ICML 2025 论文列表

Online multiple hypothesis testing has attracted a lot of attention in many applications, e.g., anomaly status detection and stock market price monitoring. The state-of-the-art generalized $\alpha$-investing (GAI) algorithms can control online false discovery rate (FDR) on p-values only under specific dependence structures, a situation that rarely occurs in practice. The e-LOND algorithm (Xu & Ramdas, 2024) utilizes e-values to achieve online FDR control under arbitrary dependence but suffers from a significant loss in power as testing levels are derived from pre-specified descent sequences. To address these limitations, we propose a novel framework on valid e-values named e-GAI. The proposed e-GAI can ensure provable online FDR control under more general dependency conditions while improving the power by dynamically allocating the testing levels. These testing levels are updated not only by relying on both the number of previous rejections and the prior costs, but also, differing from the GAI framework, by assigning less $\alpha$-wealth for each rejection from a risk aversion perspective. Within the e-GAI framework, we introduce two new online FDR procedures, e-LORD and e-SAFFRON, and provide strategies for the long-term performance to address the issue of $\alpha$-death, a common phenomenon within the GAI framework. Furthermore, we demonstrate that e-GAI can be generalized to conditionally super-uniform p-values. Both simulated and real data experiments demonstrate the advantages of both e-LORD and e-SAFFRON in FDR control and power.

Retrosynthesis, the process of breaking down a target molecule into simpler precursors through a series of valid reactions, stands at the core of organic chemistry and drug development. Although recent machine learning (ML) research has advanced single-step retrosynthetic modeling and subsequent route searches, these solutions remain restricted by the extensive combinatorial space of possible pathways. Concurrently, large language models (LLMs) have exhibited remarkable chemical knowledge, hinting at their potential to tackle complex decision-making tasks in chemistry. In this work, we explore whether LLMs can successfully navigate the highly constrained, multi-step retrosynthesis planning problem. We introduce an efficient scheme for encoding reaction pathways and present a new route-level search strategy, moving beyond the conventional step-by-step reactant prediction. Through comprehensive evaluations, we show that our LLM-augmented approach excels at retrosynthesis planning and extends naturally to the broader challenge of synthesizable molecular design.

The design of target-specific molecules such as small molecules, peptides, and antibodies is vital for biological research and drug discovery. Existing generative methods are restricted to single-domain molecules, failing to address versatile therapeutic needs or utilize cross-domain transferability to enhance model performance. In this paper, we introduce **Uni**fied generative **Mo**deling of 3D **Mo**lecules (UniMoMo), the first framework capable of designing binders of multiple molecular domains using a single model. In particular, UniMoMo unifies the representations of different molecules as graphs of blocks, where each block corresponds to either a standard amino acid or a molecular fragment. Based on these unified representations, UniMoMo utilizes a geometric latent diffusion model for 3D molecular generation, featuring an iterative full-atom autoencoder to compress blocks into latent space points, followed by an E(3)-equivariant diffusion process. Extensive benchmarks across peptides, antibodies, and small molecules demonstrate the superiority of our unified framework over existing domain-specific models, highlighting the benefits of multi-domain training.

Drug discovery is a complex process that involves multiple stages and tasks. However, existing molecular generative models can only tackle some of these tasks. We present *Generalist Molecular generative model* (GenMol), a versatile framework that uses only a *single* discrete diffusion model to handle diverse drug discovery scenarios. GenMol generates Sequential Attachment-based Fragment Embedding (SAFE) sequences through non-autoregressive bidirectional parallel decoding, thereby allowing the utilization of a molecular context that does not rely on the specific token ordering while having better sampling efficiency. GenMol uses fragments as basic building blocks for molecules and introduces *fragment remasking*, a strategy that optimizes molecules by regenerating masked fragments, enabling effective exploration of chemical space. We further propose *molecular context guidance* (MCG), a guidance method tailored for masked discrete diffusion of GenMol. GenMol significantly outperforms the previous GPT-based model in *de novo* generation and fragment-constrained generation, and achieves state-of-the-art performance in goal-directed hit generation and lead optimization. These results demonstrate that GenMol can tackle a wide range of drug discovery tasks, providing a unified and versatile approach for molecular design.

