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General Machine Learning · Evaluation

Xiang Deng, Jeff Da, Edwin Pan, Yannis Yiming He, Charles Ide, Kanak Garg, Niklas Lauffer, Andrew Park, Chetan Rane, Karmini Sampath 等

We present SWE-Bench Pro, a comprehensive benchmark designed to evaluate software engineering capabilities through complex, realistic programming challenges. This benchmark extends beyond traditional algorithmic problems to encompass the full spectrum of professional software development tasks. The dataset comprises 1,865 problems sourced from 41 active software engineering repositories, spanning 123 unique programming languages and various application domains. The benchmark is structured into public and private components, with public access to problems from 11 repositories and private evaluation sets from 12 repositories across 4 distinct problem categories. SWE-Bench Pro addresses limitations of existing evaluation frameworks by incorporating problems that reflect real-world software engineering scenarios, including substantial codebases, complex enterprise applications, and multi-file projects requiring sophisticated reasoning and code modification skills. Problems range from early-stage startup environments to enterprise-level applications, with the private commercial set remaining inaccessible to maintain evaluation integrity while enabling public access to representative problems for professional development. Our evaluation methodology employs diverse coding approaches and models under controlled conditions, ensuring robust performance assessment across multiple programming paradigms. Results demonstrate significant performance variations across different problem categories, with traditional algorithmic challenges showing notably higher success rates compared to complex, multi-file engineering tasks. The benchmark reveals substantial gaps in current capabilities for handling real-world software engineering scenarios, particularly in areas requiring deep contextual understanding, cross-file reasoning, and integration with existing large-scale systems. This work contributes a more comprehensive and realistic evaluation framework for assessing software engineering capabilities, providing insights into current limitations and establishing a foundation for future development in automated software engineering tools and methodologies.

Deep Learning · Large Language Models

Niklas Lauffer, Xiang Deng, Srivatsa Kundurthy, Brad Kenstler, Jeff Da

A popular paradigm for training LM agents relies on imitation learning, fine-tuning on expert trajectories. However, we show that the off-policy nature of imitation learning for multi-turn LM agents suffers from the fundamental limitation known as covariate shift: as the student policy's behavior diverges from the expert's, it encounters states not present in the training data, reducing the effectiveness of fine-tuning. Taking inspiration from the classic DAgger algorithm, we propose a novel data generation methodology for addressing covariate shift for multi-turn LLM training. We introduce on-policy expert corrections (OECs), partially on-policy data generated by starting rollouts with a student model and then switching to an expert model part way through the trajectory. We explore the effectiveness of our data generation technique in the domain of software engineering (SWE) tasks, a multi-turn setting where LLM agents must interact with a development environment to fix software bugs. Our experiments compare OEC data against various other on-policy and imitation learning approaches on SWE agent problems and train models using a common rejection sampling (i.e., using environment reward) combined with supervised fine-tuning technique. Experiments find that OEC trajectories show a relative 14% and 13% improvement over traditional imitation learning in the 7b and 32b setting, respectively, on SWE-bench verified. Our results demonstrate the need for combining expert demonstrations with on-policy data for effective multi-turn LM agent training.

Deep Learning · Large Language Models

Muhan Gao, Zih-Ching Chen, Kuan-Hao Huang

As large language models (LLMs) are increasingly deployed in retrieval augmented generation (RAG) and agentic systems that accumulate extensive context, understanding how distracting information affects performance in long context becomes critical. Prior work shows that semantically relevant but misleading documents can cause performance degradation, yet the quantitative relationship between the proportion of distractors and performance remains unstudied. In this work, we systematically vary the proportion of hard distractors within fixed-length contexts, revealing a striking nonlinear pattern: as the proportion of hard distractors increases, performance drops sharply within the first small fraction, while the remainder of the range yields only marginal additional decline. We term this ''The First Drop of Ink'' effect, analogous to how a single drop of ink contaminates water. We provide both theoretical and empirical analysis grounded in attention mechanics: hard distractors disproportionately capture attention even at small proportions, with diminishing marginal impact as their proportion increases. Through controlled experiments, we further show that filtering yields performance gains primarily from context length reduction rather than distractor removal, and only achieves substantial recovery when hard distractor proportion is reduced to near zero, which highlights the importance of upstream retrieval precision.

