论文检索

Applications · Genetics, Cell Biology, etc

YUXUAN SUN, Yixuan Si, Chenglu Zhu, Kai Zhang, Zhongyi Shui, Bowen Ding, Tao Lin, Lin Yang

Recent advances in computational pathology have led to the emergence of numerous foundation models. These models typically rely on general-purpose encoders with multi-instance learning for whole slide image (WSI) classification or apply multimodal approaches to generate reports directly from images. However, these models cannot emulate the diagnostic approach of pathologists, who systematically examine slides at low magnification to obtain an overview before progressively zooming in on suspicious regions to formulate comprehensive diagnoses. Instead, existing models directly output final diagnoses without revealing the underlying reasoning process. To address this gap, we introduce CPathAgent, an innovative agent-based approach that mimics pathologists' diagnostic workflow by autonomously navigating across WSI through zoom-in/out and move operations based on observed visual features, thereby generating substantially more transparent and interpretable diagnostic summaries. To achieve this, we develop a multi-stage training strategy that unifies patch-level, region-level, and WSI-level capabilities within a single model, which is essential for replicating how pathologists understand and reason across diverse image scales. Additionally, we construct PathMMU-HR², the first expert-validated benchmark for large region analysis. This represents a critical intermediate scale between patches and whole slides, reflecting a key clinical reality where pathologists typically examine several key large regions rather than entire slides at once. Extensive experiments demonstrate that CPathAgent consistently outperforms existing approaches across benchmarks at three different image scales, validating the effectiveness of our agent-based diagnostic approach and highlighting a promising direction for computational pathology.

General Machine Learning · Representation Learning

Taekyung Kim, Dongyoon Han, Byeongho Heo, Jeongeun Park, Sangdoo Yun

Deriving compact and temporally aware visual representations from dynamic scenes is essential for successful execution of sequential scene understanding tasks such as visual tracking and robotic manipulation. In this paper, we introduce Token Bottleneck (ToBo), a simple yet intuitive self-supervised learning pipeline that squeezes a scene into a bottleneck token and predicts the subsequent scene using minimal patches as hints. The ToBo pipeline facilitates the learning of sequential scene representations by conservatively encoding the reference scene into a compact bottleneck token during the squeeze step. In the expansion step, we guide the model to capture temporal dynamics by predicting the target scene using the bottleneck token along with few target patches as hints. This design encourages the vision backbone to embed temporal dependencies, thereby enabling understanding of dynamic transitions across scenes. Extensive experiments in diverse sequential tasks, including video label propagation and robot manipulation in simulated environments demonstrate the superiority of ToBo over baselines. Moreover, deploying our pre-trained model on physical robots confirms its robustness and effectiveness in real-world environments. We further validate the scalability of ToBo across different model scales. Code is available at https://github.com/naver-ai/tobo.

Applications · Robotics

Haohong Lin, Yunzhi Zhang, Wenhao Ding, Jiajun Wu, DING ZHAO

End-to-end (E2E) autonomous driving models have demonstrated strong performance in open-loop evaluations but often suffer from cascading errors and poor generalization in closed-loop settings. To address this gap, we propose Model-based Policy Adaptation (MPA), a general framework that enhances the robustness and safety of pretrained E2E driving agents during deployment. MPA first generates diverse counterfactual trajectories using a geometry-consistent simulation engine, exposing the agent to scenarios beyond the original dataset. Based on this generated data, MPA trains a diffusion-based policy adapter to refine the base policy’s predictions and a multi-step Q value model to evaluate long-term outcomes. At inference time, the adapter proposes multiple trajectory candidates, and the Q value model selects the one with the highest expected utility. Experiments on the nuScenes benchmark using a photorealistic closed-loop simulator demonstrate that MPA significantly improves performance across in-domain, out-of-domain, and safety-critical scenarios. We further investigate how the scale of counterfactual data and inference-time guidance strategies affect overall effectiveness.

