Bioinformatics

From Mechanistic Interpretability to Mechanistic Biology: Training, Evaluating, and Interpreting Sparse Autoencoders on Protein Language Models ICML 2025 GDiffRetro: Retrosynthesis Prediction with Dual Graph Enhanced Molecular Representation and Diffusion Generation AAAI 2025 Generalized Implicit Neural Representations for Dynamic Molecular Surface Modeling AAAI 2025 Geometry-Aware Generative Autoencoders for Warped Riemannian Metric Learning and Generative Modeling on Data Manifolds AISTATS 2025 Geometry Informed Tokenization of Molecules for Language Model Generation ICML 2025 Global Ground Metric Learning with Applications to scRNA data AISTATS 2025 GRNFormer: A Biologically-Guided Framework for Integrating Gene Regulatory Networks into RNA Foundation Models ACL 2025 Hotspot-Driven Peptide Design via Multi-Fragment Autoregressive Extension ICLR 2025 How to Make Large Language Models Generate 100% Valid Molecules? EMNLP 2025 Identifying Cellular Niches in Spatial Transcriptomics: An Investigation into the Capabilities of Large Language Models ACL 2025 Improving N-Glycosylation and Biopharmaceutical Production Predictions Using AutoML-Built Residual Hybrid Models AISTATS 2025 Large Language Models in Bioinformatics: A Survey ACL 2025 Learning Biomolecular Models using Signal Temporal Logic L4DC 2025 Learning Disentangled Equivariant Representation for Explicitly Controllable 3D Molecule Generation AAAI 2025 Linear System Identification from Snapshot Data by Schrodinger bridge L4DC 2025 MagNet: Multi-Level Attention Graph Network for Predicting High-Resolution Spatial Transcriptomics MIDL 2025 MING: A Functional Approach to Learning Molecular Generative Models AISTATS 2025 MOL-Mamba: Enhancing Molecular Representation with Structural & Electronic Insights AAAI 2025 Motif-Oriented Representation Learning with Topology Refinement for Drug-Drug Interaction Prediction AAAI 2025 mRNA2vec: mRNA Embedding with Language Model in the 5'UTR-CDS for mRNA Design AAAI 2025 MuCoS: Efficient Drug–Target Discovery via Multi-Context-Aware Sampling in Knowledge Graphs ACL 2025 Multi-Objective Molecular Design Through Learning Latent Pareto Set AAAI 2025 nach0-pc: Multi-task Language Model with Molecular Point Cloud Encoder AAAI 2025 Pre-Training Graph Neural Networks on Molecules by Using Subgraph-Conditioned Graph Information Bottleneck AAAI 2025 PriFold: Biological Priors Improve RNA Secondary Structure Predictions AAAI 2025