Deep Learning · Self-Supervised Learning

Antonio Torralba, Yair Weiss

Why does contrastive learning with simple images and augmentations yield useful representations for downstream tasks? We answer this by analytically computing the optimal contrastive learning (CL) weights in simple one-hidden-layer CNNs using only dataset statistics. For a range of basic augmentations and any image dataset with stationary statistics, we prove that such CNNs trained with a contrastive loss learn sinusoidal first-layer filters. With augmentations that combine translation and adding noise, the CNN learns partial whitening of the input and measures frequency contrast: differences between power at frequencies with the same expected power. The selected frequencies and their weights can be computed using a simple “waterfilling” algorithm given the dataset’s expected power spectrum. Experiments with eight image datasets show that CNNs trained with SGD empirically learn partial whitening and the predicted frequency contrasts, and the usefulness of the learned representation for recognition depends on both the augmentations and the mismatch between the training and test power spectra.

Applications · Language, Speech and Dialog

Pengfei Zhang, Tianxin Xie, Yang Minghao, Li Liu

REPresentation Alignment (REPA) improves the training of generative flow models by aligning intermediate hidden states with pretrained teacher features, but its effectiveness in token-conditioned audio Flow Matching critically depends on the choice of supervised layers, which is typically made heuristically based on the depth. In this work, we introduce **A**ttribution-**G**uided **REP**resentation **A**lignment **(AG-REPA)**, a novel causal layer selection strategy for representation alignment in audio Flow Matching. Firstly, we find that layers that best store semantic/acoustic information (high teacher-space similarity) are not necessarily the layers that contribute most to the velocity field that drives generation, and we call it **S**tore-**C**ontribute **D**issociation **(SCD)**. To turn this insight into an actionable training guidance, we propose a forward-only gate ablation (FoG-A) that quantifies each layer's causal contribution via the induced change in the predicted velocity field, enabling sparse layer selection and adaptive weighting for alignment. Across unified speech and general-audio training (LibriSpeech + AudioSet) under different token-conditioning topologies, AG-REPA consistently outperforms REPA baselines. Overall, our results show that alignment is most effective when applied to the causally dominant layers that drive the velocity field, rather than to layers that are representationally rich but functionally passive.

Applications · Everything Else

Andrea Rubbi, Arpit Merchant, Samuel Ogden, Amir Akbarnejad, Pietro Lió, Sattar Vakili, Mohammad Lotfollahi

High-throughput gene perturbation experiments can test several genetic interventions in parallel, yet experimental budgets remain limited. A central goal is hit discovery: identifying as many perturbations as possible whose phenotypic effect exceeds a predefined threshold. Pure exploration strategies are statistically inefficient, wasting budget on low-value regions. Bayesian optimization methods offer a principled alternative but target a single global optimum, over-exploiting dominant modes while neglecting other high-value regions. We formalize hit discovery as a sequential experimental design problem and propose Probability-of-Hit, an acquisition function that directly targets threshold exceedance by ranking candidates according to their posterior probability of being a hit. We prove asymptotic optimality of this approach and demonstrate strong empirical performance on both synthetic benchmarks and real biological immunology datasets, including upto 6.4\% improvement over baselines on the Schmidt IL-2 dataset.

Applications · Health / Medicine

Jiaqi Men, Hua Liu, Yiming Tang, Jinhong You, Jianghu Dong, Jiguo Cao

Accurate survival prediction in kidney transplantation is critical yet challenging due to the complex interplay between functional biomarkers and patient characteristics under censoring. To address this, we propose a functional censored quantile neural network (FunCQNet), a novel framework that integrates deep neural networks with a censoring-adjusted sequential quantile loss to approximate interaction-dependent coefficient functions. We further introduce a conformal inference approach to rigorously assess the significance of scalar-functional interactions, ensuring interpretability alongside predictive power. Extensive simulations demonstrate that FunCQNet robustly recovers functional effects under varying noise and censoring levels. When applied to kidney transplant data, the model yields precise multi-quantile predictions and reveals clinically significant, age-dependent interaction patterns between donor type and recipient survival.

