ICML 2025 Papers

Proteins exist as a dynamic ensemble of multiple conformations, and these motions are often crucial for their functions. However, current structure prediction methods predominantly yield a single conformation, overlooking the conformational heterogeneity revealed by diverse experimental modalities. Here, we present a framework for building experiment-grounded protein structure generative models that infer conformational ensembles consistent with measured experimental data. The key idea is to treat state-of-the-art protein structure predictors (e.g., AlphaFold3) as sequence-conditioned structural priors, and cast ensemble modeling as posterior inference of protein structures given experimental measurements. Through extensive real-data experiments, we demonstrate the generality of our method to incorporate a variety of experimental measurements. In particular, our framework uncovers previously unmodeled conformational heterogeneity from crystallographic densities, generates high-accuracy NMR ensembles orders of magnitude faster than status quo, and incorporates pairwise cross-link constraints. Notably, we demonstrate that our ensembles outperform AlphaFold3 and sometimes better fit experimental data than publicly deposited structures to the protein database (PDB). We believe that this approach will unlock building predictive models that fully embrace experimentally observed conformational diversity.

Deep neural networks (DNNs) excel in computer vision tasks, especially, few-shot learning (FSL), which is increasingly important for generalizing from limited examples. However, DNNs are computationally expensive with scalability issues in real world. Spiking Neural Networks (SNNs), with their event-driven nature and low energy consumption, are particularly efficient in processing sparse and dynamic data, though they still encounter difficulties in capturing complex spatiotemporal features and performing accurate cross-class comparisons. To further enhance the performance and efficiency of SNNs in few-shot learning, we propose a few-shot learning framework based on SNNs, which combines a self-feature extractor module and a cross-feature contrastive module to refine feature representation and reduce power consumption. We apply the combination of temporal efficient training loss and InfoNCE loss to optimize the temporal dynamics of spike trains and enhance the discriminative power. Experimental results show that the proposed FSL-SNN significantly improves the classification performance on the neuromorphic dataset N-Omniglot, and also achieves competitive performance to ANNs on static datasets such as CUB and miniImageNet with low power consumption.

Understanding the decision-making processes of large language models is critical given their widespread applications. To achieve this, we aim to connect a formal mathematical framework—zigzag persistence from topological data analysis —with practical and easily applicable algorithms. Zigzag persistence is particularly effective for characterizing data as it dynamically transforms across model layers. Within this framework, we introduce topological descriptors that measure how topological features, $p$-dimensional holes, persist and evolve throughout the layers. Unlike methods that assess each layer individually and then aggregate the results, our approach directly tracks the full evolutionary path of these features. This offers a statistical perspective on how prompts are rearranged and their relative positions changed in the representation space, providing insights into the system’s operation as an integrated whole. To demonstrate the expressivity and applicability of our framework, we highlight how sensitive these descriptors are to different models and a variety of datasets. As a showcase application to a downstream task, we use zigzag persistence to establish a criterion for layer pruning, achieving results comparable to state-of-the-art methods while preserving the system-level perspective.

Protein Language Models (PLMs), pre-trained on extensive evolutionary data from natural proteins, have emerged as indispensable tools for protein design. While powerful, PLMs often struggle to produce proteins with precisely specified functionalities or properties due to inherent challenges in controlling their outputs. In this work, we investigate the potential of Activation Steering, a technique originally developed for controlling text generation in Large Language Models (LLMs), to direct PLMs toward generating protein sequences with targeted properties. We propose a simple yet effective method that employs activation editing to steer PLM outputs, and extend this approach to protein optimization through a novel editing site identification module. Through comprehensive experiments on lysozyme-like sequence generation and optimization, we demonstrate that our methods can be seamlessly integrated into both auto-encoding and autoregressive PLMs without requiring additional training. These results highlight a promising direction for precise protein engineering using foundation models.

Accurate and efficient timing prediction at the register-transfer level (RTL) remains a fundamental challenge in electronic design automation (EDA), particularly in striking a balance between accuracy and computational efficiency. While static timing analysis (STA) provides high-fidelity results through comprehensive physical parameters, its computational overhead makes it impractical for rapid design iterations. Conversely, existing RTL-level approaches sacrifice accuracy due to the limited physical information available. We propose RTLDistil, a novel cross-stage knowledge distillation framework that bridges this gap by transferring precise physical characteristics from a layout-aware teacher model (Teacher GNN) to an efficient RTL-level student model (Student GNN), both implemented as graph neural networks (GNNs). RTLDistil efficiently predicts key timing metrics, such as arrival time (AT), and employs a multi-granularity distillation strategy that captures timing-critical features at node, subgraph, and global levels. Experimental results demonstrate that RTLDistil achieves significant improvement in RTL-level timing prediction error reduction, compared to state-of-the-art prediction models. This framework enables accurate early-stage timing prediction, advancing EDA's ``left-shift'' paradigm while maintaining computational efficiency. Our code and dataset will be publicly available at https://github.com/sklp-eda-lab/RTLDistil.