Dual-target molecule generation, which focuses on discovering compounds capable of interacting with two target proteins, has garnered significant attention due to its potential for improving therapeutic efficiency, safety and resistance mitigation. Existing approaches face two critical challenges. First, by simplifying the complex dual-target optimization problem to scalarized combinations of individual objectives, they fail to capture important trade-offs between target engagement and molecular properties. Second, they typically do not integrate synthetic planning into the generative process. This highlights a need for more appropriate objective function design and synthesis-aware methodologies tailored to the dual-target molecule generation task. In this work, we propose CombiMOTS, a Pareto Monte Carlo Tree Search (PMCTS) framework that generates dual-target molecules. CombiMOTS is designed to explore a synthesizable fragment space while employing vectorized optimization constraints to encapsulate target affinity and physicochemical properties. Extensive experiments on real-world databases demonstrate that CombiMOTS produces novel dual-target molecules with high docking scores, enhanced diversity, and balanced pharmacological characteristics, showcasing its potential as a powerful tool for dual-target drug discovery. The code and data is accessible through \url{https://github.com/Tibogoss/CombiMOTS}.

Leading deep learning-based methods for fixed-backbone protein sequence design do not model protein sidechain conformation during sequence generation despite the large role the three-dimensional arrangement of sidechain atoms play in protein conformation, stability, and overall protein function. Instead, these models implicitly reason about crucial sidechain interactions based solely on backbone geometry and amino-acid sequence. To address this, we present FAMPNN (Full-Atom MPNN), a sequence design method that explicitly models both sequence identity and sidechain conformation for each residue, where the per-token distribution of a residue’s discrete amino acid identity and its continuous sidechain conformation are learned with a combined categorical cross-entropy and diffusion loss objective. We demonstrate learning these distributions jointly is a highly synergistic task that both improves sequence recovery while achieving state-of-the-art sidechain packing. Furthermore, benefits from explicit full-atom modeling generalize from sequence recovery to practical protein design applications, such as zero-shot prediction of experimental binding and stability measurements.

Structure-based molecule optimization (SBMO) aims to optimize molecules with both continuous coordinates and discrete types against protein targets. A promising direction is to exert gradient guidance on generative models given its remarkable success in images, but it is challenging to guide discrete data and risks inconsistencies between modalities. To this end, we leverage a continuous and differentiable space derived through Bayesian inference, presenting Molecule Joint Optimization (MolJO), the gradient-based SBMO framework that facilitates joint guidance signals across different modalities while preserving SE(3)-equivariance. We introduce a novel backward correction strategy that optimizes within a sliding window of the past histories, allowing for a seamless trade-off between explore-and-exploit during optimization. MolJO achieves state-of-the-art performance on CrossDocked2020 benchmark (Success Rate 51.3\%, Vina Dock -9.05 and SA 0.78), more than 4x improvement in Success Rate compared to the gradient-based counterpart, and 2x ``Me-Better'' Ratio as much as 3D baselines. Furthermore, we extend MolJO to a wide range of optimization settings, including multi-objective optimization and challenging tasks in drug design such as R-group optimization and scaffold hopping, further underscoring its versatility. Code is available at https://github.com/AlgoMole/MolCRAFT.

Current causal discovery methods for time series data can effectively address a variety of scenarios; however, they remain constrained by inefficiencies. The significant inefficiencies arise primarily from the high computational costs associated with binning, the uncertainty in selecting appropriate time lags, and the extensive sets of candidate variables. To achieve both high efficiency and effectiveness of causal discovery, we introduce an accelerator termed ARROW. It incorporates an innovative concept termed “Time Weaving” that efficiently encodes time series data to well capture the dynamic trends, thereby mitigating computational complexity. We also propose a novel time lag discovery strategy utilizing XOR operations, which derives a theorem to obtain the optimal time lag and significantly enhances the efficiency using XOR operations. To optimize the search space for causal relationships, we design an efficient pruning strategy that intelligently identifies the most relevant candidate variables, enhancing the efficiency and accuracy of causal discovery. We applied ARROW to four different types of time series causal discovery algorithms and evaluated it on 25 synthetic and real-world datasets. The results demonstrate that, compared to the original algorithms, ARROW achieves up to 153x speedup while achieving higher accuracy in most cases.

