论文检索

Optimization · Learning for Optimization

Junyi Yao, Parham Eftekhar, Gene Cheung, Xujin Liu, Yao Wang, Wei Hu

Samples of brain signals collected by EEG sensors have inherent anti-correlations that are well modeled by negative edges in a finite graph. To differentiate epilepsy patients from healthy subjects using collected EEG signals, we build lightweight and interpretable transformer-like neural nets by unrolling a spectral denoising algorithm for signals on a balanced signed graph---graph with no cycles of odd number of negative edges. A balanced signed graph has well-defined frequencies that map to a corresponding positive graph via similarity transform of the graph Laplacian matrices. We implement an ideal low-pass filter efficiently on the mapped positive graph via Lanczos approximation, where the optimal cutoff frequency is learned from data. Given that two balanced signed graph denoisers learn posterior probabilities of two different signal classes during training, we evaluate their reconstruction errors for binary classification of EEG signals. Experiments show that our method achieves classification performance comparable to representative deep learning schemes, while employing dramatically fewer parameters.

Computer Vision · Vision Models & Multimodal

Qing Jiang, Xingyu Chen, Zhaoyang Zeng, Junzhi Yu, Lei Zhang

Object referring aims to detect all objects in an image that match a given natural language description. We argue that a robust object referring model should be grounded, meaning its predictions should be both explainable and faithful to the visual content. Specifically, it should satisfy two key properties: 1) Verifiable, by producing interpretable reasoning that justifies its predictions and clearly links them to visual evidence; and 2) Trustworthy, by learning to abstain when no object in the image satisfies the given expression. However, most methods treat referring as a direct bounding box prediction task, offering limited interpretability and struggling to reject expressions with no matching object. In this work, we propose Rex-Thinker, a model that formulates object referring as an explicit CoT reasoning task. Given a referring expression, we first identify all candidate object instances corresponding to the referred object category. Rex-Thinker then performs step-by-step reasoning over each candidate to assess whether it matches the given expression, before making a final prediction. To support this paradigm, we construct a large-scale CoT-style referring dataset named HumanRef-CoT by prompting GPT-4o on the HumanRef dataset. Each reasoning trace follows a structured planning, action, and summarization format, enabling the model to learn decomposed, interpretable reasoning over object candidates. We then train Rex-Thinker in two stages: a cold-start supervised fine-tuning phase to teach the model how to perform structured reasoning, followed by GRPO-based RL learning to improve accuracy and generalization. Experiments show that our approach outperforms standard baselines in both precision and interpretability on in-domain evaluation, while also demonstrating improved ability to reject hallucinated outputs and strong generalization in out-of-domain settings. Code is available at https://github.com/IDEA-Research/Rex-Thinker

Computer Vision · Vision Models & Multimodal

Lanxiang Hu, Mingjia Huo, Yuxuan Zhang, Haoyang Yu, Eric P Xing, Ion Stoica, Tajana Rosing, Haojian Jin, Hao Zhang

Playing video games requires perception, reasoning, memory, and long-horizon planning—exactly the faculties expected of modern large language and vision–language models (LLMs/VLMs). We introduce LMGame-Bench, a benchmark built on six popular games spanning platformer, puzzle, and narrative games through a unified Gym‑style API. Unlike prior game benchmarks that entangle multiple skills, LMGame-Bench employs a modular harness—including perception, memory, and reasoning modules—that can be toggled to selectively probe distinct capabilities. The benchmark further improves robustness through prompt standardization and contamination mitigation. Evaluation of 13 state-of-the-art models demonstrates that LMGame-Bench remains challenging yet effectively discriminates among models. Correlation analysis reveals that individual games align with core LLM capabilities, providing a quantitative framework for interpreting performance. Finally, LMGame-Bench exposes models’ limitations in visual state extraction, reflection, spatiotemporal reasoning, and long-context reasoning, pointing to concrete directions for model improvement.

