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Applications · Everything Else

Chao Wang, Yixin Song, Jinhui Ye, Chuan Qin, Dazhong Shen, Lingfeng Liu, Xiang Wang, Yanyong Zhang

Recently, large language models (LLMs) have been explored for integration with collaborative filtering (CF)-based recommendation systems, which are crucial for personalizing user experiences. However, a key challenge is that LLMs struggle to interpret the latent, non-semantic embeddings produced by CF approaches, limiting recommendation effectiveness and further applications. To address this, we propose FACE, a general interpretable framework that maps CF embeddings into pre-trained LLM tokens. Specifically, we introduce a disentangled projection module to decompose CF embeddings into concept-specific vectors, followed by a quantized autoencoder to convert continuous embeddings into LLM tokens (descriptors). Then, we design a contrastive alignment objective to ensure that the tokens align with corresponding textual signals. Hence, the model-agnostic FACE framework achieves semantic alignment without fine-tuning LLMs and enhances recommendation performance by leveraging their pre-trained capabilities. Empirical results on three real-world recommendation datasets demonstrate performance improvements in benchmark models, with interpretability studies confirming the interpretability of the descriptors. Code is available in \url{https://github.com/YixinRoll/FACE}.

Computer Vision · Vision Models & Multimodal

Kun Xiang, Heng Li, Terry Jingchen Zhang, Yinya Huang, Zirong Liu, Peixin Qu, Jixi He, Jiaqi Chen, Yu-Jie Yuan, Jianhua Han 等

We present SeePhys, a large-scale multimodal benchmark for LLM reasoning grounded in physics questions ranging from middle school to PhD qualifying exams. The benchmark covers 7 fundamental domains spanning the physics discipline, incorporating 21 categories of highly heterogeneous diagrams. In contrast to prior works where visual elements mainly serve auxiliary purposes, our benchmark features a substantial proportion of vision-essential problems (75%) that mandate visual information extraction for correct solutions. Through extensive evaluation, we observe that even the most advanced visual reasoning models (e.g., Gemini-2.5-pro and o4-mini) achieve sub-60% accuracy on our benchmark. These results reveal fundamental challenges in current large language models' visual understanding capabilities, particularly in: (i) establishing rigorous coupling between diagram interpretation and physics reasoning, and (ii) overcoming their persistent reliance on textual cues as cognitive shortcuts.Project Page: github.com/SeePhys/seephys-projectHugging Face: huggingface.co/datasets/SeePhys/SeePhys

Applications · Neuroscience, Cognitive Science

Zixiang Yin, Jiarui Li, Zhengming Ding

Decoding visual signals holds an appealing potential to unravel the complexities of cognition and perception. While recent reconstruction tasks leverage powerful generative models to produce high-fidelity images from neural recordings, they often pay limited attention to the underlying neural representations and rely heavily on pretrained priors. As a result, they provide little insight into how individual voxels encode and differentiate semantic content or how these representations vary across subjects. To mitigate this gap, we present an $i$nsightful **M**ulti-subject **I**nvariant **N**eural **D**ecoding ($i$MIND) model, which employs a novel dual-decoding framework--both biometric and semantic decoding--to offer neural interpretability in a data-driven manner and deepen our understanding of brain-based visual functionalities. Our $i$MIND model operates through three core steps: establishing a shared neural representation space across subjects using a ViT-based masked autoencoder, disentangling neural features into complementary subject-specific and object-specific components, and performing dual decoding to support both biometric and semantic classification tasks. Experimental results demonstrate that $i$MIND achieves state-of-the-art decoding performance with minimal scalability limitations. Furthermore, $i$MIND empirically generates voxel-object activation fingerprints that reveal object-specific neural patterns and enable investigation of subject-specific variations in attention to identical stimuli. These findings provide a foundation for more interpretable and generalizable subject-invariant neural decoding, advancing our understanding of the voxel semantic selectivity as well as the neural vision processing dynamics.

