Single-cell RNA sequencing (scRNA-seq) enables the study of cellular heterogeneity. Yet, clustering accuracy, and with it downstream analyses based on cell labels, remain challenging due to measurement noise and biological variability. In standard latent spaces (e.g., obtained through PCA), data from different cell types can be projected close together, making accurate clustering difficult. We introduce a latent plug-and-play diffusion framework that separates the observation and denoising space. This separation is operationalized through a novel Gibbs sampling procedure: the learned diffusion prior is applied in a low-dimensional latent space to perform denoising, while to steer this process, noise is reintroduced into the original high-dimensional observation space. This unique "input-space steering" ensures the denoising trajectory remains faithful to the original data structure. Our approach offers three key advantages: (1) adaptive noise handling via a tunable balance between prior and observed data; (2) uncertainty quantification through principled uncertainty estimates for downstream analysis; and (3) generalizable denoising by leveraging clean reference data to denoise noisier datasets, and via averaging, improve quality beyond the training set. We evaluate robustness on both synthetic and real single-cell genomics data. Our method improves clustering accuracy on synthetic data across varied noise levels and dataset shifts. On real-world single-cell data, our method demonstrates improved biological coherence in the resulting cell clusters, with cluster boundaries that better align with known cell type markers and developmental trajectories.

Visualization, a domain-specific yet widely used form of imagery, is an effective way to turn complex datasets into intuitive insights, and its value depends on whether data are faithfully represented, clearly communicated, and aesthetically designed. However, evaluating visualization quality is challenging: unlike natural images, it requires simultaneous judgment across data encoding accuracy, information expressiveness, and visual aesthetics. Although multimodal large language models (MLLMs) have shown promising performance in aesthetic assessment of natural images, no systematic benchmark exists for measuring their capabilities in evaluating visualizations. To address this, we propose VisJudge-Bench, the first comprehensive benchmark for evaluating MLLMs' performance in assessing visualization aesthetics and quality. It contains 3,090 expert-annotated samples from real-world scenarios, covering single visualizations, multiple visualizations, and dashboards across 32 chart types. Systematic testing on this benchmark reveals that even the most advanced MLLMs (such as GPT-5) still exhibit significant gaps compared to human experts in judgment, with a Mean Absolute Error (MAE) of 0.553 and a correlation with human ratings of only 0.428. To address this issue, we propose VisJudge, a model specifically designed for visualization aesthetics and quality assessment. Experimental results demonstrate that VisJudge significantly narrows the gap with human judgment, reducing the MAE to 0.421 (a 23.9% reduction) and increasing the consistency with human experts to 0.687 (a 60.5% improvement) compared to GPT-5. The benchmark is available at https://github.com/HKUSTDial/VisJudgeBench.

Large language models remain vulnerable to jailbreak attacks that bypass safety guardrails to elicit harmful outputs. Defending against novel jailbreaks represents a critical challenge in AI safety. Adversarial training -- designed to make models robust against worst-case perturbations -- has been the dominant paradigm for adversarial robustness. However, due to optimization challenges and difficulties in defining realistic threat models, adversarial training methods often fail on newly developed jailbreaks in practice. This paper proposes a new paradigm for improving robustness against unseen jailbreaks, centered on the Adversarial Déjà Vu hypothesis: novel jailbreaks are not fundamentally new, but largely recombinations of adversarial skills from previous attacks. We study this hypothesis through a large-scale analysis of 32 attack papers published over two years. Using an automated pipeline, we extract and compress adversarial skills into a sparse dictionary of primitives, with LLMs generating human-readable descriptions. Our analysis reveals that unseen attacks can be effectively explained as sparse compositions of earlier skills, with explanatory power increasing monotonically as skill coverage grows. Guided by this insight, we introduce Adversarial Skill Compositional Training (ASCoT), which trains on diverse compositions of skill primitives rather than isolated attack instances. ASCoT substantially improves robustness to unseen attacks, including multi-turn jailbreaks, while maintaining low over-refusal rates. We also demonstrate that expanding adversarial skill coverage, not just data scale, is key to defending against novel attacks. \textcolor{red}{\textbf{Warning: This paper contains content that may be harmful or offensive in nature.