Understanding and constructing brain communications that capture dynamic communications across multiple regions is fundamental to modern system neuroscience, yet current methods struggle to find time-varying region-level communications or scale to large neural datasets with long recording durations. We present a novel framework using Markovian Gaussian Processes to learn brain communications with time-varying temporal delays from multi-region neural recordings, named Adaptive Delay Model (ADM). Our method combines Gaussian Processes with State Space Models and employs parallel scan inference algorithms, enabling efficient scaling to large datasets while identifying concurrent communication patterns that evolve over time. This time-varying approach captures how brain region interactions shift dynamically during cognitive processes. Validated on synthetic and multi-region neural recordings datasets, our approach discovers both the directionality and temporal dynamics of neural communication. This work advances our understanding of distributed neural computation and provides a scalable tool for analyzing dynamic brain networks. Code is available at https://github.com/BRAINML-GT/Adaptive-Delay-Model.

The past few years have seen remarkable progress in the decoding of speech from brain activity, primarily driven by large single-subject datasets. However, due to individual variation, such as anatomy, and differences in task design and scanning hardware, leveraging data across subjects and datasets remains challenging. In turn, the field has not benefited from the growing number of open neural data repositories to exploit large-scale deep learning. To address this, we develop neuroscience-informed self-supervised objectives, together with an architecture, for learning from heterogeneous brain recordings. Scaling to nearly **400 hours** of MEG data and **900 subjects**, our approach shows generalisation across participants, datasets, tasks, and even to *novel* subjects. It achieves **improvements of 15-27%** over state-of-the-art models and **matches *surgical* decoding performance with *non-invasive* data**. These advances unlock the potential for scaling speech decoding models beyond the current frontier.

We train representation models with procedural data only, and apply them on visual similarity, classification, and semantic segmentation tasks without further training by using visual memory---an explicit database of reference image embeddings. Unlike prior work on visual memory, our approach achieves full compartmentalization with respect to all real-world images while retaining strong performance. Compared to a model trained on Places, our procedural model performs within 1\% on NIGHTS visual similarity, outperforms by 8\% and 15\% on CUB200 and Flowers102 fine-grained classification, and is within 10\% on ImageNet-1K classification. It also demonstrates strong zero-shot segmentation, achieving an $R^2$ on COCO within 10\% of the models trained on real data. Finally, we analyze procedural versus real data models, showing that parts of the same object have dissimilar representations in procedural models, resulting in incorrect searches in memory and explaining the remaining performance gap.

In many classification applications, the prediction of a deep neural network (DNN) based classifier needs to be accompanied by some confidence indication. Two popular approaches for that aim are: 1) *Calibration*: modifies the classifier's softmax values such that the maximal value better estimates the correctness probability; and 2) *Conformal Prediction* (CP): produces a prediction set of candidate labels that contains the true label with a user-specified probability, guaranteeing marginal coverage but not, e.g., per class coverage. In practice, both types of indications are desirable, yet, so far the interplay between them has not been investigated. Focusing on the ubiquitous *Temperature Scaling* (TS) calibration, we start this paper with an extensive empirical study of its effect on prominent CP methods. We show that while TS calibration improves the class-conditional coverage of adaptive CP methods, surprisingly, it negatively affects their prediction set sizes. Motivated by this behavior, we explore the effect of TS on CP *beyond its calibration application* and reveal an intriguing trend under which it allows to trade prediction set size and conditional coverage of adaptive CP methods. Then, we establish a mathematical theory that explains the entire non-monotonic trend. Finally, based on our experiments and theory, we offer guidelines for practitioners to effectively combine adaptive CP with calibration, aligned with user-defined goals.

