Bioinformatics

Accelerating Antibiotic Discovery with Large Language Models and Knowledge Graphs ACL 2025 Accurate Nucleic Acid-Binding Residue Identification Based Domain-Adaptive Protein Language Model and Explainable Geometric Deep Learning AAAI 2025 A Simple and Comprehensive Benchmark for Single-Cell Transcriptomics AAAI 2025 Assay2Mol: Large Language Model-based Drug Design Using BioAssay Context EMNLP 2025 Association Pattern-enhanced Molecular Representation Learning AAAI 2025 Balanced Ranking with Relative Centrality: A multi-core periphery perspective ICLR 2025 BioGraphia: A LLM-Assisted Biological Pathway Graph Annotation Platform EMNLP 2025 Blend the Separated: Mixture of Synergistic Experts for Data-Scarcity Drug-Target Interaction Prediction AAAI 2025 Boosting LLM’s Molecular Structure Elucidation with Knowledge Enhanced Tree Search Reasoning ACL 2025 Bridging Sequence-Structure Alignment in RNA Foundation Models AAAI 2025 Can Large Language Models Classify and Generate Antimicrobial Resistance Genes? ACL 2025 CFP-Gen: Combinatorial Functional Protein Generation via Diffusion Language Models ICML 2025 Cross-Modal Imputation and Uncertainty Estimation for Spatial Transcriptomics AISTATS 2025 CryoDomain: Sequence-free Protein Domain Identification from Low-resolution Cryo-EM Density Maps AAAI 2025 Deep Signature: Characterization of Large-Scale Molecular Dynamics ICLR 2025 DEPfold: RNA Secondary Structure Prediction as Dependency Parsing. ICLR 2025 Diffusion on Language Model Encodings for Protein Sequence Generation ICML 2025 dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen AAAI 2025 Efficient Trajectory Inference in Wasserstein Space Using Consecutive Averaging AISTATS 2025 Enhancing Antimicrobial Drug Resistance Classification by Integrating Sequence-Based and Text-Based Representations ACL 2025 Enhancing Generalizability in Molecular Conformation Generation with METRIZATION-Informed Geometric Diffusion Pretraining AAAI 2025 Enhancing Safe and Controllable Protein Generation via Knowledge Preference Optimization ACL 2025 Entropic Matching for Expectation Propagation of Markov Jump Processes AISTATS 2025 Exploit Your Latents: Coarse-Grained Protein Backmapping with Latent Diffusion Models AAAI 2025 FoldToken: Learning Protein Language via Vector Quantization and Beyond AAAI 2025