ICLR 2025 论文列表

Neurons in the brain are organized such that nearby cells tend to share similar functions. AI models lack this organization, and past efforts to introduce topography have often led to trade-offs between topography and task performance. In this work, we present *TopoLoss*, a new loss function that promotes spatially organized topographic representations in AI models without significantly sacrificing task performance. TopoLoss is highly adaptable and can be seamlessly integrated into the training of leading model architectures. We validate our method on both vision (ResNet-18, ResNet-50, ViT) and language models (GPT-Neo-125M, NanoGPT), collectively *TopoNets*. TopoNets are the highest performing supervised topographic models to date, exhibiting brain-like properties such as localized feature processing, lower dimensionality, and increased efficiency. TopoNets also predict responses in the brain and replicate the key topographic signatures observed in the brain’s visual and language cortices, further bridging the gap between biological and artificial systems. This work establishes a robust and generalizable framework for integrating topography into AI, advancing the development of high performing models that more closely emulate the computational strategies of the human brain. Our project page: https://toponets.github.io

Accurate protein identification from mass spectrometry (MS) data is fundamental to unraveling the complex roles of proteins in biological systems, with peptide sequencing being a pivotal step in this process. The two main paradigms for peptide sequencing are database search, which matches experimental spectra with peptide sequences from databases, and \emph{de novo} sequencing, which infers peptide sequences directly from MS without relying on pre-constructed database. Although database search methods are highly accurate, they are limited by their inability to identify novel, modified, or mutated peptides absent from the database. In contrast, \emph{de novo} sequencing is adept at discovering novel peptides but often struggles with missing peaks issue, further leading to lower precision. We introduce SearchNovo, a novel framework that synergistically integrates the strengths of database search and \emph{de novo} sequencing to enhance peptide sequencing. SearchNovo employs an efficient search mechanism to retrieve the most similar peptide spectrum match (PSM) from a database for each query spectrum, followed by a fusion module that utilizes the reference peptide sequence to guide the generation of the target sequence. Furthermore, we observed that dissimilar (noisy) reference peptides negatively affect model performance. To mitigate this, we constructed pseudo reference PSMs to minimize their impact. Comprehensive evaluations on multiple datasets reveal that SearchNovo significantly outperforms state-of-the-art models. Also, analysis indicates that many retrieved spectra contain missing peaks absent in the query spectra, and the retrieved reference peptides often share common fragments with the target peptides. These are key elements in the recipe for SearchNovo’s success. The code is available at: \textcolor{magenta}{\url{https://github.com/junxia97/SearchNovo}}.

Learning shared structure across environments facilitates rapid learning and adaptive behavior in neural systems. This has been widely demonstrated and applied in machine learning to train models that are capable of generalizing to novel settings. However, there has been limited work exploiting the shared structure in neural activity during similar tasks for learning latent dynamics from neural recordings. Existing approaches are designed to infer dynamics from a single dataset and cannot be readily adapted to account for statistical heterogeneities across recordings. In this work, we hypothesize that similar tasks admit a corresponding family of related solutions and propose a novel approach for meta-learning this solution space from task-related neural activity of trained animals. Specifically, we capture the variabilities across recordings on a low-dimensional manifold which concisely parametrizes this family of dynamics, thereby facilitating rapid learning of latent dynamics given new recordings. We demonstrate the efficacy of our approach on few-shot reconstruction and forecasting of synthetic dynamical systems, and neural recordings from the motor cortex during different arm reaching tasks.

How to balance between exploration and exploitation in an uncertain environment is a central challenge in reinforcement learning. In contrast, humans and animals have demonstrated superior exploration efficiency in novel environments. To understand how the brain’s neural network controls exploration under uncertainty, we analyzed the dynamical systems model of a biological neural network that controls explore-exploit decisions during foraging. Mathematically, this model (named the Brain Bandit Net, or BBN) is a special type of stochastic continuous Hopfield network. We show through theory and simulation that BBN can perform posterior sampling of action values with a tunable bias towards or against uncertain options. We then demonstrate that, in multi-armed bandit (MAB) tasks, BBN can generate probabilistic choice behavior with a flexible uncertainty bias resembling human and animal choice patterns. In addition to its high efficiency in MAB tasks, BBN can also be embedded with reinforcement learning algorithms to accelerate learning in MDP tasks. Altogether, our findings reveal the theoretical foundation for efficient exploration in biological neural networks and propose a general, brain-inspired algorithm for enhancing exploration in RL.

