models with latent and observed variables. We introduce the automatic Backward Filtering Forward Guiding (BFFG) paradigm (Mider et al., 2021) for programmable inference on latent states and model parameters. Our starting point is a generative model, a forward description of the probabilistic process dynamics. We backpropagate the information provided by observations through the model to transform the generative (forward) model into a pre-conditional model guided by the data. It approximates the actual conditional model with known likelihood-ratio between the two. The backward filter and the forward change of measure are suitable to be incorporated into a probabilistic programming context because they can be formulated as a set of transformation rules. The guided generative model can be incorporated in different approaches to efficiently sample latent states and parameters conditional on observations. We show applicability in a variety of settings, including Markov chains with discrete state space, interacting particle systems, state space models, branching diffusions and Gamma processes.

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

Previous studies have shown that automated text-mining tools are becoming increasingly important for successfully unlocking variant information in scientific literature at large scale. Despite multiple attempts in the past, existing tools are still of limited recognition scope and precision. We propose tmVar 3.0: an improved variant recognition and normalization tool. Compared to its predecessors, tmVar 3.0 is able to recognize a wide spectrum of variant related entities (e.g., allele and copy number variants), and to group different variant mentions belonging to the same concept in an article for improved accuracy. Moreover, tmVar3 provides additional variant normalization options such as allele-specific identifiers from the ClinGen Allele Registry. tmVar3 exhibits a state-of-the-art performance with over 90% accuracy in F-measure in variant recognition and normalization, when evaluated on three independent benchmarking datasets. tmVar3 is freely available for download. We have also processed the entire PubMed and PMC with tmVar3 and released its annotations on our FTP. Availability: ftp://ftp.ncbi.nlm.nih.gov/pub/lu/tmVar3

Neural sequence models are widely used to model time-series data. Equally ubiquitous is the usage of beam search (BS) as an approximate inference algorithm to decode output sequences from these models. BS explores the search space in a greedy left-right fashion retaining only the top-B candidates - resulting in sequences that differ only slightly from each other. Producing lists of nearly identical sequences is not only computationally wasteful but also typically fails to capture the inherent ambiguity of complex AI tasks. To overcome this problem, we propose Diverse Beam Search (DBS), an alternative to BS that decodes a list of diverse outputs by optimizing for a diversity-augmented objective. We observe that our method finds better top-1 solutions by controlling for the exploration and exploitation of the search space - implying that DBS is a better search algorithm. Moreover, these gains are achieved with minimal computational or memory over- head as compared to beam search. To demonstrate the broad applicability of our method, we present results on image captioning, machine translation and visual question generation using both standard quantitative metrics and qualitative human studies. Further, we study the role of diversity for image-grounded language generation tasks as the complexity of the image changes. We observe that our method consistently outperforms BS and previously proposed techniques for diverse decoding from neural sequence models.

The rapid scaling of Large Language Models (LLMs) has achieved remarkable performance, but it also leads to prohibitive memory costs. Existing parameter-efficient approaches such as pruning and quantization mainly compress pretrained models without enhancing architectural capacity, thereby hitting the representational ceiling of the base model. In this work, we propose VersatileFFN, a novel feed-forward network (FFN) that enables flexible reuse of parameters in both width and depth dimensions within a fixed parameter budget. Inspired by the dual-process theory of cognition, VersatileFFN comprises two adaptive pathways: a width-versatile path that generates a mixture of sub-experts from a single shared FFN, mimicking sparse expert routing without increasing parameters, and a depth-versatile path that recursively applies the same FFN to emulate deeper processing for complex tokens. A difficulty-aware gating dynamically balances the two pathways, steering "easy" tokens through the efficient width-wise route and allocating deeper iterative refinement to "hard" tokens. Crucially, both pathways reuse the same parameters, so all additional capacity comes from computation rather than memory. Experiments across diverse benchmarks and model scales demonstrate the effectiveness of the method. The code will be available at https://github.com/huawei-noah/noah-research/tree/master/VersatileFFN.

In this paper, we generalize text infilling (e.g., masked language models) by proposing Sequence Span Rewriting (SSR) as a self-supervised sequence-to-sequence (seq2seq) pre-training objective. SSR provides more fine-grained learning signals for text representations by supervising the model to rewrite imperfect spans to ground truth, and it is more consistent than text infilling with many downstream seq2seq tasks that rewrite a source sentences into a target sentence. Our experiments with T5 models on various seq2seq tasks show that SSR can substantially improve seq2seq pre-training. Moreover, we observe SSR is especially helpful to improve pre-training a small-size seq2seq model with a powerful imperfect span generator, which indicates a new perspective of transferring knowledge from a large model to a smaller model for seq2seq pre-training.

Transformer networks have lead to important progress in language modeling and machine translation. These models include two consecutive modules, a feed-forward layer and a self-attention layer. The latter allows the network to capture long term dependencies and are often regarded as the key ingredient in the success of Transformers. Building upon this intuition, we propose a new model that solely consists of attention layers. More precisely, we augment the self-attention layers with persistent memory vectors that play a similar role as the feed-forward layer. Thanks to these vectors, we can remove the feed-forward layer without degrading the performance of a transformer. Our evaluation shows the benefits brought by our model on standard character and word level language modeling benchmarks.

Large language models are usually fine-tuned to align with human preferences. However, fine-tuning a large language model can be challenging. In this work, we introduce weak-to-strong search, framing the alignment of a large language model as a test-time greedy search to maximize the log-likelihood difference between small tuned and untuned models while sampling from the frozen large model. This method serves both as (i) a compute-efficient model up-scaling strategy that avoids directly tuning the large model and as (ii) an instance of weak-to-strong generalization that enhances a strong model with weak test-time guidance. Empirically, we demonstrate the flexibility of weak-to-strong search across different tasks. In controlled-sentiment generation and summarization, we use tuned and untuned gpt2s to effectively improve the alignment of large models without additional training. Crucially, in a more difficult instruction-following benchmark, AlpacaEval 2.0, we show that reusing off-the-shelf small model pairs (e.g., zephyr-7b-beta and its untuned version) can significantly improve the length-controlled win rates of both white-box and black-box large models against gpt-4-turbo (e.g., 34.4 rightarrow 37.9 for Llama-3-70B-Instruct and 16.0 rightarrow 20.1 for gpt-3.5-turbo-instruct), despite the small models' low win rates approx 10.0.

