ICML 2026 Papers

Multistate mechanisms underlie many of the complex functions observed in natural proteins. The ability to rationally design multistate proteins would have transformative implications for many areas of biotechnology, yet lies beyond the capabilities of existing deep learning frameworks for protein design. To address this gap, we introduce SwitchCraft, a versatile and programmatic framework for designing state-switching proteins based on backpropagation through compositional design constraints parameterized by structure prediction models. In silico evaluations demonstrate success on a wide range of state-switching functional primitives, from allosteric regulation of motifs to discrimination of bound ligand identities. Using these primitives, we demonstrate an in silico strategy for de novo design of fluorescent biosensors to arbitrary small molecule analytes. These results position SwitchCraft at the inception of a powerful paradigm for higher-order functional protein design. Code is available at https://github.com/bjing2016/switchcraft.

Clinical abnormality grounding for rare diseases is often hindered by data scarcity, rendering supervised fine-tuning infeasible and single-pass inference highly unstable. Thus, we propose Dynamic Decision Learning (DDL), a framework that enables frozen LVLMs to refine their decisions across language and visual spaces by optimizing instructions and consolidating predictions under visual perturbations, thereby improving localization quality and producing a consensus-based reliability score that quantifies the model’s confidence. Results on brain-imaging benchmarks, including a rare-disease dataset with 281 pathology types across 3B–72B models, show that DDL improves mAP@75 by up to 105% on rare-disease cases and surpasses adaptation baselines and supervised fine-tuning. Moreover, we show that DDL yields stronger calibration between consensus-based reliability scores and localization accuracy under severe distribution shifts and increasing task difficulty. The code is available at https://github.com/compai-lab/2026-ICML-DDL .

Large Language Models (LLMs) hold great promise for healthcare applications, but fast-changing medical knowledge can quickly make their outputs outdated or inaccurate, limiting use in high-stakes settings. Model editing can update LLMs without full retraining, but parameter-based methods often break locality and are risky in medicine, making retrieval-based editing a better fit. However, applying model editing methods to the medical domain has two key challenges: (1) retrieval-based methods suffer from representation overlap within the medical knowledge space that causes inaccurate retrieval and reduces editing accuracy; (2) existing medical editing methods are restricted to single-sample edits, while batch-editing remains largely unexplored despite its importance for real-world applications. To address these challenges, we construct MedVersa, an expanded benchmark that evaluates single and batch edits across broader medical coverage under strict locality constraints. We then propose MedREK, a retrieval-based editing framework that integrates a shared query–key module for precise matching with an attention-based prompt encoder for informative guidance. Experiments across various medical benchmarks show that our MedREK consistently improves key metrics and provides the first validated solution for batch editing in medical LLMs.

Inferring dynamics from population snapshots is a fundamental challenge in machine learning and biology. In scRNA-sequencing (scRNA-seq), destructive measurements preclude direct tracking of individual cells across time, making trajectory inference underdetermined. Optimal Transport (OT) provides a principled framework for snapshot alignment, but a long-standing modeling question is which cost functions yield biologically meaningful couplings. Standard OT approaches rely on gene-expression distances, implicitly treating cells as independent points and neglecting structured cell-cell communication mediated by ligand-receptor signaling. We introduce CellBRIDGE (Cell-Based Regularized Interaction-Driven Gene Expression), which augments feature-based OT with a directed, typed interaction cost derived from ligand-receptor activity. By explicitly modeling cell-cell communication, CellBRIDGE improves cross-snapshot couplings and downstream trajectory estimates across synthetic and real scRNA-seq datasets relative to feature-only baselines. Notably, CellBRIDGE enables mechanistically interpretable in silico perturbations: on lung cancer data, silencing specific ligand-receptor pairs induces trajectory shifts that recapitulate expected effects of targeted pathway inhibition.

