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53 repositories

PerturbDiff
Public
Python
•6•34•4•0•Updated Apr 7, 2026Apr 7, 2026
MATH60629A_2025A
Public
Jupyter Notebook
•1•0•0•0•Updated Nov 28, 2025Nov 28, 2025
Math80648A_2025A
Public
SCSS
•2•0•0•0•Updated Nov 28, 2025Nov 28, 2025
HAX
Public
Overcoming Long-Context Limitations of State-Space Models via Context-Dependent Sparse Attention (NeurIPS 2025)
Python
•0•18•0•0•Updated Sep 30, 2025Sep 30, 2025
GearNet
Public
GearNet and Geometric Pretraining Methods for Protein Structure Representation Learning, ICLR'2023 (https://arxiv.org/abs/2203.06125)
graph-neural-networks pre-training protein-representation-learning
graph-neural-networks pre-training protein-representation-learning
Python
•
MIT License
•33•318•24•1•Updated Jun 13, 2025Jun 13, 2025
GearBind
Public
Pretrainable geometric graph neural network for antibody affinity maturation
Python
•
Apache License 2.0
•12•75•9•0•Updated Mar 18, 2025Mar 18, 2025
scCello
Public
[NeurIPS 2024 Spotlight] A cell-ontology guided transcriptome foundation model
Python
•5•22•1•1•Updated Mar 12, 2025Mar 12, 2025
ProteinTutorial_AAAI2025
Public
https://deepgraphlearning.github.io/ProteinTutorial_AAAI2025/
CSS
•
MIT License
•0•6•0•0•Updated Feb 27, 2025Feb 27, 2025
ULTRA
Public
A foundation model for knowledge graph reasoning
Python
•
MIT License
•81•609•4•0•Updated Feb 3, 2025Feb 3, 2025
GraphAny
Public
GraphAny: Fully-inductive Node Classification on Arbitrary Graphs
Python
•
MIT License
•17•154•2•1•Updated Feb 3, 2025Feb 3, 2025
S3F
Public
Sequence-Structure-Surface Model for Protein Fitness Prediction (S3F)
Python
•
MIT License
•4•51•4•0•Updated Dec 3, 2024Dec 3, 2024
MATH60630A_2024A
Public
SCSS
•0•0•0•0•Updated Nov 21, 2024Nov 21, 2024
torchdrug
Public
A powerful and flexible machine learning platform for drug discovery
deep-learning pytorch drug-discovery
deep-learning pytorch drug-discovery graph-neural-networks
Python
•
Apache License 2.0
•220•1.6k•113•11•Updated Aug 12, 2024Aug 12, 2024
graphvite
Public
GraphVite: A General and High-performance Graph Embedding System
machine-learning gpu cuda
machine-learning gpu cuda data-visualization knowledge-graph representation-learning network-embedding
C++
•
Apache License 2.0
•156•1.3k•56•0•Updated Jun 14, 2024Jun 14, 2024
esm-s
Public
Structure-Informed Protein Language Model
protein-structure protein torchdrug
protein-structure protein torchdrug
Python
•5•38•3•0•Updated Feb 15, 2024Feb 15, 2024
KnowledgeGraphEmbedding
Public
Python
•
MIT License
•271•1.4k•6•1•Updated Dec 15, 2023Dec 15, 2023
DiffPack
Public
Implementation of DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing
deep-learning protein-structure molecule
deep-learning protein-structure molecule diffusion-models score-matching score-based-generative-modeling
Python
•
MIT License
•7•90•9•0•Updated Dec 4, 2023Dec 4, 2023
ultra_torchdrug
Public
A TorchDrug version of ULTRA for reproducibility
Python
•
MIT License
•3•5•1•1•Updated Oct 29, 2023Oct 29, 2023
project
Public
Website for research projects
SCSS
•1•1•0•0•Updated Oct 25, 2023Oct 25, 2023
ESM-GearNet
Public
ESM-GearNet for Protein Structure Representation Learning (https://arxiv.org/abs/2303.06275)
Python
•13•112•2•0•Updated Oct 23, 2023Oct 23, 2023
ProtST
Public
[ICML-23 ORAL] ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts
Python
•
Apache License 2.0
•8•103•6•0•Updated Oct 16, 2023Oct 16, 2023
GNN-QE
Public
Official implementation of Graph Neural Network Query Executor (ICML 2022)
knowledge-graph fuzzy-logic reasoning
knowledge-graph fuzzy-logic reasoning graph-neural-networks
Python
•
MIT License
•12•89•5•0•Updated Sep 5, 2023Sep 5, 2023
AStarNet
Public
Official implementation of A* Networks
Python
•
MIT License
•17•155•5•0•Updated Aug 12, 2023Aug 12, 2023
NBFNet
Public
Official implementation of Neural Bellman-Ford Networks (NeurIPS 2021)
knowledge-graph link-prediction reasoning
knowledge-graph link-prediction reasoning graph-neural-networks
Python
•
MIT License
•32•232•6•1•Updated Aug 2, 2023Aug 2, 2023
torchdrug-site
Public
Website for TorchDrug
SCSS
•
MIT License
•1•6•0•1•Updated Jul 16, 2023Jul 16, 2023
SiamDiff
Public
Code for Pre-training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction (https://arxiv.org/abs/2301.12068)
protein protein-protein-interaction pre-training
protein protein-protein-interaction pre-training protein-representation-learning
Python
•6•42•4•0•Updated Jul 9, 2023Jul 9, 2023
Math80600A_2023W
Public
SCSS
•0•0•0•0•Updated Apr 22, 2023Apr 22, 2023
PEER_Benchmark
Public
PEER Benchmark, appear at NeurIPS 2022 Dataset and Benchmark Track (https://arxiv.org/abs/2206.02096)
Python
•
Apache License 2.0
•13•101•4•0•Updated Mar 18, 2023Mar 18, 2023
torchprotein-site
Public
Website for TorchProtein
SCSS
•
MIT License
•0•3•0•0•Updated Nov 11, 2022Nov 11, 2022
InductiveQE
Public
Official implementation of Inductive Logical Query Answering in Knowledge Graphs (NeurIPS 2022)
Python
•
Other
•7•47•0•0•Updated Nov 10, 2022Nov 10, 2022

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MilaGraph

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53 repositories

PerturbDiff

MATH60629A_2025A

Math80648A_2025A

HAX

GearNet

GearBind

scCello

ProteinTutorial_AAAI2025

ULTRA

GraphAny

S3F

MATH60630A_2024A

torchdrug

graphvite

esm-s

KnowledgeGraphEmbedding

DiffPack

ultra_torchdrug

project

ESM-GearNet

ProtST

GNN-QE

AStarNet

NBFNet

torchdrug-site

SiamDiff

Math80600A_2023W

PEER_Benchmark

torchprotein-site

InductiveQE

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Repositories list

53 repositories