Bioinformatics

DUSTED: Dual-Attention Enhanced Spatial Transcriptomics Denoiser AAAI 2025 Dynamics-Based Feature Augmentation of Graph Neural Networks for Variant Emergence Prediction AAAI 2025 Enhancing Antimicrobial Drug Resistance Classification by Integrating Sequence-Based and Text-Based Representations ACL 2025 Enhancing Chemical Reaction and Retrosynthesis Prediction with Large Language Model and Dual-task Learning IJCAI 2025 Enhancing Multimodal Protein Function Prediction Through Dual-Branch Dynamic Selection with Reconstructive Pre-Training IJCAI 2025 Entangled Relations: Leveraging NLI and Meta-analysis to Enhance Biomedical Relation Extraction NAACL 2025 Estimation of single-cell and tissue perturbation effect in spatial transcriptomics via Spatial Causal Disentanglement ICLR 2025 ExDDI: Explaining Drug-Drug Interaction Predictions with Natural Language AAAI 2025 From Knowledge to Treatment: Large Language Model Assisted Biomedical Concept Representation for Drug Repurposing EMNLP 2025 G2PDiffusion: Cross-Species Genotype-to-Phenotype Prediction via Evolutionary Diffusion ICCV 2025 GeLLM³O: Generalizing Large Language Models for Multi-property Molecule Optimization ACL 2025 Generative Co-Design of Antibody Sequences and Structures via Black-Box Guidance in a Shared Latent Space IJCAI 2025 Generative Flow Networks for Lead Optimization in Drug Design (Student Abstract) AAAI 2025 GoBERT: Gene Ontology Graph Informed BERT for Universal Gene Function Prediction AAAI 2025 GRAPE: Heterogeneous Graph Representation Learning for Genetic Perturbation with Coding and Non-Coding Biotype IJCAI 2025 GraphTranslate: Predicting Clinical Trial Translation using Graph Neural Networks on Biomedical Literature ACL 2025 GraPPI: A Retrieve-Divide-Solve GraphRAG Framework for Large-scale Protein-protein Interaction Exploration NAACL 2025 GRNFormer: A Biologically-Guided Framework for Integrating Gene Regulatory Networks into RNA Foundation Models ACL 2025 HeMeNet: Heterogeneous Multichannel Equivariant Network for Protein Multi-task Learning AAAI 2025 HHAN: Comprehensive Infectious Disease Source Tracing via Heterogeneous Hypergraph Neural Network AAAI 2025 Hierarchical Gradient-Based Genetic Sampling for Accurate Prediction of Biological Oscillations AAAI 2025 Hotspot-Driven Peptide Design via Multi-Fragment Autoregressive Extension ICLR 2025 How to Make Large Language Models Generate 100% Valid Molecules? EMNLP 2025 How To Make Your Cell Tracker Say "I dunno!" ICCV 2025 Improving Cancer Gene Prediction by Enhancing Common Information Between the PPI Network and Gene Functional Association AAAI 2025