Many Swedish benchmarks are translations of US-centric benchmarks and are therefore not suitable for testing knowledge that is particularly relevant, or even specific, to Sweden. We therefore introduce a manually written question-answering benchmark specifically targeted at Sweden-related personalities and events, many of which receive very limited coverage in international media. Our annotators drew inspiration from a popular radio program featuring public figures from culture and media, as well as major sports events in Sweden. The dataset can be used to measure factual recall across models of varying sizes and degrees of Swedish coverage, and allows probing of cross-lingual factual consistency, as it contains English translations. Using the dataset, we find that smaller models with stronger Swedish coverage perform comparably to a multilingual model three times larger in recalling Sweden-related facts. We also observe that continued pre-training on Swedish generally improves factual knowledge but leads to partial forgetting of previously known information. These results demonstrate the dataset's potential as a diagnostic tool for studying language adaptation and knowledge retention in multilingual models during language adaptation.

Behavior Foundation Models (BFMs) are capable of retrieving high-performing policy for any reward function specified directly at test-time, commonly referred to as zero-shot reinforcement learning (RL). While this is a very efficient process in terms of compute, it can be less so in terms of data: as a standard assumption, BFMs require computing rewards over a non-negligible inference dataset, assuming either access to a functional form of rewards, or significant labeling efforts. To alleviate these limitations, we tackle the problem of task inference purely through interaction with the environment at test-time. We propose OpTI-BFM, an optimistic decision criterion that directly models uncertainty over reward functions and guides BFMs in data collection for task inference. Formally, we provide a regret bound for well-trained BFMs through a direct connection to upper-confidence algorithms for linear bandits. Empirically, we evaluate OpTI-BFM on established zero-shot benchmarks, and observe that it enables successor-features-based BFMs to identify and optimize an unseen reward function in a handful of episodes with minimal compute overhead. Code is available at https://github.com/ThomasRupf/opti-bfm.

Tool calling has become increasingly popular for Large Language Models (LLMs). However, for large tool sets, the resulting tokens would exceed the LLM's context window limit, making it impossible to include every tool. Hence, an external retriever is used to provide LLMs with the most relevant tools for a query. Existing retrieval models rank tools based on the similarity between a user query and a tool description (TD). This leads to suboptimal retrieval as user requests are often poorly aligned with the language of TD. To remedy the issue, we propose ToolDreamer, a framework to condition retriever models to fetch tools based on hypothetical (synthetic) TD generated using an LLM, i.e., description of tools that the LLM feels will be potentially useful for the query. The framework enables a more natural alignment between queries and tools within the language space of TD's. We apply ToolDreamer on the ToolRet dataset and show that our method improves the performance of sparse and dense retrievers with and without training, thus showcasing its flexibility. Through our proposed framework, our aim is to offload a portion of the reasoning burden to the retriever so that the LLM may effectively handle a large collection of tools without inundating its context window.

Large language models (LLMs) demonstrate strong potential as autonomous agents, with promising capabilities in reasoning, tool use, and sequential decision-making. While prior benchmarks have evaluated LLM agents in various domains, the financial domain remains underexplored, despite its significant economic value and complex reasoning requirements. Most existing financial benchmarks focus on static question-answering, failing to capture the dynamics of real-market trading. To address this gap, we introduce STOCKBENCH, a contamination-free benchmark designed to evaluate LLM agents in realistic, multi-month stock trading environments. Agents receive daily market signals -- including prices, fundamentals, and news -- and make sequential buy, sell, or hold decisions. Performance is measured using financial metrics such as cumulative return, maximum drawdown, and the Sortino ratio, capturing both profitability and risk management. We evaluate a wide range of state-of-the-art proprietary and open-source LLMs. Surprisingly, most models struggle to outperform the simple buy-and-hold baseline, while some models demonstrate the potential to achieve higher returns and stronger risk management. These findings highlight both the challenges and opportunities of LLM-based trading agents, showing that strong performance on static financial question-answering do not necessarily translate into effective trading behavior. We release STOCKBENCH as an open-source benchmark to enable future research on LLM-driven financial agents.

Reward hacking, where a reasoning model exploits loopholes in a reward function to achieve high rewards without solving the intended task, poses a significant threat. This behavior may be explicit, i.e. verbalized in the model's chain-of-thought (CoT), or implicit, where the CoT appears benign thus bypasses CoT monitors. To detect implicit reward hacking, we propose TRACE (Truncated Reasoning AUC Evaluation). Our key observation is that hacking occurs when exploiting the loophole is easier than solving the actual task. This means that the model is using less 'effort' than required to achieve high reward. TRACE quantifies effort by measuring how early a model's reasoning becomes sufficient to obtain the reward. We progressively truncate a model's CoT at various lengths, force the model to answer, and estimate the expected reward at each cutoff. A hacking model, which takes a shortcut, will achieve a high expected reward with only a small fraction of its CoT, yielding a large area under the accuracy-vs-length curve. TRACE achieves over 65% gains over our strongest 72B CoT monitor in math reasoning, and over 30% gains over a 32B monitor in coding. We further show that TRACE can discover unknown loopholes during training. Overall, TRACE offers a scalable unsupervised approach for oversight where current monitoring methods prove ineffective.