As large language models (LLMs) increasingly become central to various applications and interact with diverse user populations, ensuring their reliable and consistent performance is becoming more important. This paper explores a critical issue in assessing the reliability of LLMs: the consistency between their words and deeds. To quantitatively explore this consistency, we developed a novel evaluation benchmark called the Words and Deeds Consistency Test (WDCT). The benchmark establishes a strict correspondence between word-based and deed-based questions across different domains, including opinion vs. action, non-ethical value vs. action, ethical value vs. action, and theory vs. application. The evaluation results reveal a widespread inconsistency between words and deeds across different LLMs and domains. Subsequently, we conducted experiments with either word alignment or deed alignment to observe their impact on the other aspect. The experimental results indicate that alignment only on words or deeds poorly and unpredictably influences the other aspect. This supports our hypothesis that the underlying knowledge guiding LLMs' word or deed choices is not contained within a unified space. Dataset and code are available at [https://github.com/icip-cas/Word-Deed-Consistency-Test](https://github.com/icip-cas/Word-Deed-Consistency-Test).

We provide a general framework for learning diffusion bridges that transport prior to target distributions. It includes existing diffusion models for generative modeling, but also underdamped versions with degenerate diffusion matrices, where the noise only acts in certain dimensions. Extending previous findings, our framework allows to rigorously show that score-matching in the underdamped case is indeed equivalent to maximizing a lower bound on the likelihood. Motivated by superior convergence properties and compatibility with sophisticated numerical integration schemes of underdamped stochastic processes, we propose *underdamped diffusion bridges*, where a general density evolution is learned rather than prescribed by a fixed noising process. We apply our method to the challenging task of sampling from unnormalized densities without access to samples from the target distribution. Across a diverse range of sampling problems, our approach demonstrates state-of-the-art performance, notably outperforming alternative methods, while requiring significantly fewer discretization steps and almost no hyperparameter tuning.

Quadratic approximations form a fundamental building block of machine learning methods. E.g., second-order optimizers try to find the Newton step into the minimum of a local quadratic proxy to the objective function; and the second-order approximation of a network's loss function can be used to quantify the uncertainty of its outputs via the Laplace approximation. When computations on the entire training set are intractable - typical for deep learning - the relevant quantities are computed on mini-batches. This, however, distorts and biases the shape of the associated *stochastic* quadratic approximations in an intricate way with detrimental effects on applications. In this paper, we (i) show that this bias introduces a systematic error, (ii) provide a theoretical explanation for it, (iii) explain its relevance for second-order optimization and uncertainty quantification via the Laplace approximation in deep learning, and (iv) develop and evaluate debiasing strategies.

Inspired by the Kolmogorov-Arnold representation theorem, we propose Kolmogorov-Arnold Networks (KANs) as promising alternatives to Multi-Layer Perceptrons (MLPs). While MLPs have fixed activation functions on nodes ("neurons''), KANs have learnable activation functions on edges ("weights''). KANs have no linear weights at all -- every weight parameter is replaced by a univariate function parametrized as a spline. We show that this seemingly simple change makes KANs outperform MLPs in terms of accuracy and interpretability, on small-scale AI + Science tasks. For accuracy, smaller KANs can achieve comparable or better accuracy than larger MLPs in function fitting tasks. Theoretically and empirically, KANs possess faster neural scaling laws than MLPs. For interpretability, KANs can be intuitively visualized and can easily interact with human users. Through two examples in mathematics and physics, KANs are shown to be useful ``collaborators'' helping scientists (re)discover mathematical and physical laws. In summary, KANs are promising alternatives for MLPs. Despite the slow training of KANs, their improved accuracy and interpretability show the potential to improve today's deep learning models which rely heavily on MLPs. More research is necessary to make KANs' training more efficient.