Medical Large Vision-Language Models (Med-LVLMs) suffer from severe hallucinations, posing critical safety risks in clinical deployment. Editing LVLM activations has shown promise for mitigating hallucination with minimal cost. However, due to the requirements of medical domain expertise, existing methods struggle to capture imaging manifestations and diagnostic principles that are critical for clinical interpretation, thereby limiting their effectiveness. To address these limitations, we propose the first MEDical-oriented Activation Editing (MEDA) method by integrating Query-decisive Manifestation Steering (QMS) and Principle-driven Diagnosis Induction (PDI) to promote Med-LVLM's expertise elicitation. Specifically, QMS retrieves positive query-decisive imaging manifestations as trusted guidance for activation steering, while PDI constructs positive principle-embedded diagnostic prompts to induce expert-like clinical reasoning. Extensive experiments across six benchmarks and six LVLMs demonstrate that MEDA efficiently improves the response factuality with up to a 10.2\% gain on IU-Xray, while exhibiting strong generalization and few-shot robustness.

Self-supervised pre-training methods in medical imaging typically treat each individual as an isolated instance, learning representations through augmentation-based objectives or masked reconstruction. They often do not adequately capitalize on a key characteristic of physiological features: anatomical structures maintain consistent spatial relationships across individuals (instances), such as the thalamus being medial to the basal ganglia, regardless of variations in brain size, shape, or pathology. We propose leveraging this cross-instance topological consistency as a supervisory signal. The challenge arises from the inherent variability in medical imaging, which can differ significantly across instances and modalities. To tackle this, we focus on two alignment regimes. (i) Intra-instance: with pixel-level correspondences available, a cross-modal triplet objective explicitly preserves local neighborhood topology. (ii) Inter-instance: without such supervision, we derive pseudo-correspondences to control partial neighborhood alignment and prevent topology collapse across modalities. We validate our approach across 7 downstream multi-modal tasks, achieving average improvements of 1.1\% and 5.94\% in segmentation and classification tasks, respectively, and demonstrating significantly better robustness when modalities are missing at test time.

Spatial transcriptomics offers spatially resolved gene expression profiling within tissue sections, but its cost and limited throughput hinder large-scale deployment. To extend this capability to routine practice, recent computational methods aim to infer spatial gene expression directly from ubiquitous hematoxylin and eosin-stained histology slides. However, most existing models assume Cartesian or geometry-agnostic locality, despite the hexagonal sampling of widely used spot-array platforms, and point-wise regression objectives often yield over-smoothed gene expression profiles, obscuring gene-specific spatial heterogeneity. To address these, we propose HEXST, a geometry-aligned Transformer for spatial gene expression prediction from histology. HEXST operates directly on hexagonal spot coordinates to enable efficient local-to-global contextual modeling via a tailored shifted-window attention mechanism and hexagonal rotary positional encoding. To enhance gene-wise spatial contrast, HEXST complements point-wise regression with a contrast-sensitive differential objective and transcriptomic priors from a pretrained single-cell foundation model during training. Across seven spatial transcriptomics datasets, HEXST consistently outperforms state-of-the-art models, providing accurate and robust spatial gene expression predictions while preserving gene-wise contrast and spatial heterogeneity.

Spatial proteomics enables single-cell-resolution characterization of protein expression within tissue architecture, playing a critical role in understanding tumor microenvironments and guiding precision medicine. However, current analysis workflows remain fragmented, requiring expert manual orchestration of heterogeneous tools and limiting research scalability and reproducibility. We present SP-Mind, the first autonomous AI agent designed to unify the spatial proteomics analysis pipeline, from raw multiplexed tissue imaging to downstream phenotype discovery. Equipped with expert-curated biological analysis skills and specialized computational tools, SP-Mind converts natural-language queries into end-to-end analytical workflows without task-specific fine-tuning. To rigorously evaluate its capabilities, we introduce SP-Bench, a comprehensive benchmark spanning diverse tissue types, comprising 102 tasks across 18 distinct categories. Through extensive evaluation on SP-Bench and established downstream tasks, SP-Mind achieves state-of-the-art performance compared to existing open-source biomedical agent baselines.

