graphlayouts
graphlayouts: Layout algorithms for network visualizations in R - Published in JOSS (2023)
graphsim
graphsim: An R package for simulating gene expression data from graph structures of biological pathways - Published in JOSS (2020)
Local clustering
Local clustering - Published in JOSS (2018)
graphenv
graphenv: a Python library for reinforcement learning on graph search spaces - Published in JOSS (2022)
cosasi
cosasi: Graph Diffusion Source Inference in Python - Published in JOSS (2022)
cytoscape.js-cise
An implementation of the circular layout algorithm by Dogrusoz et al. as a Cytoscape.js extension
pytextrank
Python implementation of TextRank algorithms ("textgraphs") for phrase extraction
networkit
NetworKit is a growing open-source toolkit for large-scale network analysis.
kglab
Graph Data Science: an abstraction layer in Python for building knowledge graphs, integrated with popular graph libraries – atop Pandas, NetworkX, RAPIDS, RDFlib, pySHACL, PyVis, morph-kgc, pslpython, pyarrow, etc.
BisPy
BisPy: Bisimulation in Python - Published in JOSS (2021)
suitesparse
The official SuiteSparse library: a suite of sparse matrix algorithms authored or co-authored by Tim Davis, Texas A&M University.
AtiyahBott
An implementation of the Atiyah-Bott formula for the moduli space of genus 0 stable maps.
ntpoly
A massively parallel library for computing the functions of sparse matrices.
graphtage
A semantic diff utility and library for tree-like files such as JSON, JSON5, XML, HTML, YAML, and CSV.
phd-dissertation
My "Efficient Materials Informatics between Rockets and Electrons" PhD Dissertation in Materials Science and Engineering, defended on May 20th 2024, concisely spanning 352 pages and 109 figures.
iGraphMatch
Tools to find the correspondences between vertices in different graphs.
https://github.com/cqcl/portgraph
Directed graph with first-level ports in Rust.
https://github.com/habedi/graphina
A graph data science library for Rust :crab:
https://github.com/jmrozanec/ts2g2
Generate graphs from time series and time series from graphs.
SPbLA
SPbLA: The Library of GPGPU-powered Sparse Boolean Linear Algebra Operations - Published in JOSS (2022)
https://github.com/harrymvr/absorbing-centrality
An implementation of the absorbing random-walk centrality
https://github.com/alibaba/alink
Alink is the Machine Learning algorithm platform based on Flink, developed by the PAI team of Alibaba computing platform.
IGraph/M
IGraph/M: graph theory and network analysis for Mathematica - Published in JOSS (2023)
MultilayerGraphs.jl
MultilayerGraphs.jl: Multilayer Network Science in Julia - Published in JOSS (2023)
LaplacianOpt
A Julia/JuMP Package for Maximizing Algebraic Connectivity of Undirected Weighted Graphs
signed-local-community
[WebConf 2020] Searching for polarization in signed graphs: a local spectral approach
https://github.com/kahypar/mt-kahypar
Mt-KaHyPar (Multi-Threaded Karlsruhe Hypergraph Partitioner) is a shared-memory multilevel graph and hypergraph partitioner equipped with parallel implementations of techniques used in the best sequential partitioning algorithms. Mt-KaHyPar can partition extremely large hypergraphs very fast and with high quality.
sssnet_signed_clustering
Official code for the SDM2022 paper -- SSSNET: Semi-Supervised Signed Network Clustering.
cytoscape-layout-utilities
Miscellaneous utilities for placement of nodes or components complementary to a main layout algorithm
matlab-igraph: bringing igraph to MATLAB
matlab-igraph: bringing igraph to MATLAB - Published in JOSS (2025)
https://github.com/gscholze/graphcream
using graphs to choose ice cream flavors
https://github.com/ivis-at-bilkent/cytoscape.js-c-tsm
Compound-Topology Shape Metrics Approach
https://github.com/ivis-at-bilkent/cytoscape.js-cosep
Compound Spring Embedder with Ports (CoSEP)
global-chem
A Knowledge Graph of Common Chemical Names to their Molecular Definition
basic-influence-roles
Detect and measure the Basic Influence Role each node plays in a Directed Network.
feasible-edge-replacements
Classes and algorithms for recursive amoeba trees and general framework for feasible edge replacements.
https://github.com/alondmnt/scom
algorithm for detecting Spatially Co-evolving Orthologous Modules
community-aware-graph-transformer
Community-aware Graph Transformer (CGT) is a novel Graph Transformer model that utilizes community structures to address node degree biases in message-passing mechanism and developed by NS Lab @ CUK based on pure PyTorch backend.
https://github.com/amr-yasser226/pagerank-power-method
Modular Python implementation of the PageRank algorithm via the power method, with discrete‑math foundations, end‑to‑end code, and experimental validation.
textgraphs
TextGraphs + LLMs + graph ML for entity extraction, linking, ranking, and constructing a lemma graph
https://github.com/aida-ugent/csne
Source code for CSNE: Conditional Signed Network Embeddings (CIKM2020)
hypergraphx
HGX is a multi-purpose, open-source Python library for higher-order network analysis