NeurIPS 2025 Papers

Recent work has shown that the attention maps of the widely popular DINOv2 model exhibit artifacts, which hurt both model interpretability and performance on dense image tasks. These artifacts emerge due to the model repurposing patch tokens with redundant local information for the storage of global image information. To address this problem, additional register tokens have been incorporated in which the model can store such information instead. We carefully examine the influence of these register tokens on the relationship between global and local image features, showing that while register tokens yield cleaner attention maps, these maps do not accurately reflect the integration of local image information in large models. Instead, global information is dominated by information extracted from register tokens, leading to a disconnect between local and global features. Inspired by these findings, we show that the [CLS] token itself leads to a very similar phenomenon in models without explicit register tokens. Our work shows that care must be taken when interpreting attention maps of large ViTs. Further, by clearly attributing the faulty behavior to register and [CLS] tokens, we show a path towards more interpretable vision models.

Decoding of visual stimuli from noninvasive neuroimaging techniques such as functional magnetic resonance (fMRI) has advanced rapidly in the last years; yet, most high-performing brain decoding models rely on complicated, non-interpretable latent spaces. In this study we present an interpretable brain decoding framework that inserts a semantic bottleneck into BrainDiffuser, a well established, simple and linear decoding pipeline. We firstly produce a $214-\text{dimensional}$ binary interpretable space $\mathcal{L}$ for images, in which each dimension answers to a specific question about the image (e.g., "Is there a person?", "Is it outdoors?"). A first ridge regression maps voxel activity to this semantic space. Because this mapping is linear, its weight matrix can be visualized as maps of voxel importance for each dimension of $\mathcal{L}$, revealing which cortical regions influence mostly each semantic dimension. A second regression then transforms these concept vectors into CLIP embeddings required to produce the final decoded image, conditioning the BrainDiffuser model. We found that voxel-wise weight maps for individual questions are highly consistent with canonical category-selective regions in the visual cortex (face, bodies, places, words), simultaneously revealing that activation distributions, not merely location, bear semantic meaning in the brain. Visual brain decoding performances are only slightly lower compared to the original BrainDiffuser metrics (e.g., the CLIP similarity is decreased by $\leq 4$% for the four subjects), yet offering substantial gains in interpretability and neuroscientific insights. These results show that our interpretable brain decoding pipeline enables voxel-level analysis of semantic representations in the human brain without sacrificing decoding accuracy.

Recent developments in DNN-based image watermarking techniques have achieved impressive results in protecting digital content. However, most existing methods are constrained to low-resolution images as they need to encode the entire image, leading to prohibitive memory and computational costs when applied to high-resolution images. Moreover, they lack robustness to distortions prevalent in large-image transmission, such as extreme scaling and random cropping. To address these issues, we propose a novel watermarking method based on implicit neural representations (INRs). Leveraging the properties of INRs, our method employs resolution-independent coordinate sampling mechanism to generate watermarks pixel-wise, achieving ultra-high resolution watermark generation with fixed and limited memory and computational resources. This design ensures strong robustness in watermark extraction, even under extreme cropping and scaling distortions. Additionally, we introduce a hierarchical multi-scale coordinate embedding and a low-rank watermark injection strategy to ensure high-quality watermark generation and robust decoding. Experimental results demonstrate that our method significantly outperforms existing schemes in terms of both robustness and computational efficiency while preserving high image quality. Our approach achieves an accuracy greater than 98\% in watermark extraction with only 0.4\% of the image area in 2K images. These results highlight the effectiveness of our method, making it a promising solution for large-scale and high-resolution image watermarking applications.

