Software & Tools
I develop open-source software to make topological and network analysis methods accessible to researchers across disciplines. All tools are freely available on GitHub with documentation and examples.
XGI: CompleX Group Interactions
A comprehensive Python package for the representation, manipulation, and analysis of complex systems with higher-order interactions (networks beyond pairwise connections). Co-developed with an international team of network scientists.
Features:
- Rich data structures optimized for higher-order networks with hypergraphs and simplicial complex representations
- Built-in dynamical models for: synchronization, contagion, opinion formation
- Network statistics and measures
- Visualization tools
- Integration with NetworkX ecosystem
Links: GitHub Repository Documentation Paper Tutorials
AHBA Microarray Mapper
Tools for topological analysis of gene expression data from the Allen Human Brain Atlas (AHBA). Uses the Mapper algorithm to create topological representations of high-dimensional genomic data.
Related Publication: Topological gene-expression networks recapitulate brain anatomy and function (2019)
Links: GitHub Repository Documentation & Examples
SASSAFRAS
Simple Automatic Scholar Sorter Appropriate For Researchers And Scientists
A tool for automated literature organization and management, designed to help researchers navigate large volumes of scientific papers.
Features:
- Automatic paper categorization
- Topic modeling and clustering
- Citation network analysis
- Literature review assistance
- Search and retrieval optimization
Links: GitHub Repository
Research Repositories for Topological Data Analysis:
TopTSA - Topological applications to Time Series Analysis and Dynamical Systems TDA_literature - Compendium of TDA applications and resources
More Resources: GitHub Profile - All repositories Google Scholar - Publications using these tools Research Overview - Context for software development