Safety post-training can improve the harmfulness and policy compliance of Large Language Models (LLMs), but it may also reduce general utility, a phenomenon often described as the alignment tax. We study this trade-off through the lens of continual learning: sequential alignment stages expose the model to shifted data distributions and objectives, and their gradients may interfere with directions that support previously acquired general capabilities. This view does not claim that all alignment degradation has a single cause; rather, it provides a useful first-order mechanism for mitigating one important source of capability regression. We propose Orthogonal Gradient Projection for Safety Alignment (OGPSA), a lightweight update rule that estimates a low-rank reference subspace from gradients on a small set of general-capability data and removes from each safety gradient the component lying in this subspace. The resulting update is the steepest local safety-descent direction subject to first-order preservation constraints on the reference objectives. OGPSA is compatible with standard post-training pipelines and avoids large-scale replay, although it introduces periodic reference-gradient computation. Across Supervised Fine-Tuning (SFT), Direct Preference Optimization (DPO), and sequential SFTrightarrowDPO settings, OGPSA improves the observed safety--utility trade-off over standard baselines. Under the sequential SFTrightarrowDPO pipeline, the average performance gain increases from 33.98\% to 42.74\% on Qwen2.5-7B-Instruct and from 19.74\% to 32.98\% on Llama3.1-8B-Instruct. We have open sourced our code at https://github.com/SunGL001/OGPSA.

The autoregressive nature of large language models (LLMs) limits inference speed. Each forward pass generates only a single token and is often bottlenecked by memory bandwidth. Speculative decoding alleviates this issue using a draft-then-verify approach to accelerate token generation. However, the overhead introduced during the draft phase and the training cost of the draft model limit the efficiency and adaptability of speculative decoding. In this work, we introduce PARallel Draft (PARD), a novel speculative decoding method that enables low-cost adaptation of autoregressive draft models into parallel draft models. PARD enhances inference efficiency by predicting multiple future tokens in a single forward pass of the draft phase, and incorporates a conditional drop token method to accelerate training. Its target-independence property allows a single draft model to be applied to an entire family of different models, minimizing the adaptation cost. Our proposed conditional drop token method can improves draft model training efficiency by 3x. On our optimized inference framework, PARD accelerates LLaMA3.1-8B inference by 4.08x, achieving 311.5 tokens per second.

Parameter-efficient fine-tuning optimizes large, pre-trained foundation models by updating a subset of parameters; in this class, Low-Rank Adaptation (LoRA) is particularly effective. Inspired by an effort to investigate the different roles of LoRA matrices during fine-tuning, this paper characterizes and leverages unexpected asymmetry in the importance of low-rank adapter matrices. Specifically, when updating the parameter matrices of a neural network by adding a product BA, we observe that the B and A matrices have distinct functions: A extracts features from the input, while B uses these features to create the desired output. Based on this observation, we demonstrate that fine-tuning B is inherently more effective than fine-tuning A, and that a random untrained A should perform nearly as well as a fine-tuned one. Using an information-theoretic lens, we also bound the generalization of low-rank adapters, showing that the parameter savings of exclusively training B improves the bound. We support our conclusions with experiments on RoBERTa, BART-Large, LLaMA-2, and ViTs.

Bayesian inference provides principled uncertainty quantification but is often limited by challenges of prior elicitation, likelihood misspecification, and computational burden. The martingale posterior (MGP, Fong et al., 2023) offers an alternative, replacing prior-likelihood elicitation with a predictive rule - namely, a sequence of one-step-ahead predictive distributions - for forward data generation. The utility of MGPs depends on the choice of predictive rule, yet the literature has offered few compelling examples. Foundation transformers are well-suited here, as their autoregressive generation mirrors this forward simulation and their general-purpose design enables rich predictive modeling. We introduce TabMGP, an MGP built on TabPFN, a transformer foundation model that is currently state-of-the-art for tabular data. TabMGP produces credible sets with near-nominal coverage and often outperforms both existing MGP constructions and standard Bayes.

Autonomous agents driven by Large Language Models (LLMs) have revolutionized reasoning and problem-solving but remain static after training, unable to grow with experience as intelligent beings do during deployment. We introduce Forward Learning with EXperience (FLEX), a gradient-free learning paradigm that enables LLM agents to continuously evolve through accumulated experience. Specifically, FLEX cultivates scalable and inheritable evolution by constructing a structured experience library through continual reflection on successes and failures during interaction with the environment. FLEX delivers substantial improvements on mathematical reasoning, chemical retrosynthesis, and protein fitness prediction (up to 23% on AIME25, 10% on USPTO50k, and 14% on ProteinGym). We further identify a clear scaling law of experiential growth and the phenomenon of experience inheritance across agents, marking a step toward scalable and inheritable continuous agent evolution. Project Page: https://flex-gensi-thuair.github.io.

Fine-tuning large pre-trained foundation models often yields excellent downstream performance but is prohibitively expensive when updating all parameters. Parameter-efficient fine-tuning (PEFT) methods such as LoRA alleviate this by introducing lightweight update modules, yet they commonly rely on weight-agnostic linear approximations, limiting their expressiveness. In this work, we propose PEANuT, a novel PEFT framework that introduces weight-aware neural tweakers, compact neural modules that generate task-adaptive updates conditioned on frozen pre-trained weights. PEANuT provides a flexible yet efficient way to capture complex update patterns without full model tuning. We theoretically show that PEANuT achieves equivalent or greater expressivity than existing linear PEFT methods with comparable or fewer parameters. Extensive experiments across four benchmarks with over twenty datasets demonstrate that PEANuT consistently outperforms strong baselines in both NLP and vision tasks, while maintaining low computational overhead.

Speculative decoding speeds up LLM inference by using a small draft model to propose multiple tokens that a target model verifies in parallel. Extending this idea to batches is essential for production serving, but it introduces the ragged tensor problem: sequences in the same batch accept different numbers of draft tokens, breaking right-alignment and corrupting position IDs, attention masks, and KV-cache state. We show that several existing batch implementations violate output equivalence-the fundamental requirement that speculative decoding must produce identical token sequences to standard autoregressive generation. These violations occur precisely due to improper handling of the ragged tensor problem. In response, we (1) characterize the synchronization requirements that guarantee correctness, (2) present a correctness-first batch speculative decoding EQSPEC that exposes realignment as consuming 40% of overhead, and (3) introduce EXSPEC, which maintains a sliding pool of sequences and dynamically forms same-length groups, to reduce the realignment overhead while preserving per-sequence speculative speedups. On the SpecBench dataset, across Vicuna-7B/68M, Qwen3-8B/0.6B, and GLM-4-9B/0.6B target/draft pairs, our approach achieves up to 3times throughput improvement at batch size 8 compared to batch size 1, with efficient scaling through batch size 8, while maintaining 95% output equivalence. Our method requires no custom kernels and integrates cleanly with existing inference stacks. Our code is available at https://github.com/eBay/spec_dec.