Patent examination remains an ongoing challenge in the NLP literature even after the advent of large language models (LLMs), as it requires an extensive yet nuanced human judgment on whether a submitted $\textit{claim}$ meets the statutory standards of $\textit{novelty}$ and $\textit{non-obviousness}$ against previously granted claims—$\textit{prior art}$—in expert domains. Previous NLP studies have approached this challenge as a prediction task (e.g., forecasting grant outcomes) with high-level proxies such as similarity metrics or classifiers trained on historical labels. However, this approach often overlooks the step-by-step evaluations that examiners must make with profound information, including rationales for the decisions provided in $\textit{office actions}$ documents, which also makes it harder to measure the current state of techniques in patent review processes. To fill this gap, we construct PANORAMA, a dataset of 8,143 U.S. patent examination records that preserves the full decision trails, including original applications, all cited references, $\textit{Non-Final Rejections}$, and $\textit{Notices of Allowance}$. Also, PANORAMA decomposes the trails into sequential benchmarks that emulate patent professionals' patent review processes and allow researchers to examine large language models' capabilities at each step of them. Our findings indicate that, although LLMs are relatively effective at retrieving relevant prior art and pinpointing the pertinent paragraphs, they struggle to assess the novelty and non-obviousness of patent claims. We discuss these results and argue that advancing NLP, including LLMs, in the patent domain requires a deeper understanding of real-world patent examination. Our dataset is openly available at https://huggingface.co/datasets/LG-AI-Research/PANORAMA.

Graph neural networks (GNNs) have emerged as powerful tools for learning protein structures by capturing spatial relationships at the residue level. However, existing GNN-based methods often face challenges in learning multiscale representations and modeling long-range dependencies efficiently. In this work, we propose an efficient multiscale graph-based learning framework tailored to proteins. Our proposed framework contains two crucial components: (1) It constructs a hierarchical graph representation comprising a collection of fine-grained subgraphs, each corresponding to a secondary structure motif (e.g., $\alpha$-helices, $\beta$-strands, loops), and a single coarse-grained graph that connects these motifs based on their spatial arrangement and relative orientation. (2) It employs two GNNs for feature learning: the first operates within individual secondary motifs to capture local interactions, and the second models higher-level structural relationships across motifs. Our modular framework allows a flexible choice of GNN in each stage. Theoretically, we show that our hierarchical framework preserves the desired maximal expressiveness, ensuring no loss of critical structural information. Empirically, we demonstrate that integrating baseline GNNs into our multiscale framework remarkably improves prediction accuracy and reduces computational cost across various benchmarks.

Recent studies have demonstrated that fine-tuning language models with brain data can improve their semantic understanding, although these findings have so far been limited to English. Interestingly, similar to the shared multilingual embedding space of pretrained multilingual language models, human studies provide strong evidence for a shared semantic system in bilingual individuals. Here, we investigate whether fine-tuning language models with bilingual brain data changes model representations in a way that improves them across multiple languages. To test this, we fine-tune monolingual and multilingual language models using brain activity recorded while bilingual participants read stories in English and Chinese. We then evaluate how well these representations generalize to the bilingual participants’ first language, their second language, and several other languages that the participants are not fluent in. We assess the fine-tuned language models on brain encoding performance and downstream NLP tasks. Our results show that bilingual brain-informed fine-tuned language models outperform their vanilla (pretrained) counterparts in both brain encoding performance and most downstream NLP tasks across multiple languages. These findings suggest that brain-informed fine-tuning improves multilingual understanding in language models, offering a bridge between cognitive neuroscience and NLP research. We make our code publicly available.

Machine unlearning has become a focal point in recent research, yet the specific area of feature unlearning has not been thoroughly explored. Feature unlearning involves the elimination of specific features' effects from an already trained model, presenting distinct challenges that are still not comprehensively addressed. This paper presents a novel and straightforward approach to feature unlearning that employs a tactical shuffling of the features designated for removal. By redistributing the values of the features targeted for unlearning throughout the original training dataset and subsequently fine-tuning the model with this shuffled data, our proposed method provides a theoretical guarantee for effective feature unlearning. Under mild assumptions, our method can effectively disrupt the established correlations between unlearned features and the target outcomes, while preserving the relationships between the remaining features and the predicted outcomes. Our empirical studies across various datasets,validate that our approach not only successfully removes the effects of specified features but also maintains the informational integrity of the remaining features while achieving a faster convergence rate.

