MilaGraph

MilaGraph's repositories

torchdrug

A powerful and flexible machine learning platform for drug discovery

Language:PythonApache-2.01549 27 230

KnowledgeGraphEmbedding

Language:PythonMIT1342 21 54

graphvite

GraphVite: A General and High-performance Graph Embedding System

Language:C++Apache-2.01260 28 115

ULTRA

A foundation model for knowledge graph reasoning

Language:PythonMIT575 9 25

GearNet

GearNet and Geometric Pretraining Methods for Protein Structure Representation Learning, ICLR'2023 (https://arxiv.org/abs/2203.06125)

Language:PythonMIT302 9 66

NBFNet

Official implementation of Neural Bellman-Ford Networks (NeurIPS 2021)

Language:PythonMIT228 7 19

AStarNet

Official implementation of A* Networks

Language:PythonMIT150 5 7

GraphAny

GraphAny: Fully-inductive Node Classification on Arbitrary Graphs

Language:PythonMIT148 4 3

RNNLogic

Language:C++133 6 21

ESM-GearNet

ESM-GearNet for Protein Structure Representation Learning (https://arxiv.org/abs/2303.06275)

Language:Python110 3 2

ProtST

[ICML-23 ORAL] ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts

Language:PythonApache-2.098 3 12

PEER_Benchmark

PEER Benchmark, appear at NeurIPS 2022 Dataset and Benchmark Track (https://arxiv.org/abs/2206.02096)

Language:PythonApache-2.097 4 10

DiffPack

Implementation of DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing

Language:PythonMIT89 7 12

GNN-QE

Official implementation of Graph Neural Network Query Executor (ICML 2022)

Language:PythonMIT89 3 9

GearBind

Pretrainable geometric graph neural network for antibody affinity maturation

Language:PythonApache-2.066 4 8

InductiveQE

Official implementation of Inductive Logical Query Answering in Knowledge Graphs (NeurIPS 2022)

Language:PythonNOASSERTION46 30

S3F

Sequence-Structure-Surface Model for Protein Fitness Prediction (S3F)

Language:PythonMIT46 2 4

SiamDiff

Code for Pre-training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction (https://arxiv.org/abs/2301.12068)

Language:Python42 3 4

esm-s

Structure-Informed Protein Language Model

Language:Python35 3 3

scCello

[NeurIPS 2024 Spotlight] A cell-ontology guided transcriptome foundation model

Language:Python20 3 5

HAX

Overcoming Long-Context Limitations of State-Space Models via Context-Dependent Sparse Attention (NeurIPS 2025)

Language:Python600

ProteinTutorial_AAAI2025

https://deepgraphlearning.github.io/ProteinTutorial_AAAI2025/

Language:CSSMIT6 20

torchdrug-site

Website for TorchDrug

Language:SCSSMIT6 50

ultra_torchdrug

A TorchDrug version of ULTRA for reproducibility

Language:PythonMIT5 4 1

torchprotein-site

Website for TorchProtein

Language:SCSSMIT3 20

Math80600A_2023W

Language:SCSS040

MATH60629A_2025A

Language:Jupyter Notebook000

MATH60630A_2024A

Language:SCSS020

Math80648A_2025A

Language:SCSS000

project

Website for research projects

Language:SCSS0100