Theory · Interpretability and Visualization

Bofan Gong, Shiyang Lai, James Evans, Dawn Song

Polysemanticity is pervasive in language models and remains a major challenge for interpretation and model behavioral control. Leveraging sparse autoencoders (SAEs), we map the polysemantic topology of two small models (Pythia-70M and GPT-2-Small) to identify SAE feature pairs that are semantically unrelated yet exhibit interference within models. We intervene at four loci (prompt, token, feature, neuron) and measure induced shifts in the next-token prediction distribution, uncovering polysemantic structures that expose a systematic vulnerability in these models. Critically, interventions distilled from counterintuitive interference patterns shared by two small models transfer reliably to larger instruction-tuned models (Llama-3.1-8B/70B-Instruct and Gemma-2-9B-Instruct), yielding predictable behavioral shifts without access to model internals. These findings challenge the view that polysemanticity is purely stochastic, demonstrating instead that interference structures generalize across scale and family. Such generalization suggests a convergent, higher-order organization of internal representations, which is only weakly aligned with intuition and structured by latent regularities, offering new possibilities for both black-box control and theoretical insight into human and artificial cognition.

Juntai Cao, Xiang Zhang, Raymond Li, Jiarui Ding

Understanding how transformers represent and transform internal features is a core challenge in mechanistic interpretability. Traditional tools like attention maps and probing reveal only partial structure, often blurred by polysemanticity and superposition. New model-based methods offer more principled insight: Sparse Autoencoders extract sparse, interpretable features from dense activations; Semi-Nonnegative Matrix Factorization uncovers how neuron groups themselves encode concepts; Cross-Layer Transcoders track how these representations evolve across depth; and Weight-Sparse Transformers encourage inherently modular computation through architectural sparsity. Together, these approaches provide complementary pathways for opening the black box and understanding the circuits that underpin transformer behavior.

Computer Vision · Everything Else

Rupa Kurinchi-Vendhan, Pratyusha Sharma, Antonio Torralba, Sara Beery

Scientific and environmental imagery often suffer from complex mixtures of noise related to the sensor and the environment. Existing restoration methods typically remove one degradation at a time, leading to cascading artifacts, overcorrection, or loss of meaningful signal. In scientific applications, restoration must be able to simultaneously handle compound degradations while allowing experts to selectively remove subsets of distortions without erasing important features. To address these challenges, we present PRISM (Precision Restoration with Interpretable Separation of Mixtures). PRISM is a prompted conditional diffusion framework which combines compound-aware supervision over mixed degradations with a weighted contrastive disentanglement objective that aligns primitives and their mixtures in the latent space. This compositional geometry enables high-fidelity joint removal of overlapping distortions while also allowing flexible, targeted fixes through natural language prompts. Across microscopy, wildlife monitoring, remote sensing, and urban weather datasets, PRISM outperforms state-of-the-art baselines on complex compound degradations, including zero-shot mixtures not seen during training. Importantly, we show that selective restoration significantly improves downstream scientific accuracy in several domains over standard ``black-box'' restoration. These results establish PRISM as a generalizable and controllable framework for high-fidelity restoration in domains where scientific utility is a priority.

Deep Learning · Generative Models and Autoencoders

Xiangyu Wen, Junhua Huang, Zeju LI, Min Li, Jianyuan Zhong, Zhijian Xu, Mingxuan Yuan, Yongxiang Huang, Qiang Xu

The prevailing approach to distilling reasoning from Large Language Models (LLMs)—behavioral cloning from textual rationales—is fundamentally limited. It teaches Small Language Models (SLMs) to mimic surface-level patterns rather than the underlying algorithmic structure of thought, resulting in a critical lack of logical robustness. We argue that instead of cloning text, distillation should transfer this algorithmic structure directly. We introduce Reasoning Scaffolding, a framework that reframes reasoning as a structured generation process. Our method first abstracts the teacher's thought process into a sequence of discrete, interpretable semantic signals (e.g., Contrast, Addition) that act as a scaffold. The student model is then trained via a multi-task objective to both (1) predict the next semantic signal, anticipating the reasoning flow, and (2) generate the corresponding step, conditioned on that signal. This multi-task scheme acts as a powerful regularizer, compelling the student to internalize the computational patterns of coherent reasoning. On a suite of challenging reasoning benchmarks, our method significantly outperforms state-of-the-art distillation in both accuracy and logical consistency, providing a path towards creating smaller models that are genuine reasoners, not just fluent mimics.