Growing evidence suggests that synaptic weights in the brain follow heavy-tailed distributions, yet most theoretical analyses of recurrent neural networks (RNNs) assume Gaussian connectivity. We systematically study the activity of RNNs with random weights drawn from biologically plausible Lévy alpha-stable distributions. While mean-field theory for the infinite system predicts that the quiescent state is always unstable---implying ubiquitous chaos---our finite-size analysis reveals a sharp transition between quiescent and chaotic dynamics. We theoretically predict the gain at which the finite system transitions from quiescent to chaotic dynamics, and validate it through simulations. Compared to Gaussian networks, finite heavy-tailed RNNs exhibit a broader gain regime near the edge of chaos, namely, a slow transition to chaos. However, this robustness comes with a tradeoff: heavier tails reduce the Lyapunov dimension of the attractor, indicating lower effective dimensionality. Our results reveal a biologically aligned tradeoff between the robustness of dynamics near the edge of chaos and the richness of high-dimensional neural activity. By analytically characterizing the transition point in finite-size networks---where mean-field theory breaks down---we provide a tractable framework for understanding dynamics in realistically sized, heavy-tailed neural circuits.

Spike sorting is an essential process in neural recording, which identifies and separates electrical signals from individual neurons recorded by electrodes in the brain, enabling researchers to study how specific neurons communicate and process information. Although there exist a number of spike sorting methods which have contributed to significant neuroscientific breakthroughs, many are heuristically designed, making it challenging to verify their correctness due to the difficulty of obtaining ground truth labels from real-world neural recordings. In this work, we explore a data-driven, deep learning-based approach. We begin by creating a large-scale dataset through electrophysiology simulations using biologically realistic computational models. We then present SimSort, a pretraining framework for spike sorting. Trained solely on simulated data, SimSort demonstrates zero-shot generalizability to real-world spike sorting tasks, yielding consistent improvements over existing methods across multiple benchmarks. These results highlight the potential of simulation-driven pretraining to enhance the robustness and scalability of spike sorting in experimental neuroscience.

Participating in efforts to endow generative AI with the 3D physical world perception, we propose I2-NeRF, a novel neural radiance field framework that enhances isometric and isotropic metric perception under media degradation. While existing NeRF models predominantly rely on object-centric sampling, I2-NeRF introduces a reverse-stratified upsampling strategy to achieve near-uniform sampling across 3D space, thereby preserving isometry. We further present a general radiative formulation for media degradation that unifies emission, absorption, and scattering into a particle model governed by the Beer–Lambert attenuation law. By matting direct and media-induced in-scatter radiance, this formulation extends naturally to complex media environments such as underwater, haze, and even low-light scenes. By treating light propagation uniformly in both vertical and horizontal directions, I2-NeRF enables isotropic metric perception and can even estimate medium properties such as water depth. Experiments on real-world datasets demonstrate that our method significantly improves both reconstruction fidelity and physical plausibility compared to existing approaches. The source code will be released.

The primate visual system is typically divided into two streams — the ventral stream, responsible for object recognition, and the dorsal stream, responsible for encoding spatial relations and motion. Recent studies have shown that convolutional neural networks (CNNs) pretrained on object recognition tasks are remarkably effective at predicting neuronal responses in the ventral stream, shedding light on the neural mechanisms underlying object recognition. However, similar models of the dorsal stream remain underdeveloped due to the lack of large scale datasets encompassing dorsal stream areas. To address this gap, we present STSBench, a dataset of large-scale, single neuron recordings from over 2,000 neurons in the superior temporal sulcus (STS), a nearly 50-fold increase over existing dorsal stream datasets, collected while Rhesus macaques viewed thousands of unique, natural videos. We show that our dataset can be used for benchmarking encoding models of dorsal stream neuronal responses and reconstructing visual input from neural activity.

