ICML 2025 Papers

$E(3)$-equivariant neural networks have demonstrated success across a wide range of 3D modelling tasks. A fundamental operation in these networks is the tensor product, which interacts two geometric features in an equivariant manner to create new features. Due to the high computational complexity of the tensor product, significant effort has been invested to optimize the runtime of this operation. For example, Luo et al. (2024) recently proposed the Gaunt tensor product (GTP) which promises a significant speedup. In this work, we provide a careful, systematic analysis of a number of tensor product operations. In particular, we emphasize that different tensor products are not performing the same operation. The reported speedups typically come at the cost of expressivity. We introduce measures of expressivity and interactability to characterize these differences. In addition, we realized the original implementation of GTP can be greatly simplified by directly using a spherical grid at no cost in asymptotic runtime. This spherical grid approach is faster on our benchmarks and in actual training of the MACE interatomic potential by 30\%. Finally, we provide the first systematic microbenchmarks of the various tensor product operations. We find that the theoretical runtime guarantees can differ wildly from empirical performance, demonstrating the need for careful application-specific benchmarking. Code is available at https://github.com/atomicarchitects/PriceofFreedom

Mass spectrometry plays a fundamental role in elucidating the structures of unknown molecules and subsequent scientific discoveries. One formulation of the structure elucidation task is the conditional *de novo* generation of molecular structure given a mass spectrum. Toward a more accurate and efficient scientific discovery pipeline for small molecules, we present DiffMS, a formula-restricted encoder-decoder generative network that achieves state-of-the-art performance on this task. The encoder utilizes a transformer architecture and models mass spectra domain knowledge such as peak formulae and neutral losses, and the decoder is a discrete graph diffusion model restricted by the heavy-atom composition of a known chemical formula. To develop a robust decoder that bridges latent embeddings and molecular structures, we pretrain the diffusion decoder with fingerprint-structure pairs, which are available in virtually infinite quantities, compared to structure-spectrum pairs that number in the tens of thousands. Extensive experiments on established benchmarks show that DiffMS outperforms existing models on *de novo* molecule generation. We provide several ablations to demonstrate the effectiveness of our diffusion and pretraining approaches and show consistent performance scaling with increasing pretraining dataset size. DiffMS code is publicly available at https://github.com/coleygroup/DiffMS.

Modality fusion is a cornerstone of multimodal learning, enabling information integration from diverse data sources. However, existing approaches are limited by $\textbf{(a)}$ their focus on modality correspondences, which neglects heterogeneous interactions between modalities, and $\textbf{(b)}$ the fact that they output a single multimodal prediction without offering interpretable insights into the multimodal interactions present in the data. In this work, we propose $\texttt{I$^2$MoE}$ ($\underline{I}$nterpretable Multimodal $\underline{I}$nteraction-aware $\underline{M}$ixture-$\underline{o}$f-$\underline{E}$xperts), an end-to-end MoE framework designed to enhance modality fusion by explicitly modeling diverse multimodal interactions, as well as providing interpretation on a local and global level. First, $\texttt{I$^2$MoE}$ utilizes different interaction experts with weakly supervised interaction losses to learn multimodal interactions in a data-driven way. Second, $\texttt{I$^2$MoE}$ deploys a reweighting model that assigns importance scores for the output of each interaction expert, which offers sample-level and dataset-level interpretation. Extensive evaluation of medical and general multimodal datasets shows that $\texttt{I$^2$MoE}$ is flexible enough to be combined with different fusion techniques, consistently improves task performance, and provides interpretation across various real-world scenarios. Code is available at https://github.com/Raina-Xin/I2MoE.