Deep Learning · Everything Else

Pulkit Gopalani, Wei Hu

Training Transformers on algorithmic tasks frequently demonstrates an intriguing *abrupt learning* phenomenon: an extended performance plateau followed by a sudden, sharp improvement. This work investigates the underlying mechanisms for such dynamics, primarily in shallow Transformers. We reveal that during the plateau, the model often develops an interpretable *partial solution* while simultaneously exhibiting a strong *repetition bias* in their outputs. This output degeneracy is accompanied by *internal representation collapse*, where hidden states across different tokens become nearly parallel. We further identify the slow learning of optimal attention maps as a key bottleneck. Hidden progress in attention configuration during the plateau precedes the eventual rapid convergence, and directly intervening on attention significantly alters plateau duration and the severity of repetition bias and representational collapse. We validate that these identified phenomena—repetition bias and representation collapse—are not artifacts of toy setups but also manifest in the early pre-training stage of large language models like Pythia and OLMo.

Applications · Neuroscience, Cognitive Science

Liwei Huang, Zhengyu Ma, Liutao Yu, Huihui Zhou, Yonghong Tian

Seeking high-quality representations with latent variable models (LVMs) to reveal the intrinsic correlation between neural activity and behavior or sensory stimuli has attracted much interest. In the study of the biological visual system, naturalistic visual stimuli are inherently high-dimensional and time-dependent, leading to intricate dynamics within visual neural activity. However, most work on LVMs has not explicitly considered neural temporal relationships. To cope with such conditions, we propose Time-Evolving Visual Dynamical System (TE-ViDS), a sequential LVM that decomposes neural activity into low-dimensional latent representations that evolve over time. To better align the model with the characteristics of visual neural activity, we split latent representations into two parts and apply contrastive learning to shape them. Extensive experiments on synthetic datasets and real neural datasets from the mouse visual cortex demonstrate that TE-ViDS achieves the best decoding performance on naturalistic scenes/movies, extracts interpretable latent trajectories that uncover clear underlying neural dynamics, and provides new insights into differences in visual information processing between subjects and between cortical regions. In summary, TE-ViDS is markedly competent in extracting stimulus-relevant embeddings from visual neural activity and contributes to the understanding of visual processing mechanisms. Our codes are available at https://github.com/Grasshlw/Time-Evolving-Visual-Dynamical-System.

Deep Learning · Graph Neural Networks

Sofiane Ennadir, Oleg Smirnov, Yassine ABBAHADDOU, Lele Cao, Johannes Lutzeyer

Graph Neural Networks (GNNs) have achieved strong performance across a range of graph representation learning tasks, yet their adversarial robustness in graph classification remains underexplored compared to node classification. While most existing defenses focus on the message-passing component, this work investigates the overlooked role of pooling operations in shaping robustness. We present a theoretical analysis of standard flat pooling methods (sum, average and max), deriving upper bounds on their adversarial risk and identifying their vulnerabilities under different attack scenarios and graph structures. Motivated by these insights, we propose Robust Singular Pooling (RS-Pool), a novel pooling strategy that leverages the dominant singular vector of the node embedding matrix to construct a robust graph-level representation. We theoretically investigate the robustness of RS-Pool and interpret the resulting bound leading to improved understanding of our proposed pooling operator. While our analysis centers on Graph Convolutional Networks (GCNs), RS-Pool is model-agnostic and can be implemented efficiently via power iteration. Empirical results on real-world benchmarks show that RS-Pool provides better robustness than the considered pooling methods when subject to state-of-the-art adversarial attacks while maintaining competitive clean accuracy.

Social Aspects · Accountability, Transparency and Interpretability

蕾蕾 温, Liwei Zheng, Hongda Li, Lijun Sun, Zhihua Wei, Wen Shen

In recent years, large language models (LLMs) have made significant advancements in arithmetic reasoning. However, the internal mechanism of how LLMs solve arithmetic problems remains unclear. In this paper, we propose explaining arithmetic reasoning in LLMs using game-theoretic interactions. Specifically, we disentangle the output score of the LLM into numerous interactions between the input words. We quantify different types of interactions encoded by LLMs during forward propagation to explore the internal mechanism of LLMs for solving arithmetic problems. We find that (1) the internal mechanism of LLMs for solving simple one-operator arithmetic problems is their capability to encode operand-operator interactions and high-order interactions from input samples. Additionally, we find that LLMs with weak one-operator arithmetic capabilities focus more on background interactions. (2) The internal mechanism of LLMs for solving relatively complex two-operator arithmetic problems is their capability to encode operator interactions and operand interactions from input samples. (3) We explain the task-specific nature of the LoRA method from the perspective of interactions.

