ICML 2025 论文列表

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.

*De novo* peptide sequencing is a fundamental computational technique for ascertaining amino acid sequences of peptides directly from tandem mass spectrometry data, eliminating the need for reference databases. Cutting-edge models encode the observed mass spectra into latent representations from which peptides are predicted auto-regressively. However, the issue of missing fragmentation, attributable to factors such as suboptimal fragmentation efficiency and instrumental constraints, presents a formidable challenge in practical applications. To tackle this obstacle, we propose a novel computational paradigm called $\underline{\textbf{L}}$atent $\underline{\textbf{I}}$mputation before $\underline{\textbf{P}}$rediction (LIPNovo). LIPNovo is devised to compensate for missing fragmentation information within observed spectra before executing the final peptide prediction. Rather than generating raw missing data, LIPNovo performs imputation in the latent space, guided by the theoretical peak profile of the target peptide sequence. The imputation process is conceptualized as a set-prediction problem, utilizing a set of learnable peak queries to reason about the relationships among observed peaks and directly generate the latent representations of theoretical peaks through optimal bipartite matching. In this way, LIPNovo manages to supplement missing information during inference and thus boosts performance. Despite its simplicity, experiments on three benchmark datasets demonstrate that LIPNovo outperforms state-of-the-art methods by large margins. Code is available at https://github.com/usr922/LIPNovo.

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.

We present a novel, and effective, approach to achieve optimal mesh relocation in finite element methods (FEMs). The cost and accuracy of FEMs is critically dependent on the choice of mesh points. Mesh relocation (r-adaptivity) seeks to optimise the mesh geometry to obtain the best solution accuracy at given computational budget. Classical r-adaptivity relies on the solution of a separate nonlinear ``meshing'' PDE to determine mesh point locations. This incurs significant cost at remeshing, and relies on estimates that relate interpolation- and FEM-error. Recent machine learning approaches have focused on the construction of fast surrogates for such classical methods. Instead, our new approach trains a graph neural network (GNN) to determine mesh point locations by directly minimising the FE solution error from the PDE system Firedrake to achieve higher solution accuracy. Our GNN architecture closely aligns the mesh solution space to that of classical meshing methodologies, thus replacing classical estimates for optimality with a learnable strategy. This allows for rapid and robust training and results in an extremely efficient and effective GNN approach to online r-adaptivity. Our method outperforms both classical, and prior ML, approaches to r-adaptive meshing. In particular, it achieves lower FE solution error, whilst retaining the significant speed-up over classical methods observed in prior ML work.

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.

To address the challenge of scarce computational resources in genomic modeling, we introduce GERM, a genomic foundation model optimized for accessibility and adaptability. GERM improves upon models like DNABERT-2 by eliminating outliers that hinder low-rank adaptation and post-training quantization, enhancing both efficiency and robustness. We replace the vanilla attention layer with an outlier-free mechanism inspired by associative memory models. By removing outliers during both pre-training and fine-tuning, this approach accelerates adaptation, reduces computational costs, and enhances quantization robustness within acceptable loss margins. Additionally, we propose GERM-T, a strategy that employs small-step continual learning within the outlier-free framework, leveraging original checkpoints to avoid retraining from scratch. Empirically, GERM improves fine-tuning performance by 37.98% and quantization by 64.34% over the baseline model. It also reduces average kurtosis by 92.14% and maximum infinity norm by 82.77%. Compared to leading methods, GERM consistently delivers superior performance, offering a practical solution for genomic modeling in resource-constrained settings.

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.

We develop a novel physics informed deep learning approach for solving nonlinear drift-diffusion equations on metric graphs. These models represent an important model class with a large number of applications in areas ranging from transport in biological cells to the motion of human crowds. While traditional numerical schemes require a large amount of tailoring, especially in the case of model design or parameter identification problems, physics informed deep operator networks (DeepONets) have emerged as a versatile tool for the solution of partial differential equations with the particular advantage that they easily incorporate parameter identification questions. We here present an approach where we first learn three DeepONet models for representative inflow, inner and outflow edges, resp., and then subsequently couple these models for the solution of the drift-diffusion metric graph problem by relying on an edge-based domain decomposition approach. We illustrate that our framework is applicable for the accurate evaluation of graph-coupled physics models and is well suited for solving optimization or inverse problems on these coupled networks.