How much can we infer about an emotional voice solely from an expressive face? This intriguing question holds great potential for applications such as virtual character dubbing and aiding individuals with expressive language disorders. Existing face-to-speech methods offer great promise in capturing identity characteristics but struggle to generate diverse vocal styles with emotional expression. In this paper, we explore a new task, termed *emotional face-to-speech*, aiming to synthesize emotional speech directly from expressive facial cues. To that end, we introduce **DEmoFace**, a novel generative framework that leverages a discrete diffusion transformer (DiT) with curriculum learning, built upon a multi-level neural audio codec. Specifically, we propose multimodal DiT blocks to dynamically align text and speech while tailoring vocal styles based on facial emotion and identity. To enhance training efficiency and generation quality, we further introduce a coarse-to-fine curriculum learning algorithm for multi-level token processing. In addition, we develop an enhanced predictor-free guidance to handle diverse conditioning scenarios, enabling multi-conditional generation and disentangling complex attributes effectively. Extensive experimental results demonstrate that DEmoFace generates more natural and consistent speech compared to baselines, even surpassing speech-driven methods. Demos of DEmoFace are shown at our project https://demoface.github.io.

Quantum control is concerned with the realisation of desired dynamics in quantum systems, serving as a linchpin for advancing quantum technologies and fundamental research. Analytic approaches and standard optimisation algorithms do not yield satisfactory solutions for more complex quantum systems, and especially not for real world quantum systems which are open and noisy. We devise a physics-constrained Reinforcement Learning (RL) algorithm that restricts the space of possible solutions. We incorporate priors about the desired time scales of the quantum state dynamics - as well as realistic control signal limitations - as constraints to the RL algorithm. These constraints improve solution quality and enhance computational scaleability. We evaluate our method on three broadly relevant quantum systems and incorporate real-world complications, arising from dissipation and control signal perturbations. We achieve both higher fidelities - which exceed 0.999 across all systems - and better robustness to time-dependent perturbations and experimental imperfections than previous methods. Lastly, we demonstrate that incorporating multi-step feedback can yield solutions robust even to strong perturbations. Our implementation can be found at: https://github.com/jan-o-e/RL4qcWpc.

The contextual multi-armed bandit (MAB) is a widely used framework for problems requiring sequential decision-making under uncertainty, such as recommendation systems. In applications involving a large number of users, the performance of contextual MAB can be significantly improved by facilitating collaboration among multiple users. This has been achieved by the clustering of bandits (CB) methods, which adaptively group the users into different clusters and achieve collaboration by allowing the users in the same cluster to share data. However, classical CB algorithms typically rely on numerical reward feedback, which may not be practical in certain real-world applications. For instance, in recommendation systems, it is more realistic and reliable to solicit preference feedback between pairs of recommended items rather than absolute rewards. To address this limitation, we introduce the first "clustering of dueling bandit algorithms" to enable collaborative decision-making based on preference feedback. We propose two novel algorithms: (1) Clustering of Linear Dueling Bandits (COLDB) which models the user reward functions as linear functions of the context vectors, and (2) Clustering of Neural Dueling Bandits (CONDB) which uses a neural network to model complex, non-linear user reward functions. Both algorithms are supported by rigorous theoretical analyses, demonstrating that user collaboration leads to improved regret bounds. Extensive empirical evaluations on synthetic and real-world datasets further validate the effectiveness of our methods, establishing their potential in real-world applications involving multiple users with preference-based feedback.

Foundation models that are capable of automating cognitive tasks represent a pivotal technological shift, yet their societal implications remain unclear. These systems promise exciting advances, yet they also risk flooding our information ecosystem with formulaic, homogeneous, and potentially misleading synthetic content. Developing benchmarks grounded in real use cases where these risks are most significant is therefore critical. Through a thematic analysis using 2 million language model user prompts, we identify *creative composition tasks* as a prevalent usage category where users seek help with personal tasks that require everyday creativity. Our fine-grained analysis identifies mismatches between current benchmarks and usage patterns among these tasks. Crucially, we argue that the same use cases that currently lack thorough evaluations can lead to negative downstream impacts. This position paper argues that benchmarks focused on creative composition tasks is a necessary step towards understanding the societal harms of AI-generated content. We call for greater transparency in usage patterns to inform the development of new benchmarks that can effectively measure both the progress and the impacts of models with creative capabilities.