Applications · Health / Medicine

Yaxuan Song, Jianan Fan, Tianyi Wang, Qiuyue Hu, Hang Chang, Heng Huang, Weidong Cai

Histopathology whole-slide images (WSIs) are routinely acquired in clinical practice and contain rich tissue morphology but lack direct molecular architecture and functional programs defining pathological states, whereas RNA sequencing (RNA-seq) provides genome-wide transcriptional profiles at substantial cost, thereby motivating WSI-based genome-wide transcriptomic prediction. Existing approaches for predicting gene expression from WSIs predominantly rely on deterministic regression with one-to-one mapping, limiting their ability to capture biological heterogeneity and predictive uncertainty. We propose RNA-FM, a flow-matching generative framework for genome-wide bulk RNA-seq prediction from histopathology images. RNA-FM formulates transcriptomic prediction as a continuous-time conditional transport problem, learning a velocity field that maps a simple prior to the target gene expression distribution conditioned on morphological features. By incorporating pathway-level structure, RNA-FM enables scalable, biologically interpretable, and genome-wide gene expression imputation. Extensive experiments across multiple anatomical regions, pathway-level analysis, and external validation cohorts demonstrate that RNA-FM consistently outperforms state-of-the-art approaches while effectively capturing both inter-patient and intra-tumoral heterogeneity.

Optimization · Large Scale, Parallel and Distributed

Davide DAscenzo, Sebastiano Cultrera di Montesano

Training deep learning models on single-cell datasets with hundreds of millions of cells requires loading data from disk, as these datasets exceed available memory. While random sampling provides the data diversity needed for effective training, it is prohibitively slow due to the random access pattern overhead, whereas sequential streaming achieves high throughput but introduces biases that degrade model performance. We present scDataset, a PyTorch data loader that enables efficient training from on-disk data with seamless integration across diverse storage formats. Our approach combines block sampling and batched fetching to achieve quasi-random sampling that balances I/O efficiency with minibatch diversity. On Tahoe-100M, a dataset of 100 million cells, scDataset achieves more than two orders of magnitude speedup compared to true random sampling while working directly with AnnData files. We provide theoretical bounds on minibatch diversity and empirically show that scDataset matches the performance of true random sampling across multiple classification tasks.

Applications · Health / Medicine

Marie Brockschmidt, Maresa Schröder, Stefan Feuerriegel

Survival analysis is a cornerstone of clinical research by modeling time-to-event outcomes such as metastasis, disease relapse, or patient death. Unlike standard tabular data, survival data often come with incomplete event information due to dropout, or loss to follow-up. This poses unique challenges for synthetic data generation, where it is crucial for clinical research to faithfully reproduce both the event-time distribution and the censoring mechanism. In this paper, we propose SurvDiff, an end-to-end diffusion model specifically designed for generating synthetic data in survival analysis. SurvDiff is tailored to capture the data-generating mechanism by jointly generating mixed-type covariates, event times, and right-censoring, guided by a survival-tailored loss function. The loss encodes the time-to-event structure and directly optimizes for downstream survival tasks, which ensures that SurvDiff (i) reproduces realistic event-time distributions and (ii) preserves the censoring mechanism. Across multiple datasets, we show that SurvDiff consistently outperforms state-of-the-art generative baselines in both distributional fidelity and survival model evaluation metrics across multiple medical datasets. To the best of our knowledge, SurvDiff is the first end-to-end diffusion model explicitly designed for generating synthetic survival data.