Recent advances in operator learning have produced two distinct approaches for solving partial differential equations (PDEs): attention-based methods offering point-level adaptability but lacking spectral constraints, and spectral-based methods providing domain-level continuity priors but limited in local flexibility. This dichotomy has hindered the development of PDE solvers with both strong flexibility and generalization capability. This work introduces Holistic Physics Mixer (HPM), a novel framework that bridges this gap by integrating spectral and physical information in a unified space. HPM unifies both approaches as special cases while enabling more powerful spectral-physical interactions beyond either method alone. This enables HPM to inherit both the strong generalization of spectral methods and the flexibility of attention mechanisms while avoiding their respective limitations. Through extensive experiments across diverse PDE problems, we demonstrate that HPM consistently outperforms state-of-the-art methods in both accuracy and computational efficiency, while maintaining strong generalization capabilities with limited training data and excellent zero-shot performance on unseen resolutions.

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.

Geometry is a ubiquitous tool in computer graphics, design, and engineering. However, the lack of large shape datasets limits the application of state-of-the-art supervised learning methods and motivates the exploration of alternative learning strategies. To this end, we introduce geometry-informed neural networks (GINNs) -- a framework for training shape-generative neural fields without data by leveraging user-specified design requirements in the form of objectives and constraints. By adding diversity as an explicit constraint, GINNs avoid mode-collapse and can generate multiple diverse solutions, often required in geometry tasks. Experimentally, we apply GINNs to several problems spanning physics, geometry, and engineering design, showing control over geometrical and topological properties, such as surface smoothness or the number of holes. These results demonstrate the potential of training shape-generative models without data, paving the way for new generative design approaches without large datasets.

Recent years have witnessed a surge in the development of protein structural tokenization methods, which chunk protein 3D structures into discrete or continuous representations. Structure tokenization enables the direct application of powerful techniques like language modeling for protein structures, and large multimodal models to integrate structures with protein sequences and functional texts. Despite the progress, the capabilities and limitations of these methods remain poorly understood due to the lack of a unified evaluation framework. We first introduce **StructTokenBench**, a framework that comprehensively evaluates the quality and efficiency of structure tokenizers, focusing on fine-grained local substructures rather than global structures, as typical in existing benchmarks. Our evaluations reveal that no single model dominates all benchmarking perspectives. Observations of codebook under-utilization led us to develop **AminoAseed**, a simple yet effective strategy that enhances codebook gradient updates and optimally balances codebook size and dimension for improved tokenizer utilization and quality. Compared to the leading model ESM3, our method achieves an average of 6.31\% performance improvement across 24 supervised tasks, with sensitivity and utilization rates increased by 12.83\% and 124.03\%, respectively. Source code and model weights are available at https://github.com/KatarinaYuan/StructTokenBench.

Molecular machine learning has gained popularity with the advancements of geometric deep learning. In parallel, retrieval-augmented generation has become a principled approach commonly used with language models. However, the optimal integration of retrieval augmentation into molecular machine learning remains unclear. Graph neural networks stand to benefit from clever matching to understand the structural alignment of retrieved molecules to a query molecule. Neural graph matching offers a compelling solution by explicitly modeling node and edge affinities between two structural graphs while employing a noise-robust, end-to-end neural network to learn affinity metrics. We apply this approach to mass spectrum simulation and introduce MARASON, a novel model that incorporates neural graph matching to enhance a fragmentation-based neural network. Experimental results highlight the effectiveness of our design, with MARASON achieving 27% top-1 accuracy, a substantial improvement over the non-retrieval state-of-the-art accuracy of 19%. Moreover, MARASON outperforms both naive retrieval-augmented generation methods and traditional graph matching approaches. Code is publicly available at https://github.com/coleygroup/ms-pred.

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.

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.

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.