Ziyuan He, Yuxuan Wang, Jiaqi Li, Kexin Liang, Muhan Zhang

Large language models (LLMs) are equipped with increasingly extended context windows recently, yet their long context understanding capabilities over long dependency tasks remain fundamentally limited and underexplored. This gap is especially significant in many real-world long-context applications that were rarely benchmarked. In this paper, we introduce $\textbf{LooGLE v2}$, a novel benchmark designed to evaluate LLMs' long context ability in real-world applications and scenarios. Our benchmark consists of automatically collected real-world long texts, ranging from 16k to 2M tokens, encompassing domains in law, finance, game and code. Accordingly, we delicately design 10 types of domain-specific long-dependency tasks and generate 1,934 QA instances with various diversity and complexity in a scalable data curation pipeline for further practical needs. We conduct a comprehensive assessment of 6 locally deployed and 4 API-based LLMs. The evaluation results show that even the best-performing model achieves only a 59.2\% overall score on our benchmark. Despite the extensive context windows, popular LLMs are only capable of understanding a much shorter length of context than they claim to be, revealing significant limitations in their ability to handle real-world tasks with long dependencies and highlighting substantial room for model improvement in practical long-context understanding.

Reinforcement Learning · Deep RL

Xiangqi Wang, Yue Huang, Yanbo Wang, Xiaonan Luo, Kehan Guo, Yujun Zhou, Xiangliang Zhang

LLMs often need effective configurations, like temperature and reasoning steps, to handle tasks requiring sophisticated reasoning and problem-solving, ranging from joke generation to mathematical reasoning. Existing prompting approaches usually adopt general-purpose, fixed configurations that work “well enough” across tasks but seldom achieve task-specific optimality. To address this gap, we introduce AdaReasoner, an LLM-agnostic plugin designed for any LLM to automate adaptive reasoning configurations for tasks requiring different types of thinking. AdaReasoner is trained using a reinforcement learning (RL) framework, combining a factorized action space with a targeted exploration strategy, along with a pretrained reward model to optimize the policy model for reasoning configurations with only a few-shot guide. AdaReasoner is backed by theoretical guarantees and experiments of fast convergence and a sublinear policy gap. Across six different LLMs and a variety of reasoning tasks, it consistently outperforms standard baselines, preserves out-of-distribution robustness, and yield gains on knowledge-intensive tasks through tailored prompts.

Rongyang Zhang, Yuqing Huang, Chengqiang Lu, Qimeng Wang, Yan Gao, YIWU, Yao Hu, Yin Xu, Wei Wang, Hao Wang 等

In real-world scenarios, providing user queries with visually enhanced responses can considerably benefit understanding and memory, underscoring the great value of interleaved image-text generation. Despite recent progress, like the visual autoregressive model that unifies text and image processing in a single transformer architecture, generating high-quality interleaved content remains challenging. Moreover, evaluations of these interleaved sequences largely remain underexplored, with existing benchmarks often limited by unimodal metrics that inadequately assess the intricacies of combined image-text outputs. To address these issues, we present RAG-IGBench, a thorough benchmark designed specifically to evaluate the task of Interleaved Generation based on Retrieval-Augmented Generation (RAG-IG) in open-domain question answering. RAG-IG integrates multimodal large language models (MLLMs) with retrieval mechanisms, enabling the models to access external image-text information for generating coherent multimodal content. Distinct from previous datasets, RAG-IGBench draws on the latest publicly available content from social platforms and introduces innovative evaluation metrics that measure the quality of text and images, as well as their consistency. Through extensive experiments with state-of-the-art MLLMs (both open-source and proprietary) on RAG-IGBench, we provide an in-depth analysis examining the capabilities and limitations of these models. Additionally, we validate our evaluation metrics by demonstrating their high correlation with human assessments. Models fine-tuned on RAG-IGBench's training set exhibit improved performance across multiple benchmarks, confirming both the quality and practical utility of our dataset. Our benchmark is available at https://github.com/zry13/RAG-IGBench.