Biomedical regression tasks require predicting continuous targets from heterogeneous and unstructured evidence. While Large Language Models (LLMs) provide a robust interface for reasoning over mixed modalities, they are inherently limited by their discrete tokenization and cross-entropy objectives, which lack awareness of numerical proximity. To bridge this gap, we present \textbf{SPR-RAFT}, a parameter-efficient and regression-aware framework that adapts frozen LLMs for high-precision regression. SPR-RAFT introduces a dual-module architecture: a learnable soft prompt that conditions the LLM to route numerical reasoning into a specific latent state, and a lightweight regression head anchored on a dedicated readout token for numerical reasoning consolidation. Crucially, we align these two modalities via a hybrid objective that combines distribution-based text generation with representation-based robust regression. This ensures the model remains both semantically coherent and numerically calibrated. With only about 1.6M trainable parameters ($\sim$0.04\% of a 4B-parameter backbone), SPR-RAFT consistently outperforms prompting strategies, standard fine-tuning, and non-LLM baselines across diverse biomedical benchmarks, including clinical trial duration, biological age estimation, and molecular property prediction.

Unifying multimodal understanding and generation is a compelling frontier that is beginning to emerge in the medical field. However, the limited existing unified medical models typically treat understanding and generation as disjoint objectives, lacking a meaningful functional synergy. In this work, we identify and address a critical question in unified medical modeling: what form of “understanding” truly benefits generation. We present SynerMedGen, a unified framework built on the proposed principle of generation-aligned understanding, which synergizes understanding objectives with generation tasks via task alignment. SynerMedGen introduces three generation-aligned understanding tasks and a two-stage training strategy that transfers generation-beneficial representations learned during understanding training to medical image synthesis. Remarkably, even with understanding training alone, our SynerMedGen achieves strong zero-shot performance across 22 medical image synthesis tasks and demonstrates robust generalization. When combined with generation training, SynerMedGen consistently outperforms state-of-the-art specialized medical image synthesis models as well as recent unified medical models. We also release SynerMed, a large-scale dataset of 1M paired synthesis samples and 2M understanding instances for studying understanding–generation synergy. Our project can be accessed at https://github.com/piooip/SynerMedGen.

Computational protein design holds immense promise across diverse domains, but existing approaches face significant challenges: traditional physics-based methods require substantial domain expertise, while emerging deep learning methods often rely on restricted functional ontologies, struggle to bridge the semantic gap between text and protein sequences, or lack closed-loop optimization mechanisms. In this paper, we present PDAgent, an LLM-driven autonomous agent framework that enables *in silico* protein design through template-based directed mutation. Our framework accepts natural language specifications of desired protein properties and employs a ReAct-style reasoning loop comprising five phases: THINK, PLAN, ACT, OBSERVE, and REFLECT. PDAgent integrates template retrieval, conservation-aware mutation strategies, and domain-specific computational tools for property optimization across seven biophysical dimensions. Experiments on 100 diverse protein design tasks demonstrate that PDAgent achieves a 91.86% average constraint satisfaction rate with high structural quality (mean pLDDT 87.69), substantially outperforming both direct LLM generation and specialized deep learning methods. We provide the source code at https://github.com/Gift-OYS/PDAgent.

Surgical video datasets are essential for scene understanding, enabling procedural modeling and intra-operative support. However, these datasets are often heavily imbalanced, with rare actions and tools under-represented, which limits the robustness of downstream models. We address this challenge with *SurgiFlowVid*, a sparse and controllable video diffusion framework for generating surgical videos of under-represented classes. Our approach introduces a dual-prediction diffusion module that jointly denoises RGB frames and optical flow, providing temporal inductive biases to improve motion modeling from limited samples. In addition, a sparse visual encoder conditions the generation process on lightweight signals (e.g., sparse segmentation masks or RGB frames), enabling controllability without dense annotations. We validate our approach on three surgical datasets across tasks including action recognition, tool presence detection, and laparoscope motion prediction. Synthetic data generated by our method yields consistent gains of $10$–$20$% over competitive baselines, establishing *SurgiFlowVid* as a promising strategy to mitigate data imbalance and advance surgical video understanding methods.