Social Aspects · Accountability, Transparency and Interpretability

Aleksandar Petrov, Shruti Agarwal, Philip Torr, Adel Bibi, John Collomosse

Watermarking, the practice of embedding imperceptible information into media such as images, videos, audio, and text, is essential for intellectual property protection, content provenance and attribution. The growing complexity of digital ecosystems necessitates watermarks for different uses to be embedded in the same media. However, to detect and decode all watermarks, they need to coexist well with one another. We perform the first study of coexistence of deep image watermarking methods and, contrary to intuition, we find that various open-source watermarks can coexist with only minor impacts on image quality and decoding robustness. The coexistence of watermarks also opens the avenue for ensembling watermarking methods. We show how ensembling can increase the overall message capacity and enable new trade-offs between capacity, accuracy, robustness and image quality, without needing to retrain the base models.

Chengzhuo Tong, Ziyu Guo, Renrui Zhang, Wenyu Shan, Xinyu Wei, Zhenghao Xing, Hongsheng Li, Pheng-Ann Heng

Recent advancements underscore the significant role of Reinforcement Learning (RL) in enhancing the Chain-of-Thought (CoT) reasoning capabilities of large language models (LLMs). Two prominent RL algorithms, Direct Preference Optimization (DPO) and Group Relative Policy Optimization (GRPO), are central to these developments, showcasing different pros and cons. Autoregressive image generation, also interpretable as a sequential CoT reasoning process, presents unique challenges distinct from LLM-based CoT reasoning. These encompass ensuring text-image consistency, improving image aesthetic quality, and designing sophisticated reward models, rather than relying on simpler rule-based rewards. While recent efforts have extended RL to this domain, these explorations typically lack an in-depth analysis of the domain-specific challenges and the characteristics of different RL strategies. To bridge this gap, we provide the first comprehensive investigation of the GRPO and DPO algorithms in autoregressive image generation, evaluating their ***in-domain*** performance and ***out-of-domain*** generalization, while scrutinizing the impact of ***different reward models*** on their respective capabilities. Our findings reveal that GRPO and DPO exhibit distinct advantages, and crucially, that reward models possessing stronger intrinsic generalization capabilities potentially enhance the generalization potential of the applied RL algorithms. Furthermore, we systematically explore ***three prevalent scaling strategies*** to enhance both their in-domain and out-of-domain proficiency, deriving unique insights into efficiently scaling performance for each paradigm. We hope our study paves a new path for inspiring future work on developing more effective RL algorithms to achieve robust CoT reasoning in the realm of autoregressive image generation.

Applications · Physics

Haoran Li, CHENHAN XIAO, Muhao Guo, Yang Weng

Learning dynamics is essential for model-based control and Reinforcement Learning in systems operating in changing environments, such as robotics, autonomous vehicles, and power systems. However, limited system measurements, such as those from low-resolution meters, demand sample-efficient learning. Symmetry provides a powerful inductive bias by characterizing equivalent relations in system behavior to improve sample efficiency. While recent methods attempt to discover symmetries from data, they typically assume a single global symmetry group and treat symmetry discovery and dynamic learning as separate tasks, leading to limited expressiveness and error accumulation. In this paper, we propose the Latent Mixture of Symmetries (Latent MoS), an expressive model that captures symmetry-governed latent factors from complex dynamical measurements. Latent MoS focuses on dynamic learning while locally preserving the underlying symmetric transformations. To further capture long-range temporal equivalence, we introduce a hierarchical architecture that stacks Latent MoS blocks across multiple time scales. Numerical experiments across diverse physical systems demonstrate that Latent MoS significantly outperforms state-of-the-art baselines in interpolation and extrapolation tasks while offering interpretable latent representations suitable for future geometric and safety-critical analysis.