Theory · Learning Theory

Julian Asilis, Mikael Møller Høgsgaard, Grigoris Velegkas

Binary classification in the classic PAC model exhibits a curious phenomenon: Empirical Risk Minimization (ERM) learners are suboptimal in the realizable case yet optimal in the agnostic case. Roughly speaking, this owes itself to the fact that non-realizable distributions $\\mathcal{D}$ are more difficult to learn than realizable distributions -- even when one discounts a learner's error by $\\mathrm{err}(h^\\ast_\\mathcal{D})$, i.e., the error of the best hypothesis in $\\mathcal{H}$. Thus, optimal agnostic learners are permitted to incur excess error on (easier-to-learn) distributions $\\mathcal{D}$ for which $\\tau = \\mathrm{err}(h^\\ast_\\mathcal{D})$ is small. Recent work of Hanneke, Larsen, and Zhivotovskiy (FOCS '24) addresses this shortcoming by including $\\tau$ itself as a parameter in the agnostic error term. In this more fine-grained model, they demonstrate tightness of the error lower bound $\\tau + \\Omega \\left(\\sqrt{\\frac{\\tau (d + \\log(1 / \\delta))}{m}} + \\frac{d + \\log(1 / \\delta)}{m} \\right)$ in a regime where $\\tau > d/m$, and leave open the question of whether there may be a higher lower bound when $\\tau \\approx d/m$, with $d$ denoting $\\mathrm{VC}(\\mathcal{H})$. In this work, we resolve this question by exhibiting a learner which achieves error $c \\cdot \\tau + O \\left(\\sqrt{\\frac{\\tau (d + \\log(1 / \\delta))}{m}} + \\frac{d + \\log(1 / \\delta)}{m} \\right)$ for a constant $c \\leq 2.1$, matching the lower bound and demonstrating optimality when $\\tau =O( d/m)$. Further, our learner is computationally efficient and is based upon careful aggregations of ERM classifiers, making progress on two other questions of Hanneke, Larsen, and Zhivotovskiy (FOCS '24). We leave open the interesting question of whether our approach can be refined to lower the constant from 2.1 to 1, which would completely settle the complexity of agnostic learning.

Theory · Learning Theory

Antoine Ledent, Rodrigo Alves, Yunwen Lei

It has been recently observed in much of the literature that neural networks exhibit a bottleneck rank property: for larger depths, the activation and weights of neural networks trained with gradient-based methods tend to be of approximately low rank. In fact, the rank of the activations of each layer converges to a fixed value referred to as the ``bottleneck rank", which is the minimum rank required to represent the training data. This perspective is in line with the observation that regularizing linear networks (without activations) with weight decay is equivalent to minimizing the Schatten $p$ quasi norm of the neural network. In this paper we investigate the implications of this phenomenon for generalization. More specifically, we prove generalization bounds for neural networks which exploit the approximate low rank structure of the weight matrices if present. The final results rely on the Schatten $p$ quasi norms of the weight matrices: for small p, the bounds exhibit a sample complexity $ \widetilde{O}(WrL^2)$ where $W$ and $L$ are the width and depth of the neural network respectively and where $r$ is the rank of the weight matrices. As $p$ increases, the bound behaves more like a norm-based bound instead. The proof techniques involve a careful interpolation between the parametric and norm based regimes. We also demonstrate in experiments that this bound outperforms both classic parameter counting and norm based bounds in the typical overparametrized regime.

Applications · Chemistry and Drug Discovery

Nayoung Kim, Seongsu Kim, Sungsoo Ahn

Designing metal-organic frameworks (MOFs) with novel chemistries is a longstanding challenge due to their large combinatorial space and complex 3D arrangements of the building blocks. While recent deep generative models have enabled scalable MOF generation, they assume (1) a fixed set of building blocks and (2) known local 3D coordinates of building blocks. However, this limits their ability to (1) design novel MOFs and (2) generate the structure using novel building blocks. We propose a two-stage MOF generation framework that overcomes these limitations by modeling both chemical and geometric degrees of freedom. First, we train an SMILES-based autoregressive model to generate metal and organic building blocks, paired with a cheminformatics toolkit for 3D structure initialization. Second, we introduce a flow matching model that predicts translations, rotations, and torsional angles to assemble the blocks into valid 3D frameworks. Our experiments demonstrate improved reconstruction accuracy, the generation of valid, novel, and unique MOFs, and the ability to create novel building blocks. Our code is available at https://github.com/nayoung10/MOFFlow-2.