Computational imaging methods increasingly rely on powerful generative diffusion models to tackle challenging image restoration tasks. In particular, state-of-the-art zero-shot image inverse solvers leverage distilled text-to-image latent diffusion models (LDMs) to achieve unprecedented accuracy and perceptual quality with high computational efficiency. However, extending these advances to high-definition video restoration remains a significant challenge, due to the need to recover fine spatial detail while capturing subtle temporal dependencies. Consequently, methods that naively apply image-based LDM priors on a frame-by-frame basis often result in temporally inconsistent reconstructions. We address this challenge by leveraging recent advances in Video Consistency Models (VCMs), which distill video latent diffusion models into fast generators that explicitly capture temporal causality. Building on this foundation, we propose LVTINO, the first zero-shot or plug-and-play inverse solver for high definition video restoration with priors encoded by VCMs. Our conditioning mechanism bypasses the need for automatic differentiation and achieves state-of-the-art video reconstruction quality with only a few neural function evaluations, while ensuring strong measurement consistency and smooth temporal transitions across frames. Extensive experiments on a diverse set of video inverse problems show significant perceptual improvements over current state-of-the-art methods that apply image LDMs frame by frame, establishing a new benchmark in both reconstruction fidelity and computational efficiency. The code is available on GitHub.

Learning the dynamics of a process given sampled observations at several time points is an important but difficult task in many scientific applications. When no ground-truth trajectories are available, but one has only snapshots of data taken at discrete time steps, the problem of modelling the dynamics, and thus inferring the underlying trajectories, can be solved by multi-marginal generalisations of flow matching algorithms. This paper proposes a novel flow matching method that overcomes the limitations of existing multi-marginal trajectory inference algorithms. Our proposed method, ALI-CFM, uses a GAN-inspired adversarial loss to fit neurally parametrised interpolant curves between source and target points such that the marginal distributions at intermediate time points are close to the observed distributions. The resulting interpolants are smooth trajectories that, as we show, are unique under mild assumptions. These interpolants are subsequently marginalised by a flow matching algorithm, yielding a trained vector field for the underlying dynamics. We showcase the versatility and scalability of our method by outperforming the existing baselines on spatial transcriptomics and cell tracking datasets, while performing on par with them on single-cell trajectory prediction. Code: https://github.com/mmacosha/adversarially-learned-interpolants.

The Schrödinger bridge problem is concerned with finding a stochastic dynamical system bridging two marginal distributions that minimises a certain transportation cost. This problem, which represents a generalisation of optimal transport to the stochastic case, has received attention due to its connections to diffusion models and flow matching, as well as its applications in the natural sciences. However, all existing algorithms allow to infer such dynamics only for cases where samples from both distributions are available. In this paper, we propose the first general method for modelling Schrödinger bridges when one (or both) distributions are given by their unnormalised densities, with no access to data samples. Our algorithm relies on a generalisation of the iterative proportional fitting (IPF) procedure to the data-free case, inspired by recent developments in off-policy reinforcement learning for training of diffusion samplers. We demonstrate the efficacy of the proposed data-to-energy IPF on synthetic problems, finding that it can successfully learn transports between multimodal distributions. As a secondary consequence of our reinforcement learning formulation, which assumes a fixed time discretisation scheme for the dynamics, we find that existing data-to-data Schrödinger bridge algorithms can be substantially improved by learning the diffusion coefficient of the dynamics. Finally, we apply the newly developed algorithm to the problem of sampling posterior distributions in latent spaces of generative models, thus creating a data-free image-to-image translation method. Code: https://github.com/mmacosha/d2e-stochastic-dynamics