Reinforcement Learning · Multi-agent

HyunJi Nam, Yanming Wan, Mickel Liu, Peter Ahnn, Jianxun Lian, Natasha Jaques

As everyday use cases of large language model (LLM) AI assistants have expanded, it is becoming increasingly important to personalize responses to align to different users' preferences and goals. While reinforcement learning from human feedback (RLHF) is effective at improving LLMs to be generally more helpful and fluent, it does not account for variability across users, as it models the entire user population with a single reward model, meaning it assumes that everyone's preferences are the same. We present a novel framework, **P**reference **L**earning **U**sing **S**ummarization (**PLUS**), that uses reinforcement learning (RL) to learn to produce text-based summaries of each user's preferences, characteristics, and past conversations. These summaries condition the reward model, enabling it to make personalized predictions about the types of responses valued by each user. Both the user-summarization model and reward model are trained simultaneously, creating an online co-adaptation loop. We show that in contrast to the standard Bradley–Terry model, summaries produced by PLUS capture diverse aspects of user preferences, achieving a 11–77\% improvement in reward model accuracy. Key strengths of PLUS are: (1) robust performance with new users and conversation topics, achieving a 25\% improvement over the best personalized reward model technique used for RLHF; (2) zero-shot personalization with state-of-the-art proprietary models like GPT-4 (e.g., PLUS-summary-conditioned responses achieved a 72\% win rate compared to 28\% for default GPT-4o); (3) learning from flexible user contexts beyond preference labels, and (4) interpretable representation of users, enabling greater transparency and user control in pluralistic LLM alignment.

Theory · Interpretability and Visualization

Aideen Fay, Inés García-Redondo, Qiquan Wang, Haim Dubossarsky, Anthea Monod

Existing interpretability methods for Large Language Models (LLMs) predominantly capture linear directions or isolated features. This overlooks the high-dimensional, relational, and nonlinear geometry of model representations. We apply persistent homology (PH) to characterize how adversarial inputs reshape the geometry and topology of internal representation spaces of LLMs. This phenomenon, especially when considered across operationally different attack modes, remains poorly understood. We analyze six models (3.8B to 70B parameters) under two distinct attacks, indirect prompt injection and backdoor fine-tuning, and show that a consistent topological signature persists throughout. Adversarial inputs induce topological compression, where the latent space becomes structurally simpler, collapsing the latent space from varied, compact, small-scale features into fewer, dominant, large-scale ones. This signature is architecture-agnostic, emerges early in the network, and is highly discriminative across layers. By quantifying the shape of activation point clouds and neuron-level information flow, our framework reveals geometric invariants of representational change that complement existing linear interpretability methods.

Computer Vision · Classification and Understanding

Aymene Mohammed Bouayed, Samuel Deslauriers-gauthier, Adrian IACOVELLI, David Naccache, Aymene Mohammed Bouayed

Interpreting the decisions of Convolutional Neural Networks (CNNs) is essential for understanding their behavior, yet it remains a significant challenge, particularly for self-supervised models. Most existing methods for generating saliency maps rely on reference labels, restricting their use to supervised tasks. EigenCAM is the only notable label-independent alternative, leveraging Singular Value Decomposition to generate saliency maps applicable across CNN models, but it does not fully exploit the tensorial structure of feature maps. In this work, we introduce the Tucker Saliency Map (TSM) method, which applies Tucker tensor decomposition to better capture the inherent structure of feature maps, producing more accurate singular vectors and values. These are used to generate high-fidelity saliency maps, effectively highlighting objects of interest in the input. We further extend EigenCAM and TSM into multivector variants—Multivec-EigenCAM and Multivector Tucker Saliency Maps (MTSM)—which utilize all singular vectors and values, further improving saliency map quality. Quantitative evaluations on supervised classification models demonstrate that TSM, Multivec-EigenCAM, and MTSM achieve competitive performance with label-dependent methods. Moreover, TSM enhances interpretability by approximately $50\%$ over EigenCAM for both supervised and self-supervised models. Multivec-EigenCAM and MTSM further advance state-of-the-art interpretability performance on self-supervised models, with MTSM achieving the best results.

