Machine Learning and Computational Biology Lab

Repositories

• topo-ae-distances
  Python BSD-3-Clause 1 5 0 0 Updated Mar 30, 2021

• topological-autoencoders

  Code for the paper "Topological Autoencoders" by Michael Moor, Max Horn, Bastian Rieck, and Karsten Borgwardt.

  autoencoder persistent-homology topological-data-analysis tda
  Python BSD-3-Clause 10 41 0 0 Updated Mar 30, 2021

• sc-autoencoding

  student internship of Simon Streib to reduce single cell data
  Python 1 1 0 0 Updated Mar 29, 2021

• maldi-learn

  Software library for Maldi-Tof preprocessing and machine learning analysis.
  Python 0 4 1 0 Updated Mar 29, 2021

• FindComb

  Scientifica app for finding the most significant combinations of features
  Python 2 3 1 0 Updated Mar 23, 2021

• Set_Functions_for_Time_Series

  Repository of the ICML 2020 paper "Set Functions for Time Series"
  Python BSD-3-Clause 9 56 0 0 Updated Feb 25, 2021

• mgp-tcn

  Sepsis Prediction on MIMIC
  Python BSD-3-Clause 10 29 1 0 Updated Feb 16, 2021

• neighborGWAS
  Python 1 0 0 0 Updated Feb 4, 2021

• BaselEpi

  SEIR model framework used to describe the spread of the first SARS-CoV-2 wave within Basel-City
  Python 0 0 0 0 Updated Feb 4, 2021

• graphkernels-review

  Code and data sets for the review on graph kernels
  Python BSD-3-Clause 2 1 0 0 Updated Jan 7, 2021

• SAPIENs

  Forked from LaetitiaPapaxanthos/SAPIENs
  Jupyter Notebook 1 1 0 0 Updated Jan 3, 2021

• ripser

  Forked from Ripser/ripser

  Ripser: efficient computation of Vietoris–Rips persistence barcodes
  C++ MIT 47 0 0 0 Updated Nov 24, 2020

• homebrew-mlcb

  Homebrew taps of the Machine Learning and Computational Biology group of Prof. Karsten Borgwardt

  homebrew homebrew-tap
  Ruby 0 1 0 0 Updated Nov 24, 2020

• TDA-CNN-AD

  Model combining topological descriptors with patch based MR imaging features
  Python 1 0 0 0 Updated Nov 13, 2020

• fMRI_Cubical_Persistence

  Code of our NeurIPS 2020 publication 'Uncovering the Topology of Time-Varying fMRI Data using Cubical Persistence'

  persistent-homology topological-data-analysis tda neurips cubical-complex cubical-complexes neurips-2020
  Python BSD-3-Clause 1 8 0 0 Updated Oct 22, 2020

• pathogenex-scores
  Jupyter Notebook BSD-3-Clause 0 0 0 0 Updated Oct 20, 2020

• biobank_genomics
  Shell 1 0 0 0 Updated Oct 2, 2020

• GP-PoM
  TypeScript 0 4 0 0 Updated Sep 23, 2020

• Imputing_Signatures
  Python BSD-3-Clause 0 1 0 0 Updated Sep 23, 2020

• persim

  Forked from scikit-tda/persim

  Distances and representations of persistence diagrams
  Python MIT 33 0 0 0 Updated Sep 21, 2020

• ARDISS

  Automatic Relevance Determination for Imputation of Summary Statistics
  Python Apache-2.0 3 3 3 0 Updated Sep 7, 2020

• sepsis-prediction-review
  Python 1 0 0 0 Updated Aug 31, 2020

• SiNIMin

  Significant Network Interval Mining

  networks interactions statistical-testing
  C++ GPL-3.0 1 4 0 0 Updated Aug 21, 2020

• LSH-WTK

  Locality-Sensitive Hashing for the Wasserstein Time Series Kernel.
  Python 0 2 0 0 Updated Aug 17, 2020

• uea_ucr_datasets

  A small package for loading and handling UEA UCR time series classification datasets.
  Python 0 3 0 0 Updated Aug 7, 2020

• WWL

  Wasserstein Weisfeiler-Lehman Graph Kernels
  Python BSD-3-Clause 7 34 0 0 Updated Aug 4, 2020

• maldi_amr

  Code for the paper "Antimicrobial resistance prediction in clinical isolates through machine learning on MALDI-TOF mass spectra"

  python maldi-tof-ms maldi-tof-mass-spectrometry antimicrobial-resistance
  Jupyter Notebook BSD-3-Clause 1 0 0 0 Updated Jul 30, 2020

• Topf

  Topological peak filtering

  persistent-homology topological-data-analysis peak-detection
  Python BSD-3-Clause 0 0 0 0 Updated Jul 29, 2020

• Graph-Classification-with-TDA

  Forked from e-sollier/Graph-Classification-with-TDA
  Jupyter Notebook 3 1 0 0 Updated Jul 15, 2020

• MoProEmbeddings

  Implementation of moment propagation embeddings.
  Python 1 0 0 0 Updated Jul 13, 2020