Social Aspects · Privacy-preserving Statistics and Machine Learning

Ming Wen, Jiaqi Zhu, Yuedong Xu, Yipeng Zhou, DINGDING HAN

Large language models (LLMs) typically require fine-tuning for domain-specific tasks, and LoRA offers a computationally efficient approach by training low-rank adaptors. LoRA is also communication-efficient for federated LLMs when multiple users collaboratively fine-tune a global LLM model without sharing their proprietary raw data. However, even the transmission of local adaptors between a server and clients risks serious privacy leakage. Applying differential privacy (DP) to federated LoRA encounters a dilemma: adding noise to both adaptors amplifies synthetic noise on the model, while fixing one adaptor impairs the learnability of fine-tuning. In this paper, we propose FedASK (Differentially Private Federated Low Rank Adaptation with Double SKetching) , a novel federated LoRA framework to enable effective updating of both low-rank adaptor matrices with robust differential privacy. Inspired by randomized SVD, our key idea is a two-stage sketching pipeline. This pipeline first aggregates carefully sketched, privacy-preserving local updates, and then reconstructs the global matrices on the server to facilitate effective updating of both adaptors. We theoretically prove FedASK's differential privacy guarantee and its exact aggregation property. Comprehensive experiments demonstrate that FedASK consistently outperforms baseline methods across a variety of privacy settings and data distributions.

Applications · Neuroscience, Cognitive Science

HaiYang Li, Liao Yu, Qiang Yu, Yunliang Zang

Biological circuits have evolved to incorporate multiple modules that perform similar functions. In the fly olfactory circuit, both lateral inhibition (LI) and neuronal spike frequency adaptation (SFA) are thought to enhance pattern separation for odor learning. However, it remains unclear whether these mechanisms play redundant or distinct roles in this process. In this study, we present a computational model of the fly olfactory circuit to investigate odor discrimination under varying noise conditions that simulate complex environments. Our results show that LI primarily enhances odor discrimination in low‑ and medium‑noise scenarios, but this benefit diminishes and may reverse under higher‑noise conditions. In contrast, SFA consistently improves discrimination across all noise levels. LI is preferentially engaged in low‑ and medium‑noise environments, whereas SFA dominates in high‑noise settings. When combined, these two sparsification mechanisms enable optimal discrimination performance. This work demonstrates that seemingly redundant modules in biological circuits can, in fact, be essential for achieving optimal learning in complex contexts.

Computer Vision · Vision Models & Multimodal

Cheng Luo, Jianghui Wang, Bing Li, Siyang Song, Bernard Ghanem

In this paper, we introduce Online Multimodal Conversational Response Generation (OMCRG), a novel task designed to produce synchronized verbal and non-verbal listener feedback online, based on the speaker's multimodal inputs. OMCRG captures natural dyadic interactions and introduces new challenges in aligning generated audio with listeners' facial responses. To tackle these challenges, we incorporate text as an intermediate modality to connect audio and facial responses. We propose OmniResponse, a Multimodal Large Language Model (MLLM) that autoregressively generates accurate multimodal listener responses. OmniResponse leverages a pretrained LLM enhanced with two core components: Chrono-Text Markup, which precisely timestamps generated text tokens, and TempoVoice, a controllable online text-to-speech (TTS) module that outputs speech synchronized with facial responses. To advance OMCRG research, we offer ResponseNet, a dataset of 696 detailed dyadic interactions featuring synchronized split-screen videos, multichannel audio, transcripts, and annotated facial behaviors. Comprehensive evaluations on ResponseNet demonstrate that OmniResponse outperforms baseline models in terms of semantic speech content, audio-visual synchronization, and generation quality. Our dataset, code, and models are publicly available at https://omniresponse.github.io/.

Probabilistic Methods · Monte Carlo and Sampling Methods

Dongyeop Woo, Minsu Kim, Minkyu Kim, Kiyoung Seong, Sungsoo Ahn

We propose Energy-based generator matching (EGM), a modality-agnostic approach to train generative models from energy functions in the absence of data. Extending the recently proposed generator matching, EGM enables training of arbitrary continuous-time Markov processes, e.g., diffusion, flow, and jump, and can generate data from continuous, discrete, and a mixture of two modalities. To this end, we propose estimating the generator matching loss using self-normalized importance sampling with an additional bootstrapping trick to reduce variance in the importance weight. We validate EGM on both discrete and multimodal tasks up to 100 and 20 dimensions, respectively.