Computer Vision · Vision Models & Multimodal

Jiyoon Pyo, Yuankun Jiao, Dongwon Jung, Zekun Li, Leeje Jang, Sofia Kirsanova, Jina Kim, Yijun Lin, Qin Liu, Junyi Xie 等

Cartographic reasoning is the skill of interpreting geographic relationships by aligning legends, map scales, compass directions, map texts, and geometries across one or more map images. Although essential as a concrete cognitive capability and for critical tasks such as disaster response and urban planning, it remains largely unevaluated. Building on progress in chart and infographic understanding, recent large vision language model (LVLM) works on map visual question-answering (VQA) often simplify maps as a special case of charts. In contrast, map VQA demands comprehension of layered symbology (e.g., symbols, geometries, and text labels) as well as spatial relations tied to orientation and distance that often span multiple maps and are not captured by chart-style evaluations. To address this gap, we introduce FRIEDA, a benchmark for testing complex open-ended cartographic reasoning in LVLMs. FRIEDA sources real map images from documents and reports in various domains (e.g., geology, urban planning, and environmental assessment) and geographical areas. Following classifications in Geographic Information System (GIS) literature, FRIEDA targets all three categories of spatial relations: topological (border, equal, intersect, within), metric (distance), and directional (orientation). All questions require multi-step inference, and many require cross-map grounding and reasoning. We evaluate eleven state-of-the-art LVLMs under two settings: (1) the direct setting, where we provide the maps relevant to the question, and (2) the contextual setting, where the model may have to identify the maps relevant to the question before reasoning. Even the strongest models, Gemini-2.5-Pro and GPT-5-Think, achieve only 38.20\% and 37.20\% accuracy, respectively, far below human performance of 84.87\%. These results reveal a persistent gap in multi-step cartographic reasoning, positioning FRIEDA as a rigorous benchmark to drive progress on spatial intelligence in LVLMs.

General Machine Learning · Representation Learning

Jan-Philipp von Bassewitz, Adeel Pervez, Marco Fumero, Matthew Robinson, THEOFANIS KARALETSOS, Francesco Locatello

Modeling the dynamics of cellular differentiation is fundamental to advancing the understanding and treatment of diseases associated with this process, such as cancer. With the rapid growth of single-cell datasets, this has also become a particularly promising and active domain for machine learning. Current state-of-the-art models, however, rely on computationally expensive optimal transport preprocessing and multi-stage training, while also not discovering explicit gene interactions. To address these challenges we propose Cell-Mechanistic Neural Networks (*Cell-MNN*), an encoder-decoder architecture whose latent representation is a *locally linearized ODE* governing the dynamics of cellular evolution from stem to tissue cells. Cell-MNN is fully end-to-end (besides a standard PCA pre-processing) and its ODE representation learns interpretable gene interactions. Empirically, we show that Cell-MNN achieves competitive performance on single-cell benchmarks, surpasses state-of-the-art baselines in scaling to larger datasets and joint training across multiple datasets, while also learning interpretable gene interactions that we validate against the TRRUST database of gene interactions.

Applications · Time Series

Akash Pandey, Payal Mohapatra, Wei Chen, Qi Zhu, Sinan Keten

Identifying the extent to which every temporal segment influences a model’s predictions is essential for explaining model decisions and increasing transparency. While post-hoc explainable methods based on gradients and feature-based attributions have been popular, they suffer from reference state sensitivity and struggle to generalize across time-series datasets, as they treat time points independently and ignore sequential dependencies. Another perspective on explainable time-series classification is through interpretable components of the model, for instance, leveraging self-attention mechanisms to estimate temporal attribution; however, recent findings indicate that these attention weights often fail to provide faithful measures of temporal importance. In this work, we advance this perspective and present a novel explainability-driven deep learning framework, TimeSliver, which jointly utilizes raw time-series data and its symbolic abstraction to construct a representation that maintains the original temporal structure. Each element in this representation linearly encodes the contribution of each temporal segment to the final prediction, allowing us to assign a meaningful importance score to every time point. For time-series classification, TimeSliver outperforms other temporal attribution methods by 11\% on 7 distinct synthetic and real-world multivariate time-series datasets. TimeSliver also achieves predictive performance within 2\% of state-of-the-art baselines across 26 UEA benchmark datasets, positioning it as a strong and explainable framework for general time-series classification.