As Generative AI (GenAI) systems see growing adoption, a key concern involves the external validity of evaluations, or the extent to which they generalize from lab-based to real-world deployment conditions. Threats to the external validity of GenAI evaluations arise when the source sample of human raters and system outputs used to obtain a system quality estimate differs from the target distribution at deployment time. In this work, we propose a doubly-robust estimation framework designed to address this evaluation sampling bias. Key to our approach is the use of "persona" ratings produced by prompting an LLM evaluator (i.e., an LLM-as-a-judge) to behave as a human rater with specific sociodemographic characteristics. Our doubly-robust framework combines these informative yet imperfect persona ratings with human ratings obtained under evaluation sampling bias to produce statistically valid system quality estimates. In particular, we show that our approach yields valid system quality estimates when either (i) a model trained to predict human ratings using persona ratings and source data observed under sampling bias, or (ii) a reweighting model that corrects for sampling bias is of sufficient quality. We validate our framework theoretically and via a novel Persona Simulation Framework (PSF) designed to systematically manipulate persona quality and the degree of evaluation sampling bias present in source data. Our work provides a principled foundation for combining imperfect persona ratings with human ratings observed under sampling bias to obtain valid system quality estimates.

Flow matching has emerged as a competitive framework for learning high-quality generative policies in robotics; however, we find that generalisation arises and saturates early along the flow trajectory, in accordance with recent findings in the literature. We further observe that increasing the number of Euler integration steps during inference counter-intuitively and universally degrades policy performance. We attribute this to (i) additional, uniformly spaced integration steps oversample the late-time region, thereby constraining actions towards the training trajectories and reducing generalisation; and (ii) the learned velocity field becoming non-Lipschitz as integration time approaches 1, causing instability. To address these issues, we propose a novel policy that utilises non-uniform time scheduling (e.g., U-shaped) during training, which emphasises both early and late temporal stages to regularise policy training, and a dense-jump integration schedule at inference, which uses a single-step integration to replace the multi-step integration beyond a jump point, to avoid unstable areas around 1. Essentially, our policy is an efficient one-step learner that still pushes forward performance through multi-step integration, yielding up to 23.7% performance gains over state-of-the-art baselines across diverse robotic tasks.

We present a learnable physics-based predictive model that provides accurate motion and force-torque prediction of the robot end effector in contact-rich manipulation. The proposed model extends the state-of-the-art GNN-based simulator (FIGNet) with novel node and edge types, enabling action-conditional predictions for control and state estimation in the context of robotic peg insertion. Our model learns in a self-supervised manner, using only joint encoder and force-torque data while the robot is touching the environment. In simulation, the MPC agent using our model matches the performance of the same controller with the ground truth dynamics model in a challenging peg-in-hole task, while in the real-world experiment, our model achieves a 50$\%$ improvement in motion prediction accuracy and 3$\times$ increase in force-torque prediction precision over the baseline physics simulator. Finally, we apply the model to track the robot end effector with a particle filter during real-world peg insertion, demonstrating a practical application of its predictive accuracy.

Autonomous-driving perception systems require robust Multi-Object Tracking (MOT) to operate reliably in dynamic environments. MOT maintains consistent object identities across frames while preserving spatial accuracy. Recent foundation models, such as SAM2, provide promptable video segmentation without task-specific fine-tuning. However, their direct application to Multi-Object Tracking and Segmentation (MOTS) remains limited by the absence of explicit identity management mechanisms and by growing memory requirements during tracking. This work introduces Seg2Track-SAM2, a framework that integrates pretrained object detectors with SAM2 and a dedicated Seg2Track module to support track initialization, data association, and track refinement. The method operates without dataset-specific fine-tuning and remains detector-agnostic. Experimental evaluation on the KITTI MOTS and MOTS Challenge benchmarks shows that Seg2Track-SAM2 ranks fourth overall in both datasets while achieving the highest association accuracy (AssA) among compared methods. In addition, a sliding-window memory strategy reduces memory usage by up to 75% with minimal impact on tracking performance, enabling deployment under resource constraints. Together, these results indicate that Seg2Track-SAM2 improves identity consistency and memory efficiency in MOTS without requiring dataset-specific training. The code is available at https://github.com/hcmr-lab/Seg2Track-SAM2.

