ICML 2026 Papers

Computational approaches have become central to Protein–Protein Interaction (PPI) research, complementing experimental techniques that remain costly and incomplete. While modern deep learning methods capture diverse biological signals and hold promise in expanding the known interactome, empirical validation remains a critical bottleneck due to its long and expensive procedures. To address this challenge, we introduce the problem of PPI candidate ranking, aiming to prioritize interactions for experimental testing. We propose a novel framework that leverages domain knowledge through interpretability-guided ranking and further refines prioritization by integrating complementary sources of evidence, including interaction scores, structural plausibility, and biomedical language features. Evaluations on a large-scale dataset constructed from successive STRING releases demonstrate that our approach yields significant improvements over two state-of-the-art PPI prediction models, providing more accurate and biologically coherent rankings.

The rapid evolution of generative models has unlocked new potentials in protein binder design, a pivotal task in structural biology, by facilitating end-to-end generation via joint sequence-structure modeling or hallucination. However, existing approaches are predominantly implemented under a single-target, single-state assumption, limiting their ability to model multi-target or multi-state interactions required for advanced function-oriented protein design. Here, we introduce Chamaileon, which unifies multi-target and multi-state binder design by formulating the problem as cross-context binding landscape modeling. The framework is underpinned by a training paradigm termed \textit{In-Context Complex Co-Design (I3CD)} for context-aware sequence-structure co-modeling. During inference, we employ \textit{Mixture-of-Paths Sampling (MoPS)}, a scalable strategy that optimizes a single sequence across contexts while alleviating the scarcity of high-quality multi-conformational paired data. Extensive evaluation on our newly constructed benchmark, \textit{CROSS}, demonstrates that Chamaileon effectively generates sequences adaptable to diverse conformational landscapes and multi-target requirements.

Structural nested mean models (SNMMs) are a principled approach to estimate the treatment effects over time. A particular strength of SNMMs is to break the joint effect of treatment sequences over time into localized, time-specific ``blip effects''. This decomposition promotes interpretability through the incremental effects and enables the efficient offline evaluation of optimal treatment policies without re-computation. However, neural frameworks for SNMMs are lacking, as their inherently sequential g-estimation scheme prevents end-to-end, gradient-based training. Here, we propose DeepBlip, the first neural framework for SNMMs, which overcomes this limitation with a novel double optimization trick to enable simultaneous learning of all blip functions. Our DeepBlip seamlessly integrates sequential neural networks like LSTMs or transformers to capture complex temporal dependencies. By design, our method correctly adjusts for time-varying confounding to produce unbiased estimates, and its Neyman-orthogonal loss function ensures robustness to nuisance model misspecification. Finally, we evaluate our DeepBlip across various clinical datasets, where it achieves state-of-the-art performance.

Electronic Health Records (EHRs) possess unique characteristics distinct from natural language, yet existing EHR foundation models often rely on suboptimal NLP-based approaches. We propose a pretraining method tailored to EHRs' distinct features. First, we introduce Pathology-Focused Binning, a density-based quantization strategy that prioritizes clinically significant numerical ranges over usual values. Second, to jointly capture both the exact timing of clinical events and the relative intervals between them, we propose Dual-Calendar Rotary Positional Embedding (RoPE), which encodes absolute and relative temporal signals. Third, we introduce the Time-Conditioned Foreseeing (TCF) objective, aligning with clinical treatment planning to forecast events across multiple temporal horizons by explicitly modeling event timing. Our approach establishes a temporal generative EHR model that outperforms existing foundation models on eleven diverse downstream tasks—achieving up to a 54% improvement in AUPRC—and enables the generation of realistic, temporally consistent patient trajectories. Code is available at https://github.com/Pusheen-cat/TCF_PFM.

Antibodies originate from germline templates and are diversified by somatic hypermutation, producing sequences in which conserved germline residues scaffold structure while rare non-germline (NGL) substitutions refine antigen binding. Current antibody language models (ALMs) treat all residues equivalently and inherit a germline bias that systematically down-weights functionally critical NGL mutations as statistical noise. We introduce PRISM, a germline-aware ALM that explicitly represents germline and non-germline residues as distinct token types over a factorized 53-token vocabulary. PRISM achieves state-of-the-art pseudo-perplexity in hypervariable CDRs and is uniquely positively correlated with experimental binding affinity across three deep mutational scanning landscapes on which all compared ALMs anti-correlate. The dual-vocabulary further enables property-specific controllable generation previously unattainable with entangled ALMs. NGL-directed sampling improves physics-based binding scores while GL-directed sampling preserves stability and solubility. These results establish disentangled germline/non-germline representation as a substantive advance in antibody language modeling.

