IBM / otter-knowledgeLinks
Knowledge-enhanced learned representation enriches protein sequence and SMILES drug databases with a large Knowledge Graph fused from different sources. This improves results on TDC drug target binding affinity prediction benchmarks.
☆61Updated last month
Alternatives and similar repositories for otter-knowledge
Users that are interested in otter-knowledge are comparing it to the libraries listed below
Sorting:
- Code and data for the Nature Machine Intelligence paper "Knowledge graph-enhanced molecular contrastive learning with functional prompt".☆127Updated last year
- BioT5 (EMNLP 2023) and BioT5+ (ACL 2024 Findings)☆116Updated 10 months ago
- The code for "Learning Molecular Representation in a Cell"☆36Updated 5 months ago
- [ICLR 2022] OntoProtein: Protein Pretraining With Gene Ontology Embedding☆149Updated 4 months ago
- Code for "Unifying Molecular and Textual Representations via Multi-task Language Modelling" @ ICML 2023☆40Updated 10 months ago
- Code for the paper Enhancing Activity Prediction Models in Drug Discovery with the Ability to Understand Human Language☆98Updated 10 months ago
- A new retrieval-based framework for controllable molecule generation.☆49Updated 2 years ago
- [ACL 2024] ProtLLM: An Interleaved Protein-Language LLM with Protein-as-Word Pre-Training☆49Updated last year
- PyTorch code for KDD 2023 paper "Pre-training Antibody Language Models for Antigen-Specific Computational Antibody Design"☆53Updated last year
- Implementation of ICLR23 paper "Molecule Generation for Target Protein Binding with Structural Motifs"☆69Updated last year
- [ICML-23 ORAL] ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts☆98Updated last year
- SSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction (Briefings in Bioinformatics 2023)☆52Updated last year
- A comprehensive repository dedicated to the collection and exploration of studies utilizing Large Language Models for molecular design, p…☆42Updated 2 years ago
- Associated Repository for "Translation between Molecules and Natural Language"☆180Updated last year
- ☆43Updated last year
- ☆50Updated last year
- [Briefings in Bioinformatics] A Survey of Generative AI for de novo Drug Design☆89Updated 8 months ago
- The official implementation of dual-view molecule pre-training.☆42Updated 3 years ago
- Source code and data repository for "Ensembles of knowledge graph embedding models improve predictions for drug discovery"☆20Updated last year
- ☆36Updated last year
- Chemical-Reaction-Aware Molecule Representation Learning☆79Updated 3 years ago
- LLM for Drug Editing, ICLR 2024☆152Updated last year
- codes for KPGT (Knowledge-guided Pre-training of Graph Transformer)☆114Updated 10 months ago
- Fine-tuning of ChemBERTA LLMs to predict molecules' HIV inhibition replication.☆30Updated last year
- PEER Benchmark, appear at NeurIPS 2022 Dataset and Benchmark Track (https://arxiv.org/abs/2206.02096)☆92Updated 2 years ago
- A Text-guided Protein Design Framework, Nat Mach Intell 2025 (https://www.nature.com/articles/s42256-025-01011-z)☆90Updated 6 months ago
- a novel DTA predition method using graph neural network☆74Updated 2 years ago
- ☆16Updated 2 years ago
- ☆19Updated last year
- The Clinical Trials Knowledge Graph☆57Updated 2 years ago