Optimization · Stochastic & Convex Optimization

Konstantinos Oikonomidis, Jan Quan, Panagiotis Patrinos

We study nonlinearly preconditioned gradient methods for smooth nonconvex optimization problems, focusing on sigmoid preconditioners that inherently perform a form of gradient clipping akin to the widely used gradient clipping technique. Building upon this idea, we introduce a novel heavy ball-type algorithm and provide convergence guarantees under a generalized smoothness condition that is less restrictive than traditional Lipschitz smoothness, thus covering a broader class of functions. Additionally, we develop a stochastic variant of the base method and study its convergence properties under different noise assumptions. We compare the proposed algorithms with baseline methods on diverse tasks from machine learning including neural network training.

General Machine Learning · Everything Else

Jan Quan, Johan Suykens, Panagiotis Patrinos

Motivated by the recently shown connection between self-attention and (kernel) principal component analysis (PCA), we revisit the fundamentals of PCA. Using the difference-of-convex (DC) framework, we present several novel formulations and provide new theoretical insights. In particular, we show the kernelizability and out-of-sample applicability for a PCA-like family of problems. Moreover, we uncover that simultaneous iteration, which is connected to the classical QR algorithm, is an instance of the difference-of-convex algorithm (DCA), offering an optimization perspective on this longstanding method. Further, we describe new algorithms for PCA and empirically compare them with state-of-the-art methods. Lastly, we introduce a kernelizable dual formulation for a robust variant of PCA that minimizes the $l_1$-deviation of the reconstruction errors.

Theory · Game Theory

Javier Cembrano, Felix Fischer, Max Klimm

We study the selection of agents based on mutual nominations, a theoretical problem with many applications from committee selection to AI alignment. As agents both select and are selected, they may be incentivized to misrepresent their true opinion about the eligibility of others to influence their own chances of selection. Impartial mechanisms circumvent this issue by guaranteeing that the selection of an agent is independent of the nominations cast by that agent. Previous research has established strong bounds on the performance of impartial mechanisms, measured by their ability to approximate the number of nominations for the most highly nominated agents. We study to what extent the performance of impartial mechanisms can be improved if they are given a prediction of a set of agents receiving a maximum number of nominations. Specifically, we provide bounds on the consistency and robustness of such mechanisms, where consistency measures the performance of the mechanisms when the prediction is correct and robustness its performance when the prediction is incorrect. For the general setting where up to $k$ agents are to be selected and agents nominate any number of other agents, we give a mechanism with consistency $1-O\big(\frac{1}{k}\big)$ and robustness $1-\frac{1}{e}-O\big(\frac{1}{k}\big)$. For the special case of selecting a single agent based on a single nomination per agent, we prove that $1$-consistency can be achieved while guaranteeing $\frac{1}{2}$-robustness. A close comparison with previous results shows that (asymptotically) optimal consistency can be achieved with little to no sacrifice in terms of robustness.

Applications · Chemistry and Drug Discovery

Daniel D. Richman, Jessica Karaguesian, Carl-Mikael Suomivuori, Ron Dror

The function of biomolecules such as proteins depends on their ability to interconvert between a wide range of structures or conformations. Researchers have endeavored for decades to develop computational methods to predict the distribution of conformations, which is far harder to determine experimentally than a static folded structure. We present ConforMix, an inference-time algorithm that enhances sampling of conformational distributions using a combination of classifier guidance, filtering, and free energy estimation. Our approach upgrades diffusion models---whether trained for static structure prediction or conformational generation---to enable more efficient discovery of conformational variability without requiring prior knowledge of major degrees of freedom. ConforMix is orthogonal to improvements in model pretraining and would benefit even a hypothetical model that perfectly reproduced the Boltzmann distribution. Remarkably, when applied to a diffusion model trained for static structure prediction, ConforMix captures structural changes including domain motion, cryptic pocket flexibility, and transporter cycling, while avoiding unphysical states. Case studies of biologically critical proteins demonstrate the scalability, accuracy, and utility of this method.