Calibration is a fundamental concept that aims at ensuring the reliability of probabilistic predictions by aligning them with real-world outcomes. There is a surge of studies on new calibration measures that are easier to optimize compared to the classical $\ell_1$-Calibration while still having strong implications for downstream applications. One recent such example is the work by Fishelson et al. (2025) who show that it is possible to achieve $\tilde{\mathcal{O}}(T^{1/3})$ pseudo $\ell_{2}$-Calibration error via minimizing pseudo swap regret of the squared loss, which in fact implies the same bound for all bounded proper losses with a smooth univariate form. In this work, we significantly generalize their result in the following ways: (a) in addition to smooth univariate forms, our algorithm also simultaneously achieves $\tilde{\mathcal{O}}(T^{1/3})$ swap regret for any proper loss with a twice continuously differentiable univariate form (such as Tsallis entropy); (b) our bounds hold not only for pseudo swap regret that measures losses using the forecaster's distributions on predictions, but also hold for the actual swap regret that measures losses using the forecaster's actual realized predictions. We achieve so by introducing a new stronger notion of calibration called (pseudo) KL-Calibration, which we show is equivalent to the (pseudo) swap regret with respect to log loss. We prove that there exists an algorithm that achieves $\tilde{\mathcal{O}}(T^{1/3})$ KL-Calibration error and provide an explicit algorithm that achieves $\tilde{\mathcal{O}}(T^{1/3})$ pseudo KL-Calibration error. Moreover, we show that the same algorithm achieves ${\mathcal{O}}(T^{1/3} (\log T) ^ {-\frac{1}{3}}\log (T/{\delta}))$ swap regret with probability at least $1-\delta$ for any proper loss with a smooth univariate form, which implies $\tilde{\mathcal{O}}(T^{1/3})$ $\ell_2$-Calibration error. A technical contribution of our work is a new randomized rounding procedure and a non-uniform discretization scheme to minimize the swap regret for log loss.

We introduce *Error Broadcast and Decorrelation* (EBD), a novel learning framework for neural networks that addresses credit assignment by directly broadcasting output errors to individual layers, circumventing weight transport of backpropagation. EBD is rigorously grounded in the stochastic orthogonality property of Minimum Mean Square Error estimators. This fundamental principle states that the error of an optimal estimator is orthogonal to functions of the input. Guided by this insight, EBD defines layerwise loss functions that directly penalize correlations between layer activations and output errors, thereby establishing a principled foundation for error broadcasting. This theoretically sound mechanism naturally leads to the experimentally observed three-factor learning rule and integrates with biologically plausible frameworks to enhance performance and plausibility. Numerical experiments demonstrate EBD’s competitive or better performance against other error-broadcast methods on benchmark datasets. Our findings establish EBD as an efficient, biologically plausible, and principled alternative for neural network training.

Biological function arises through the dynamical interactions of multiple subsystems, including those between brain areas, within gene regulatory networks, and more. A common approach to understanding these systems is to model the dynamics of each subsystem and characterize communication between them. An alternative approach is through the lens of control theory: how the subsystems control one another. This approach involves inferring the directionality, strength, and contextual modulation of control between subsystems. However, methods for understanding subsystem control are typically linear and cannot adequately describe the rich contextual effects enabled by nonlinear complex systems. To bridge this gap, we devise a data-driven nonlinear control-theoretic framework to characterize subsystem interactions via the Jacobian of the dynamics. We address the challenge of learning Jacobians from time-series data by proposing the JacobianODE, a deep learning method that leverages properties of the Jacobian to directly estimate it for arbitrary dynamical systems from data alone. We show that JacobianODE models outperform existing Jacobian estimation methods on challenging systems, including high-dimensional chaos. Applying our approach to a multi-area recurrent neural network (RNN) trained on a working memory selection task, we show that the “sensory” area gains greater control over the “cognitive” area over learning. Furthermore, we leverage the JacobianODE to directly control the trained RNN, enabling precise manipulation of its behavior. Our work lays the foundation for a theoretically grounded and data-driven understanding of interactions among biological subsystems.