While multi-task learning based automatic radiology report generation (RRG) is widely adopted to ensure clinical consistency, most focus on architectural designs yet remain limited to coarse linear scalarization strategies. These strategies cannot effectively balance the hard constraints of discriminative clinical supervision with the smoothness requirements of report generation. To address these problems, we analyze the failure mechanism of linear scalarization from the perspective of gradient dynamics, utilizing the stochastic differential equation (SDE) framework to characterize it as a "Double Dilemma" of drift term deviation and diffusion term decay. Based on this, we propose a backbone-agnostic optimizer named **C**onflict-**A**verse **M**agnitude-**E**nhanced **Grad**ient Descent (CAME-Grad). Through conflict-averse direction rectification and magnitude-enhanced energy injection, the algorithm not only ensures geometric validity, but also avoids local optimal solutions. Then, the adaptive gradient fusion mechanism is used to establish a dynamic balance between the theoretical optimal direction and the task-specific inductive bias. Experiments show that as a universal plug-and-play optimizer, CAME-Grad brings substantial and consistent improvements across eight diverse RRG methods, elevating overall clinical efficacy performance by an average of 2.3\% on MIMIC-CXR and 1.9\% on IU X-Ray. Our code is available at https://github.com/vpsg-research/CAME-Grad.

In clinical practice, patients often present with multiple co-occurring diseases, yet most existing Multi-Label-Diagnosis (MLD) methods treat diagnosis as a rigid discriminative partitioning task, implicitly assuming that overlapping pathologies are separable. This assumption is problematic in medical images, where identical or highly similar visual observations may simultaneously support multiple disease labels, and disease concepts are inherently correlated rather than independent. Enforcing hard decision boundaries under such overlap suppresses shared evidence, biases feature representations, and ultimately undermines model reliability. To address this limitation, we propose Fuzzy Alignment with Comorbidity Topology FACT, a novel paradigm that reformulates MLD as a fuzzy alignment problem between atomic visual evidence and disease semantic anchors. FACT is characterized by three key features: (1) modeling visual polysemy through shared and reusable atomic visual evidence; (2) encoding disease correlation via semantic anchors structured by comorbidity topology; and (3) employing a metric-based fuzzy membership function for non-discriminative visual-semantic alignment. Extensive experiments on three public clinical benchmarks demonstrate that FACT consistently improves diagnostic performance while delivering clinically plausible predictions. The code is available at \url{https://github.com/yyuChen9/FACT}.

Efficiently designing high-quality molecules targeting disease-relevant targets is a critical challenge. Most existing methods can capture pairwise amino acid relations, neglecting the higher-order relations among multiple amino acids. This paper proposes a target-specific molecule generation framework, namely TSMGen, to comprehensively capture the local and global structural information of the protein pocket by modeling higher-order spatial dependencies both at the atomic and the amino acid levels. Furthermore, we design a context-aware bidirectional fusion module to learn the more detailed structural information about the protein pocket. This module simultaneously attends to features from both the protein pocket and the molecule, fully leveraging the structural information from both to optimize the generation process of targeted molecules, thereby enhancing the quality of generated molecules. Experiments show that TSMGen outperforms state-of-the-art methods in terms of Vina Score, High Affinity, QED, SA and Diversity, and a case study on $\beta$-secretase enzyme further confirms its ability to generate molecules with stronger binding affinity.

Millimeter-wave (mmWave) enables privacy-preserving, illumination-robust human pose estimation (HPE), with each mmWave frame represented as a range--angle--Doppler tensor, providing spatial magnitude for localization and Doppler signatures for motion-related cues. However, existing mmWave-based HPE methods either underutilize or naïvely fuse Doppler signatures with spatial magnitude, disregarding their distinct physical semantics. As a result, non-human Doppler signatures can be misinterpreted as human motion cues, leading to jittery trajectories. We propose \textbf{PULSE}, which converts Doppler signatures into confidence-aware motion prompts and injects them into spatial magnitude reasoning through constrained interactions. By screening Doppler prompts before they influence prediction, PULSE first suppresses spurious spectral motion cues and then uses the screened prompts to stabilize prediction. Across three datasets spanning single- and multi-person settings, PULSE consistently improves pose accuracy and temporal stability, indicating that controlled Doppler prompting is a practical direction for stable mmWave HPE. Codes are available in supplementary materials.