Ran Xin, Zeyu Zheng, Yanchen Nie, Kun Yuan, Xia Xiao

The integration of Large Language Models (LLMs) with automated theorem proving has shown immense promise, yet is constrained by challenges in scaling up both training-time reinforcement learning (RL) and inference-time compute. This paper introduces BFS-Prover-V2, a step-level theorem proving system designed to address this dual scaling problem. We present two primary innovations. The first is a novel multi-turn off-policy RL framework for continually improving the performance of the LLM step-prover at training time. This framework, inspired by the principles of AlphaZero, utilizes a multi-stage expert iteration pipeline featuring adaptive tactic-level data filtering and periodic retraining to surmount the performance plateaus that typically curtail long-term RL in LLM-based agents. The second innovation is a planner-enhanced multi-agent system that scales reasoning capabilities at inference time. This architecture employs a general reasoning model as a high-level planner to iteratively decompose complex theorems into a sequence of simpler subgoals. This hierarchical approach substantially reduces the search space, enabling a team of parallel prover agents to collaborate efficiently by leveraging a shared proof cache. We demonstrate that this dual approach to scaling yields state-of-the-art results on established formal mathematics benchmarks. BFS-Prover-V2 achieves 95.08% and 41.4% on the miniF2F and ProofNet test sets respectively. While demonstrated in the domain of formal mathematics, the RL and inference techniques presented in this work are of broader interest and may be applied to other domains requiring long-horizon multi-turn reasoning and complex search.

Reinforcement Learning · Batch/Offline

Tianwei Ni, Esther Derman, Vineet Jain, Vincent Taboga, Siamak Ravanbakhsh, Pierre-Luc Bacon

Popular offline reinforcement learning (RL) methods rely on conservatism, penalizing out-of-dataset actions or restricting rollout horizons. We question the universality of this principle and revisit a complementary Bayesian perspective. By modeling a posterior over plausible world models and training a history-dependent agent to maximize expected return, the Bayesian approach directly addresses epistemic uncertainty and enables test-time generalization, without conservatism. We first illustrate in a bandit setting that Bayesianism excels on low-quality datasets where conservatism fails. Scaling to realistic tasks, we find that long-horizon rollouts are essential to control value overestimation once conservatism is removed. We introduce design choices that enable learning from long-horizon rollouts while mitigating compounding errors, yielding our algorithm, NEUBAY, grounded in the neutral Bayesian principle. On D4RL and NeoRL benchmarks, NEUBAY is competitive with leading conservative algorithms, achieving new state-of-the-art on 7 datasets with rollout horizons of several hundred steps. Finally, we characterize datasets by quality and coverage to identify when NEUBAY is preferable to conservative methods.

Applications · Health / Medicine

Bowen Jing, Mihir Bafna, Anisha Parsan, Heyuan Ni, David Kwabi-Addo, Bryan Bryson, Adam Klivans, Bonnie Berger

Multistate mechanisms underlie many of the complex functions observed in natural proteins. The ability to rationally design multistate proteins would have transformative implications for many areas of biotechnology, yet lies beyond the capabilities of existing deep learning frameworks for protein design. To address this gap, we introduce SwitchCraft, a versatile and programmatic framework for designing state-switching proteins based on backpropagation through compositional design constraints parameterized by structure prediction models. In silico evaluations demonstrate success on a wide range of state-switching functional primitives, from allosteric regulation of motifs to discrimination of bound ligand identities. Using these primitives, we demonstrate an in silico strategy for de novo design of fluorescent biosensors to arbitrary small molecule analytes. These results position SwitchCraft at the inception of a powerful paradigm for higher-order functional protein design.

Applications · Health / Medicine

Mingcheng Zhu, Zhiyao Luo, Yu Liu, Tingting Zhu

By processing electronic health records (EHRs) as natural language sequences, large language models (LLMs) have shown potential in clinical prediction tasks such as mortality prediction and phenotyping. However, longitudinal or highly frequent EHRs often yield excessively long token sequences that result in high computational costs and even reduced performance. Existing solutions either add modules for compression or remove less important tokens, which introduce additional inference latency or risk losing clinical information. To achieve lossless compression of token sequences without additional cost or loss of performance, we propose Medical Token-Pair Encoding (MedTPE), a layered method that extends standard tokenisation for EHR sequences. MedTPE merges frequently co-occurring medical token pairs into composite tokens, providing lossless compression while preserving the computational complexity through a dependency-aware replacement strategy. Only the embeddings of the newly introduced tokens of merely 0.5-1.0\% of the LLM’s parameters are fine-tuned via self-supervised learning. Experiments on real-world datasets for two clinical scenarios demonstrate that MedTPE reduces input token length by up to 31% and inference latency by 34-63%, while maintaining or even improving both predictive performance and output format compliance across three LLMs and four clinical prediction tasks. Furthermore, MedTPE demonstrates robustness across different input context lengths and generalisability to scientific and financial domains.

