Bioinformatics

Biology-Instructions: A Dataset and Benchmark for Multi-Omics Sequence Understanding Capability of Large Language Models EMNLP 2025 BIOPSY - Biomarkers In Oncology: Pipeline for Structured Yielding EMNLP 2025 BOE-ViT: Boosting Orientation Estimation with Equivariance in Self-Supervised 3D Subtomogram Alignment CVPR 2025 BounDr.E: Predicting Drug-likeness via Biomedical Knowledge Alignment and EM-like One-Class Boundary Optimization ICML 2025 BrainMAP: Learning Multiple Activation Pathways in Brain Networks AAAI 2025 Bridging the Gap between Database Search and \emph{De Novo} Peptide Sequencing with SearchNovo ICLR 2025 Bridging the Gap between Learning and Inference for Diffusion-Based Molecule Generation ACML 2025 BudgetIV: Optimal Partial Identification of Causal Effects with Mostly Invalid Instruments AISTATS 2025 Can Large Language Models Classify and Generate Antimicrobial Resistance Genes? ACL 2025 CFD: Learning Generalized Molecular Representation via Concept-Enhanced Feedback Disentanglement ICLR 2025 Classifying Copy Number Variations Using State Space Modeling of Targeted Sequencing Data: A Case Study in Thalassemia MLHC 2025 CombiMOTS: Combinatorial Multi-Objective Tree Search for Dual-Target Molecule Generation ICML 2025 Compositional Flows for 3D Molecule and Synthesis Pathway Co-design ICML 2025 Conditional Causal Representation Learning for Heterogeneous Single-cell RNA Data Integration and Prediction IJCAI 2025 Context Matters: Query-aware Dynamic Long Sequence Modeling of Gigapixel Images ICML 2025 CRAB: A Benchmark for Evaluating Curation of Retrieval-Augmented LLMs in Biomedicine EMNLP 2025 Cradle-VAE: Enhancing Single-Cell Gene Perturbation Modeling with Counterfactual Reasoning-based Artifact Disentanglement AAAI 2025 Cross-modality Matching and Prediction of Perturbation Responses with Labeled Gromov-Wasserstein Optimal Transport AISTATS 2025 CryoDomain: Sequence-free Protein Domain Identification from Low-resolution Cryo-EM Density Maps AAAI 2025 CryoMAE: Few-Shot Cryo-EM Particle Picking with Masked Autoencoders WACV 2025 CycSeq: Leveraging Cyclic Data Generation for Accurate Perturbation Prediction in Single-Cell RNA-Seq IJCAI 2025 Divide and Conquer: Coordinating Multiplex Mixture of Graph Learners to Handle Multi-Omics Analysis IJCAI 2025 DO-CoLM: Dynamic 3D Conformation Relationships Capture with Self-Adaptive Ordering Molecular Relational Modeling in Language Models IJCAI 2025 DrugHash: Hashing Based Contrastive Learning for Virtual Screening AAAI 2025 Drug-TTA: Test-Time Adaptation for Drug Virtual Screening via Multi-task Meta-Auxiliary Learning ICML 2025