Machine Learning and Systems Biology Research Department (@BorgwardtLab)
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BorgwardtLab

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Top repositories

1

SAT

Official Pytorch code for Structure-Aware Transformer.
Python
226
star
2

topological-autoencoders

Code for the paper "Topological Autoencoders" by Michael Moor, Max Horn, Bastian Rieck, and Karsten Borgwardt.
Python
131
star
3

Set_Functions_for_Time_Series

Repository of the ICML 2020 paper "Set Functions for Time Series"
Python
118
star
4

TOGL

Topological Graph Neural Networks (ICLR 2022)
Python
101
star
5

GraphKernels

A package for computing Graph Kernels
C++
97
star
6

proteinshake

Protein structure datasets for machine learning.
Python
82
star
7

WWL

Wasserstein Weisfeiler-Lehman Graph Kernels
Python
76
star
8

mgp-tcn

Sepsis Prediction on MIMIC
Python
64
star
9

P-WL

A Persistent Weisfeilerโ€“Lehman Procedure for Graph Classification
Python
58
star
10

graph-kernels

Graph kernels
C++
55
star
11

S3M

A software package for statistically significant shapelet mining
C++
52
star
12

sampling-outlier-detection

Rapid computation of distance-based outlierness scores via sampling
C
33
star
13

maldi_amr

Code for the paper "Antimicrobial resistance prediction in clinical isolates through machine learning on MALDI-TOF mass spectra"
Jupyter Notebook
30
star
14

Neural-Persistence

Code for the paper 'Neural Persistence: A Complexity Measure for Deep Neural Networks Using Algebraic Topology'
Python
29
star
15

maldi-learn

Software library for Maldi-Tof preprocessing and machine learning analysis.
Python
28
star
16

PyChange

Multiple change detection with python
C++
22
star
17

WTK

A Wasserstein Subsequence Kernel for Time Series.
Python
21
star
18

JointMDS

Official implementation of Joint Multidimensional Scaling
Python
20
star
19

PST

Protein Structure Transformer (PST): Endowing pretrained protein language models with structural knowledge
Python
19
star
20

fMRI_Cubical_Persistence

Code of our NeurIPS 2020 publication 'Uncovering the Topology of Time-Varying fMRI Data using Cubical Persistence'
Python
19
star
21

filtration_curves

Code for the KDD 2021 paper 'Filtration Curves for Graph Representation'
Python
17
star
22

MvKDR

Multi-view Spectral Clustering on Conflicting Views
Python
16
star
23

fisher_information_embedding

Official code for Fisher information embedding for node and graph learning (ICML 2023)
Python
16
star
24

Kernelized-Rank-Learning

Kernelized rank learning for personalized drug recommendation
Jupyter Notebook
15
star
25

ggme

Official repository for the ICLR 2022 paper "Evaluation Metrics for Graph Generative Models: Problems, Pitfalls, and Practical Solutions" https://openreview.net/forum?id=tBtoZYKd9n
Python
14
star
26

HOGImine

Higher-order genetic interaction discovery with network-based biological priors.
C++
13
star
27

MotiFiesta

Approximate subgraph motif mining through learnable edge contraction.
Python
12
star
28

multicenter-sepsis

Python
10
star
29

networkGWAS

Method for performing genome-wide association like studies on neighborhoods identified on biological networks relevant for the phenotype of interest.
Python
10
star
30

MID

MID (Mutual Information Dimension) for measuring statistical dependence between two random variables
C
10
star
31

maldi_PIKE

Code for 'Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra'
Python
9
star
32

graphkernels-review

Code and data sets for the review on graph kernels
Python
9
star
33

reComBat

reComBat package to correct batch effects
Jupyter Notebook
9
star
34

topo-ae-distances

Python
8
star
35

CAsMap

Detection of statistically significant combinations of SNPs in association mapping
C++
7
star
36

proteinshake_models

Python
7
star
37

Kernel-Conditional-Clustering

Kernel Conditional Clustering
MATLAB
7
star
38

ADNI_3DCNNvsTDA

This is a summary of the model code used in "Back to the basics with inclusion of clinical domain knowledge - A simple, scalable and effective model of Alzheimer's Disease classification". It comprised the relevant 3D CNNs for hippocampus, patch and full inner brain image subsets, the TDA 2D CNN with relevant dense models to combine models trained on persistence images from different homological dimensions. Moreover, the models (GNN and LR) to combine multiple image patches are included, as well as the data splits in terms of ADNI database patient IDs (partitions).
Python
7
star
39