Deep Learning · Large Language Models

Ido Pinto, Yizhak Elboher, Haoze Wu, Nina Narodytska, Guy Katz

The synthesis of inductive loop invariants is a critical bottleneck in automated program verification. While Large Language Models (LLMs) show promise in mitigating this issue, they often fail on hard instances, generating invariants that are invalid or computationally ineffective. While fine-tuning is a natural route to mitigate this limitation, obtaining high-quality training data for invariant generation remains an open challenge. We present a rigorous data curation pipeline designed to extract high-quality training signals from raw verifier-generated invariants. First, we formalize the properties required for a high-quality training invariant. Second, we propose \textsc{Wonda}, a pipeline that refines noisy data via AST-based normalization, followed by LLM-driven semantic rewriting and augmentation with provable quality guarantees. We demonstrate that fine-tuning Small Language Models (SLMs) on this curated dataset result in consistent and significant performance gain. In particular, a fine-tuned 4B parameter model matches the utility of a GPT-OSS-120B baseline and approaches the state-of-the-art GPT-5.2, without incurring reasoning-time overhead. On challenging instances from the recent InvBench evaluation suite, our approach doubles the invariant correctness rate of base models; and improves their Virtual Best Performance (VBP) rates on the verification task by up to 14.2\%.

Applications · Health / Medicine

Lina Zhang, Jiarui Cui, Tonmoy Monsoor, Peizheng Li, Xinyi Peng, Chong Han, Prateik Sinha, Siyuan Dai, Jessica Pasqua, Colin McCrimmon 等

While Multimodal Large Language Models (MLLMs) have demonstrated remarkable proficiency in general video understanding, their capacity to interpret involuntary, and spatio-temporally evolving pathologic motor behaviors such as seizure semiology remains largely untested. To address this gap, we introduce Seizure-Semiology-Suite (S³), a clinically grounded dataset and benchmark for fine-grained, structured seizure semiology understanding. The dataset includes 438 seizure videos annotated with over 35,000 dense labels covering 20 ILAE-defined semiological features. Building on this dataset, we propose a seven-task hierarchical benchmark that systematically evaluates MLLMs from low-level visual perception to temporal sequencing, narrative report generation, and seizure diagnosis. To enable clinically meaningful evaluation of generated reports, we further introduce the Report Quality Index for Seizure Semiology (Seizure-RQI). Extensive baselines across 11 open-weight MLLMs reveal systematic weaknesses in laterality reasoning, temporal localization, symptom sequencing, and clinically faithful reporting. We show that seizure-specific fine-tuning substantially improves performance across tasks, and that a two-stage neuro-symbolic framework achieves an F1 score of 0.96 on epileptic versus non-epileptic seizure classification. Seizure-Semiology-Suite establishes a rigorous benchmark for evaluating multimodal models in safety-critical medical video understanding and guides the development of clinically reliable, domain-adaptive multimodal intelligence.

Applications · Everything Else

Hong-Jie You, Jie-Jing Shao, Xiao-Wen Yang, Lin-Han Jia, Lan-Zhe Guo, Yu-Feng Li

Existing methods for expressive music performance rendering rely on supervised learning over small labeled datasets, which limits scaling of both data volume and model size, despite the availability of vast unlabeled music, as in vision and language. To address this gap, we introduce Pianist Transformer, with three key contributions: 1) introducing large-scale self-supervised learning into expressive piano performance rendering through a unified Musical Instrument Digital Interface (MIDI) representation, enabling pre-training on 10B tokens of unlabeled MIDI data; 2) an efficient asymmetric Transformer with note-level compression, substantially improving training efficiency, memory usage, and inference speed for long-context music modeling; 3) a state-of-the-art rendering model with an editable workflow, achieving strong objective and subjective results and enabling integration into real-world music production workflows. Overall, Pianist Transformer outlines a scalable path toward human-like performance synthesis in the music domain. An anonymous demo with audio examples is available at: https://anonymous.4open.science/r/JSKJDHKIOWBBCGFBDKS/.

