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Bioinformatics

638 directly classified papers

Papers per year

Papers

Shared Task at Biolaysumm2025 : Extract then summarize approach Augmented with UMLS based Definition Retrieval for Lay Summary generation. ACL 2025
SMAFIRA Shared Task at the BioNLP’2025 Workshop: Assessing the Similarity of the Research Goal ACL 2025
Automatic Annotation Augmentation Boosts Translation between Molecules and Natural Language NAACL 2025
Towards Better Multi-task Learning: A Framework for Optimizing Dataset Combinations in Large Language Models NAACL 2025
Spatially Resolved Transcriptomics Data Clustering with Tailored Spatial-scale Modulation IJCAI 2025
scRAG: Hybrid Retrieval-Augmented Generation for LLM-based Cross-Tissue Single-Cell Annotation ACL 2025
PreClinIE: An Annotated Corpus for Information Extraction in Preclinical Studies ACL 2025
Improving Cancer Gene Prediction by Enhancing Common Information Between the PPI Network and Gene Functional Association AAAI 2025
Can Large Language Models Classify and Generate Antimicrobial Resistance Genes? ACL 2025
AutoProteinEngine: A Large Language Model Driven Agent Framework for Multimodal AutoML in Protein Engineering COLING 2025
GRNFormer: A Biologically-Guided Framework for Integrating Gene Regulatory Networks into RNA Foundation Models ACL 2025
Learning from Negative Samples in Biomedical Generative Entity Linking ACL 2025
GraPPI: A Retrieve-Divide-Solve GraphRAG Framework for Large-scale Protein-protein Interaction Exploration NAACL 2025
Whole Genome Transformer for Gene Interaction Effects in Microbiome Habitat Specificity AAAI 2025
BOE-ViT: Boosting Orientation Estimation with Equivariance in Self-Supervised 3D Subtomogram Alignment CVPR 2025
Zero-Shot Cross-Sentential Scientific Relation Extraction via Entity-Guided Summarization IJCNLP 2025
ASCENT: Annotation-free Self-supervised Contrastive Embeddings for 3D Neuron Tracking in Fluorescence Microscopy ICCV 2025
Biological Sequence Kernels with Guaranteed Flexibility JMLR 2025
CryoMAE: Few-Shot Cryo-EM Particle Picking with Masked Autoencoders WACV 2025
Assay2Mol: Large Language Model-based Drug Design Using BioAssay Context EMNLP 2025
STINR: Deciphering Spatial Transcriptomics via Implicit Neural Representation CVPR 2025
Virtual CRISPR: Can LLMs Predict CRISPR Screen Results? ACL 2025
GeLLM³O: Generalizing Large Language Models for Multi-property Molecule Optimization ACL 2025
LIDDIA: Language-based Intelligent Drug Discovery Agent EMNLP 2025
A SAT-based Method for Counting All Singleton Attractors in Boolean Networks IJCAI 2025