Abstract Visual Reasoning (AVR) entails discerning latent patterns in visual data and inferring underlying rules. Existing solutions often lack scalability and adaptability, as deep architectures tend to overfit training data, and static neural networks fail to dynamically capture diverse rules. To tackle the challenges, we propose a Dynamic and Scalable Reasoning Framework (DSRF) that greatly enhances the reasoning ability by widening the network instead of deepening it, and dynamically adjusting the reasoning network to better fit novel samples instead of a static network. Specifically, we design a Multi-View Reasoning Pyramid (MVRP) to capture complex rules through layered reasoning to focus features at each view on distinct combinations of attributes, widening the reasoning network to cover more attribute combinations analogous to complex reasoning rules. Additionally, we propose a Dynamic Domain-Contrast Prediction (DDCP) block to handle varying task-specific relationships dynamically by introducing a Gram matrix to model feature distributions, and a gate matrix to capture subtle domain differences between context and target features. Extensive experiments on six AVR tasks demonstrate DSRF’s superior performance, achieving state-of-the-art results under various settings. Code is available here: https://github.com/UNNCRoxLi/DSRF.

Model merging has emerged as a promising technique for enhancing large language models, though its application in large-scale pre-training remains relatively unexplored. In this paper, we present a comprehensive investigation of model merging techniques during the pre-training process. Through extensive experiments with both dense and Mixture-of-Experts (MoE) architectures ranging from millions to over 100 billion parameters, we demonstrate that merging checkpoints trained with constant learning rates not only achieves significant performance improvements but also enables accurate prediction of annealing behavior. These improvements lead to both more efficient model development and significantly lower training costs. Our detailed ablation studies on merging strategies and hyperparameters provide new insights into the underlying mechanisms while uncovering novel applications. Through comprehensive experimental analysis, we offer the open-source community practical pre-training guidelines for effective model merging.

Riemannian symmetric spaces (RSS) such as hyperbolic spaces and symmetric positive definite (SPD) manifolds have become popular spaces for representation learning. In this paper, we propose a novel approach for building discriminative neural networks on Siegel spaces, a family of RSS that is largely unexplored in machine learning tasks. For classification applications, one focus of recent works is the construction of multiclass logistic regression (MLR) and fully-connected (FC) layers for hyperbolic and SPD neural networks. Here we show how to build such layers for Siegel neural networks. Our approach relies on the quotient structure of those spaces and the notation of vector-valued distance on RSS. We demonstrate the relevance of our approach on two applications, i.e., radar signal classification and node classification. Our results successfully demonstrate state-of-the-art performance across all datasets.

Brain-computer interfaces have shown great potential in motor and speech rehabilitation, but still suffer from low performance stability across days, mostly due to the instabilities in neural signals. These instabilities, partially caused by neuron deaths and electrode shifts, leading to channel-level variabilities among different recording days. Previous studies mostly focused on aligning multi-day neural signals of onto a low-dimensional latent manifold to reduce the variabilities, while faced with difficulties when neural signals exhibit significant drift. Here, we propose to learn a channel-level invariant neural representation to address the variabilities in channels across days. It contains a channel-rearrangement module to learn stable representations against electrode shifts, and a channel reconstruction module to handle the missing neurons. The proposed method achieved the state-of-the-art performance with cross-day decoding tasks over two months, on multiple benchmark BCI datasets. The proposed approach showed good generalization ability that can be incorporated to different neural networks.

The energy paradigm, exemplified by Hopfield networks, offers a principled framework for memory in neural systems by interpreting dynamics as descent on an energy surface. While powerful for static associative memories, it falls short in modeling sequential memory, where transitions between memories are essential. We introduce the Exponential Dynamic Energy Network (EDEN), a novel architecture that extends the energy paradigm to temporal domains by evolving the energy function over multiple timescales. EDEN combines a static high-capacity energy network with a slow, asymmetrically interacting modulatory population, enabling robust and controlled memory transitions. We formally derive short-timescale energy functions that govern local dynamics and use them to analytically compute memory escape times, revealing a phase transition between static and dynamic regimes. The analysis of capacity, defined as the number of memories that can be stored with minimal error rate as a function of the dimensions of the state space (number of feature neurons), for EDEN shows that it achieves exponential sequence memory capacity $\mathcal{O}(\gamma^N)$, outperforming the linear capacity $\mathcal{O}(N)$ of conventional models. Furthermore, EDEN's dynamics resemble the activity of time and ramping cells observed in the human brain during episodic memory tasks, grounding its biological relevance. By unifying static and sequential memory within a dynamic energy framework, EDEN offers a scalable and interpretable model for high-capacity temporal memory in both artificial and biological systems.