ICML 2026 Papers

Deep protein structure predictors such as AlphaFold provide confidence estimates (e.g., pLDDT) that are not calibrated and degrade under distribution shifts across experimental modalities, temporal changes, and disordered regions. We introduce \textbf{CalPro}, a prior-aware evidential conformal framework for shift-robust uncertainty quantification. CalPro combines three components: (i) a geometric evidential head outputting Normal Inverse Gamma distributions via graph neural networks; (ii) a differentiable calibration surrogate that shapes representations during training, followed by split-conformal calibration for finite-sample coverage; and (iii) domain priors (disorder, flexibility) encoded as soft constraints on predicted uncertainty. Theoretically, we derive structure-aware \emph{sensitivity bounds} for coverage degradation under distribution shift using PAC-Bayesian control over ambiguity sets, quantifying how miscoverage increases with model complexity and shift magnitude. Empirically, CalPro achieves at most 5 percentage points coverage degradation across modalities compared to 15 to 25 points for baselines, reduces calibration error by 30\% to 50\%, and improves downstream docking success from 52\% to 75\% when filtering by uncertainty. The framework extends beyond proteins to structured regression tasks where priors encode local reliability.

We introduce BioAgent Bench, an evaluation suite designed for measuring the performance and robustness of AI agents in common bioinformatics tasks. The suite consists of manually curated end-to-end tasks (e.g., RNA-seq, variant calling, metagenomics) accompanied by task-specific prompts and concrete output artifacts to support automated assessment. We evaluate frontier closed- and open-weight models across multiple agent harnesses, and use an LLM-based grader to score pipeline progress and outcome validity. We find that agents based on frontier LLMs can complete multi-step bioinformatics pipelines without elaborate custom scaffolding, often producing the requested final artifacts reliably. However, robustness tests reveal failure modes under controlled perturbations (corrupted inputs, decoy files, and prompt bloat), indicating that correct high-level pipeline construction does not guarantee reliable step-level reasoning. Finally, bioinformatics workflows often involve sensitive patient data or unpublished intellectual property, thereby making the use of cost-effective yet reliable local agents an imperative. Therefore, by releasing the code and the complementary resources comprising our suite, we aim to accelerate the development of such privacy-preserving agents.

Recent advances in 3D molecular modeling have achieved high-fidelity structural synthesis, yet these models often lack an explicit and manipulable representation space. To address this, MolFLAE introduced a fixed-dimensional, E(3)-equivariant latent space, providing a novel framework for molecular editing independent of atom counts. However, because its latent space was primarily optimized for geometric reconstruction, it remains semantically shallow and inadequate for comprehensive representation learning. In this work, we propose **MolAlign3D**, which evolves this architecture into a unified semantic-generative engine. By anchoring MolFLAE’s manipulable latents with embeddings from a pre-trained molecular encoder, we yield a manifold that is both semantically dense and geometrically precise. Experiments show that MolAlign3D achieves high-fidelity molecular reconstruction and attains comparable performance on molecular property prediction benchmarks. Notably, the integration of rich semantic priors significantly enhances zero-shot molecular manipulation, including atom-number editing and latent-space interpolation, outperforming prior fixed-dimensional equivariant latent baseline.

While Large Language Models (LLMs) have achieved remarkable success in dyadic (one-on-one) instruction, they face significant challenges in One-to-Many alignment, such as clinical ward rounds, where an instructor must simultaneously guide a diverse group of trainees. Current models often suffer from context dilution and goal misalignment, failing to balance individual scaffolding with collective learning progress. To address this, we introduce ClinEdu, a multi-agent pedagogical simulator that model the complexity of group dynamics. Leveraging this platform, we construct ClinTeach, a large-scale dataset of Socratic teaching dialogues, and propose ClinTutor-R1, the first multimodal agent explicitly architected to achieve one-to-many alignment in clinical education, employing an explicit internal thinking mechanism to model both individual belief states and group consensus. We validate our framework through a comprehensive protocol covering both standard static benchmarks and rigorous in-situ interactive evaluation within ClinEdu. Experimental results demonstrate that ClinTutor-R1 outperforms base models by over 20% and achieves parity with proprietary reasoning models , while exhibiting exceptional scalability in maintaining instructional quality across expanding student cohorts.

De novo ligand design is a fundamental task that seeks to generate protein or molecule candidates that can effectively dock with protein receptors and achieve strong binding affinity entirely from scratch. It holds paramount significance for a wide spectrum of biomedical applications. However, most existing studies are constrained by the \textbf{Pseudo De Novo}, \textbf{Limited Docking Modeling}, and \textbf{Inflexible Ligand Type}. To address these issues, we propose MagicDock, a forward-looking framework grounded in the progressive pipeline and differentiable surface modeling. (1) We adopt a well-designed gradient inversion framework. To begin with, general docking knowledge of receptors and ligands is incorporated into the backbone model. Subsequently, the docking knowledge is instantiated as reverse gradient flows by binding prediction, which iteratively guide the de novo generation of ligands. (2) We emphasize differentiable surface modeling in the \textit{generation process}, leveraging learnable 3D point-cloud representations to precisely capture docking details, thereby ensuring that the generated ligands preserve docking validity through interpretable spatial fingerprints. (3) We introduce customized designs for different ligand types and integrate them into a unified gradient inversion framework with flexible triggers, thereby ensuring broad applicability. Moreover, we provide sufficient theoretical guarantees for MagicDock. Extensive experiments across 9 scenarios demonstrate that MagicDock achieves average improvements of 7.0\% and 7.4\% over SOTA baselines specialized for protein or molecule ligand design, respectively.

Public health reasoning requires population level inference grounded in scientific evidence, expert consensus, and safety constraints. However, it remains underexplored as a structured machine learning problem with limited supervised signals and benchmarks. We introduce GlobalHealthAtlas, a large scale multilingual dataset of 280,210 instances spanning 15 public health domains and 17 languages. We further propose a large language model (LLM) assisted construction and quality control pipeline with retrieval, deduplication, evidence grounding checks, and label validation to improve consistency at scale. Finally, we present a domain aligned evaluator distilled from high confidence judgments of diverse LLMs to assess outputs along six dimensions: Accuracy, Reasoning, Completeness, Consensus Alignment, Terminology Norms, and Insightfulness. Together, these contributions enable reproducible training and evaluation of LLMs for safety critical public health reasoning beyond conventional QA benchmarks. We publicly release project codebase, evaluator, and model at:: https://github.com/Jan8217/GlobalHealthAtlas, https://huggingface.co/aerovane0/GlobalHealthAtlas_Public_Evaluator and https://huggingface.co/aerovane0/GlobalHealthAtlas_Public_Model