Deep Learning · Everything Else

Floris Holstege, Shauli Ravfogel, Bram Wouters

Modern neural networks often encode unwanted concepts alongside task-relevant information, leading to fairness and interpretability concerns. Existing post-hoc approaches can remove undesired concepts but often degrade useful signals. We introduce SPLINCE—Simultaneous Projection for LINear concept removal and Covariance prEservation—which eliminates sensitive concepts from representations while exactly preserving their covariance with a target label. SPLINCE achieves this via an oblique projection that ``splices out'' the unwanted direction yet protects important label correlations. Theoretically, it is the unique solution that removes linear concept predictability and maintains target covariance with minimal embedding distortion. Empirically, SPLINCE outperforms baselines on benchmarks such as Bias in Bios and Winobias, removing protected attributes while minimally damaging main-task information.

Probabilistic Methods

Shengyuan Chen, Zheng Yuan, Qinggang Zhang, Wen Hua, Jiannong Cao, Xiao Huang

Entity alignment (EA) aims to merge two knowledge graphs (KGs) by identifying equivalent entity pairs. Existing methods can be categorized into symbolic and neural models. Symbolic models, while precise, struggle with substructure heterogeneity and sparsity, whereas neural models, although effective, generally lack interpretability and cannot handle uncertainty. We propose NeuSymEA, a unified neuro-symbolic reasoning framework that combines the strengths of both methods to fully exploit the cross-KG structural pattern for robust entity alignment. NeuSymEA models the joint probability of all possible pairs' truth scores in a Markov random field, regulated by a set of rules, and optimizes it with the variational EM algorithm. In the E-step, a neural model parameterizes the truth score distributions and infers missing alignments. In the M-step, the rule weights are updated based on the observed and inferred alignments, handling uncertainty. We introduce an efficient symbolic inference engine driven by logic deduction, enabling reasoning with extended rule lengths. NeuSymEA achieves a significant 7.6\% hit@1 improvement on $DBP15K_{ZH-EN}$ compared with strong baselines and demonstrates robustness in low-resource settings, achieving 73.7\% hit@1 accuracy on $DBP15K_{FR-EN}$ with only 1\% pairs as seed alignments. Codes are released at https://github.com/chensyCN/NeuSymEA-NeurIPS25.

Applications · Genetics, Cell Biology, etc

Xiaotang Wang, Xuanwei Lin, Yun Zhu, Hao Li, Yongqi Zhang

Crossmodal matching in single-cell omics is essential for explaining biological regulatory mechanisms and enhancing downstream analyses. However, current single-cell crossmodal models often suffer from three limitations: sparse modality signals, underutilization of biological attributes, and insufficient modeling of regulatory interactions. These challenges hinder generalization in data-scarce settings and restrict the ability to uncover fine-grained biologically meaningful crossmodal relationships. Here, we present a novel framework which reformulates crossmodal matching as a graph classification task on Attributed Bipartite Graphs (ABGs). It models single-cell ATAC-RNA data as an ABG, where each expressed ATAC and RNA is treated as a distinct node with unique IDs and biological features. To model crossmodal interaction patterns on the constructed ABG, we propose $\text{Bi}^2\text{Former}$, a **bi**ologically-driven **bi**partite graph trans**former** that learns interpretable attention over ATAC–RNA pairs. This design enables the model to effectively learn and explain biological regulatory relationships between ATAC and RNA modalities. Extensive experiments demonstrate that $\text{Bi}^2\text{Former}$ achieves state-of-the-art performance in crossmodal matching across diverse datasets, remains robust under sparse training data, generalizes to unseen cell types and datasets, and reveals biologically meaningful regulatory patterns. This work pioneers an ABG-based approach for single-cell crossmodal matching, offering a powerful framework for uncovering regulatory interactions at the single-cell omics. Our code is available at: https://github.com/wangxiaotang0906/Bi2Former.