Large language models (LLMs) serve as an active and promising field of generative artificial intelligence and have demonstrated abilities to perform complex tasks in multiple domains, including mathematical and scientific reasoning. In this work, we construct a novel agent framework for solving representative problems in scientific computing. The proposed agent, incorporating a "rewriting-resolution-review-revision" logical chain via three reasoning LLMs (functioning as the Consultant, Reviewer, and Programmer, respectively), is integrated in a collaborative and interactive manner. The Consultant module endows the agent with knowledge transfer capabilities to link problems to professional domain insights, thereby rewriting problem descriptions through text augmentation. The Programmer module is responsible for generating and executing well-structured code to deliver the problem resolution. The Reviewer module equips the agent with the capacity for self-debugging and self-refinement through interactive feedback with code runtime outputs. By leveraging the end-to-end review mechanism, the executable code provided by the Programmer attains the iterative revision. A comprehensive evaluation is conducted on the performance of the proposed agent framework in solving partial differential equations (PDEs), ill-conditioned linear systems, and data-driven physical analysis problems. Compared to single-model, this collaborative framework significantly improves the bug-free code generation rate and reduces the occurrence of non-physical solutions, thereby establishing a highly reliable framework for autonomous code generation based on natural language descriptions. The review mechanism improved the average execution success rate of the modern reasoning models. Our code is available at https://github.com/ChengAo21/Re4_Sci_Agent

Accurate 3D medical image segmentation requires a delicate balance between fine-grained local details and global contextual understanding. While spatial-domain models often struggle with long-range dependencies, existing frequency-based approaches frequently overlook intrinsic spectral properties such as Hermitian symmetry, leading to suboptimal feature integration. In this paper, we propose SSFMamba, a Mamba based Symmetry-driven Spatial-Frequency fusion framework tailored for 3D medical imaging. Our architecture employs a complementary dual-branch design: the spatial branch preserves intricate anatomical textures, while the frequency branch captures global contextual dependencies in the frequency domain. A core innovation is the 3D Multi-Directional Scanning Mechanism (MDSM), which integrates Hermitian symmetry with the causal nature of State Space Models (SSMs) to enable direction-aware global modeling. Crucially, by shifting the modeling focus to frequency-domain spectral components, SSFMamba captures the underlying structural characteristics of anatomical tissues. This leads to a highly adaptable framework that excels in both MRI and CT applications, regardless of the significant variations in intensity distributions. Extensive evaluations on the BraTS2020, BraTS2023, and BTCV datasets demonstrate that SSFMamba consistently outperforms state-of-the-art methods. Notably, our approach achieves exceptional performance on low-contrast organs such as the pancreas (81.97% Dice), underscoring its potential as a unified and physically consistent perception framework for diverse 3D clinical applications.

Maximum A Posteriori (MAP) estimation is a cornerstone framework for blind inverse problems, where an image and a forward operator are jointly estimated as the maximizers of a posterior distribution. In this paper, we analyze the recovery guarantees of MAP-based methods by adopting a Morse-Bott framework. We model the image prior potential as a Morse-Bott function, where natural images are modeled as residing locally on a critical submanifold. This means that while the potential is locally flat along the natural directions of the image manifold, it is strictly convex in the directions normal to it. We demonstrate that this Morse-Bott hypothesis aligns with the structural properties of state-of-the-art learned priors, a finding we validate through an experimental analysis of the potential landscape and its Hessian spectrum. Our theoretical results show that, in a neighborhood of the ground-truth image and operator, the posterior admits local minimizers that are stable both with respect to initialization (gradient steps converge to the same minimizer) and to small noise perturbations (solutions vary smoothly). This local stability explains the empirical success of well-designed gradient-based optimization in these settings. However, we also demonstrate that this stability is a local property: the blurry trap, well-known for sparse priors in blind deconvolution, persists even with state-of-the-art learned priors. Our findings demonstrate that the failure of MAP in blind deconvolution is not a limitation of prior quality, but an intrinsic characteristic of the landscape. We conclude that successful recovery of posterior maximization depends on strategic initialization within the basin of favorable local minima, and we validate this with numerical experiments on both synthetic and real-world data.

While diffusion models excel at image generation, their growing adoption raises critical concerns about copyright issues and model transparency. Existing attribution methods identify training examples influencing an entire image, but fall short in isolating contributions to specific elements, such as styles or objects, that are of primary concern to stakeholders. To address this gap, we introduce concept-level attribution through a novel method called Concept-TRAK, which extends influence functions with a key innovation: specialized training and utility loss functions designed to isolate concept-specific influences rather than overall reconstruction quality. We evaluate Concept-TRAK on novel concept attribution benchmarks using Synthetic and CelebA-HQ datasets, as well as the established AbC benchmark, showing substantial improvements over prior methods in concept-level attribution scenarios. We further demonstrate its versatility on real-world text-to-image generation with compositional and multi-concept prompts.