Merging multiple expert models offers a promising approach for performing multi-task learning without accessing their original data. Existing methods attempt to alleviate task conflicts by sparsifying task vectors or promoting orthogonality among them. However, they overlook the fundamental target of model merging: the merged model performs as closely as possible to task-specific models on respective tasks. We find these methods inevitably discard task-specific information that, while causing conflicts, is crucial for performance. Based on our findings, we frame model merging as a constrained optimization problem ($\textit{i.e.}$, minimizing the gap between the merged model and individual models, subject to the constraint of retaining shared knowledge) and solve it via adaptive projective gradient descent. Specifically, we align the merged model with individual models by decomposing and reconstituting the loss function, alleviating conflicts through $\textit{data-free}$ optimization of task vectors. To retain shared knowledge, we optimize this objective by projecting gradients within a $\textit{shared subspace}$ spanning all tasks. Moreover, we view merging coefficients as adaptive learning rates and propose a task-aware, training-free strategy. Experiments show that our plug-and-play approach consistently outperforms previous methods, achieving state-of-the-art results across diverse architectures and tasks in both vision and NLP domains.

Accurate predictions rely on the expressiveness power of graph deep learning frameworks like graph neural networks and graph transformers, where a positional encoding mechanism has become much more indispensable in recent state-of-the-art (SOTA) works to record the canonical position information. However, the current positional encoding limits in three aspects, at least: (1) most positional encodings are pre-defined, and fixed functions, which are inadequate to adapt to the complex attributed graphs; (2) a few pioneering works propose the learnable positional encoding but still limited to the structural information, leaving the real-world time-evolving topological and feature information untouched; (3) most positional encodings should be equipped with transformer's attention mechanism to fully release the power, where the dense or relational attention is often unaffordable on large-scale structured data. Hence, we study the possibility of Learnable Spatial-Temporal Positional Encoding in an effective and efficient manner and then propose a simple temporal link prediction model named L-STEP. Briefly, for L-STEP, we (1) prove the proposed positional learning scheme can preserve the graph property from the spatial-temporal spectral viewpoint, (2) verify that MLPs can fully exploit the expressiveness and reach Transformers' performance on that encoding, (3) change different initial positional encoding inputs to show robustness, (4) analyze the theoretical complexity and obtain less empirical running time than SOTA, and (5) demonstrate its temporal link prediction out-performance on 13 classic datasets and with 10 algorithms in both transductive and inductive settings using 3 different sampling strategies. Also, L-STEP obtains the leading performance in the newest large-scale TGB benchmark.

On-device LLMs have gained increasing attention for their ability to enhance privacy and provide a personalized user experience. To facilitate private learning with scarce data, Federated Learning has become a standard approach. However, it faces challenges such as computational resource heterogeneity and data heterogeneity among end users. We propose CoMiGS ($\textbf{Co}$llaborative learning with a $\textbf{Mi}$xture of $\textbf{G}$eneralists and $\textbf{S}$pecialists), the first approach to address both challenges. A key innovation of our method is the bi-level optimization formulation of the Mixture-of-Experts learning objective, where the router is optimized using a separate validation set to ensure alignment with the target distribution. We solve our objective with alternating minimization, for which we provide a theoretical analysis. Our method shares generalist experts across users while localizing a varying number of specialist experts, thereby adapting to users’ computational resources and preserving privacy. Through extensive experiments, we show CoMiGS effectively balances general and personalized knowledge for each token generation. We demonstrate that CoMiGS remains robust against overfitting—due to the generalists' regularizing effect—while adapting to local data through specialist expertise. We open source our codebase for collaborative LLMs.

Accurate estimation of mutational effects on protein-protein binding energies is an open problem with applications in structural biology and therapeutic design. Several deep learning predictors for this task have been proposed but, presumably due to the scarcity of binding data, these methods under-perform computationally expensive estimates based on empirical force-fields. In response, we propose a transfer-learning approach that leverages advances in protein sequence modeling and folding stability prediction for this task. The key idea is to parameterize the binding energy as the difference between the folding energy of the protein complex and the sum of the folding energies of its binding partners. We show that using a pre-trained inverse-folding model as a proxy for folding energy provides strong zero-shot performance, and can be fine-tuned with (1) copious folding energy measurements and (2) more limited binding energy measurements. The resulting predictor, StaB-ddG, is the first deep learning predictor to match the accuracy of the state-of-the-art empirical force-field method Flex ddG, while offering an over 10,000x speed-up.