A major challenge for Multi-Agent Systems (MAS) is enabling agents to adapt dynamically to diverse environments in which opponents and teammates may continually change. Agents trained using conventional methods tend to excel only within the confines of their training cohorts; their performance drops significantly when confronting unfamiliar agents. To address this shortcoming, we introduce Inverse Attention Agents that adopt concepts from the Theory of Mind (ToM) implemented algorithmically using an attention mechanism trained in an end-to-end manner. Crucial to determining the final actions of these agents, the weights in their attention model explicitly represent attention to different goals. We furthermore propose an inverse attention network that deduces the ToM of agents based on observations and prior actions. The network infers the attentional states of other agents, thereby refining the attention weights to adjust the agent's final action. We conduct experiments in a continuous environment, tackling demanding tasks encompassing cooperation, competition, and a blend of both. They demonstrate that the inverse attention network successfully infers the attention of other agents, and that this information improves agent performance. Additional human experiments show that, compared to baseline agent models, our inverse attention agents exhibit superior cooperation with humans and better emulate human behaviors.

The fine-tuning of deep pre-trained models has revealed compositional properties, with multiple specialized modules that can be arbitrarily composed into a single, multi-task model. However, identifying the conditions that promote compositionality remains an open issue, with recent efforts concentrating mainly on linearized networks. We conduct a theoretical study that attempts to demystify compositionality in standard non-linear networks through the second-order Taylor approximation of the loss function. The proposed formulation highlights the importance of staying within the pre-training basin to achieve composable modules. Moreover, it provides the basis for two dual incremental training algorithms: the one from the perspective of multiple models trained individually, while the other aims to optimize the composed model as a whole. We probe their application in incremental classification tasks and highlight some valuable skills. In fact, the pool of incrementally learned modules not only supports the creation of an effective multi-task model but also enables unlearning and specialization in certain tasks. Code available at <https://github.com/aimagelab/mammoth>

Current AI frameworks for brain decoding and encoding, typically train and test models within the same datasets. This limits their utility for cognitive training (neurofeedback) for which it would be useful to pool experiences across individuals to better simulate stimuli not sampled during training. A key obstacle to model generalisation is the degree of variability of inter-subject cortical organisation, which makes it difficult to align or compare cortical signals across participants. In this paper we address this through use of surface vision transformers, which build a generalisable model of cortical functional dynamics, through encoding the topography of cortical networks and their interactions as a moving image across a surface. This is then combined with tri-modal self-supervised contrastive (CLIP) alignment of audio, video, and fMRI modalities to enable the retrieval of visual and auditory stimuli from patterns of cortical activity (and vice-versa). We validate our approach on 7T task-fMRI data from 174 healthy participants engaged in the movie-watching experiment from the Human Connectome Project (HCP). Results show that it is possible to detect which movie clips an individual is watching purely from their brain activity, even for individuals and movies *not seen during training*. Further analysis of attention maps reveals that our model captures individual patterns of brain activity that reflect semantic and visual systems. This opens the door to future personalised simulations of brain function. Code \& pre-trained models will be made available at https://github.com/metrics-lab/sim.

Current approaches to genomic sequence modeling often struggle to align the inductive biases of machine learning models with the evolutionarily-informed structure of biological systems. To this end, we formulate a novel application of hyperbolic CNNs that exploits this structure, enabling more expressive DNA sequence representations. Our strategy circumvents the need for explicit phylogenetic mapping while discerning key properties of sequences pertaining to core functional and regulatory behavior. Across 37 out of 42 genome interpretation benchmark datasets, our hyperbolic models outperform their Euclidean equivalents. Notably, our approach even surpasses state-of-the-art performance on seven GUE benchmark datasets, consistently outperforming many DNA language models while using orders of magnitude fewer parameters and avoiding pretraining. Our results include a novel set of benchmark datasets---the Transposable Elements Benchmark---which explores a major but understudied component of the genome with deep evolutionary significance. We further motivate our work by exploring how our hyperbolic models recognize genomic signal under various data-generating conditions and by constructing an empirical method for interpreting the hyperbolicity of dataset embeddings. Throughout these assessments, we find persistent evidence highlighting the potential of our hyperbolic framework as a robust paradigm for genome representation learning. Our code and benchmark datasets are available at https://github.com/rrkhan/HGE.