Multi-vector dense retrieval methods like ColBERT systematically use a single-layer linear projection to reduce the dimensionality of individual vectors. In this study, we explore the implications of the MaxSim operator on the gradient flows of the training of multi-vector models and show that such a simple linear projection has inherent, if non-critical, limitations in this setting. We then discuss the theoretical improvements that could result from replacing this single-layer projection with well-studied alternative feedforward linear networks (FFN), such as deeper, non-linear FFN blocks, GLU blocks, and skip-connections, could alleviate these limitations. Through the design and systematic evaluation of alternate projection blocks, we show that better-designed final projections positively impact the downstream performance of ColBERT models. We highlight that many projection variants outperform the original linear projections, with the best-performing variants increasing average performance on a range of retrieval benchmarks across domains by over 2 NDCG@10 points. We then conduct further exploration on the individual parameters of these projections block in order to understand what drives this empirical performance, highlighting the particular importance of upscaled intermediate projections and residual connections. As part of these ablation studies, we show that numerous suboptimal projection variants still outperform the traditional single-layer projection across multiple benchmarks, confirming our hypothesis. Finally, we observe that this effect is consistent across random seeds, further confirming that replacing the linear layer of ColBERT models is a robust, drop-in upgrade.

In the artificial neuron, I replace the dot product with the weighted Lehmer mean, which may emulate different cases of a generalized mean. The single neuron instance is replaced by a multiplet of neurons which have the same averaging weights. A group of outputs feed forward, in lieu of the single scalar. The generalization parameter is typically set to a different value for each neuron in the multiplet. I further extend the concept to a multiplet taken from the Gini mean. Derivatives with respect to the weight parameters and with respect to the two generalization parameters are given. Some properties of the network are investigated, showing the capacity to emulate the classical exclusive-or problem organically in two layers and perform some multiplication and division. The network can instantiate truncated power series and variants, which can be used to approximate different functions, provided that parameters are constrained. Moreover, a mean case slope score is derived that can facilitate a learning-rate novelty based on homogeneity of the selected elements. The multiplet neuron equation provides a way to segment regularization timeframes and approaches.

Gradient-based data selection offers a principled framework for estimating sample utility in large language model (LLM) fine-tuning, but existing methods are mostly designed for offline settings. They are therefore less suited to online fine-tuning, where data arrives sequentially, sample utility is step-dependent, and the effective update geometry is shaped by adaptive optimizers. We propose an optimizer-aware framework for gradient-based online data selection and reweighting in LLM fine-tuning. Our key idea is to view online selection not as static sample ranking, but as shaping the next target-oriented update under the optimizer state. We formulate this as an optimizer-aware update-matching problem, establish its connection to second-order target utility, and show why subset-level construction must account for interactions and redundancy among selected samples. Based on this view, we develop a two-stage Filter-then-Weight algorithm that first filters geometrically useful candidates and then optimizes their coefficients. To make the framework practical for LLMs, we introduce a factorized outer-product gradient representation and optimized matrix computations for long-context data. Experiments show that our method consistently improves convergence and downstream performance over existing online data selection baselines under the same data budget.

We present protein autoregressive modeling (PAR), the first multi-scale autoregressive framework for protein backbone generation via coarse-to-fine next-scale prediction. Using the hierarchical nature of proteins, PAR generates structures that mimic sculpting a statue, forming a coarse topology and refining structural details over scales. To achieve this, PAR consists of three key components: (i) multi-scale downsampling operations that represent protein structures across multiple scales during training; (ii) an autoregressive transformer that encodes multi-scale information and produces conditional embeddings to guide structure generation; (iii) a flow-based backbone decoder that generates backbone atoms conditioned on these embeddings. Moreover, autoregressive models suffer from exposure bias, caused by the training and the generation procedure mismatch, and substantially degrades structure generation quality. We effectively alleviate this issue by adopting noisy context learning and scheduled sampling, enabling robust backbone generation. Notably, PAR exhibits strong zero-shot generalization, supporting flexible human-prompted conditional generation and motif scaffolding without requiring fine-tuning. On the unconditional generation benchmark, PAR effectively learns protein distributions and produces backbones of high design quality, and exhibits favorable scaling behavior. Together, these properties establish PAR as a promising framework for protein structure generation.

We propose Beam Tree Recursive Cell (BT-Cell) - a backpropagation-friendly framework to extend Recursive Neural Networks (RvNNs) with beam search for latent structure induction. We further extend this framework by proposing a relaxation of the hard top-k operators in beam search for better propagation of gradient signals. We evaluate our proposed models in different out-of-distribution splits in both synthetic and realistic data. Our experiments show that BTCell achieves near-perfect performance on several challenging structure-sensitive synthetic tasks like ListOps and logical inference while maintaining comparable performance in realistic data against other RvNN-based models. Additionally, we identify a previously unknown failure case for neural models in generalization to unseen number of arguments in ListOps. The code is available at: https://github.com/JRC1995/BeamTreeRecursiveCells.

This study introduces PV-RNN, a novel variational RNN inspired by the predictive-coding ideas. The model learns to extract the probabilistic structures hidden in fluctuating temporal patterns by dynamically changing the stochasticity of its latent states. Its architecture attempts to address two major concerns of variational Bayes RNNs: how can latent variables learn meaningful representations and how can the inference model transfer future observations to the latent variables. PV-RNN does both by introducing adaptive vectors mirroring the training data, whose values can then be adapted differently during evaluation. Moreover, prediction errors during backpropagation, rather than external inputs during the forward computation, are used to convey information to the network about the external data. For testing, we introduce error regression for predicting unseen sequences as inspired by predictive coding that leverages those mechanisms. The model introduces a weighting parameter, the meta-prior, to balance the optimization pressure placed on two terms of a lower bound on the marginal likelihood of the sequential data. We test the model on two datasets with probabilistic structures and show that with high values of the meta-prior the network develops deterministic chaos through which the data's randomness is imitated. For low values, the model behaves as a random process. The network performs best on intermediate values, and is able to capture the latent probabilistic structure with good generalization. Analyzing the meta-prior's impact on the network allows to precisely study the theoretical value and practical benefits of incorporating stochastic dynamics in our model. We demonstrate better prediction performance on a robot imitation task with our model using error regression compared to a standard variational Bayes model lacking such a procedure.