Reinforcement Learning · Planning

Yao Zhang, Shijie Tang, Zeyu Li, Zhen Han, Volker Tresp

Web agents hold great potential for automating complex computer tasks, yet their interactions involve long-horizon, sequential decision-making with irreversible actions. In such settings, outcome-based supervision is sparse and delayed, often rewarding incorrect trajectories and failing to support inference-time scaling. This motivates the use of Process Reward Models (WebPRMs) for web navigation, but existing approaches remain limited: scalar WebPRMs collapse progress into coarse, weakly grounded signals, while checklist-based WebPRMs rely on brittle template matching that fails under layout or semantic changes and often mislabels superficially correct actions as successful, providing little insight or interpretability. To address these challenges, we introduce WebArbiter, a reasoning-first, principle-inducing WebPRM that formulates reward modeling as text generation, producing structured justifications that conclude with a preference verdict and identify the action most conducive to task completion under the current context. Training follows a two-stage pipeline: reasoning distillation equips the model with coherent principle-guided reasoning, and reinforcement learning corrects teacher biases by directly aligning verdicts with correctness, enabling stronger generalization. To support systematic evaluation, we release WebPRMBench, a comprehensive benchmark spanning four diverse web environments with rich tasks and high-quality preference annotations. On WebPRMBench, WebArbiter-7B outperforms the strongest baseline, GPT-5, by 9.1 points. In reward-guided trajectory search on WebArena-Lite, it surpasses the best prior WebPRM by up to 7.2 points, underscoring its robustness and practical value in complex web tasks.

Applications · Genetics, Cell Biology, Health, etc

Zhijian Wei, Runze Ma, Zichen Wang, Zhongmin Li, Shuotong Song, Shuangjia Zheng

Virtual cell modeling aims to predict cellular responses to perturbations. Existing virtual cell models rely heavily on large-scale single-cell datasets, learning explicit mappings between gene expression and perturbations. Although recent models attempt to incorporate multi-source biological information, their generalization remains constrained by data quality, coverage, and batch effects. More critically, these models often function as black boxes, offering predictions without interpretability or consistency with biological principles, which undermines their credibility in scientific research. To address these challenges, we present VCWorld, a cell-level white-box simulator that integrates structured biological knowledge with the iterative reasoning capabilities of large language models to instantiate a biological world model. VCWorld operates in a data-efficient manner to reproduce perturbation-induced signaling cascades and generates interpretable, stepwise predictions alongside explicit mechanistic hypotheses. In drug perturbation benchmarks, VCWorld achieves state-of-the-art predictive performance, and the inferred mechanistic pathways are consistent with publicly available biological evidence. Our code is publicly available at https://anonymous.4open.science/r/VCWorld-B970.

Applications · Time Series

Andrea Zerio, Maya Bechler-Speicher, Maor Huri, Marie Vestergaard, Tine Jess, Ran Gilad-Bachrach, Samir Bhatt, Aleksejs Sazonovs

Real-world temporal data often consists of multiple signal types recorded at irregular, asynchronous intervals. For instance, in the medical domain, different types of blood tests can be measured at different times and frequencies, resulting in fragmented and unevenly scattered temporal data. Similar issues of irregular sampling occur in other domains, such as the monitoring of large systems using event log files. Effectively learning from such data requires handling sets of temporal sparse and heterogeneous signals. In this work, we propose Super Mixing Additive Networks (SuperMAN), a novel and interpretable-by-design framework for learning directly from such heterogeneous signals, by modeling them as sets of implicit graphs. SuperMAN provides diverse interpretability capabilities, including node-level, graph-level, and subset-level importance, and enables practitioners to trade finer-grained interpretability for greater expressivity when domain priors are available. SuperMAN achieves state-of-the-art performance in real-world high-stakes tasks, including predicting Crohn’s disease onset and hospital length of stay from routine blood test measurements and detecting fake news. Furthermore, we demonstrate how SuperMAN’s interpretability properties assist in revealing disease development phase transitions and provide crucial insights in the healthcare domain.