Applications · Neuroscience, Cognitive Science

Nima Hadidi, Jason Chan, Ebrahim Feghhi, Jonathan Kao

Surface electromyography (sEMG) at the wrists could enable natural, keyboard‑free text entry, yet the state‑of‑the‑art emg2qwerty baseline still misrecognizes 51.8\% of characters zero‑shot on unseen users and 7.0\% after user‑specific fine‑tuning. We trace much of these errors to mismatched cross‑user signal statistics, fragile reliance on high‑order feature dependencies, and the absence of architectural inductive biases aligned with the bilateral nature of typing. To address these issues, we introduce three simple modifications: (i) Rolling Time Normalization which adaptively aligns input distributions across users; (ii) Aggressive Channel Masking, which encourages reliance on low‑order feature combinations more likely to generalize across users; and (iii) a Split‑and‑Share encoder that processes each hand independently with weight‑shared streams to reflect the bilateral symmetry of the neuromuscular system. Combined with a five‑fold reduction in spectral resolution (33$\rightarrow$6 frequency bands), these components yield a compact Split-and-Share model, SplashNet‑mini, which uses only ¼ the parameters and 0.6× the FLOPs of the baseline while reducing character error rate (CER) to 36.4\% zero‑shot and 5.9\% after fine‑tuning. An upscaled variant, SplashNet (½ parameters, 1.15× FLOPs of the baseline), further lowers error to 35.7\% and 5.5\%, representing 31\% and 21\% relative improvements in the zero-shot and finetuned settings, respectively. SplashNet therefore establishes a new state-of-the-art without requiring additional data.

Optimization · Bayesian & Black-box Optimization

Xunzhao Yu

Meta-learning has been demonstrated to be useful to improve the sampling efficiency of Bayesian optimization (BO) and surrogate-assisted evolutionary algorithms (SAEAs) when solving expensive optimization problems (EOPs). Existing studies mainly focus on either combinations of existing meta-learning modeling methods with optimization algorithms, or the development of meta-learning acquisition functions for specific meta BO. However, the meta-learning models used in the literature are not designed for optimization purpose, and the generalization ability of meta-learning acquisition functions is limited. In this work, we develop a novel architecture of meta-learning model for optimization purpose and propose a generalized few-shot evolutionary optimization (FSEO) framework to solve EOPs. We focus on the scenario of expensive multi-objective EOPs (EMOPs) in the context of few-shot optimization as there are few studies on it and its high requirement on surrogate modeling performance. The surrogates in FSEO framework combines neural network with Gaussian Processes (GPs), their network parameters and some parameters of GPs represent task-independent experience and are meta-learned across related optimization tasks, the remaining GPs parameters are task-specific parameters that represent unique features of the target task. We demonstrate that our FSEO framework is able to improve the sampling efficiency of existing SAEAs on EMOPs.

Social Aspects · Trustworthy Machine Learning

Sang Truong, Yuheng Tu, Michael Hardy, Anka Reuel-Lamparth, Zeyu Tang, Jirayu Burapacheep, Jonathan Perera, Chibuike Uwakwe, Benjamin Domingue, Nick Haber 等

Benchmarks are pivotal in driving AI progress, and invalid benchmark questions frequently undermine their reliability. Manually identifying and correcting errors among thousands of benchmark questions is not only infeasible but also a critical bottleneck for reliable evaluation. In this work, we introduce a framework for systematic benchmark revision that leverages statistical analysis of response patterns to flag potentially invalid questions for further expert review. Our approach builds on a core assumption commonly used in AI evaluations that the mean score sufficiently summarizes model performance. This implies a unidimensional latent construct underlying the measurement experiment, yielding expected ranges for various statistics for each item. When empirically estimated values for these statistics fall outside the expected range for an item, the item is more likely to be problematic. Across nine widely used benchmarks, our method guides expert review to identify problematic questions with up to 84\% precision. In addition, we introduce an LLM‑judge first pass to review questions, further reducing human effort. Together, these components provide an efficient and scalable framework for systematic benchmark revision.