MilaGraph

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49 repositories

scCello
Public
[NeurIPS 2024 Spotlight] A cell-ontology guided transcriptome foundation model
Python
•0•7•0•0•Updated Feb 7, 2025Feb 7, 2025
ProteinTutorial_AAAI2025
Public
https://deepgraphlearning.github.io/ProteinTutorial_AAAI2025/
CSS
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MIT License
•0•3•0•0•Updated Feb 6, 2025Feb 6, 2025
ULTRA
Public
A foundation model for knowledge graph reasoning
Python
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MIT License
•68•506•2•0•Updated Feb 3, 2025Feb 3, 2025
GraphAny
Public
GraphAny: Fully-inductive Node Classification on Arbitrary Graphs
Python
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MIT License
•9•119•0•0•Updated Feb 3, 2025Feb 3, 2025
S3F
Public
Sequence-Structure-Surface Model for Protein Fitness Prediction (S3F)
Python
•
MIT License
•2•23•1•0•Updated Dec 3, 2024Dec 3, 2024
MATH60630A_2024A
Public
SCSS
•0•0•0•0•Updated Nov 21, 2024Nov 21, 2024
GearBind
Public
Pretrainable geometric graph neural network for antibody affinity maturation
Python
•
Apache License 2.0
•5•42•6•0•Updated Aug 21, 2024Aug 21, 2024
torchdrug
Public
A powerful and flexible machine learning platform for drug discovery
deep-learning drug-discovery pytorch graph-neural-networks
Python
•
Apache License 2.0
•203•1.5k•110•12•Updated Aug 12, 2024Aug 12, 2024
graphvite
Public
GraphVite: A General and High-performance Graph Embedding System
machine-learning gpu cuda data-visualization knowledge-graph representation-learning network-embedding
C++
•
Apache License 2.0
•154•1.2k•53•0•Updated Jun 14, 2024Jun 14, 2024
esm-s
Public
Structure-Informed Protein Language Model
protein-structure protein torchdrug
Python
•4•27•3•0•Updated Feb 15, 2024Feb 15, 2024
KnowledgeGraphEmbedding
Public
Python
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MIT License
•267•1.3k•6•2•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 diffusion-models score-matching score-based-generative-modeling
Python
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MIT License
•7•81•8•0•Updated Dec 4, 2023Dec 4, 2023
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
Python
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MIT License
•30•280•23•0•Updated Nov 20, 2023Nov 20, 2023
ultra_torchdrug
Public
A TorchDrug version of ULTRA for reproducibility
Python
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MIT License
•2•5•1•1•Updated Oct 29, 2023Oct 29, 2023
project
Public
Website for research projects
SCSS
•1•0•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
•10•84•2•0•Updated Oct 23, 2023Oct 23, 2023
ProtST
Public
[ICML-23 ORAL] ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts
Python
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Apache License 2.0
•7•92•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 graph-neural-networks
Python
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MIT License
•11•89•5•0•Updated Sep 5, 2023Sep 5, 2023
AStarNet
Public
Official implementation of A* Networks
Python
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MIT License
•16•140•5•0•Updated Aug 12, 2023Aug 12, 2023
NBFNet
Public
Official implementation of Neural Bellman-Ford Networks (NeurIPS 2021)
knowledge-graph link-prediction reasoning graph-neural-networks
Python
•
MIT License
•29•203•6•1•Updated Aug 2, 2023Aug 2, 2023
torchdrug-site
Public
Website for TorchDrug
SCSS
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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-representation-learning
Python
•5•40•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
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Apache License 2.0
•10•86•3•0•Updated Mar 18, 2023Mar 18, 2023
torchprotein-site
Public
Website for TorchProtein
SCSS
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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
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Other
•6•47•0•0•Updated Nov 10, 2022Nov 10, 2022
RNNLogic
Public
C++
•25•129•15•0•Updated Oct 25, 2022Oct 25, 2022
SPN
Public
Python
•2•29•4•0•Updated Jul 12, 2022Jul 12, 2022
Math80600A_2022W
Public
SCSS
•1•0•0•0•Updated Apr 6, 2022Apr 6, 2022
ContinuousGNN
Public
Python
•
MIT License
•13•45•2•0•Updated Nov 17, 2021Nov 17, 2021