Speculative decoding (SD) has emerged as a promising technique to accelerate LLM inference by employing a small draft model to propose draft tokens in advance, and validating them in parallel with the large target model. However, the existing SD methods still remain constrained by their serialized execution, which causes the mutual waiting bubbles between the draft and target models. To address this challenge, we draw inspiration from branch prediction in modern processors and propose a novel framework SpecBranch to unlock branch parallelism in SD. Specifically, we first take an in-depth analysis of the potential of branch parallelism in SD, and recognize that the key challenge lies in the trade-offs between parallelization and token rollback. Based on the analysis, we introduce parallel speculative branches to preemptively hedge against likely rejections. Meanwhile, to enhance parallelism, we jointly orchestrate adaptive draft lengths with a hybrid combination of the implicit draft model confidence and explicit reusing of target model features. Extensive experiments across various models and benchmarks show that SpecBranch achieves over 1.8times sim 4.5times speedups against the auto-regressive decoding and reduces rollback tokens by 50\% for poorly aligned models, while maintaining an identical sampling distribution.

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights are available at https://github.com/DeepGraphLearning/esm-s.

Protein family design emerges as a promising alternative by combining the advantages of de novo protein design and mutation-based directed evolution.In this paper, we propose ProfileBFN, the Profile Bayesian Flow Networks, for specifically generative modeling of protein families. ProfileBFN extends the discrete Bayesian Flow Network from an MSA profile perspective, which can be trained on single protein sequences by regarding it as a degenerate profile, thereby achieving efficient protein family design by avoiding large-scale MSA data construction and training. Empirical results show that ProfileBFN has a profound understanding of proteins. When generating diverse and novel family proteins, it can accurately capture the structural characteristics of the family. The enzyme produced by this method is more likely than the previous approach to have the corresponding function, offering better odds of generating diverse proteins with the desired functionality.

Text generation with Large Language Models (LLMs) is known to be memory bound due to the combination of their auto-regressive nature, huge parameter counts, and limited memory bandwidths, often resulting in low token rates. Speculative decoding has been proposed as a solution for LLM inference acceleration. However, since draft models are often unavailable in the modern open-source LLM families, e.g., for Llama 2 7B, training a high-quality draft model is required to enable inference acceleration via speculative decoding. In this paper, we propose a simple draft model training framework for direct alignment to chat-capable target models. With the proposed framework, we train Llama 2 Chat Drafter 115M, a draft model for Llama 2 Chat 7B or larger, with only 1.64\% of the original size. Our training framework only consists of pretraining, distillation dataset generation, and finetuning with knowledge distillation, with no additional alignment procedure. For the finetuning step, we use instruction-response pairs generated by target model for distillation in plausible data distribution, and propose a new Total Variation Distance++ (TVD++) loss that incorporates variance reduction techniques inspired from the policy gradient method in reinforcement learning. Our empirical results show that Llama 2 Chat Drafter 115M with speculative decoding achieves up to 2.3 block efficiency and 2.4times speed-up relative to autoregressive decoding on various tasks with no further task-specific fine-tuning.

Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the evolutionary trajectories of protein families. The accuracy of protein structure predictions is often compromised for protein sequences that lack sufficient homologous information to construct high quality MSA. Although various methods have been proposed to generate virtual MSA under these conditions, they fall short in comprehensively capturing the intricate coevolutionary patterns within MSA or require guidance from external oracle models. Here we introduce MSAGPT, a novel approach to prompt protein structure predictions via MSA generative pretraining in the low MSA regime. MSAGPT employs a simple yet effective 2D evolutionary positional encoding scheme to model complex evolutionary patterns. Endowed by this, its flexible 1D MSA decoding framework facilitates zero or few shot learning. Moreover, we demonstrate that leveraging the feedback from AlphaFold2 can further enhance the model capacity via Rejective Fine tuning (RFT) and Reinforcement Learning from AF2 Feedback (RLAF). Extensive experiments confirm the efficacy of MSAGPT in generating faithful virtual MSA to enhance the structure prediction accuracy. The transfer learning capabilities also highlight its great potential for facilitating other protein tasks.

Autoregressive models have achieved promising results in natural language processing. However, for image generation tasks, they encounter substantial challenges in effectively capturing long-range dependencies, managing computational costs, and most crucially, defining meaningful autoregressive sequences that reflect natural image hierarchies. To address these issues, we present Next-Frequency Image Generation (NFIG), a novel framework that decomposes the image generation process into multiple frequency-guided stages. Our approach first generates low-frequency components to establish global structure with fewer tokens, then progressively adds higher-frequency details, following the natural spectral hierarchy of images. This principled autoregressive sequence not only improves the quality of generated images by better capturing true causal relationships between image components, but also significantly reduces computational overhead during inference. Extensive experiments demonstrate that NFIG achieves state-of-the-art performance with fewer steps, offering a more efficient solution for image generation, with 1.25times speedup compared to VAR-d20 while achieving better performance (FID: 2.81) on the ImageNet-256 benchmark. We hope that our insight of incorporating frequency-domain knowledge to guide autoregressive sequence design will shed light on future research. We will make our code publicly available upon acceptance of the paper.

Fine-tuning the bias terms of large language models (LLMs) has the potential to achieve unprecedented parameter efficiency while maintaining competitive performance, particularly in low-data regimes. However, the link between fine-tuning different bias terms (i.e., b_q, b_k, and b_v in the query, key, or value projections) and downstream performance remains largely unclear to date. In this paper, we investigate the link between fine-tuning b_q, b_k, and b_v with the performance of the downstream task. Our key finding is that directly fine-tuning b_v generally leads to higher downstream performance in low-data regimes, in comparison to b_q and b_k. We extensively evaluate this unique property across a wide range of LLMs spanning encoder-only and decoder-only architectures up to 6.7B parameters (including bias-free LLMs). Our results provide strong evidence for the effectiveness of directly fine-tuning b_v across various downstream tasks. The implementation code is available at https://github.com/whubaichuan/BEFT.