Circuit discovery has recently attracted attention as a potential research direction to explain the non-trivial behaviors of language models. It aims to find the computational subgraphs, also known as circuits, within the model that are responsible for solving specific tasks. However, most existing studies overlook the holistic nature of these circuits and require designing specific corrupted activations for different tasks, which is inaccurate and inefficient. In this work, we propose an end-to-end approach based on the principle of Information Bottleneck, called IBCircuit, to holistically identify informative circuits. In contrast to traditional causal interventions, IBCircuit is an optimization framework for holistic circuit discovery and can be applied to any given task without tediously corrupted activation design. In both the Indirect Object Identification (IOI) and Greater-Than tasks, IBCircuit identifies more faithful and minimal circuits in terms of critical node components and edge components compared to recent related work.

We present Mechanistic PDE Networks -- a model for discovery of governing *partial differential equations* from data. Mechanistic PDE Networks represent spatiotemporal data as space-time dependent *linear* partial differential equations in neural network hidden representations. The represented PDEs are then solved and decoded for specific tasks. The learned PDE representations naturally express the spatiotemporal dynamics in data in neural network hidden space, enabling increased modeling power. Solving the PDE representations in a compute and memory-efficient way, however, is a significant challenge. We develop a native, GPU-capable, parallel, sparse and differentiable multigrid solver specialized for linear partial differential equations that acts as a module in Mechanistic PDE Networks. Leveraging the PDE solver we propose a discovery architecture that can discovers nonlinear PDEs in complex settings, while being robust to noise. We validate PDE discovery on a number of PDEs including reaction-diffusion and Navier-Stokes equations.

We demonstrate how neural networks can drive mathematical discovery through a case study of the Hadwiger-Nelson problem, a long-standing open problem at the intersection of discrete geometry and extremal combinatorics that is concerned with coloring the plane while avoiding monochromatic unit-distance pairs. Using neural networks as approximators, we reformulate this mixed discrete-continuous geometric coloring problem with hard constraints as an optimization task with a probabilistic, differentiable loss function. This enables gradient-based exploration of admissible configurations that most significantly led to the discovery of two novel six-colorings, providing the first improvement in thirty years to the off-diagonal variant of the original problem (Mundinger et al., 2024a). Here, we establish the underlying machine learning approach used to obtain these results and demonstrate its broader applicability through additional numerical insights.

Recent advances in molecular generative models have demonstrated great promise for accelerating scientific discovery, particularly in drug design. However, these models often struggle to generate high-quality molecules, especially in conditional scenarios where specific molecular properties must be satisfied. In this work, we introduce GeoRCG, a general framework to improve molecular generative models by integrating geometric representation conditions with provable theoretical guarantees. We decompose the generation process into two stages: first, generating an informative geometric representation; second, generating a molecule conditioned on the representation. Compared with single-stage generation, the easy-to-generate representation in the first stage guides the second stage generation toward a high-quality molecule in a goal-oriented way. Leveraging EDM and SemlaFlow as base generators, we observe significant quality improvements in unconditional molecule generation on the widely used QM9 and GEOM-DRUG datasets. More notably, in the challenging conditional molecular generation task, our framework achieves an average 50\% performance improvement over state-of-the-art approaches, highlighting the superiority of conditioning on semantically rich geometric representations. Furthermore, with such representation guidance, the number of diffusion steps can be reduced to as small as 100 while largely preserving the generation quality achieved with 1,000 steps, thereby significantly reducing the generation iterations needed.

Many generative applications, such as synthesis-based 3D molecular design, involve constructing compositional objects with continuous features. Here, we introduce Compositional Generative Flows (CGFlow), a novel framework that extends flow matching to generate objects in compositional steps while modeling continuous states. Our key insight is that modeling compositional state transitions can be formulated as a straightforward extension of the flow matching interpolation process. We further build upon the theoretical foundations of generative flow networks (GFlowNets), enabling reward-guided sampling of compositional structures. We apply CGFlow to synthesizable drug design by jointly designing the molecule's synthetic pathway with its 3D binding pose. Our approach achieves state-of-the-art binding affinity and synthesizability on all 15 targets from the LIT-PCBA benchmark, and 4.2x improvement in sampling efficiency compared to 2D synthesis-based baseline. To our best knowledge, our method is also the first to achieve state of-art-performance in both Vina Dock (-9.42) and AiZynth success rate (36.1\%) on the CrossDocked2020 benchmark.