Autoregressive generative models for irregularly sampled clinical time-series data are increasingly used for zero-shot risk forecasting. Prior work typically adopts a single fine-grained discretization of time, where tokens are generated at one fixed, predetermined temporal resolution. We demonstrate that the zero-shot accuracy of individual generative forecasters varies with temporal resolution: performance can degrade when the model resolution is poorly matched to the temporal dynamics of the endpoint being evaluated. We then propose MoRGen (Mixture-of-Resolutions Generation), which fuses forecasts from generative experts trained at multiple temporal resolutions using a low-capacity task-specific mixture, improving performance across tasks with different temporal dynamics. Across multiple horizons and outcomes on three independent clinical datasets, MoRGen achieves lower binary cross-entropy (BCE) and statistically significant AUROC gains over autoregressive generative models that forecast tokens at a fixed temporal resolution.

Online matching has been a mainstay in domains such as Internet advertising and organ allocation, but practical algorithms often lack strong theoretical guarantees. We take an important step toward addressing this by developing new online matching algorithms based on a coarsening approach. Although coarsening typically implies a loss of granularity, we show that, to the contrary, aggregating offline nodes into capacitated clusters can yield near-optimal theoretical guarantees. We apply our methodology to heart transplant allocation to develop theoretically grounded policies based on structural properties of historical data. Furthermore, in simulations based on real data, our policy closely matches the performance of the omniscient benchmark, achieving competitive ratio 0.91, drastically higher than the US status quo policy's 0.51. Our work bridges the gap between data-driven heuristics and pessimistic theoretical lower bounds.

Antimicrobial peptide discovery is challenged by the astronomical size of peptide space and the relative scarcity of active peptides. While generative models provide latent maps of this space, they typically ignore decoder-induced geometry and rely on flat Euclidean metrics, making exploration distorted and inefficient. Existing manifold-based approaches assume fixed intrinsic dimensionality, which fails for real peptide data. We introduce **PepCompass**, a geometry-aware framework based on a **Union of $\kappa$-Stable Riemannian Manifolds** that captures local decoder geometry while maintaining computational stability. PepCompass performs global interpolation via **Potential-minimizing Geodesic Search (PoGS)** to bias discovery toward promising seeds and enables local exploration through **Second-Order Riemannian Brownian Efficient Sampling** and **Mutation Enumeration in Tangent Space**, which together form **Local Enumeration Bayesian Optimization (LE-BO)**. PepCompass achieves a 100% *in-vitro* validation rate: PoGS identifies four novel seeds and LE-BO optimizes them into 25 highly active, broad-spectrum peptides, demonstrating that geometry-informed exploration is a powerful paradigm for antimicrobial peptide design.

Federated learning (FL) offers a promising framework for collaborative digital pathology by enabling model training across institutions. However, real-world deployments face heterogeneity arising from diverse multiple instance learning (MIL) architectures and heterogeneous feature extractors across institutions. We propose FedHD, a novel FL framework that performs local Gaussian-mixture feature alignment tailored for WSI analysis. Instead of exchanging model parameters, each client independently distills semantically rich synthetic feature representations aligned with the distribution of real WSIs. To preserve diagnostic diversity, FedHD adopts a one-to-one distillation strategy, generating a synthetic counterpart for each real slide to avoid over-compression. During federation, a curriculum-based integration strategy progressively incorporates cross-site synthetic features into local training once performance plateaus. Furthermore, an optional interpretation module reconstructs pseudo-patches from synthetic embeddings, enhancing transparency. FedHD is architecture-agnostic, privacy-preserving, and supports personalized yet collaborative training across diverse institutions. Experiments on TCGA-IDH, CAMELYON16, and CAMELYON17 show that FedHD consistently outperforms state-of-the-art federated and distillation baselines.

As LLM-powered agents have been used for high-stakes decision-making, such as clinical diagnosis, it becomes critical to develop reliable verification of their decisions to facilitate trustworthy deployment. Yet, existing verifiers usually underperform owing to a lack of domain knowledge and limited calibration. To address this, we establish **GLEAN**, an agent verification framework with **G**uide**L**ine-grounded **E**vidence **A**ccumulatio**N** that compiles expert-curated protocols into trajectory-informed, well-calibrated correctness signals. GLEAN evaluates the step-wise alignment with domain guidelines and aggregates multi-guideline ratings into surrogate features, which are accumulated along the trajectory and calibrated into correctness probabilities using Bayesian logistic regression. Moreover, the estimated uncertainty triggers active verification, which selectively collects additional evidence for uncertain cases via expanding guideline coverage and performing differential checks. We empirically validate GLEAN with agentic clinical diagnosis across three diseases from the MIMIC-IV dataset, surpassing the best baseline by 12\% in AUROC and 50\% in Brier score reduction, which confirms the effectiveness in both discrimination and calibration. In addition, the expert study with clinicians recognizes GLEAN's utility in practice.

