boxorange / BioIE-LLMLinks
Biological Information Extraction from Large Language Models (LLMs) (Journal of Computational Biology 2025)
☆12Updated 7 months ago
Alternatives and similar repositories for BioIE-LLM
Users that are interested in BioIE-LLM are comparing it to the libraries listed below
Sorting:
- SkipGNN: Predicting Molecular Interactions with Skip-Graph Networks (Scientific Reports)☆65Updated 5 years ago
- [Bioinformatics 2021] This is the repo for the paper `SumGNN: Multi-typed Drug Interaction Prediction via Efficient Knowledge Graph Summa…☆88Updated last year
- Bi-Level Graph Neural Networks for Drug-Drug Interaction Prediction. ICML 2020 Graph Representation Learning and Beyond (GRL+) Workshop☆30Updated 5 years ago
- A Knowledge Graph for Relational Learning On Biological Data☆108Updated last year
- Knowledge-enhanced learned representation enriches protein sequence and SMILES drug databases with a large Knowledge Graph fused from dif…☆62Updated 4 months ago
- ☆34Updated 5 years ago
- Code to accompany the "Understanding the Performance of Knowledge Graph Embeddings in Drug Discovery" manuscript (Artificial Intelligence…☆34Updated last month
- ☆10Updated 5 years ago
- DeepDrug: A general graph-based deep learning framework for drug relation prediction☆62Updated 3 years ago
- Graph Positional and Structural Encoder☆54Updated last year
- ☆16Updated 3 years ago
- [ICLR 2022] OntoProtein: Protein Pretraining With Gene Ontology Embedding☆151Updated 10 months ago
- ☆58Updated 5 years ago
- ☆52Updated last year
- Code and data for the Nature Machine Intelligence paper "Knowledge graph-enhanced molecular contrastive learning with functional prompt".☆136Updated last year
- An end-to-end heterogeneous graph representation learning-based framework for drug-target interaction prediction☆31Updated 3 years ago
- ☆29Updated 5 years ago
- OTGNN code☆56Updated 5 years ago
- Official implementation of NeurIPS'21 paper"Motif-based Graph Self-Supervised Learning for Molecular Property Prediction"☆127Updated 2 years ago
- DPPIN: A Biological Repository of Dynamic Protein-Protein Interaction Network Data, IEEE BigData 2022☆32Updated 2 years ago
- Source code and data repository for "Ensembles of knowledge graph embedding models improve predictions for drug discovery"☆20Updated 2 years ago
- Code of our IJCAI2021 paper: "Learning Attributed Graph Representation with Communicative Message Passing Transformer"☆40Updated 3 years ago
- TIP: Tri-graph Interaction Propagation model for Polypharmacy Side Effect Prediction (GRL@NeurIPS, 2019)☆25Updated 3 years ago
- OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data.☆157Updated last year
- [ACL 2024] ProtLLM: An Interleaved Protein-Language LLM with Protein-as-Word Pre-Training☆50Updated last year
- LLM for Drug Editing, ICLR 2024☆156Updated last year
- Code and Data for the paper: Molecular Contrastive Learning with Chemical Element Knowledge Graph [AAAI 2022]☆91Updated 2 years ago
- Chemical-Reaction-Aware Molecule Representation Learning☆83Updated 3 years ago
- Must-read papers on NLP for science.☆56Updated 2 years ago
- Python package is for paper 'Predicting potential drug-drug interactions by integrating chemical, biological, phenotypic and network data…☆39Updated 9 years ago