Current generative models for drug discovery primarily use molecular docking as an oracle to guide the generation of active compounds. However, such models are often not useful in practice because even compounds with high docking scores do not consistently show real-world experimental activity. More accurate methods for activity prediction exist, such as molecular dynamics based binding free energy calculations, but they are too computationally expensive to use in a generative model. To address this challenge, we propose Multi-Fidelity Latent space Active Learning (MF-LAL), a generative modeling framework that integrates a set of oracles with varying cost-accuracy tradeoffs. Using active learning, we train a surrogate model for each oracle and use these surrogates to guide generation of compounds with high predicted activity. Unlike previous approaches that separately learn the surrogate model and generative model, MF-LAL combines the generative and multi-fidelity surrogate models into a single framework, allowing for more accurate activity prediction and higher quality samples. Our experiments on two disease-relevant proteins show that MF-LAL produces compounds with significantly better binding free energy scores than other single and multi-fidelity approaches (~50% improvement in mean binding free energy score). The code is available at https://github.com/Rose-STL-Lab/MF-LAL.

For researchers and practitioners in finance, finding synergistic formulaic alphas is very important but challenging. In this paper, we reconsider the discovery of synergistic formulaic alphas from the viewpoint of sequential decision-making, and conceptualize the entire alpha discovery process as a non-stationary and reward-sparse Markov decision process. To overcome the challenges of non-stationarity and reward-sparsity, we propose the AlphaQCM method, a novel distributional reinforcement learning method designed to search for synergistic formulaic alphas efficiently. The AlphaQCM method first learns the Q function and quantiles via a Q network and a quantile network, respectively. Then, the AlphaQCM method applies the quantiled conditional moment method to learn unbiased variance from the potentially biased quantiles. Guided by the learned Q function and variance, the AlphaQCM method navigates the non-stationarity and reward-sparsity to explore the vast search space of formulaic alphas with high efficacy. Empirical applications to real-world datasets demonstrate that our AlphaQCM method significantly outperforms its competitors, particularly when dealing with large datasets comprising numerous stocks.

Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlux, an image-generative model that simulates cellular morphology changes induced by chemical and genetic perturbations using flow matching. Unlike prior methods, CellFlux models distribution-wise transformations from unperturbed to perturbed cell states, effectively distinguishing actual perturbation effects from experimental artifacts such as batch effects—a major challenge in biological data. Evaluated on chemical (BBBC021), genetic (RxRx1), and combined perturbation (JUMP) datasets, CellFlux generates biologically meaningful cell images that faithfully capture perturbation-specific morphological changes, achieving a 35% improvement in FID scores and a 12% increase in mode-of-action prediction accuracy over existing methods. Additionally, CellFlux enables continuous interpolation between cellular states, providing a potential tool for studying perturbation dynamics. These capabilities mark a significant step toward realizing virtual cell modeling for biomedical research. Project page: https://yuhui-zh15.github.io/CellFlux/.

Neural causal discovery methods have recently improved in terms of scalability and computational efficiency. However, our systematic evaluation highlights significant room for improvement in their accuracy when uncovering causal structures. We identify a fundamental limitation: \textit{unavoidable likelihood score estimation errors disallow distinguishing the true structure}, even for small graphs and relatively large sample sizes. Furthermore, we identify the faithfulness property as a critical bottleneck: (i) it is likely to be violated across any reasonable dataset size range, and (ii) its violation directly undermines the performance of neural penalized-likelihood discovery methods. These findings lead us to conclude that progress within the current paradigm is fundamentally constrained, necessitating a paradigm shift in this domain.

We develop Latent Exploration Score (LES) to mitigate over-exploration in Latent Space Optimization (LSO), a popular method for solving black-box discrete optimization problems. LSO utilizes continuous optimization within the latent space of a Variational Autoencoder (VAE) and is known to be susceptible to over-exploration, which manifests in unrealistic solutions that reduce its practicality. LES leverages the trained decoder’s approximation of the data distribution, and can be employed with any VAE decoder–including pretrained ones–without additional training, architectural changes or access to the training data. Our evaluation across five LSO benchmark tasks and twenty-two VAE models demonstrates that LES always enhances the quality of the solutions while maintaining high objective values, leading to improvements over existing solutions in most cases. We believe that new avenues to LSO will be opened by LES’ ability to identify out of distribution areas, differentiability, and computational tractability.