Many LLM-based open-ended search systems freeze the foundation model that proposes improvements to existing solutions, which may bottleneck long-run progress. Recent work has explored updating the proposal model at test time [arXiv:2511.23473], but the update strategy is still typically hand-specified. Therefore, this study investigated whether an LLM can use task feedback to decide how it should update its weights. For tractability, we focused on the simpler case where there is only one round of self-improvement, and restricted the update operator to self-supervised next token prediction (NTP), leaving the model freedom in choosing its training data and key NTP hyperparameters. Using the Self-Adapting Language Models (SEAL) [arXiv:2506.10943] framework as a testbed, we relaxed its fixed human template constraint and allowed the model to generate its own self-edit templates, thereby giving it more control over its training data and hyperparameters. Two variants were studied, differing in whether template generation was conditioned on a lightweight archive of past templates. In SEAL's Single-Passage Knowledge Incorporation setting with Qwen3-8B on SQuAD [arXiv:1606.05250], the no-archive variant performed comparably to the weaker "Implications" baseline, while the archive variant outperformed "Implications" and approached the strongest human-designed "Rewrite" baseline without surpassing it. Further analysis of collapse in the model's exploration revealed that a naive archive can confer some short-term robustness but can also accelerate homogenization, suggesting that explicit novelty pressure may be required to consistently advance beyond carefully optimized human strategies. Our code is available at https://github.com/cheongalc/search-self-edit-strategies .

The proliferation of pretrained models, as a result of advancements in pretraining techniques, has led to the emergence of a vast zoo of publicly available models. Effectively utilizing these resources to obtain models with robust out-of-distribution generalization capabilities for downstream tasks has become a crucial area of research. Previous research has primarily focused on identifying the most powerful models within the model zoo, neglecting to fully leverage the diverse inductive biases contained within. This paper argues that the knowledge contained in weaker models is valuable and presents a method for leveraging the diversity within the model zoo to improve out-of-distribution generalization capabilities. Specifically, we investigate the behaviors of various pretrained models across different domains of downstream tasks by characterizing the variations in their encoded representations in terms of two dimensions: diversity shift and correlation shift. This characterization enables us to propose a new algorithm for integrating diverse pretrained models, not limited to the strongest models, in order to achieve enhanced out-of-distribution generalization performance. Our proposed method demonstrates state-of-the-art empirical results on a variety of datasets, thus validating the benefits of utilizing diverse knowledge.

Alignment with human preference is a desired property of large language models (LLMs). Currently, the main alignment approach is based on reinforcement learning from human feedback (RLHF). Despite the effectiveness of RLHF, it is intricate to implement and train, thus recent studies explore how to develop alternative alignment approaches based on supervised fine-tuning (SFT). A major limitation of SFT is that it essentially does imitation learning, which cannot fully understand what are the expected behaviors. To address this issue, we propose an improved alignment approach named FIGA. Different from prior methods, we incorporate fine-grained (i.e., token or phrase level) quality signals that are derived by contrasting good and bad responses. Our approach has made two major contributions. Firstly, we curate a refined alignment dataset that pairs initial responses and the corresponding revised ones. Secondly, we devise a new loss function can leverage fine-grained quality signals to instruct the learning of LLMs for alignment. Extensive experiments have demonstrated the effectiveness of our approaches by comparing a number of competitive baselines.

Autoregressive models, such as the GPT family, use a fixed order, usually left-to-right, to generate sequences. However, this is not a necessity. In this paper, we challenge this assumption and show that by simply adding a positional encoding for the output, this order can be modulated on-the-fly per-sample which offers key advantageous properties. It allows for the sampling of and conditioning on arbitrary subsets of tokens, and it also allows sampling in one shot multiple tokens dynamically according to a rejection strategy, leading to a sub-linear number of model evaluations. We evaluate our method across various domains, including language modeling, path-solving, and aircraft vertical rate prediction, decreasing the number of steps required for generation by an order of magnitude.

Protein language models are trained primarily with masked language modeling (MLM), which predicts amino-acid identities at masked positions. We ask whether latent-space prediction can complement these token-level objectives under matched wall-clock budget. Across pretrained and random-init protein sequence encoders at 35--150M parameters, we find that the best protein-JEPA design is not all-position latent prediction but a variant: predicting latent targets only at masked positions, and retaining the MLM cross-entropy. We call this recipe masked-position MLM+JEPA. On a 16-task downstream suite (15 frozen linear probes plus SCOPe-40 zero-shot fold retrieval), under matched wall-clock budgets, this recipe wins more tasks than it loses against MLM-only continuation: 10 wins / 3 losses / 3 ties (hereafter W/L/T) on pretrained ESM2-35M, 11/2/3 on ESM2-150M while results in pretraining from scratch are mixed (6/8/2). Gains are seen for multiple models on 11 of 16 tasks, including stability, etaβeta-lactamase fitness, variant effect, intrinsic disorder, remote homology, enzyme classification, and SCOPe-40 fold retrieval. Tasks with more losses than wins are Fluorescence (TAPE) and Peptide-HLA Binding. All-position MLM+JEPA matches MLM-only overall but does not reproduce the masked-position gains. JEPA-only (no MLM) collapses in nearly every experiment. We conclude that JEPA, when combined with MLM, is competitive and can outperform pure MLM in pretraining and continued training, even under matched wall-clock budgets.

Predicting protein function from sequence is a central challenge in computational biology. While existing methods rely heavily on structured ontologies or similarity-based techniques, they often lack the flexibility to express structure-free functional descriptions and novel biological functions. In this work, we introduce Prot2Text-V2, a novel multimodal sequence-to-text model that generates free-form natural language descriptions of protein function directly from amino acid sequences. Our method combines a protein language model as a sequence encoder (ESM-3B) and a decoder-only language model (LLaMA-3.1-8B-Instruct) through a lightweight nonlinear modality projector. A key innovation is our Hybrid Sequence-level Contrastive Alignment Learning (H-SCALE), which improves cross-modal learning by matching mean- and std-pooled protein embeddings with text representations via contrastive loss. After the alignment phase, we apply instruction-based fine-tuning using LoRA on the decoder to teach the model how to generate accurate protein function descriptions conditioned on the protein sequence. We train Prot2Text-V2 on about 250K curated entries from SwissProt and evaluate it under low-homology conditions, where test sequences have low similarity with training samples. Prot2Text-V2 consistently outperforms traditional and LLM-based baselines across various metrics.