Social Aspects · Fairness, Equity, Justice and Safety

Eunseo Choi, Ho-Yeon Kim, Jaewon Lee, Taeyong jo, Myungjun lee, Heejin Ahn

Quantifying uncertainty in neural network predictions is essential for deploying models in high-stakes domains such as autonomous driving, healthcare, and manufacturing. While conventional approaches often depend on costly sampling or parametric distributional assumptions, we propose Hyperspherical Confidence Mapping (HCM), a simple yet principled framework for uncertainty estimation that is both sampling-free and distribution-free. HCM decomposes model outputs into a magnitude and a normalized direction vector constrained to lie on a unit hypersphere, enabling a novel interpretation of uncertainty as the degree of violation of a geometric constraint. Grounded in this geometric constraint formulation, our method provides deterministic and interpretable uncertainty estimates applicable to both regression and classification. We validate the effectiveness of HCM across diverse benchmarks and real-world industrial tasks, demonstrating competitive or superior performance to ensemble and evidential approaches, while significantly reducing inference cost and ensuring strong confidence–error alignment. Our results highlight the value of geometric structure in uncertainty estimation and position HCM as a versatile alternative to conventional techniques.

Applications · Language, Speech and Dialog

Lucas McCabe, Rimon Melamed, Tom Hartvigsen, H Howie Huang

Many black-box techniques for quantifying the uncertainty of large language models (LLMs) rely on repeated LLM sampling, which can be computationally expensive. Therefore, practical applicability demands reliable estimation from few samples. Semantic entropy (SE) is a popular sample-based uncertainty estimator with a discrete formulation attractive for the black-box setting. Recent extensions of SE exhibit improved LLM hallucination detection, but do so with less interpretable methods that admit additional hyperparameters. For this reason, we revisit the canonical discrete semantic entropy (DSE) estimator, finding that it underestimates the ``true'' semantic entropy, as expected from theory. We propose a modified semantic alphabet size estimator, and illustrate that using it to adjust DSE for sample coverage results in more accurate SE estimation in our setting of interest. Furthermore, we find that two semantic alphabet size estimators, including our proposed, flag incorrect LLM responses as well or better than many top-performing alternatives, with the added benefit of remaining highly interpretable.

Shijie Xia, Yuhan Sun, Pengfei Liu

Recently, Large Language Models (LLMs) have been applied to scientific equation discovery, leveraging their embedded scientific knowledge for hypothesis generation. However, current methods typically confine LLMs to the role of an equation proposer within search algorithms like genetic programming. In this paper, we present SR-Scientist, a framework that elevates the LLM from a simple equation proposer to an autonomous AI scientist that writes code to analyze data, implements the equation as code, submits it for evaluation, and optimizes the equation based on experimental feedback. Specifically, we wrap the code interpreter into a set of tools for data analysis and equation evaluation. The agent is instructed to optimize the equation by utilizing these tools over a long horizon with minimal human-defined pipelines. Empirical results show that SR-Scientist outperforms baseline methods by an absolute margin of 6\% to 35\% on datasets covering four science disciplines. Additionally, we demonstrate our method's robustness to noise, the generalization of the discovered equations to out-of-domain data, and their symbolic accuracy. Furthermore, we develop an end-to-end reinforcement learning framework to enhance the agent's capabilities.

Applications · Genetics, Cell Biology, Health, etc

Yicheng Hu, Xinyu Lin, Shulin Li, Wenjie Wang, Fengbin ZHU, Fuli Feng

Subcellular localization is a crucial biological task for drug target identification and function annotation. Although it has been biologically realized that subcellular localization is closely associated with protein structure, no existing dataset offers comprehensive 3D structural information with detailed subcellular localization annotations, thus severely hindering the application of promising structure-based models on this task. To address this gap, we introduce a new benchmark called $\textbf{CAPSUL}$, a $\textbf{C}$omprehensive hum$\textbf{A}$n $\textbf{P}$rotein benchmark for $\textbf{SU}$bcellular $\textbf{L}$ocalization. It features a dataset that integrates diverse 3D structural representations with fine-grained subcellular localization annotations carefully curated by domain experts. We evaluate this benchmark using a variety of state-of-the-art sequence-based and structure-based models, showcasing the importance of involving structural features in this task. Furthermore, we explore reweighting and single-label classification strategies to facilitate future investigation on structure-based methods for this task. Lastly, we showcase the powerful interpretability of structure-based methods through a case study on the Golgi apparatus, where we discover a decisive localization pattern $\alpha$-helix from attention mechanisms, demonstrating the potential for bridging the gap with intuitive biological interpretability and paving the way for data-driven discoveries in cell biology.