Applications · Neuroscience, Cognitive Science

Muquan Yu, Mu Nan, Hossein Adeli, Jacob Prince, John A. Pyles, Leila Wehbe, Maggie Henderson, Michael Tarr, Andrew Luo

Understanding functional representations within higher visual cortex is a fundamental question in computational neuroscience. While artificial neural networks pretrained on large-scale datasets exhibit striking representational alignment with human neural responses, learning image-computable models of visual cortex relies on individual-level, large-scale fMRI datasets. The necessity for expensive, time-intensive, and often impractical data acquisition limits the generalizability of encoders to new subjects and stimuli. **BraInCoRL** uses in-context learning to predict voxelwise neural responses from few-shot examples *without any additional finetuning* for novel subjects and stimuli. We leverage a transformer architecture that can flexibly condition on a variable number of in-context image stimuli, learning an inductive bias over multiple subjects. During training, we explicitly optimize the model for in-context learning. By jointly conditioning on image features and voxel activations, our model learns to directly generate better performing voxelwise models of higher visual cortex. We demonstrate that BraInCoRL consistently outperforms existing voxelwise encoder designs in a low-data regime when evaluated on entirely novel images, while also exhibiting strong test-time scaling behavior. The model also generalizes to an entirely new visual fMRI dataset, which uses different subjects and fMRI data acquisition parameters. Further, BraInCoRL facilitates better interpretability of neural signals in higher visual cortex by attending to semantically relevant stimuli. Finally, we show that our framework enables interpretable mappings from natural language queries to voxel selectivity.

Applications · Time Series

Jiaming Ma, Binwu Wang, Qihe Huang, Guanjun Wang, Pengkun Wang, Zhengyang Zhou, Yang Wang

The stable periodic patterns present in the time series data serve as the foundation for long-term forecasting. However, existing models suffer from limitations such as continuous and chaotic input partitioning, as well as weak inductive biases, which restrict their ability to capture such recurring structures. In this paper, we propose MoFo, which interprets periodicity as both the correlation of period-aligned time steps and the trend of period-offset time steps. We first design period-structured patches—2D tensors generated through discrete sampling—where each row contains only period-aligned time steps, enabling direct modeling of periodic correlations. Period-offset time steps within a period are aligned in columns. To capture trends across these offset time steps, we introduce a period-aware modulator. This modulator introduces an adaptive strong inductive bias through a regulated relaxation function, encouraging the model to generate attention coefficients that align with periodic trends. This function is end-to-end trainable, enabling the model to adaptively capture the distinct periodic patterns across diverse datasets. Extensive empirical results on widely used benchmark datasets demonstrate that MoFo achieves competitive performance while maintaining high memory efficiency and fast training speed.

Social Aspects · Fairness, Equity, Justice and Safety

Daniel Jarne Ornia, Nicholas Bishop, Joel Dyer, Wei-Chen Lee, Anisoara Calinescu, Doyne Farmer, Michael Wooldridge

Advanced reasoning models with agentic capabilities (AI agents) are deployed to interact with humans and to solve sequential decision‑making problems under (often approximate) utility functions and internal models. When such problems have resource or failure constraints where action sequences may be forcibly terminated once resources are exhausted, agents face implicit trade‑offs that reshape their utility-driven (rational) behaviour. Additionally, since these agents are typically commissioned by a human principal to act on their behalf, asymmetries in constraint exposure can give rise to previously unanticipated misalignment between human objectives and agent incentives. We formalise this setting through a survival bandit framework, provide theoretical and empirical results that quantify the impact of survival‑driven preference shifts, identify conditions under which misalignment emerges and propose mechanisms to mitigate the emergence of risk-seeking or risk-averse behaviours. As a result, this work aims to increase understanding and interpretability of emergent behaviours of AI agents operating under such survival pressure, and offer guidelines for safely deploying such AI systems in critical resource‑limited environments.