Low-Rank Adaptation (LoRA) has become one of the most widely used fine-tuning mechanisms for adapting large language models to new domains, tasks, and users. Yet adaptation performance alone can obscure an important failure mode: LoRA updates may improve performance on the target distribution while degrading prior capabilities learned during pretraining and alignment. We show that this forgetting becomes especially severe when the adaptation distribution differs substantially from the models original training or alignment distributions. The challenge is amplified in practical settings, where the original training and alignment data are typically unavailable. Motivated by this constraint, we study how LoRA based adaptation balances new learning against forgetting in a replay-free setting, and introduce a simple output space regularizer that can be added directly to existing training pipelines. Our method removes the ground-truth token from both the base and adapted model distributions, renormalizes the remaining probabilities, and applies KL regularization only over the non-target vocabulary. This preserves the base models relative preferences among alternative tokens without directly opposing the cross-entropy signal required for adaptation. As the regularizer acts only at the loss level, it requires no replay data, architectural changes, adapter redesign, or inference-time overhead, and can be applied directly to existing LoRA variants. Across all LoRA variants tested and across various backbones, our method improves the frontier between new learning and forgetting when the adaptation distribution differs substantially from the base models original training or alignment distributions, suggesting a broadly applicable route toward more reliable LLM updating.

Recent advances in large language model (LLM) embeddings have enabled powerful representations for biological data, but most applications to date focus only on gene-level information. We present one of the first systematic frameworks to generate variant-level embeddings across the entire human genome. Using curated annotations from FAVOR, ClinVar, and the GWAS Catalog, we constructed semantic text descriptions for 8.9 billion possible variants and generated embeddings at three scales: 1.5 million HapMap3+MEGA variants, ~90 million imputed UK Biobank variants, and ~9 billion all possible variants. Embeddings were produced with both OpenAI's text-embedding-3-large and the open-source Qwen3-Embedding-0.6B models. Baseline experiments demonstrate high predictive accuracy for variant properties, validating the embeddings as structured representations of genomic variation. We outline two downstream applications: embedding-informed hypothesis testing by extending the Frequentist And Bayesian framework to genome-wide association studies, and embedding-augmented genetic risk prediction that enhances standard polygenic risk scores. These resources, publicly available on Hugging Face, provide a foundation for advancing large-scale genomic discovery and precision medicine.

Parameter-efficient fine-tuning (PEFT) has shown its effectiveness in adapting the pre-trained language models to downstream tasks while only updating a small number of parameters. Despite the success, most existing methods independently adapt to each task without considering knowledge transfer between tasks and are limited to low-data regimes. To overcome this issue, we propose Prototype-based HyperAdapter (PHA), a novel framework built on the adapter-tuning and hypernetwork. It introduces an instance-dense retriever and a prototypical hypernetwork to generate the conditional modules in a sample-efficient manner. This leads to comparable performance improvements against existing PEFT methods on multi-task learning and few-shot transfer learning. More importantly, when the available data size gets smaller, our method outperforms other strong baselines by a large margin. Based on our extensive empirical experiments across various datasets, we demonstrate that PHA strikes a better trade-off between trainable parameters, accuracy on stream tasks, and sample efficiency.

Generative machine learning models are increasingly being used to design novel proteins for therapeutic and biotechnological applications. However, the current methods mostly focus on the design of proteins with a fixed backbone structure, which leads to their limited ability to account for protein flexibility, one of the crucial properties for protein function. Learning to engineer protein flexibility is problematic because the available data are scarce, heterogeneous, and costly to obtain using computational as well as experimental methods. Our contributions to address this problem are three-fold. First, we comprehensively compare methods for quantifying protein flexibility and identify data relevant to learning. Second, we design and train flexibility predictors utilizing sequential or both sequential and structural information on the input. We overcome the data scarcity issue by leveraging a pre-trained protein language model. Third, we introduce a method for fine-tuning a protein inverse folding model to steer it toward desired flexibility in specified regions. We demonstrate that our method Flexpert-Design enables guidance of inverse folding models toward increased flexibility. This opens up new possibilities for protein flexibility engineering and the development of proteins with enhanced biological activities.

Recent works have revealed the great potential of speculative decoding in accelerating the autoregressive generation process of large language models. The success of these methods relies on the alignment between draft candidates and the sampled outputs of the target model. Existing methods mainly achieve draft-target alignment with training-based methods, e.g., EAGLE, Medusa, involving considerable training costs. In this paper, we present a training-free alignment-augmented speculative decoding algorithm. We propose alignment sampling, which leverages output distribution obtained in the prefilling phase to provide more aligned draft candidates. To further benefit from high-quality but non-aligned draft candidates, we also introduce a simple yet effective flexible verification strategy. Through an adaptive probability threshold, our approach can improve generation accuracy while further improving inference efficiency. Experiments on 8 datasets (including question answering, summarization and code completion tasks) show that our approach increases the average generation score by 3.3 points for the LLaMA3 model. Our method achieves a mean acceptance length up to 2.39 and speed up generation by 2.23.

TabPFN [Hollmann et al., 2023], a Transformer model pretrained to perform in-context learning on fresh tabular classification problems, was presented at the last ICLR conference. To better understand its behavior, we treat it as a black-box function approximator generator and observe its generated function approximations on a varied selection of training datasets. Exploring its learned inductive biases in this manner, we observe behavior that is at turns either brilliant or baffling. We conclude this post with thoughts on how these results might inform the development, evaluation, and application of prior-data fitted networks (PFNs) in the future.

In practice, we usually need to build variable-sized models adapting for diverse resource constraints in different application scenarios, where weight initialization is an important step prior to training. The Learngene framework, introduced recently, firstly learns one compact part termed as learngene from a large well-trained model, after which learngene is expanded to initialize variable-sized models. In this paper, we start from analysing the importance of guidance for the expansion of well-trained learngene layers, inspiring the design of a simple but highly effective Learngene approach termed SWS (Stage-wise Weight Sharing), where both learngene layers and their learning process critically contribute to providing knowledge and guidance for initializing models at varying scales. Specifically, to learn learngene layers, we build an auxiliary model comprising multiple stages where the layer weights in each stage are shared, after which we train it through distillation. Subsequently, we expand these learngene layers containing stage information at their corresponding stage to initialize models of variable depths. Extensive experiments on ImageNet-1K demonstrate that SWS achieves consistent better performance compared to many models trained from scratch, while reducing around 6.6x total training costs. In some cases, SWS performs better only after 1 epoch tuning. When initializing variable-sized models adapting for different resource constraints, SWS achieves better results while reducing around 20x parameters stored to initialize these models and around 10x pre-training costs, in contrast to the pre-training and fine-tuning approach.