Understanding how the brain learns may be informed by studying biologically plausible learning rules. These rules, often approximating gradient descent learning to respect biological constraints such as locality, must meet two critical criteria to be considered an appropriate brain model: (1) good neuroscience task performance and (2) alignment with neural recordings. While extensive research has assessed the first criterion, the second remains underexamined. Employing methods such as Procrustes analysis on well-known neuroscience datasets, this study demonstrates the existence of a biologically plausible learning rule — namely e-prop, which is based on gradient truncation and has demonstrated versatility across a wide range of tasks — that can achieve neural data similarity comparable to Backpropagation Through Time (BPTT) when matched for task accuracy. Our findings also reveal that model architecture and initial conditions can play a more significant role in determining neural similarity than the specific learning rule. Furthermore, we observe that BPTT-trained models and their biologically plausible counterparts exhibit similar dynamical properties at comparable accuracies. These results underscore the substantial progress made in developing biologically plausible learning rules, highlighting their potential to achieve both competitive task performance and neural data similarity.

In physics, complex systems are often simplified into minimal, solvable models that retain only the core principles. In machine learning, layerwise linear models (e.g., linear neural networks) act as simplified representations of neural network dynamics. These models follow the dynamical feedback principle, which describes how layers mutually govern and amplify each other's evolution. This principle extends beyond the simplified models, successfully explaining a wide range of dynamical phenomena in deep neural networks, including neural collapse, emergence, lazy and rich regimes, and grokking. In this position paper, we call for the use of layerwise linear models retaining the core principles of neural dynamical phenomena to accelerate the science of deep learning.

Coupled dynamical systems govern essential phenomena across physics, biology, and engineering, where components interact through complex dependencies. While Graph Ordinary Differential Equations (GraphODE) offer a powerful framework to model these systems, their **generalization** capabilities degrade severely under limited observational training data due to two fundamental flaws: (i) the entanglement of static attributes and dynamic states in the initialization process, and (ii) the reliance on context-specific coupling patterns during training, which hinders performance in unseen scenarios. In this paper, we propose a Generalizable GraphODE with disentanglement and regularization (GREAT) to address these challenges. Through systematic analysis via the Structural Causal Model, we identify backdoor paths that undermine generalization and design two key modules to mitigate their effects. The *Dynamic-Static Equilibrium Decoupler (DyStaED)* disentangles static and dynamic states via orthogonal subspace projections, ensuring robust initialization. Furthermore, the *Causal Mediation for Coupled Dynamics (CMCD)* employs variational inference to estimate latent causal factors, reducing spurious correlations and enhancing universal coupling dynamics. Extensive experiments across diverse dynamical systems demonstrate that ours outperforms state-of-the-art methods within both in-distribution and out-of-distribution.

The primary goal of brain-computer interfaces (BCIs) is to establish a direct linkage between neural activities and behavioral actions via neural decoders. Due to the nonstationary property of neural signals, BCIs trained on one day usually obtain degraded performance on other days, hindering the user experience. Existing studies attempted to address this problem by aligning neural signals across different days. However, these neural adaptation methods may exhibit instability and poor performance when only a few trials are available for alignment, limiting their practicality in real-world BCI deployment. To achieve efficient and stable neural adaptation with few trials, we propose Flow-Based Distribution Alignment (FDA), a novel framework that utilizes flow matching to learn flexible neural representations with stable latent dynamics, thereby facilitating source-free domain alignment through likelihood maximization. The latent dynamics of FDA framework is theoretically proven to be stable using Lyapunov exponents, allowing for robust adaptation. Further experiments across multiple motor cortex datasets demonstrate the superior performance of FDA, achieving reliable results with fewer than five trials. Our FDA approach offers a novel and efficient solution for few-trial neural data adaptation, offering significant potential for improving the long-term viability of real-world BCI applications.

In the maximum coverage problem we are given $d$ subsets from a universe $[n]$, and the goal is to output $k$ subsets such that their union covers the largest possible number of distinct items. We present the first algorithm for maximum coverage in the turnstile streaming model, where updates which insert or delete an item from a subset come one-by-one. Notably our algorithm only uses $poly\log n$ update time. We also present turnstile streaming algorithms for targeted and general fingerprinting for risk management where the goal is to determine which features pose the greatest re-identification risk in a dataset. As part of our work, we give a result of independent interest: an algorithm to estimate the complement of the $p^{\text{th}}$ frequency moment of a vector for $p \geq 2$. Empirical evaluation confirms the practicality of our fingerprinting algorithms demonstrating a speedup of up to $210$x over prior work.