Deep Learning · Everything Else

Seonghwan Park, Jueun Mun, Donghyun Oh, Namhoon Lee

Concept bottleneck models (CBMs) ensure interpretability by decomposing predictions into human interpretable concepts. Yet the annotations used for training CBMs that enable this transparency are often noisy, and the impact of such corruption is not well understood. In this study, we present the first systematic study of noise in CBMs and show that even moderate corruption simultaneously impairs prediction performance, interpretability, and the intervention effectiveness. Our analysis identifies a susceptible subset of concepts whose accuracy declines far more than the average gap between noisy and clean supervision and whose corruption accounts for most performance loss. To mitigate this vulnerability we propose a two-stage framework. During training, sharpness-aware minimization stabilizes the learning of noise-sensitive concepts. During inference, where clean labels are unavailable, we rank concepts by predictive entropy and correct only the most uncertain ones, using uncertainty as a proxy for susceptibility. Theoretical analysis and extensive ablations elucidate why sharpness-aware training confers robustness and why uncertainty reliably identifies susceptible concepts, providing a principled basis that preserves both interpretability and resilience in the presence of noise.

Applications · Neuroscience, Cognitive Science

Xiuning Zhang, Xincheng Lu, Nihong Chen, Yuanyuan Mi

Serial dependence reflects how recent sensory history shapes current perception, producing two opposing biases: repulsion, where perception is repelled from recent stimuli, and attraction, where perception is drawn toward them. Repulsion typically occurs at the sensory perception stage, while attraction arises at the post-perception stage. To uncover the neural basis of these effects, we developed a two-layer continuous attractor neural network model incorporating synaptic short-term plasticity (STP). The lower layer, dominated by synaptic depression, models sensory processing and drives repulsion due to sustained neurotransmitter depletion. The higher layer, dominated by synaptic facilitation, models post-perception processing and drives attraction by sustained high neurotransmitter release probability. Our model successfully explains the serial dependence phenomena observed in the visual orientation judgment experiments, highlighting STP as the critical mechanism, with its time constants defining the temporal windows of repulsion and attraction. Furthermore, the model provides a neural foundation for the Bayesian interpretation of serial dependence. This study advances our understanding of how the neural system leverages STP to balance sensitivity in sensory perception with stability in post-perceptual cognition.

Social Aspects · Accountability, Transparency and Interpretability

Samuele Bortolotti, Emanuele Marconato, Paolo Morettin, Andrea Passerini, Stefano Teso

Concept-based Models are neural networks that learn a concept extractor to map inputs to high-level concepts and an inference layer to translate these into predictions. Ensuring these modules produce interpretable concepts and behave reliably in out-of-distribution is crucial, yet the conditions for achieving this remain unclear. We study this problem by establishing a novel connection between Concept-based Models and reasoning shortcuts (RSs), a common issue where models achieve high accuracy by learning low-quality concepts, even when the inference layer is fixed and provided upfront. Specifically, we extend RSs to the more complex setting of Concept-based Models and derive theoretical conditions for identifying both the concepts and the inference layer. Our empirical results highlight the impact of RSs and show that existing methods, even combined with multiple natural mitigation strategies, often fail to meet these conditions in practice.

Applications · Neuroscience, Cognitive Science

Vinam Arora, Divyansha Lachi, Ian Knight, Mehdi Azabou, Blake Richards, Cole Hurwitz, Joshua H Siegle, Eva L Dyer

Identifying the functional identity of individual neurons is essential for interpreting circuit dynamics, yet it remains a major challenge in large-scale _in vivo_ recordings where anatomical and molecular labels are often unavailable. Here we introduce NuCLR, a self-supervised framework that learns context-aware representations of neuron identity by modeling each neuron's role within the broader population. NuCLR employs a spatio-temporal transformer that captures both within-neuron dynamics and across-neuron interactions. It is trained with a sample-wise contrastive objective that encourages temporally-stable and discriminative embeddings. Across multiple open-access datasets, NuCLR outperforms prior methods in both cell type and brain region classification. Critically, it exhibits strong zero-shot generalization to entirely new populations, without any retraining or access to stimulus labels. Furthermore, we demonstrate that our framework scales effectively with data size. Overall, our results demonstrate that modeling population context is crucial for understanding neuron identity and that rich signal for cell-typing and neuron localization is present in neural activity alone. Code available at: https://github.com/nerdslab/nuclr.