General Machine Learning · Supervised Learning

Mohamed Chiheb Yaakoubi, Cosme Louart, Malik TIOMOKO, Zhenyu Liao

We study high-dimensional convex empirical risk minimization (ERM) under general non-Gaussian data designs. By heuristically extending the Convex Gaussian Min–Max Theorem (CGMT) to non-Gaussian settings, we derive an asymptotic min–max characterization of key statistics, enabling approximation of the mean $\mu_{\hat{\theta}}$ and covariance $C_{\hat{\theta}}$ of the ERM estimator $\hat{\theta}$. Specifically, under a concentration assumption on the data matrix and standard regularity conditions on the loss and regularizer, we show that for a test covariate $x$ independent of the training data, the projection $\hat{\theta}^\top x$ approximately follows the convolution of the (generally non-Gaussian) distribution of $\mu_{\hat{\theta}}^\top x$ with an independent centered Gaussian variable of variance $\mathrm{tr}\!\big(C_{\hat{\theta}}\,\mathbb{E}[xx^\top]\big)$. This result clarifies the scope and limits of Gaussian universality for ERMs. Additionally, we prove that any $\mathcal{C}^2$ regularizer is asymptotically equivalent to a quadratic form determined solely by its Hessian at zero and gradient at $\mu_{\hat{\theta}}$. Numerical simulations across diverse losses and models are provided to validate our theoretical predictions and qualitative insights.

Deep Learning · Large Language Models

Zhangquan Chen, Jiale Tao, Ruihuang Li, Yihao Hu, Ruitao Chen, Zhantao Yang, Xinlei Yu, Haodong Jing, Manyuan Zhang, Shuai Shao 等

Humans perceive the world through diverse modalities that operate synergistically to support a holistic understanding of their surroundings. However, existing omnimodal models still exhibit substantial performance degradation on visual tasks when the audio modality is incorporated. We identify this “modality interference” as a consequence of pre-training data imbalances, where the scarcity of mixed modality supervision induces a bias towards isolated modalities, resulting in an inherent trade-off. To address this challenge, we propose OmniVideo-R1, a novel reinforced reasoning framework that leverages post-training to rectify modality bias. OmniVideo-R1 empowers models to “think with omnimodal cues” and integrate cross-modal information. The framework consists of two key strategies: (1) query-intensive grounding based on self-supervised learning paradigms; and (2) modality- attentive fusion built upon contrastive learning paradigms. Extensive experiments on multiple benchmarks demonstrate that OmniVideo-R1 consistently outperforms strong baselines, highlighting its effectiveness and robust generalization capabilities.

Applications · Health / Medicine

Dian Ding, Liren Dong, Yu Lu, Juntao Zhou, Ran Wang, Peng Li, Zhenyi Jia, Guangtao Xue

Gastrointestinal (GI) motility assessment via bowel sounds (BS) offers a non-invasive alternative to resource-intensive clinical standards. However, the diagnostic utility of BS is often compromised by its spectral overlap with non-stationary speech interference. While generative models have advanced signal restoration, traditional Gaussian-based diffusion frameworks struggle with the impulsive, heavy-tailed nature of real-world clinical noise. In this paper, we propose a novel Cauchy-driven Diffusion Bridge framework to isolate high-fidelity bowel sounds from complex interference. Our contributions are three-fold: (1) We introduce ClinBS, a large-scale clinical dataset (over 25 hours) containing rare pathological transients verified by experts; (2) We mathematically formulate a Cauchy bridge driver, deriving closed-form expressions for the score and density to better model heavy-tailed perturbations; and (3) We implement an efficient sampling procedure via Gaussian scale-mixture reparameterization. Extensive experiments show our framework achieves state-of-the-art performance, outperforming baselines by 13.4%–49.8% across core metrics and elevating abnormal BS recognition accuracy to 88.01%. These results demonstrate the system's potential for robust clinical GI monitoring and diagnosis.