Neural circuits produce signals that are complex and nonlinear. To facilitate the understanding of neural dynamics, a popular approach is to fit state space models (SSM) to the data and analyze the dynamics of the low-dimensional latent variables. Despite the power of SSM to explain the dynamics of neural circuits, these models have been shown to merely capture statistical associations in the data and cannot be causally interpreted. Therefore, an important research problem is to build models that can predict neural dynamics under causal manipulations. Here, we propose interventional state-space models (iSSM), a class of causal models that can predict neural responses to novel perturbations. We draw on recent advances in causal dynamical systems and present theoretical results for the identifiability of iSSM. In simulations of the motor cortex, we show that iSSM can recover the true latents and the underlying dynamics. In addition, we illustrate two applications of iSSM in biological datasets. First, we applied iSSM to a dataset of calcium recordings from ALM neurons in mice during photostimulation. Second, we applied iSSM to a dataset of electrophysiological recordings from macaque dlPFC during micro-stimulation. In both cases, we show that iSSM outperforms SSM and results in identifiable parameters. The code is available at https://github.com/amin-nejat/issm.

In online platforms, incentives (\textit{e.g}., discounts, coupons) are used to boost user engagement and revenue. Uplift modeling methods are developed to estimate user responses from observational data, often incorporating distribution balancing to address selection bias. However, these methods are limited by in-distribution testing data, which mirrors the training data distribution. In reality, user features change continuously due to time, geography, and other factors, especially on complex online marketing platforms. Thus, effective uplift modeling method for out-of-distribution data is crucial. To address this, we propose a novel uplift modeling method \textbf{I}nvariant \textbf{D}eep \textbf{U}plift \textbf{M}odeling, namely \textbf{IDUM}, which uses invariant learning to enhance out-of-distribution generalization by identifying causal factors that remain consistent across domains. IDUM further refines these features into necessary and sufficient factors and employs a masking component to reduce computational costs by selecting the most informative invariant features. A balancing discrepancy component is also introduced to mitigate selection bias in observational data. We conduct extensive experiments on public and real-world datasets to demonstrate IDUM's effectiveness in both in-distribution and out-of-distribution scenarios in online marketing. Furthermore, we also provide theoretical analysis and related proofs to support our IDUM's generalizability.

Incorporating permutation equivariance into neural networks has proven to be useful in ensuring that models respect symmetries that exist in data. Symmetric tensors, which naturally appear in statistics, machine learning, and graph theory, are essential for many applications in physics, chemistry, and materials science, amongst others. However, existing research on permutation equivariant models has not explored symmetric tensors as inputs, and most prior work on learning from these tensors has focused on equivariance to Euclidean groups. In this paper, we present two different characterisations of all linear permutation equivariant functions between symmetric power spaces of $\mathbb{R}^{n}$. We show on two tasks that these functions are highly data efficient compared to standard MLPs and have potential to generalise well to symmetric tensors of different sizes.

ANN-to-SNN conversion has emerged as a key approach to train Spiking Neural Networks (SNNs), particularly for Transformer architectures, as it maps pre-trained ANN parameters to SNN equivalents without requiring retraining, thereby preserving ANN accuracy while eliminating training costs. Among various coding methods used in ANN-to-SNN conversion, time-to-first-spike (TTFS) coding, which allows each neuron to at most one spike, offers significantly lower energy consumption. However, while previous TTFS-based SNNs have achieved comparable performance with convolutional ANNs, the attention mechanism and nonlinear layers in Transformer architectures remains a challenge by existing SNNs with TTFS coding. This paper proposes a new neuron structure for TTFS coding that expands its representational range and enhances the capability to process nonlinear functions, along with detailed designs of nonlinear neurons for different layers in Transformer. Experimental results on different models demonstrate that our proposed method can achieve high accuracy with significantly lower energy consumption. To the best of our knowledge, this is the first work to focus on converting Transformer to SNN with TTFS coding.

We develop a framework for capturing the instrumental value of data production processes, which accounts for two key factors: (a) the context of the agent’s decision-making; (b) how much data or information the buyer already possesses. We "micro-found" our data valuation function by establishing its connection to classic notions of signals and information design in economics. When instantiated in Bayesian linear regression, our value naturally corresponds to information gain. Applying our proposed data value in Bayesian linear regression for monopoly pricing, we show that if the seller can fully customize data production, she can extract the first-best revenue (i.e., full surplus) from any population of buyers, i.e., achieving first-degree price discrimination. If data can only be constructed from an existing data pool, this limits the seller’s ability to customize, and achieving first-best revenue becomes generally impossible. However, we design a mechanism that achieves seller revenue at most $\log(\kappa)$ less than the first-best, where $\kappa$ is the condition number associated with the data matrix. As a corollary, the seller extracts the first-best revenue in the multi-armed bandits special case.