Pre-trained language models (PLMs) have become a prevalent technique in deep learning for code, utilizing a two-stage pre-training and fine-tuning procedure to acquire general knowledge about code and specialize in a variety of downstream tasks. However, the dynamic nature of software codebases poses a challenge to the effectiveness and robustness of PLMs. In particular, world-realistic scenarios potentially lead to significant differences between the distribution of the pre-training and test data, i.e., distribution shift, resulting in a degradation of the PLM's performance on downstream tasks. In this paper, we stress the need for adapting PLMs of code to software data whose distribution changes over time, a crucial problem that has been overlooked in previous works. The motivation of this work is to consider the PLM in a non-stationary environment, where fine-tuning data evolves over time according to a software evolution scenario. Specifically, we design a scenario where the model needs to learn from a stream of programs containing new, unseen APIs over time. We study two widely used PLM architectures, i.e., a GPT2 decoder and a RoBERTa encoder, on two downstream tasks, API call and API usage prediction. We demonstrate that the most commonly used fine-tuning technique from prior work is not robust enough to handle the dynamic nature of APIs, leading to the loss of previously acquired knowledge i.e., catastrophic forgetting. To address these issues, we implement five continual learning approaches, including replay-based and regularization-based methods. Our findings demonstrate that utilizing these straightforward methods effectively mitigates catastrophic forgetting in PLMs across both downstream tasks while achieving comparable or superior performance.

Instruction tuning enables language models to generalize more effectively and better follow user intent. However, obtaining instruction data can be costly and challenging. Prior works employ methods such as expensive human annotation, crowd-sourced datasets with alignment issues, or generating noisy examples via LLMs. We introduce the LongForm dataset, which is created by leveraging English corpus examples with augmented instructions. We select a diverse set of human-written documents from existing corpora such as C4 and Wikipedia and generate instructions for the given documents via LLMs. This approach provides a cheaper and cleaner instruction-tuning dataset and one suitable for long text generation. We finetune T5, OPT, and LLaMA models on our dataset and show that even smaller LongForm models have good generalization capabilities for text generation. Our models outperform 10x larger language models without instruction tuning on various tasks such as story/recipe generation and long-form question answering. Moreover, LongForm models outperform prior instruction-tuned models such as FLAN-T5 and Alpaca by a large margin. Finally, our models can effectively follow and answer multilingual instructions; we demonstrate this for news generation. We publicly release our data and models: https://github.com/akoksal/LongForm.

Large language models (LLMs) consistently benefit from further fine-tuning on various tasks. However, we observe that directly tuning the INSTRUCT (i.e., instruction tuned) models often leads to marginal improvements and even performance degeneration. Notably, paired BASE models, the foundation for these INSTRUCT variants, contain highly similar weight values (i.e., less than 2% on average for Llama 3.1 8B). Therefore, we propose a novel Shadow-FT framework to tune the INSTRUCT models by leveraging the corresponding BASE models. The key insight is to fine-tune the BASE model, and then directly graft the learned weight updates to the INSTRUCT model. Our proposed Shadow-FT introduces no additional parameters, is easy to implement, and significantly improves performance. We conduct extensive experiments on tuning mainstream LLMs, such as Qwen 3 and Llama 3 series, and evaluate them across 19 benchmarks covering coding, reasoning, and mathematical tasks. Experimental results demonstrate that Shadow-FT consistently outperforms conventional full-parameter and parameter-efficient tuning approaches. Further analyses indicate that Shadow-FT can be applied to multimodal large language models (MLLMs) and combined with direct preference optimization (DPO). Codes and weights are available at https://github.com/wutaiqiang/Shadow-FT{Github}.

Despite significant progress of generative models in the natural sciences, their controllability remains challenging. One fundamentally missing aspect of molecular or protein generative models is an inductive bias that can reflect continuous properties of interest. To that end, we propose the Regression Transformer (RT), a novel method that abstracts regression as a conditional sequence modeling problem. This introduces a new paradigm of multitask language models which seamlessly bridge sequence regression and conditional sequence generation. We thoroughly demonstrate that, despite using a nominal-scale training objective, the RT matches or surpasses the performance of conventional regression models in property prediction tasks of small molecules, proteins and chemical reactions. Critically, priming the same model with continuous properties yields a highly competitive conditional generative model that outperforms specialized approaches in a substructure-constrained, property-driven molecule generation benchmark. Our dichotomous approach is facilitated by a novel, alternating training scheme that enables the model to decorate seed sequences by desired properties, e.g., to optimize reaction yield. In sum, the RT is the first report of a multitask model that concurrently excels at predictive and generative tasks in biochemistry. This finds particular application in property-driven, local exploration of the chemical or protein space and could pave the road toward foundation models in material design. The code to reproduce all experiments of the paper is available at: https://github.com/IBM/regression-transformer

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

To combat the memory bandwidth-bound nature of autoregressive LLM inference, previous research has proposed the speculative decoding framework. To perform speculative decoding, a small draft model proposes candidate continuations of the input sequence, that are then verified in parallel by the base model. One way to specify the draft model, as used in the recent Medusa decoding framework, is as a collection of light-weight heads, called draft heads, that operate on the base model's hidden states. To date, all existing draft heads have been sequentially independent, meaning that they speculate tokens in the candidate continuation independently of any preceding tokens in the candidate continuation. In this work, we propose Hydra heads, a sequentially dependent, drop-in replacement for standard draft heads that significantly improves speculation accuracy. Decoding with Hydra heads improves throughput compared to Medusa decoding with standard draft heads. We further explore the design space of Hydra head training objectives and architectures, and propose a carefully-tuned Hydra head recipe, which we call Hydra++, that improves decoding throughput by 1.31x and 2.71x compared to Medusa decoding and autoregressive decoding, respectively. Overall, Hydra heads are a simple intervention on standard draft heads that significantly improve the end-to-end speed of draft head based speculative decoding.

Reinforcement Learning from Human Feedback (RLHF) has become a cornerstone for aligning large language models (LLMs). However, its effectiveness depends on high-quality instruction data. Most existing alignment datasets are either private or require costly human annotation, which limits reproducibility and scalability. Even with Reinforcement Learning from AI Feedback (RLAIF), concerns about data quality remain. Moreover, it is unclear how much data is actually required to fine-tune a base model into a strong instruction-following model. Current approaches often rely on over 300k examples even at the supervised fine-tuning (SFT) stage, yet they still underperform compared to proprietary models, creating barriers for academic and resource-limited communities. To address this gap, we introduce PiKa, a data-efficient family of expert-level alignment datasets. In particular, the PiKa-SFT dataset uses only 30k SFT examples, far fewer than state-of-the-art datasets like Magpie. Through evaluations by fine-tuning Llama-3-8B-Base on PiKa and other public datasets, we show that PiKa-SFT outperforms models trained on much larger data. On AlpacaEval 2.0 and Arena-Hard benchmarks, PiKa-SFT fine-tuning even surpasses the official Llama-3-8B-Instruct model trained on over 10 million proprietary examples. We further extend our study by training the Qwen2.5 series (0.5B to 7B) on PiKa-SFT, achieving consistent gains. These findings demonstrate that high-quality alignment can be achieved with significantly less data, offering a scalable path for open-source LLM alignment. Code and data: https://github.com/SJY8460/PiKa.