Disease screening is critical for early detection and timely intervention in clinical practice. However, most current screening models for medical images suffer from limited interpretability and suboptimal performance. They often lack effective mechanisms to reference historical cases or provide transparent reasoning pathways. To address these challenges, we introduce EviScreen, an evidential reasoning framework for disease screening that leverages region-level evidence from historical cases. The proposed EviScreen offers retrospection interpretability through regional evidence retrieved from dual knowledge banks. Using this evidential mechanism, the subsequent evidence-aware reasoning module makes predictions using both the current case and evidence from historical cases, thereby enhancing disease screening performance. Furthermore, rather than relying on post-hoc saliency maps, EviScreen enhances localization interpretability by leveraging abnormality maps derived from contrastive retrieval. Our method achieves superior performance on our carefully established benchmarks for real-world disease screening, yielding notably higher specificity at clinical-level recall. Code is publicly available at https://github.com/DopamineLcy/EviScreen.

High-order relations involving multiple interacting entities are commonly encountered, particularly in biomedical domains. Existing relational learning methods typically learn static entity representations and assume symmetric relation inference, which can be inadequate for capturing context-dependent entity functions and the inherent asymmetry of high-order relations. In this paper, we propose Contextualized High-order Contrastive Learning (CONTEXTOR), a general and plug-and-play framework that formulates high-order relation inference as a dynamic query–response process. Specifically, CONTEXTOR decomposes each high-order relation into multiple incomplete query tuples and their corresponding response entities. Given a query tuple, we contextualize candidate response entity representations via an asymmetric conditional modulation, and align queries with their corresponding contextualized responses through multi-fold contrastive learning. Extensive experiments on benchmark datasets spanning multiple biomedical tasks demonstrate that CONTEXTOR consistently outperforms existing methods across diverse evaluation settings. Code is available at https://github.com/ZJUDataIntelligence/CONTEXTOR.

Fast Healthcare Interoperability Resources (FHIR) is the dominant standard for interoperable exchange of healthcare data. In FHIR, electronic health records form a directed graph of resources. Answering clinically meaningful questions over FHIR requires agents to perform multi-step reasoning, filtering, and aggregation across multiple resource types. Prior work shows that even tool-augmented LLM agents (retrieval, code execution, multi-turn planning) often select the wrong resources or violate traversal constraints. We study this problem in the context of FHIR-AgentBench, a benchmark for realistic question answering over real-world hospital data, and frame reasoning on FHIR as a sequential decision-making problem over a queryable structured graph. We implement a multi-turn CodeAct agent and post-train it with reinforcement learning using a custom harness and tools. A LLM Judge provides execution-grounded rewards. Compared to prompt-based, closed-model baselines, RL post-training improves performance while enforcing data-integrity constraints. Empirically, our approach improves answer correctness from 50% (o4-mini) to 77% on FHIR-AgentBench using a smaller and cheaper Qwen3-8B model. We present an end-to-end post-training pipeline (environment building, harness construction, model training and custom evaluation) that reliably improves multi-turn reasoning over structured clinical graphs.

Gastrointestinal (GI) motility assessment via bowel sounds (BS) offers a non-invasive alternative to resource-intensive clinical standards. However, the diagnostic utility of BS is often compromised by its spectral overlap with non-stationary speech interference. While generative models have advanced signal restoration, traditional Gaussian-based diffusion frameworks struggle with the impulsive, heavy-tailed nature of real-world clinical noise. In this paper, we propose a novel Cauchy-driven Diffusion Bridge framework to isolate high-fidelity bowel sounds from complex interference. Our contributions are three-fold: (1) We introduce ClinBS, a large-scale clinical dataset (over 25 hours) containing rare pathological transients verified by experts; (2) We mathematically formulate a Cauchy bridge driver, deriving closed-form expressions for the score and density to better model heavy-tailed perturbations; and (3) We implement an efficient sampling procedure via Gaussian scale-mixture reparameterization. Extensive experiments show our framework achieves state-of-the-art performance, outperforming baselines by 13.4%–49.8% across core metrics and elevating abnormal BS recognition accuracy to 88.01%. These results demonstrate the system's potential for robust clinical GI monitoring and diagnosis.