By processing electronic health records (EHRs) as natural language sequences, large language models (LLMs) have shown potential in clinical prediction tasks such as mortality prediction and phenotyping. However, longitudinal or highly frequent EHRs often yield excessively long token sequences that result in high computational costs and even reduced performance. Existing solutions either add modules for compression or remove less important tokens, which introduce additional inference latency or risk losing clinical information. To achieve lossless compression of token sequences without additional cost or loss of performance, we propose Medical Token-Pair Encoding (MedTPE), a layered method that extends standard tokenisation for EHR sequences. MedTPE merges frequently co-occurring medical token pairs into composite tokens, providing lossless compression while preserving the computational complexity through a dependency-aware replacement strategy. Only the embeddings of the newly introduced tokens of merely 0.5-1.0\% of the LLM’s parameters are fine-tuned via self-supervised learning. Experiments on real-world datasets for two clinical scenarios demonstrate that MedTPE reduces input token length by up to 31\% and inference latency by 34-63\%, while maintaining or even improving both predictive performance and output format compliance across multiple LLMs and four clinical prediction tasks. Furthermore, MedTPE demonstrates robustness across different input context lengths and generalisability to scientific and financial domains and different languages. The code is available in the GitHub repository.

Inferring spatial transcriptomics (ST) from histology enables scalable histogenomic profiling, yet current methods are largely restricted to single-tissue models. This fragmentation fails to leverage biological principles shared across cancer types and hinders application to data-scarce scenarios. While pan-cancer training offers a solution, the resulting heterogeneity challenges monolithic architectures. To bridge this gap, we introduce **MoLF** (*Mixture-of-Latent-Flow*), a generative model for pan-cancer histogenomic prediction. MoLF leverages a conditional Flow Matching objective to map noise to the gene latent manifold, parameterized by a Mixture-of-Experts (MoE) velocity field. By dynamically routing inputs to specialized sub-networks, this architecture effectively decouples the optimization of diverse tissue patterns. Our experiments demonstrate that MoLF establishes a new state-of-the-art, consistently outperforming both specialized and foundation model baselines on pan-cancer benchmarks. Furthermore, MoLF exhibits zero-shot generalization to cross-species data, suggesting it captures fundamental, conserved histo-molecular mechanisms.

Large Language Models (LLMs) exhibit high reasoning capacity in medical question-answering, but their tendency to produce hallucinations and outdated knowledge poses critical risks in healthcare fields. While Retrieval-Augmented Generation (RAG) mitigates these issues, existing methods rely on noisy token-level signals and lack the multi-round refinement required for complex reasoning. In this paper, we propose **MA-RAG** (**M**ulti-Round **A**gentic RAG), a framework that facilitates test-time scaling for complex medical reasoning by iteratively evolving both external evidence and internal reasoning history within an agentic refinement loop. At each round, the agent transforms semantic **conflict** among candidate responses into actionable queries to retrieve external evidence, while optimizing history reasoning traces to mitigate long-context degradation. MA-RAG extends the *self-consistency* principle by leveraging the lack of consistency as a proactive signal for multi-round agentic reasoning and retrieval, and mirrors a *boosting* mechanism that iteratively minimizes the residual error toward a stable, high-fidelity medical **consensus**. Extensive evaluations across 7 medical Q\&A benchmarks show that MA-RAG consistently surpasses competitive inference-time scaling and RAG baselines, delivering **substantial +6.8 points** on average accuracy over the backbone model. Our code is available at https://github.com/NJU-RL/MA-RAG.