Bioinformatics

Protein Fitness Landscape: Spectral Graph Theory Perspective AISTATS 2025 Protein Structure Tokenization: Benchmarking and New Recipe ICML 2025 PScalpel: A Machine Learning-based Guider for Protein Phase-Separating Behaviour Alteration AAAI 2025 R-DTI: Drug Target Interaction Prediction Based on Second-Order Relevance Exploration AAAI 2025 Recovering Manifold Structure Using Ollivier Ricci Curvature ICLR 2025 Relation-Aware Equivariant Graph Networks for Epitope-Unknown Antibody Design and Specificity Optimization AAAI 2025 Rethinking Cancer Gene Identification Through Graph Anomaly Analysis AAAI 2025 Rethinking Text-based Protein Understanding: Retrieval or LLM? EMNLP 2025 Robust Heterogeneous Graph Classification for Molecular Property Prediction with Information Bottleneck AAAI 2025 SpotDiff: Spatial Gene Expression Imputation Diffusion with Single-Cell RNA Sequencing Data Integration AAAI 2025 SWAMamba: A Sliding Window Attention Mamba Framework for Predicting Translation Elongation Rates AAAI 2025 Synergy of GFlowNet and Protein Language Model Makes a Diverse Antibody Designer AAAI 2025 Variational Combinatorial Sequential Monte Carlo for Bayesian Phylogenetics in Hyperbolic Space AISTATS 2025 VenusFactory: An Integrated System for Protein Engineering with Data Retrieval and Language Model Fine-Tuning ACL 2025 Virtual CRISPR: Can LLMs Predict CRISPR Screen Results? ACL 2025 Whole Genome Transformer for Gene Interaction Effects in Microbiome Habitat Specificity AAAI 2025 AI for Science in the Era of Large Language Models EMNLP 2024 Atom-Level Optical Chemical Structure Recognition with Limited Supervision CVPR 2024 Biomedical Knowledge Graph Embedding with Householder Projection (Student Abstract) AAAI 2024 BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning ACL 2024 Bridge-IF: Learning Inverse Protein Folding with Markov Bridges NeurIPS 2024 Conditional Synthesis of 3D Molecules with Time Correction Sampler NeurIPS 2024 Contrastive losses as generalized models of global epistasis NeurIPS 2024 CrossBind: Collaborative Cross-Modal Identification of Protein Nucleic-Acid-Binding Residues AAAI 2024 CryoGEM: Physics-Informed Generative Cryo-Electron Microscopy NeurIPS 2024