Polypharmacology provides a powerful strategy for treating complex diseases, but identifying molecules that simultaneously satisfy coupled constraints across multiple biological targets remains difficult. Existing methods typically model protein pockets in isolation and struggle to jointly account for multiple heterogeneous binding sites when designing a single shared ligand. To address these limitations, we propose a pocket-structure-centric generative framework for polypharmacology. This framework introduces a novel protein topological representation that selectively masks ligand-irrelevant residues while explicitly modeling backbone folding geometry and inter-residue spatial proximity within binding pockets. In addition, structural representations are jointly fused with amino acid and nucleotide sequences to capture their complementary information across targets. Experiments on COVID-19, schizophrenia, and tumor targets show that this framework generates valid candidates with significantly improved binding affinities compared to state-of-the-art methods.

Common deep learning approaches for antibody engineering focus on modeling the marginal distribution of sequences. By treating sequences as independent samples, however, these methods overlook affinity maturation as a rich and largely untapped source of information about the evolutionary process by which antibodies explore the underlying fitness landscape. In contrast, classical phylogenetic models explicitly represent evolutionary dynamics but lack the expressivity to capture complex epistatic interactions. We bridge this gap with **CoSiNE**, a continuous-time Markov chain parameterized by a deep neural network. Mathematically, we prove that CoSiNE provides a first-order approximation to the intractable sequential point mutation process, capturing epistatic effects with an error bound that is quadratic in branch length. Empirically, CoSiNE outperforms state-of-the-art language models in zero-shot variant effect prediction by explicitly disentangling selection from context-dependent somatic hypermutation. Finally, we introduce *Guided Gillespie*, a classifier-guided sampling scheme that steers CoSiNE at inference time, enabling efficient optimization of antibody binding affinity toward specific antigens.

Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce RiboSphere, a framework that learns discrete geometric representations of RNA by combining vector quantization with flow matching. Our design is motivated by the modular organization of RNA architecture: complex folds are composed from recurring structural motifs. RiboSphere uses a geometric transformer encoder to produce approximately SE(3)-invariant (rotation/translation-invariant) features, which are discretized with finite scalar quantization (FSQ) into a finite vocabulary of latent codes. Conditioned on these discrete codes, a flow-matching decoder reconstructs atomic coordinates, enabling high-fidelity structure generation. We find that the learned code indices are enriched for specific RNA motifs, suggesting that the model captures motif-level compositional structure rather than acting as a purely compressive bottleneck. Across benchmarks, RiboSphere achieves strong performance in structure reconstruction (RMSD 1.25\,\AA, TM-score 0.84), and its pretrained discrete representations transfer effectively to inverse folding and RNA--ligand binding prediction, with robust generalization in data-scarce regimes.

Mislabeled samples in training datasets severely degrade the performance of deep networks, as overparameterized models tend to memorize erroneous labels. We address this challenge by proposing a novel approach for mislabeled data detection that leverages training dynamics. Our method is grounded in the key observation that correctly labeled samples exhibit consistent entropy decrease during training, while mislabeled samples maintain relatively high entropy throughout the training process. Building on this insight, we introduce a signed entropy integral (SEI) statistic that captures both the magnitude and temporal trend of prediction entropy across training epochs. SEI is broadly applicable to classification networks and demonstrates particular effectiveness when integrated with contrastive language-image pretraining (CLIP) architectures. Through extensive experiments on four medical imaging datasets---a domain particularly susceptible to labeling errors due to diagnostic complexity---spanning diverse modalities and pathologies, we demonstrate that SEI achieves state-of-the-art performance in mislabeled data identification, outperforming existing methods while maintaining computational efficiency and implementation simplicity. Our code is available at https://github.com/MedAITech/SEI.

Data augmentation is a widely used strategy to improve model robustness and generalization by enriching training datasets with synthetic examples. While large language models (LLMs) have demonstrated strong generative capabilities for this purpose, their applications in high-stakes domains like healthcare present unique challenges due to the risk of generating clinically incorrect or misleading information. In this work, we propose a novel query-based model collaboration framework that integrates expert-level domain knowledge to guide the augmentation process to preserve critical medical information. Compared to existing LLM-based and traditional augmentation methods, our generated data significantly improves preservation of critical medical information and reduces hallucinations at both the token and concept levels. Experiments on downstream clinical prediction tasks demonstrate consistent performance gains over existing augmentation methods. This lightweight collaborative framework addresses the gap between LLM augmentation potential and the safety requirements of specialized domains.