Large language models (LLMs) have demonstrated remarkable capabilities in solving complex reasoning tasks, particularly in mathematics. However, the domain of physics reasoning presents unique challenges that have received significantly less attention. Existing benchmarks often fall short in evaluating LLMs’ abilities on the breadth and depth of undergraduate-level physics, underscoring the need for a comprehensive evaluation. To fill this gap, we introduce UGPhysics, a large-scale and diverse benchmark specifically designed to evaluate **U**nder**G**raduate-level **Physics** (**UGPhysics**) reasoning with LLMs. UGPhysics includes 5,520 undergraduate-level physics problems in both English and Chinese across 13 subjects with seven different answer types and four distinct physics reasoning skills, all rigorously screened for data leakage. Additionally, we develop a Model-Assistant Rule-based Judgment (**MARJ**) pipeline specifically tailored for assessing physics problems, ensuring accurate evaluation. Our evaluation of 31 leading LLMs shows that the highest overall accuracy, 49.8% (achieved by OpenAI-o1-mini), emphasizes the need for models with stronger physics reasoning skills, beyond math abilities. We hope UGPhysics, along with MARJ, will drive future advancements in AI for physics reasoning. Codes and data are available at \href{https://github.com/YangLabHKUST/UGPhysics}{https://github.com/YangLabHKUST/UGPhysics}.

Leveraging long contexts is crucial for advanced AI systems, but attention computation poses a scalability challenge. While scaled dot-product attention (SDPA) exhibits token sparsity, i.e. only a few pivotal tokens significantly contribute to output, exploiting this sparsity remains challenging. Existing methods either suffer from quality degradation or require substantial additional resources. We show that identifying pivotal tokens is a Maximum Inner Product Search (MIPS) problem. However, existing MIPS solutions are not well-suited for SDPA, as they are not GPU-friendly and often underperform due to the separated query and key distributions. This paper introduces HashAttention, framing pivotal token identification as a recommendation problem. Given a query, HashAttention encodes keys and queries in Hamming space, capturing the required semantic similarity, using learned mapping functions. HashAttention efficiently identifies pivotal tokens for a given query using bitwise operations and computes attention using only these tokens, improving the overall attention efficiency. Trained on generic data, HashAttention reduces tokens used by up to $16\times$ with minimal quality loss, requiring only 32 bits of auxiliary memory per token. Sparsity can be further improved to $32\times$ through task-specific fine-tuning. On A100 GPU, at $32\times$ sparsity, incorporating HashAttention reduces attention latency by up to $4.3\times$ in GPT-FAST and $2.54\times$ in FlashDecode, and achieves up to $3.12\times$ higher throughput for GPT-FAST.

Plasticity, or the ability of an agent to adapt to new tasks, environments, or distributions, is crucial for continual learning. In this paper, we study the loss of plasticity in deep continual RL from the lens of churn: network output variability induced by the data in each training batch. We demonstrate that (1) the loss of plasticity is accompanied by the exacerbation of churn due to the gradual rank decrease of the Neural Tangent Kernel (NTK) matrix; (2) reducing churn helps prevent rank collapse and adjusts the step size of regular RL gradients adaptively. Moreover, we introduce Continual Churn Approximated Reduction (C-CHAIN) and demonstrate it improves learning performance and outperforms baselines in a diverse range of continual learning environments on OpenAI Gym Control, ProcGen, DeepMind Control Suite, and MinAtar benchmarks.

Inverse problems (IPs) involve reconstructing signals from noisy observations. Recently, diffusion models (DMs) have emerged as a powerful framework for solving IPs, achieving remarkable reconstruction performance. However, existing DM-based methods frequently encounter issues such as heavy computational demands and suboptimal convergence. In this work, building upon the idea of the recent work DMPlug, we propose two novel methods, DMILO and DMILO-PGD, to address these challenges. Our first method, DMILO, employs intermediate layer optimization (ILO) to alleviate the memory burden inherent in DMPlug. Additionally, by introducing sparse deviations, we expand the range of DMs, enabling the exploration of underlying signals that may lie outside the range of the diffusion model. We further propose DMILO-PGD, which integrates ILO with projected gradient descent (PGD), thereby reducing the risk of suboptimal convergence. We provide an intuitive theoretical analysis of our approaches under appropriate conditions and validate their superiority through extensive experiments on diverse image datasets, encompassing both linear and nonlinear IPs. Our results demonstrate significant performance gains over state-of-the-art methods, highlighting the effectiveness of DMILO and DMILO-PGD in addressing common challenges in DM-based IP solvers.

