A collection of important graph embedding, classification and representation learning papers with implementations.

deepwalk kernel-methods attention-mechanism network-embedding graph-kernel graph-kernels graph-convolutional-networks classification-algorithm node2vec weisfeiler-lehman graph-embedding graph-classification graph-attention-networks graph-representation-learning graph2vec deep-graph-kernels netlsd graph-attention-model structural-attention node-embedding

• Updated Mar 18, 2023
• Python

PyTorch Geometric Temporal: Spatiotemporal Signal Processing with Neural Machine Learning Models (CIKM 2021)

deep-learning network-science pytorch temporal-networks spatial-analysis spatial-data spatiotemporal network-embedding spatio-temporal-analysis graph-convolutional-networks gcn spatio-temporal-data temporal-data graph-embedding graph-neural-networks node-embedding graph-convolution gnn temporal-graphs

• Updated May 30, 2026
• Python

Karate Club: An API Oriented Open-source Python Framework for Unsupervised Learning on Graphs (CIKM 2020)

machine-learning sklearn community-detection network-science deepwalk networkx supervised-learning louvain unsupervised-learning network-embedding scikit label-propagation gcn graph-clustering node2vec networkx-graph graph-embedding graph2vec node-embedding 2vec

• Updated Jul 17, 2024
• Python

PyTorch Implementation and Explanation of Graph Representation Learning papers: DeepWalk, GCN, GraphSAGE, ChebNet & GAT.

pytorch deepwalk graph-convolutional-networks graph-embedding graph-attention-networks chebyshev-polynomials graph-representation-learning node-embedding graph-sage

• Updated Mar 28, 2025
• Jupyter Notebook

A parallel implementation of "graph2vec: Learning Distributed Representations of Graphs" (MLGWorkshop 2017).

machine-learning kernel word2vec deepwalk matrix-factorization transformer unsupervised-learning graph-kernel node2vec weisfeiler-lehman noise-contrastive-estimation graph-embedding graph2vec subgraph2vec graph-wavelet node-embedding struc2vec implicit-matrix-factorization diff2vec gemsec

• Updated Nov 6, 2022
• Python

Little Ball of Fur - A graph sampling extension library for NetworKit and NetworkX (CIKM 2020)

machine-learning deep-learning graph graph-algorithms network-science networkx sampling network-embedding random-walk metropolis-hastings minimum-spanning-tree graph-embedding forest-fire graph-sampling network-analytics node-embedding graph-sparsification community-structure network-sampling

• Updated Dec 20, 2025
• Python

A repository of pretty cool datasets that I collected for network science and machine learning research.

data-science benchmark machine-learning community-detection network-science deepwalk dataset dimensionality-reduction network-analysis network-embedding link-prediction gcn node2vec graph-embedding node-classification graph2vec node-embedding graph-convolution gnn graph-neural-network

• Updated Dec 20, 2025

A PyTorch implementation of "Predict then Propagate: Graph Neural Networks meet Personalized PageRank" (ICLR 2019).

machine-learning deep-neural-networks research deep-learning pagerank pytorch deepwalk attention network-embedding gcn iclr node2vec graph-embedding graph-classification node-embedding graph-attention graph-convolutional-neural-networks graph-neural-network ppnp appnp

• Updated Nov 6, 2022
• Python

A collection of graph foundation models including papers, codes, and datasets.

machine-learning deep-learning molecule transfer-learning representation-learning unsupervised-learning data-augmentation link-prediction zero-shot-learning graph-classification node-classification few-shot-learning graph-neural-networks self-supervised-learning knowlege-graph graph-representation-learning node-embedding pre-training foundation-models graph-foundation-model

• Updated Jul 10, 2025

A Pytorch implementation of "Splitter: Learning Node Representations that Capture Multiple Social Contexts" (WWW 2019).