Recent advances in reinforcement learning have shown that language models can develop sophisticated reasoning through training on tasks with verifiable rewards, but these approaches depend on human-curated problem-answer pairs and domain-specific reward engineering. We introduce SPIRAL, a self-play framework where models learn by playing multi-turn, zero-sum games against continuously improving versions of themselves, generating an automatic curriculum of stronger opponents, and eliminating the need for human supervision. To enable this self-play training at scale, we implement a fully online, multi-turn, multi-agent reinforcement learning system for LLMs and propose role-conditioned advantage estimation (RAE) to stabilize multi-agent training. SPIRAL produces reasoning capabilities that transfer broadly, improving performance by up to 10% across a suite of 8 reasoning benchmarks on 4 different models spanning Qwen and Llama model families, outperforming supervised fine-tuning on 25,000 expert game trajectories. Multi-game training (TicTacToe, Kuhn Poker, Simple Negotiation) yields the strongest results, with improvements observed across both base and instruction-tuned models. Analysis of chain-of-thought traces reveals that games develop distinct cognitive patterns that transfer to improve reasoning performance, with different games developing complementary strengths. Even models which have already been trained on reasoning tasks using RLVR, like DeepSeek-R1-Distill-Qwen-7B, still benefit from our approach. These results demonstrate that zero-sum games naturally develop transferable reasoning capabilities across diverse model architectures and training stages, highlighting a promising direction for autonomous reasoning development. Our code can be found in https://github.com/spiral-rl/spiral.

Process or step-wise supervision has played a crucial role in advancing complex multi-step reasoning capabilities of Large Language Models (LLMs). However, efficient, high-quality automated process annotation remains a significant challenge. To address this, we introduce Single-Pass Annotation with Reference-Guided Evaluation (SPARE), a novel structured framework that enables efficient per-step annotation by jointly aligning solution steps to reference solutions and determine its accuracy with explicit reasoning in single generation. We demonstrate SPARE's effectiveness across four diverse datasets spanning mathematical reasoning (GSM8K, MATH), multi-hop question answering (MuSiQue-Ans), and spatial reasoning (SpaRP), showing consistent improvements in two applications: (1) training Process Reward Models (PRMs) for ranking and aggregating multiple generations, and (2) fine-tuning models via offline reinforcement learning for greedy decoding. On ProcessBench, SPARE demonstrates data-efficient out-of-distribution generalization, using only $\sim$16% of training samples compared to human-labeled and other synthetically trained baselines. Additionally, it achieves competitive performance with MCTS-based methods while offering 2.3$\times$ speedup in terms of total token count. Manual analysis reveals complementary precision-recall characteristics with MCTS approaches, suggesting potential for ensemble methods. These results establish SPARE as a practical and scalable solution for automatic process supervision in LLM reasoning.

The de novo design of ligand-binding proteins with tailored functions is essential for advancing biotechnology and molecular medicine, yet existing AI approaches are limited by scarce protein-ligand complex data. To circumvent this data bottleneck, we leverage the abundant natural language descriptions characterizing protein-ligand interactions. Here, we introduce InstructPro, a family of generative models that design proteins following the guidance of natural language instructions and ligand formulas. InstructPro produces protein sequences consistent with specified function descriptions and ligand targets. To enable training and evaluation, we develop InstructProBench, a large-scale dataset of 9.6 million (function description, ligand, protein) triples. We train two model variants -- InstructPro-1B and InstructPro-3B -- that substantially outperform strong baselines. InstructPro-1B achieves an AlphaFold3 ipTM of 0.918 and a binding affinity of -8.764 on seen ligands, while maintaining robust performance in a zero-shot setting with scores of 0.869 and -6.713, respectively. These results are accompanied by novelty scores of 70.1% and 68.8%, underscoring the model's ability to generalize beyond the training set. Furthermore, the model yields a superior binding free energy of -20.9 kcal/mol and an average of 5.82 intermolecular hydrogen bonds, validating its proficiency in designing high-affinity ligand-binding proteins. Notably, scaling to InstructPro-3B further improves the zero-shot ipTM to 0.882, binding affinity to -6.797, and binding free energy to -25.8 kcal/mol, demonstrating clear performance gains associated with increased model capacity. These findings highlight the power of natural language-guided generative models to mitigate the data bottlenecks in traditional structure-based methods, significantly broadening the scope of de novo protein design.

