Bioinformatics

Accelerating Antibiotic Discovery with Large Language Models and Knowledge Graphs ACL 2025 Accelerating Cross-Encoders in Biomedical Entity Linking ACL 2025 Accurate Nucleic Acid-Binding Residue Identification Based Domain-Adaptive Protein Language Model and Explainable Geometric Deep Learning AAAI 2025 AdaBioBERT: Adaptive Token Sequence Learning for Biomedical Named Entity Recognition ACL 2025 ADIOS: Antibody Development via Opponent Shaping ICML 2025 Antibody Design and Optimization with Multi-scale Equivariant Graph Diffusion Models for Accurate Complex Antigen Binding IJCAI 2025 A Physics-Augmented Deep Learning Framework for Classifying Single Molecule Force Spectroscopy Data ICML 2025 ARTeFACT: Benchmarking Segmentation Models on Diverse Analogue Media Damage WACV 2025 Artificial Intelligence in Spectroscopy: Advancing Chemistry from Prediction To Generation and Beyond IJCAI 2025 A SAT-based Method for Counting All Singleton Attractors in Boolean Networks IJCAI 2025 ASCENT: Annotation-free Self-supervised Contrastive Embeddings for 3D Neuron Tracking in Fluorescence Microscopy ICCV 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 A Survey on Foundation Language Models for Single-cell Biology ACL 2025 A Unified Framework for Human-Allied Learning of Probabilistic Circuits AAAI 2025 Automatic Annotation Augmentation Boosts Translation between Molecules and Natural Language NAACL 2025 AutoProteinEngine: A Large Language Model Driven Agent Framework for Multimodal AutoML in Protein Engineering COLING 2025 BAnG: Bidirectional Anchored Generation for Conditional RNA Design ICML 2025 Benchmarking zero-shot biomedical relation triplet extraction across language model architectures ACL 2025 Beyond Atoms: Enhancing Molecular Pretrained Representations with 3D Space Modeling ICML 2025 Beyond Sequence: Impact of Geometric Context for RNA Property Prediction ICLR 2025 BioGraphia: A LLM-Assisted Biological Pathway Graph Annotation Platform EMNLP 2025 BioHopR: A Benchmark for Multi-Hop, Multi-Answer Reasoning in Biomedical Domain ACL 2025 Biological Sequence Kernels with Guaranteed Flexibility JMLR 2025