Graph Node Embeddings Embedding Tools

Tools for learning vector representations of nodes and graphs through unsupervised or self-supervised methods. Includes multi-scale embeddings, domain-specific graph embedding techniques (roads, stations, GO terms), and graph classification via embeddings. Does NOT include general graph neural networks, knowledge graph embeddings, or downstream task applications like drug discovery or influence maximization.

There are 50 graph node embeddings tools tracked. 1 score above 70 (verified tier). The highest-rated is eliorc/node2vec at 72/100 with 1,293 stars and 43,847 monthly downloads.

Get all 50 projects as JSON

curl "https://pt-edge.onrender.com/api/v1/datasets/quality?domain=embeddings&subcategory=graph-node-embeddings&limit=20"

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#	Tool	Score	Tier	Stars	Language
1	eliorc/node2vec Implementation of the node2vec algorithm.	72	Verified	1,293	Python
2	ferencberes/online-node2vec Node Embeddings in Dynamic Graphs	54	Established	57	Jupyter Notebook
3	mims-harvard/nimfa Nimfa: Nonnegative matrix factorization in Python	51	Established	557	Python
4	mims-harvard/decagon Graph convolutional neural network for multirelational link prediction	51	Established	469	Jupyter Notebook
5	claws-lab/jodie A PyTorch implementation of ACM SIGKDD 2019 paper "Predicting Dynamic...	49	Emerging	414	Python
6	mims-harvard/graphml-tutorials Tutorials for Machine Learning on Graphs	48	Emerging	230	Jupyter Notebook
7	mims-harvard/Raindrop Graph Neural Networks for Irregular Time Series	48	Emerging	219	Python
8	dawenl/cofactor CoFactor: Regularizing Matrix Factorization with Item Co-occurrence	48	Emerging	166	Jupyter Notebook
9	mims-harvard/scikit-fusion scikit-fusion: Data fusion via collective latent factor models	47	Emerging	151	Python
10	abojchevski/graph2gauss Gaussian node embeddings. Implementation of "Deep Gaussian Embedding of...	47	Emerging	179	Python
11	mims-harvard/SubGNN Subgraph Neural Networks (NeurIPS 2020)	46	Emerging	202	Python
12	eugeneyan/ml-surveys 📋 Survey papers summarizing advances in deep learning, NLP, CV, graphs,...	46	Emerging	2,881	—
13	mims-harvard/GraphXAI GraphXAI: Resource to support the development and evaluation of GNN explainers	46	Emerging	206	Python
14	snash4/GAT2VEC embedding attributed graphs	44	Emerging	57	Python
15	neo4j-product-examples/graph-machine-learning-examples Neo4j Graph Data Science with Graph ML & GNNs	43	Emerging	47	Jupyter Notebook
16	xgfs/verse Reference implementation of the paper VERSE: Versatile Graph Embeddings from...	43	Emerging	134	C++
17	sashakolpakov/graphem-rapids Graph embedding for influence maximization in networks	42	Emerging	4	Python
18	uhh-lt/path2vec Learning to represent shortest paths and other graph-based measures of node...	41	Emerging	33	Jupyter Notebook
19	nate-russell/Network-Embedding-Resources Network Embedding Survey and Resources	40	Emerging	41	—
20	benedekrozemberczki/diff2vec Reference implementation of Diffusion2Vec (Complenet 2018) built on Gensim...	40	Emerging	127	Python
21	rodrigo-arenas/Graph-Embeddings Graph and Nodes embeddings for downstream tasks	38	Emerging	5	Python
22	pedugnat/dynnode2vec dynnode2vec is a python package that implements algorithms to embed dynamic graphs	37	Emerging	12	Python
23	specialprocedures/semnet Semnet efficiently constructs graph structures from embeddings, enabling...	37	Emerging	5	Python
24	aedera/anc2vec Unsupervised neural network for learning embeddings of GO terms.	32	Emerging	21	Python
25	HKUST-KnowComp/SRBRW Source Code for IJCAI 2018 paper "Biased Random Walk based Social...	30	Emerging	9	C
26	talshapira/BGP2Vec We introduce a novel approach for Autonomous System (AS) embedding using...	29	Experimental	9	Jupyter Notebook
27	bio-ontology-research-group/DL2Vec Convert Description Logic axioms into a graph, and generate embedding...	27	Experimental	19	Python
28	arangoml/fastgraphml Given an input graph (ArangoDB or PyG) it generates graph embeddings using...	27	Experimental	68	Python
29	aida-ugent/DeBayes DeBayes: a Bayesian Method for Debiasing Network Embeddings (ICML 2020).	26	Experimental	8	Python
30	OlegDurandin/dtree2vec This project contain implementation the system, proposed in the "Adapting...	25	Experimental	3	HTML
31	vedashree29296/PyEmbeo graph embeddings for neo4j in python	24	Experimental	27	Python
32	Calychas/highway2vec highway2vec: representing OpenStreetMap microregions with respect to their...	24	Experimental	4	Jupyter Notebook
33	joisino/gnnrecover Code for "Graph Neural Networks can Recover the Hidden Features Solely from...	22	Experimental	24	Python
34	mims-harvard/fastGNMF Fast graph-regularized matrix factorization	22	Experimental	20	Python
35	sayalaruano/DengueDrugRep A project to predict new repurposed drugs for dengue using a biomedical...	22	Experimental	3	Jupyter Notebook
36	pietrocinaglia/dante DANTE is a software tool for pairwise alignment of dynamic networks. It...	22	Experimental	1	—
37	GemsLab/RGM Fast embedding-based graph classification with connections to kernels	21	Experimental	13	Python
38	meowoodie/Regularized-RBM A regularized version of RBM for unsupervised feature selection.	17	Experimental	13	Python
39	ErikLundin98/hermitian_laplacian_graph Node embedding extraction using GraphWave and the Hermitian Laplacian	15	Experimental	2	Jupyter Notebook
40	FOCS-AI/linkwise Topology-Driven Edge Predictions with Graph Machine Learning for Optical...	15	Experimental	2	Jupyter Notebook
41	RMilock/multi-scale-node-embeddings Official repository for the paper "Multi-Scale Node Embeddings for Graph...	15	Experimental	—	Python
42	shan1322/Hyperwalk embeddings for hyperedges in a hypergraph	14	Experimental	7	Python
43	GemsLab/EMBER Node embedding for directed, weighted networks	14	Experimental	7	Python
44	monomonedula/sten Simple algorithm for generating graph nodes embeddings	13	Experimental	6	Python
45	SmartData-Polito/gnn-for-darknet This repo contains the codes and the notebooks used for the paper "Exploring...	13	Experimental	8	Jupyter Notebook
46	kevinbdsouza/graph_embed_hic SCI and LINE to form Hi-C graph embeddings. Comparison with Hi-C-LSTM....	12	Experimental	3	Python
47	SelimWaly/Neural-Network-Graph-Learning SDNE and LINE Deep Learning Graph Embeddings Implementation	12	Experimental	3	Jupyter Notebook
48	OxfordRSE/L2Gv2 Infer global embeddings from local graph embeddings	11	Experimental	—	Python
49	Birunda3000/GNNs_X_GAE-S_cla Repositório de TCC com pipeline completo para experimentos com GNNs: geração...	11	Experimental	—	Python
50	pyvandenbussche/node2vec-arxiv Experiment using node2vec on arxiv papers metadata	10	Experimental	1	Python