Large Language Models (LLMs) are increasingly being used in workflows involving generating content to be consumed by humans (*e.g.,* marketing) and also in directly interacting with humans (*e.g.,* through chatbots). The development of such systems that are capable of generating verifiably persuasive messages presents both opportunities and challenges for society. On the one hand, such systems could positively impact domains like advertising and social good, such as addressing drug addiction, and on the other, they could be misused for spreading misinformation and shaping political opinions. To channel LLMs' impact on society, we need to develop systems to measure and benchmark their persuasiveness. With this motivation, we introduce **PersuasionBench** and **PersuasionArena**, the first large-scale benchmark and arena containing a battery of tasks to automatically measure the simulative and generative persuasion abilities of large language models. We introduce **transsuasion** (trans = carrying across, suasion = the act of persuading), a novel task of transforming non-persuasive language into persuasive content while preserving other factors determining persuasiveness (sender, receiver, time, and channel). Our findings indicate that the simulative persuasion capabilities of LLMs are barely above random; however, their generative persuasion capabilities are much better. For instance, GPT-4o loses only 36% of the time when playing against the best human persuader. Further, we find that LLMs' persuasiveness correlates positively with model size, but smaller models can also be made to have a higher persuasiveness than much larger models. Notably, targeted training using synthetic and natural datasets significantly enhances smaller models' persuasive capabilities, challenging scale-dependent assumptions. Our findings carry key implications for both model developers and policymakers. For instance, while the EU AI Act and California's SB-1047 aim to regulate AI models based on the number of floating point operations, we demonstrate that simple metrics like this alone fail to capture the full scope of AI's societal impact. We invite the community to explore and contribute to PersuasionArena and PersuasionBench, available at [behavior-in-the-wild.github.io/measure-persuasion](https://behavior-in-the-wild.github.io/measure-persuasion), to advance our understanding of AI-driven persuasion and its societal implications.

Motivated by applications in chemistry and other sciences, we study the expressive power of message-passing neural networks for geometric graphs, whose node features correspond to 3-dimensional positions. Recent work has shown that such models can separate generic pairs of non-isomorphic geometric graphs, though they may fail to separate some rare and complicated instances. However, these results assume a fully connected graph, where each node possesses complete knowledge of all other nodes. In contrast, often, in application, every node only possesses knowledge of a small number of nearest neighbors. This paper shows that generic pairs of non-isomorphic geometric graphs can be separated by message-passing networks with rotation equivariant features as long as the underlying graph is connected. When only invariant intermediate features are allowed, generic separation is guaranteed for generically globally rigid graphs. We introduce a simple architecture, EGENNET, which achieves our theoretical guarantees and compares favorably with alternative architecture on synthetic and chemical benchmarks

Electroencephalography (EEG) is a non-invasive technique to measure and record brain electrical activity, widely used in various BCI and healthcare applications. Early EEG decoding methods rely on supervised learning, limited by specific tasks and datasets, hindering model performance and generalizability. With the success of large language models, there is a growing body of studies focusing on EEG foundation models. However, these studies still leave challenges: Firstly, most of existing EEG foundation models employ full EEG modeling strategy. It models the spatial and temporal dependencies between all EEG patches together, but ignores that the spatial and temporal dependencies are heterogeneous due to the unique structural characteristics of EEG signals. Secondly, existing EEG foundation models have limited generalizability on a wide range of downstream BCI tasks due to varying formats of EEG data, making it challenging to adapt to. To address these challenges, we propose a novel foundation model called CBraMod. Specifically, we devise a criss-cross transformer as the backbone to thoroughly leverage the structural characteristics of EEG signals, which can model spatial and temporal dependencies separately through two parallel attention mechanisms. And we utilize an asymmetric conditional positional encoding scheme which can encode positional information of EEG patches and be easily adapted to the EEG with diverse formats. CBraMod is pre-trained on a very large corpus of EEG through patch-based masked EEG reconstruction. We evaluate CBraMod on up to 10 downstream BCI tasks (12 public datasets). CBraMod achieves the state-of-the-art performance across the wide range of tasks, proving its strong capability and generalizability. The source code is publicly available at https://github.com/wjq-learning/CBraMod.

