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TDA Bioinformatics Foundry

Packages Environments Molds Papers Tags

Glossary Design

Software

Packages

A Package is the software project we study and harden. Runnable environments and build recipes are related artifacts, not part of the package's identity.

HiPoNet A multi-view simplicial complex network predicting cohort-level labels from high-dimensional cellular point clouds. method/simplicial-learning method/topological-deep-learning application/single-cell modality/high-dim-tabular
open-topodockq-featurizer The MIT clean-room TopoDockQ interface featurizer, bit-exact against the bytecode-only original it replaces. method/persistent-laplacian application/structure-qa modality/molecular-structure
open-topoqa-featurizer The MIT clean-room TopoQA interface featurizer, written from the paper because the published implementation carries no license. method/persistent-homology application/structure-qa modality/molecular-structure
open-topoqa-scorer The MIT clean-room ProteinGAT interface-quality scorer, retrained from the paper rather than reusing an unlicensed checkpoint. method/topological-deep-learning application/structure-qa modality/molecular-structure
PETLS A C++ library with Python bindings for building persistent topological Laplacians and computing their matrices and spectra. method/persistent-laplacian application/molecular-sciences modality/point-cloud modality/graph
petls-pytorch An Apache-2.0 PyTorch implementation of persistent topological Laplacians and the Foundry's shippable PETLS substitute. method/persistent-laplacian
TopoDockQ A persistent-Laplacian scorer predicting DockQ interface quality to rank and filter peptide-protein docking poses. method/persistent-homology method/persistent-laplacian method/topological-deep-learning application/structure-qa modality/molecular-structure
TopoMetry An MIT-licensed toolkit for learning and evaluating spectral manifold representations of high-dimensional single-cell data. method/spectral-geometry application/single-cell modality/high-dim-tabular
TopoQA A topological deep learning model ranking predicted protein-complex structures by the quality of their interface. method/persistent-homology method/topological-deep-learning application/structure-qa modality/molecular-structure

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