machine-learning deep-learning clustering word2vec community-detection pytorch deepwalk gensim factorization network-embedding node2vec graph-embedding overlapping-community-detection deep-neural-network graph-representation-learning node-embedding implicit-factorization graph-neural-network ego-splitting word-vector

• Updated Jun 6, 2023
• Python

A sparsity aware implementation of "Deep Autoencoder-like Nonnegative Matrix Factorization for Community Detection" (CIKM 2018).

data-science machine-learning deep-learning clustering word2vec sklearn community-detection deepwalk autoencoder dimensionality-reduction unsupervised-learning cikm embedding nmf coordinate-descent node2vec node-embedding gemsec mnmf danmf

• Updated Mar 18, 2023
• Python

Py3plex - A multilayer complex network visualization and analysis library in python3

visualization data-science library bioinformatics command-line graph-algorithms docker-compose network-science python3 complex-networks biological-data-analysis network-visualization multiplex-networks network-analysis social-sciences multilayer-networks node-embedding centrality-measures heterogeneous-networks network-mining

• Updated Nov 11, 2026
• Python

The reference implementation of "Multi-scale Attributed Node Embedding". (Journal of Complex Networks 2021)

deep-learning word2vec deepwalk gensim network-analysis embedding network-embedding node2vec graph-embedding node-embedding gemsec implicit-factorization asonam tadw attributed-embedding aane asne musae walklets graph-neural-network

• Updated Sep 19, 2022
• Python

A scalable Gensim implementation of "Learning Role-based Graph Embeddings" (IJCAI 2018).

machine-learning research deep-learning tensorflow word2vec sklearn network-science pytorch deepwalk gensim representation-learning network-embedding node2vec weisfeiler-lehman graph-embedding graph-wavelet node-embedding struc2vec implicit-factorization graph-neural-network

• Updated Nov 6, 2022
• Python

Reference implementation of Diffusion2Vec (Complenet 2018) built on Gensim and NetworkX.

machine-learning deep-learning neural-network tensorflow embeddings deepwalk gensim complex-networks factorization unsupervised-learning embedding network-embedding diffusion node2vec graph-embedding node-embedding struc2vec diff2vec implicit-factorization semisupervised-learning

• Updated Nov 6, 2022
• Python

Variational Graph Recurrent Neural Networks - PyTorch

representation-learning variational-inference link-prediction graph-convolutional-networks variational-autoencoder variational-autoencoders graph-embedding graph-neural-networks graph-representation-learning node-embedding dynamic-graphs graph-auto-encoder graph-neural-network

• Updated Jul 8, 2020
• Python

A lightweight implementation of Walklets from "Don't Walk Skip! Online Learning of Multi-scale Network Embeddings" (ASONAM 2017).

machine-learning deep-learning word2vec deepwalk dimensionality-reduction gensim edge-prediction multiscale graph-mining embedding node2vec word-embedding graph-embedding node-classification graph-neural-networks node-embedding walklet graphlet dont-walk-skip graph-convolution

• Updated Mar 18, 2023
• Python

TigerLily: Finding drug interactions in silico with the Graph.

machine-learning node deep-learning graph ddi biology network-science knowledge-graph graph-database unsupervised-learning embedding graph-machine-learning gradient-boosting graph-embedding pharmaceuticals node-embedding tigergraph drug-drug-interaction heterogeneous-graph

• Updated Dec 17, 2022
• Jupyter Notebook

Representation learning-based graph alignment based on implicit matrix factorization and structural embeddings

scalability matrix-factorization representation-learning network-embedding graph-matching network-alignment node-embedding

• Updated Mar 30, 2021
• Python

A sparsity aware and memory efficient implementation of "Attributed Social Network Embedding" (TKDE 2018).

data-science tensorflow word2vec deepwalk feature-extraction dimensionality-reduction factorization representation-learning embedding network-embedding node2vec graph-embedding attributed node-embedding diff2vec gemsec attributed-embedding 2vec aane asne

• Updated Nov 6, 2022
• Python