Brain-inspired Spiking Neural Networks (SNNs) leverage sparse spikes to encode information and operate in an asynchronous event-driven manner, offering a highly energy-efficient paradigm for machine intelligence. However, the current SNN community focuses primarily on performance improvement by developing large-scale models, which limits the applicability of SNNs in resource-limited edge devices. In this paper, we propose a hardware-friendly and lightweight SNN, aimed at effectively deploying high-performance SNN in resource-limited scenarios. Specifically, we first develop a baseline model that integrates uniform quantization and structured pruning, called QP-SNN baseline. While this baseline significantly reduces storage demands and computational costs, it suffers from performance decline. To address this, we conduct an in-depth analysis of the challenges in quantization and pruning that lead to performance degradation and propose solutions to enhance the baseline's performance. For weight quantization, we propose a weight rescaling strategy that utilizes bit width more effectively to enhance the model's representation capability. For structured pruning, we propose a novel pruning criterion using the singular value of spatiotemporal spike activities to enable more accurate removal of redundant kernels. Extensive experiments demonstrate that integrating two proposed methods into the baseline allows QP-SNN to achieve state-of-the-art performance and efficiency, underscoring its potential for enhancing SNN deployment in edge intelligence computing.

With the recent development and advancement of Transformer and MLP architectures, significant strides have been made in time series analysis. Conversely, the performance of Convolutional Neural Networks (CNNs) in time series analysis has fallen short of expectations, diminishing their potential for future applications. Our research aims to enhance the representational capacity of Convolutional Neural Networks (CNNs) in time series analysis by introducing novel perspectives and design innovations. To be specific, We introduce a novel time series reshaping technique that considers the inter-patch, intra-patch, and cross-variable dimensions. Consequently, we propose TVNet, a dynamic convolutional network leveraging a 3D perspective to employ time series analysis. TVNet retains the computational efficiency of CNNs and achieves state-of-the-art results in five key time series analysis tasks, offering a superior balance of efficiency and performance over the state-of-the-art Transformer-based and MLP-based models. Additionally, our findings suggest that TVNet exhibits enhanced transferability and robustness. Therefore, it provides a new perspective for applying CNN in advanced time series analysis tasks.

Cognition arises from the coordinated interaction of brain regions with distinct computational roles. Despite improvements in our ability to extract the dynamics underlying circuit computation from population activity recorded in individual areas, understanding how multiple areas jointly support distributed computation remains a challenge. As part of this effort, we propose a multi-region neural dynamics model composed of two building blocks: _i)_ within-region (potentially driven) nonlinear dynamics and _ii)_ communication channels between regions, parameterized through their impulse response. Together, these choices make it possible to learn nonlinear neural population dynamics and understand the flow of information between regions by drawing from the rich literature of linear systems theory. We develop a state noise inversion free variational filtering and learning algorithm for our model and show, through neuroscientifically inspired numerical experiments, how the proposed model can reveal interpretable characterizations of the local computations within and the flow of information between neural populations. We further validate the efficacy of our approach using simultaneous population recordings from areas V1 and V2.

What can we learn from comparing video models to human brains, arguably the most efficient and effective video processing systems in existence? Our work takes a step towards answering this question by performing the first large-scale benchmarking of deep video models on representational alignment to the human brain, using publicly available models and a recently released video brain imaging (fMRI) dataset. We disentangle four factors of variation in the models (temporal modeling, classification task, architecture, and training dataset) that affect alignment to the brain, which we measure by conducting Representational Similarity Analysis across multiple brain regions and model layers. We show that temporal modeling is key for alignment to brain regions involved in early visual processing, while a relevant classification task is key for alignment to higher-level regions. Moreover, we identify clear differences between the brain scoring patterns across layers of CNNs and Transformers, and reveal how training dataset biases transfer to alignment with functionally selective brain areas. Additionally, we uncover a negative correlation of computational complexity to brain alignment. Measuring a total of 99 neural networks and 10 human brains watching videos, we aim to forge a path that widens our understanding of temporal and semantic video representations in brains and machines, ideally leading towards more efficient video models and more mechanistic explanations of processing in the human brain.