2019-06-Machine-Learning-for-Biology

Introduction to Machine Learning for Biology (Workshop @ D-BSSE Retreat 2019)
TeX
7
star
40

SiNIMin

Significant Network Interval Mining
C++
6
star
41

significant-subgraph-mining

Finding statistically significant subgraphs while correcting for multiple testing
C++
6
star
42

LSH-WTK

Locality-Sensitive Hashing for the Wasserstein Time Series Kernel.
Python
6
star
43

LMM-Lasso

An implementation of the Lasso model for association mapping and phenotype prediction which corrects for population strucure (Rakitsch et al., Bioinformatics 2013): http://goo.gl/FRmXwI
Python
6
star
44

sepsis-prediction-review

Python
5
star
45

uea_ucr_datasets

A small package for loading and handling UEA UCR time series classification datasets.
Python
5
star
46

GP-PoM

TypeScript
5
star
47

graphhopper-kernels

Scalable kernels for graphs with continuous attributes (Feragen et al., NIPS 2013) http://goo.gl/VxSfzZ
MATLAB
5
star
48

ARDISS

Automatic Relevance Determination for Imputation of Summary Statistics
Python
4
star
49

Epistasis-GLIDE

A C and CUDA implementation of tabulating linear regression for an exhaustive pairwise interaction search on a CUDA enabled GPU (Kam-Thong et al., Human Heredity 2012) http://goo.gl/XE54ir
Cuda
4
star
50

Topf

Topological peak filtering
Python
3
star
51

simbsig

The official implementation for the SIMBSIG package
Python
3
star
52

FindComb

Scientifica app for finding the most significant combinations of features
Python
3
star
53

Multi-SConES

Multi-task feature selection coupled with multiple network regularizers
R
3
star
54

Imputing_Signatures

Python
2
star
55

PheGeMIL

Python
2
star
56

ccSVM

Confounder-corrected Classification with Support Vector Machines (Li et al., Bioinformatics 2011) http://goo.gl/Qz9Ap5
C++
2
star
57

DeepEST

Python
2
star
58

NeuralWalker

Official Pytorch implementation of NeuralWalker
Python
2
star
59

proteinshake_release

Python
2
star
60

MODS-recovery

Codes for prediction of the recovery of pediatric sepsis patients with MODS
Python
2
star
61

GraphMatchingSubstitutionMatrices

Code and Data for the paper: Structure- and Function-Aware Substitution Matrices via Learnable Graph Matching (RECOMB 2024)
Python
2
star
62

sc-autoencoding

student internship of Simon Streib to reduce single cell data
Python
2
star
63

Epistasis-lightbulb

Efficient algorithms and GPU implementations for genome-wide epistasis screens as described in (Achlioptas et al., KDD 2011) http://goo.gl/jX8kPi
Python
2
star
64

batchCorrectionPublicData

Summary of the code published in 'reComBat: Batch effect removal in large-scale, multi-source omics data integration'.
Python
1
star
65

biobank_genomics

Shell
1
star
66

LongCOVID

Prediction of long COVID from proteomic and clinical data
Python
1
star
67

gene-representations-in-networks

A systematic evaluation of gene representations in network based genetic analysis
Python
1
star
68

homebrew-mlcb

Homebrew taps of the Machine Learning and Computational Biology group of Prof. Karsten Borgwardt
Ruby
1
star
69

glide-scripts

Companion scripts to the GLIDE software
Python
1
star
70

SignificantPatternMiningFDR

Code and Data for the paper: FASM and FAST-YB: Significant Pattern Mining with False Discovery Rate Control (ICDM 2023).
C
1
star
71

SCIRecoveryPredictionPublic

We provide a simple matching algorithm to identify digital twins for spinal cord injury patients in the acute injury phase.
Python
1
star
72

MoProEmbeddings

Implementation of moment propagation embeddings.
Python
1
star
73

Genetic-Heterogeneity-Discovery-FAIS

Genome-wide detection of intervals of genetic heterogeneity (Llinares-Lopez et al., ISMB/Bioinformatics 2015) http://goo.gl/h9gl6K
C
1
star