We present a novel reasoning approach called Flow-of-Options (FoO), designed to address intrinsic biases in Large Language Models (LLMs). Flow-of-Options enables LLMs to systematically explore a diverse range of possibilities in their reasoning, as demonstrated by an FoO-based agentic framework developed for autonomously solving Machine Learning (ML) tasks. FoO enforces diversity in LLM solutions through compressed and interpretable task representations, resulting in improvements of 38.2% - 69.2% on standard data science tasks, and 37.4% - 47.9% on therapeutic chemistry tasks, as compared to state-of-the-art baselines. With an overall operation cost under $1 per task, our framework is well-suited for cost-sensitive applications. Going beyond tabular classification and regression, we show the broader applicability of our FoO-based agentic system to tasks such as reinforcement learning and image generation. Our code is open-sourced at: https://github.com/flagshippioneering/Flow-of-Options.

Existing PLMs generate protein sequences based on a single-condition constraint from a specific modality, struggling to simultaneously satisfy multiple constraints across different modalities. In this work, we introduce CFP-GEN, a novel diffusion language model for Combinatorial Functional Protein GENeration. CFP-GEN facilitates the de novo protein design by integrating multimodal conditions with functional, sequence, and structural constraints. Specifically, an Annotation-Guided Feature Modulation (AGFM) module is introduced to dynamically adjust the protein feature distribution based on composable functional annotations, e.g., GO terms, IPR domains and EC numbers. Meanwhile, the ResidueControlled Functional Encoding (RCFE) module captures residue-wise interaction to ensure more precise control. Additionally, off-the-shelf 3D structure encoders can be seamlessly integrated to impose geometric constraints. We demonstrate that CFP-GEN enables high-throughput generation of novel proteins with functionality comparable to natural proteins, while achieving a high success rate in designing multifunctional proteins.

Decoding functional magnetic resonance imaging (fMRI) signals into text has been a key challenge in the neuroscience community, with the potential to advance brain-computer interfaces and uncover deeper insights into brain mechanisms. However, existing approaches often struggle with suboptimal predictive performance, limited task variety, and poor generalization across subjects. In response to this, we propose MindLLM, a model designed for subject-agnostic and versatile fMRI-to-text decoding. MindLLM consists of an fMRI encoder and an off-the-shelf LLM. The fMRI encoder employs a neuroscience-informed attention mechanism, which is capable of accommodating subjects with varying input shapes and thus achieves high-performance subject-agnostic decoding. Moreover, we introduce Brain Instruction Tuning (BIT), a novel approach that enhances the model's ability to capture diverse semantic representations from fMRI signals, facilitating more versatile decoding. We evaluate MindLLM on comprehensive fMRI-to-text benchmarks. Results demonstrate that our model outperforms the baselines, improving downstream tasks by $12.0\%$, unseen subject generalization by $24.5\%$, and novel task adaptation by $25.0\%$. Furthermore, the attention patterns in MindLLM provide interpretable insights into its decision-making process.

Circular and non-flat data distribution are prevalent across diverse domains of data science, yet their specific geometric structures often remain underutilized in machine learning frameworks. A principled approach to accounting for the underlying geometry of such data is pivotal, particularly when extending statistical models, like the pervasive Gaussian distribution. In this work, we tackle those issue by focusing on the manifold of symmetric positive definite matrices, a key focus in information geometry. We introduced a non-isotropic wrapped Gaussian by leveraging the exponential map, we derive theoretical properties of this distribution and propose a maximum likelihood framework for parameter estimation. Furthermore, we reinterpret established classifiers on SPD through a probabilistic lens and introduce new classifiers based on the wrapped Gaussian model. Experiments on synthetic and real-world datasets demonstrate the robustness and flexibility of this geometry-aware distribution, underscoring its potential to advance manifold-based data analysis. This work lays the groundwork for extending classical machine learning and statistical methods to more complex and structured data.