We propose expanding the shared Transformer module to produce and initialize Transformers of varying depths, enabling adaptation to diverse resource constraints. Drawing an analogy to genetic expansibility, we term such module as learngene. To identify the expansion mechanism, we delve into the relationship between the layer's position and its corresponding weight value, and find that linear function appropriately approximates this relationship. Building on this insight, we present Transformer as Linear Expansion of learnGene (TLEG), a novel approach for flexibly producing and initializing Transformers of diverse depths. Specifically, to learn learngene, we firstly construct an auxiliary Transformer linearly expanded from learngene, after which we train it through employing soft distillation. Subsequently, we can produce and initialize Transformers of varying depths via linearly expanding the well-trained learngene, thereby supporting diverse downstream scenarios. Extensive experiments on ImageNet-1K demonstrate that TLEG achieves comparable or better performance in contrast to many individual models trained from scratch, while reducing around 2x training cost. When transferring to several downstream classification datasets, TLEG surpasses existing initialization methods by a large margin (e.g., +6.87% on iNat 2019 and +7.66% on CIFAR-100). Under the situation where we need to produce models of varying depths adapting for different resource constraints, TLEG achieves comparable results while reducing around 19x parameters stored to initialize these models and around 5x pre-training costs, in contrast to the pre-training and fine-tuning approach. When transferring a fixed set of parameters to initialize different models, TLEG presents better flexibility and competitive performance while reducing around 2.9x parameters stored to initialize, compared to the pre-training approach.

Prior-data fitted networks (PFNs) were recently proposed as a new paradigm for machine learning. Instead of training the network to an observed training set, a fixed model is pre-trained offline on small, simulated training sets from a variety of tasks. The pre-trained model is then used to infer class probabilities in-context on fresh training sets with arbitrary size and distribution. Empirically, PFNs achieve state-of-the-art performance on tasks with similar size to the ones used in pre-training. Surprisingly, their accuracy further improves when passed larger data sets during inference. This article establishes a theoretical foundation for PFNs and illuminates the statistical mechanisms governing their behavior. While PFNs are motivated by Bayesian ideas, a purely frequentistic interpretation of PFNs as pre-tuned, but untrained predictors explains their behavior. A predictor's variance vanishes if its sensitivity to individual training samples does and the bias vanishes only if it is appropriately localized around the test feature. The transformer architecture used in current PFN implementations ensures only the former. These findings shall prove useful for designing architectures with favorable empirical behavior.

Supervised fine-tuning (SFT) is crucial in adapting large language models (LLMs) to a specific domain or task. However, only a limited amount of labeled data is available in practical applications, which poses a severe challenge for SFT in yielding satisfactory results. Therefore, a data-efficient framework that can fully exploit labeled and unlabeled data for LLM fine-tuning is highly anticipated. Towards this end, we introduce a semi-supervised fine-tuning framework named SemiEvol for LLM adaptation from a propagate-and-select manner. For knowledge propagation, SemiEvol adopts a bi-level approach, propagating knowledge from labeled data to unlabeled data through both in-weight and in-context methods. For knowledge selection, SemiEvol incorporates a collaborative learning mechanism, selecting higher-quality pseudo-response samples. We conducted experiments using GPT-4o-mini and Llama-3.1 on seven general or domain-specific datasets, demonstrating significant improvements in model performance on target data. Furthermore, we compared SemiEvol with SFT and self-evolution methods, highlighting its practicality in hybrid data scenarios.

Reinforcement Learning from Human Feedback (RLHF) has become the standard for aligning Large Language Models (LLMs), yet its efficacy is bottlenecked by the high cost of acquiring preference data, especially in low-resource and expert domains. To address this, we introduce ACTIVEULTRAFEEDBACK, a modular active learning pipeline that leverages uncertainty estimates to dynamically identify the most informative responses for annotation. Our pipeline facilitates the systematic evaluation of standard response selection methods alongside DOUBLE REVERSE THOMPSON SAMPLING (DRTS) and DELTAUCB, two novel methods prioritizing response pairs with large predicted quality gaps, leveraging recent results showing that such pairs provide good signals for fine-tuning. Our experiments demonstrate that ACTIVEULTRAFEEDBACK yields high-quality datasets that lead to significant improvements in downstream performance, notably achieving comparable or superior results with as little as one-sixth of the annotated data relative to static baselines. Our pipeline is available at https://github.com/lasgroup/ActiveUltraFeedback and our preference datasets at https://huggingface.co/ActiveUltraFeedback.

This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential evolutionary knowledge from the universe of natural protein sequences, to acquire an immediate capability to design preferable protein sequences for given folds. We conduct a structural surgery on pLMs, where a lightweight structural adapter is implanted into pLMs and endows it with structural awareness. During inference, iterative refinement is performed to effectively optimize the generated protein sequences. Experiments show that LM-Design improves the state-of-the-art results by a large margin, leading to up to 4% to 12% accuracy gains in sequence recovery (e.g., 55.65%/56.63% on CATH 4.2/4.3 single-chain benchmarks, and >60% when designing protein complexes). We provide extensive and in-depth analyses, which verify that LM-Design can (1) indeed leverage both structural and sequential knowledge to accurately handle structurally non-deterministic regions, (2) benefit from scaling data and model size, and (3) generalize to other proteins (e.g., antibodies and de novo proteins)

There have been various types of pretraining architectures including autoencoding models (e.g., BERT), autoregressive models (e.g., GPT), and encoder-decoder models (e.g., T5). However, none of the pretraining frameworks performs the best for all tasks of three main categories including natural language understanding (NLU), unconditional generation, and conditional generation. We propose a General Language Model (GLM) based on autoregressive blank infilling to address this challenge. GLM improves blank filling pretraining by adding 2D positional encodings and allowing an arbitrary order to predict spans, which results in performance gains over BERT and T5 on NLU tasks. Meanwhile, GLM can be pretrained for different types of tasks by varying the number and lengths of blanks. On a wide range of tasks across NLU, conditional and unconditional generation, GLM outperforms BERT, T5, and GPT given the same model sizes and data, and achieves the best performance from a single pretrained model with 1.25x parameters of BERT Large , demonstrating its generalizability to different downstream tasks.