Predicting the intermediate trajectories between an initial and target distribution is a central problem in generative modeling. Existing approaches, such as flow matching and Schrödinger bridge matching, effectively learn mappings between two distributions by modeling a single stochastic path. However, these methods are inherently limited to unimodal transitions and cannot capture branched or divergent evolution from a common origin to multiple distinct modes. To address this, we introduce Branched Schrödinger Bridge Matching (BranchSBM), a novel framework that learns branched Schrödinger bridges. BranchSBM parameterizes multiple time-dependent velocity fields and growth processes, enabling the representation of population-level divergence into multiple terminal distributions. We show that BranchSBM is not only more expressive but also essential for tasks involving multi-path surface navigation, modeling cell fate bifurcations from homogeneous progenitor states, and simulating diverging cellular responses to perturbations.

Understanding the implicit bias of optimization algorithms is key to explaining and improving the generalization of deep models. The hyperbolic implicit bias induced by pointwise overparameterization promotes sparsity, but also yields a small inverse Riemannian metric near zero, slowing down parameter movement and impeding meaningful parameter sign flips. To overcome this obstacle, we propose Hyperbolic Aware Minimization (HAM), which alternates a standard optimizer step with a lightweight hyperbolic mirror step. The mirror step incurs less compute and memory than pointwise overparameterization, reproduces its beneficial hyperbolic geometry for feature learning, and mitigates the small-inverse-metric bottleneck. Our characterization of the implicit bias in the context of underdetermined linear regression provides insights into the mechanism how HAM consistently increases performance --even in the case of dense training, as we demonstrate in experiments with standard vision benchmarks. HAM is especially effective in combination with different sparsification methods, advancing the state of the art.

Large Language Models (LLMs) have achieved remarkable success in complex reasoning tasks, but their inference remains computationally inefficient. We observe a common failure mode in many prevalent LLMs, overthinking, where models generate verbose and tangential reasoning traces even for simple queries. Recent work has tried to mitigate this by enforcing fixed token budgets, however, this can lead to underthinking, especially on harder problems. Through empirical analysis, we identify that this inefficiency often stems from unclear problem-solving strategies. To formalize this, we develop a theoretical model, BAM (Budget Allocation Model), which models reasoning as a sequence of sub-questions with varying uncertainty, and introduce the E3 metric to capture the trade-off between correctness and computation efficiency. Building on theoretical results from BAM, we propose Plan-and-Budget, a model-agnostic, test-time framework that decomposes complex queries into sub-questions and allocates token budgets based on estimated complexity using adaptive scheduling. Plan-and-Budget improves reasoning efficiency across a range of tasks and models, achieving up to 70% accuracy gains, 39% token reduction, and 193.8% improvement in E3. Notably, it improves the efficiency of a smaller model (DS-Qwen-32B) to match the efficiency of a larger model (DS-LLaMA-70B), demonstrating Plan-and-Budget's ability to close performance gaps without retraining. Our code is available at https://github.com/junhongmit/P-and-B.

Few-shot Whole Slide Image (WSI) classification is severely hampered by overfitting. We argue that this is not merely a data-scarcity issue but a fundamentally geometric problem. Grounded in the manifold hypothesis, our analysis shows that features from pathology foundation models exhibit a low-dimensional manifold geometry that is easily perturbed by downstream models. This insight reveals a key potential issue in downstream multiple instance learning models: linear layers are geometry-agnostic and, as we show empirically, can distort the manifold geometry of the features. To address this, we propose the Manifold Residual (MR) block, a plug-and-play module that is explicitly geometry-aware. The MR block reframes the linear layer as residual learning and decouples it into two pathways: (1) a fixed, random matrix serving as a geometric anchor that approximately preserves topology while also acting as a spectral shaper to sharpen the feature spectrum; and (2) a trainable, low-rank residual pathway that acts as a residual learner for task-specific adaptation, with its structural bottleneck explicitly mirroring the low effective rank of the features. This decoupling imposes a structured inductive bias and reduces learning to a simpler residual fitting task. Through extensive experiments, we demonstrate that our approach achieves state-of-the-art results with significantly fewer parameters, offering a new paradigm for few-shot WSI classification. Code is available in https://github.com/BearCleverProud/MR-Block.

