protein sequence

PatchET: Learning Enzyme Temperature Properties Through Patch-Based Neural Architectures AAAI 2026 S²Drug: Bridging Protein Sequence and 3D Structure in Contrastive Representation Learning for Virtual Screening AAAI 2026 Sequence-Free for Compound Protein Interaction Prediction AAAI 2026 TIGER: Text-Informed Generalized Enzyme-Reaction Retrieval ACL 2026 AutoProteinEngine: A Large Language Model Driven Agent Framework for Multimodal AutoML in Protein Engineering COLING 2025 A Variational Perspective on Generative Protein Fitness Optimization ICML 2025 Biological Sequence Kernels with Guaranteed Flexibility JMLR 2025 Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences ICLR 2025 Bridging Protein Sequences and Microscopy Images with Unified Diffusion Models ICML 2025 Curriculum Learning for Biological Sequence Prediction: The Case of De Novo Peptide Sequencing ICML 2025 Fast Uncovering of Protein Sequence Diversity from Structure ICLR 2025 FoldToken: Learning Protein Language via Vector Quantization and Beyond AAAI 2025 Immunogenicity Prediction with Dual Attention Enables Vaccine Target Selection ICLR 2025 Large Language and Protein Assistant for Protein-Protein Interactions Prediction ACL 2025 Rethinking Text-based Protein Understanding: Retrieval or LLM? EMNLP 2025 Steering Protein Family Design through Profile Bayesian Flow ICLR 2025 The OMG dataset: An Open MetaGenomic corpus for mixed-modality genomic language modeling ICLR 2025 BioBridge: Bridging Biomedical Foundation Models via Knowledge Graphs ICLR 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 CARE: a Benchmark Suite for the Classification and Retrieval of Enzymes NeurIPS 2024 Enhancing Transcription Factor Prediction through Multi-Task Learning (Student Abstract) AAAI 2024 Multi-modal Transfer Learning between Biological Foundation Models NeurIPS 2024 ProtT3: Protein-to-Text Generation for Text-based Protein Understanding ACL 2024 PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction AAAI 2024