This paper explores the challenges of integrating tactile sensing into intelligent systems for multimodal reasoning, particularly in enabling commonsense reasoning about the open-ended physical world. We identify two key challenges: modality discrepancy, where existing large touch-language models often treat touch as a mere sub-modality of language, and open-ended tactile data scarcity, where current datasets lack the diversity, open-endness and complexity needed for reasoning. To overcome these challenges, we introduce SToLa, a Self-Adaptive Touch-Language framework. SToLa utilizes Mixture of Experts (MoE) to dynamically process, unify, and manage tactile and language modalities, capturing their unique characteristics. Crucially, we also present a comprehensive tactile commonsense reasoning dataset and benchmark featuring free-form questions and responses, 8 physical properties, 4 interactive characteristics, and diverse commonsense knowledge. Experiments show SToLa exhibits competitive performance compared to existing models on the PhysiCLeAR benchmark and self-constructed datasets, proving the effectiveness of the Mixture of Experts architecture in multimodal management and the performance advantages for open-scenario tactile commonsense reasoning tasks.

Radiology report generation is critical for efficiency but current models lack the structured reasoning of experts, hindering clinical trust and explainability by failing to link visual findings to precise anatomical locations. This paper introduces BoxMed-RL, a groundbreaking unified training framework for generating spatially verifiable and explainable radiology reports. Built on a large vision-language model, BoxMed-RL revolutionizes report generation through two integrated phases: (1) In the Pretraining Phase, we refine the model via medical concept learning, using Chain-of-Thought supervision to internalize the radiologist-like workflow, followed by spatially verifiable reinforcement, which applies reinforcement learning to align medical findings with bounding boxes. (2) In the Downstream Adapter Phase, we freeze the pretrained weights and train a downstream adapter to ensure fluent and clinically credible reports. This framework precisely mimics radiologists' workflow, compelling the model to connect high-level medical concepts with definitive anatomical evidence. Extensive experiments on public datasets demonstrate that BoxMed-RL achieves an average 7% improvement in both METEOR and ROUGE-L metrics compared to state-of-the-art methods. An average 5% improvement in large language model-based metrics further underscores BoxMed-RL's robustness in generating high-quality radiology reports.

Mixture of Experts (MoE) models enhance neural network scalability by dynamically selecting relevant experts per input token, enabling larger model sizes while maintaining manageable computation costs. However, efficient training of large-scale MoE models across thousands of GPUs presents significant challenges due to limitations in existing parallelism strategies. We introduce an end-to-end training framework for large-scale MoE models that utilizes five-dimensional hybrid parallelism: Tensor Parallelism, Expert Parallelism, Context Parallelism, Data Parallelism, and Pipeline Parallelism. Central to our approach is MoE Parallel Folding, a novel strategy that decouples the parallelization of attention and MoE layers in Transformer models, allowing each layer type to adopt optimal parallel configurations. Additionally, we develop a flexible token-level dispatcher that supports both token-dropping and token-dropless MoE training across all five dimensions of parallelism. This dispatcher accommodates dynamic tensor shapes and coordinates different parallelism schemes for Attention and MoE layers, facilitating complex parallelism implementations. Our experiments demonstrate significant improvements in training efficiency and scalability. We achieve up to 49.3% Model Flops Utilization (MFU) for the Mixtral 8x22B model and 39.0% MFU for the Qwen2-57B-A14B model on H100 GPUs, outperforming existing methods. The framework scales efficiently up to 1,024 GPUs and maintains high performance with sequence lengths up to 128K tokens, validating its effectiveness for large-scale MoE model training. The code is available in Megatron-Core.

In this paper, we present a comprehensive analysis and monitoring framework for the impact of Large Language Models (LLMs) on Wikipedia, examining the evolution of Wikipedia through existing data and using simulations to explore potential risks. We begin by analyzing article content and page views to study the recent changes in Wikipedia and assess the impact of LLMs. Subsequently, we evaluate how LLMs affect various Natural Language Processing (NLP) tasks related to Wikipedia, including machine translation and retrieval-augmented generation (RAG). Our findings and simulation results reveal that Wikipedia articles have been affected by LLMs, with an impact of approximately 1% in certain categories. If the machine translation benchmark based on Wikipedia is influenced by LLMs, the scores of the models may become inflated, and the comparative results among models could shift. Moreover, the effectiveness of RAG might decrease if the knowledge has been contaminated by LLMs. While LLMs have not yet fully changed Wikipedia's language and knowledge structures, we believe that our empirical findings signal the need for careful consideration of potential future risks in NLP research. We release all the experimental dataset and source code at: https://github.com/HSM316/LLM_Wikipedia