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An open API service indexing awesome lists of open source software.

Projects in Awesome Lists by BorgwardtLab

A curated list of projects in awesome lists by BorgwardtLab .

https://github.com/borgwardtlab/sat

Official Pytorch code for Structure-Aware Transformer.

graph-neural-networks graph-representation-learning graph-transformer icml-2022

Last synced: 09 Apr 2025

https://github.com/borgwardtlab/set_functions_for_time_series

Repository of the ICML 2020 paper "Set Functions for Time Series"

deep-learning icml-2020 set-functions time-series-analysis

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/proteinshake

Protein structure datasets for machine learning.

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/wwl

Wasserstein Weisfeiler-Lehman Graph Kernels

Last synced: 03 Apr 2025

https://github.com/BorgwardtLab/P-WL

A Persistent Weisfeiler–Lehman Procedure for Graph Classification

graph-classification graph-kernels machine-learning persistent-homology topological-data-analysis weisfeiler-lehman

Last synced: 27 Mar 2025

https://github.com/borgwardtlab/p-wl

A Persistent Weisfeiler–Lehman Procedure for Graph Classification

graph-classification graph-kernels machine-learning persistent-homology topological-data-analysis weisfeiler-lehman

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/mgp-tcn

Sepsis Prediction on MIMIC

Last synced: 19 Oct 2025

https://github.com/BorgwardtLab/graph-kernels

Graph kernels

Last synced: 27 Mar 2025

https://github.com/borgwardtlab/graph-kernels

Graph kernels

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/sampling-outlier-detection

Rapid computation of distance-based outlierness scores via sampling

Last synced: 25 Aug 2025

https://github.com/borgwardtlab/pst

Protein Structure Transformer (PST): Endowing pretrained protein language models with structural knowledge

evolutionary-scale-modeling graph-transformer protein-representation-learning protein-structure

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/neural-persistence

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

algebraic-topology deep-learning iclr iclr2019 machine-learning neural-networks persistent-homology

Last synced: 16 Aug 2025

https://github.com/borgwardtlab/maldi-learn

Software library for Maldi-Tof preprocessing and machine learning analysis.

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/pychange

Multiple change detection with python

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/wtk

A Wasserstein Subsequence Kernel for Time Series.

data-mining machine-learning optimal-transport time-series-classification

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/maldi_amr

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

antimicrobial-resistance maldi-tof-mass-spectrometry maldi-tof-ms python

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/filtration_curves

Code for the KDD 2021 paper 'Filtration Curves for Graph Representation'

graph-classification graph-representation kdd2021 topological-data-analysis

Last synced: 27 Feb 2026

https://github.com/borgwardtlab/mvkdr

Multi-view Spectral Clustering on Conflicting Views

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/jointmds

Official implementation of Joint Multidimensional Scaling

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/fmri_cubical_persistence

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

cubical-complex cubical-complexes neurips neurips-2020 persistent-homology tda topological-data-analysis

Last synced: 07 Mar 2026

https://github.com/borgwardtlab/motifiesta

Approximate subgraph motif mining through learnable edge contraction.

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/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

evaluation-framework evaluation-metrics generative-model graph-learning machine-learning

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/kernelized-rank-learning

Kernelized rank learning for personalized drug recommendation

Last synced: 10 Sep 2025

https://github.com/borgwardtlab/recombat

reComBat package to correct batch effects

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/fisher_information_embedding

Official code for Fisher information embedding for node and graph learning (ICML 2023)

attention-model graph-kernels graph-learning graph-neural-networks icml-2023 information-geometry

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/mid

MID (Mutual Information Dimension) for measuring statistical dependence between two random variables

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/networkgwas

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

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/graphkernels-review

Code and data sets for the review on graph kernels

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/casmap

Detection of statistically significant combinations of SNPs in association mapping

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/maldi_pike

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

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/sinimin

Significant Network Interval Mining

interactions networks statistical-testing

Last synced: 21 Aug 2025

https://github.com/borgwardtlab/2019-06-machine-learning-for-biology

Introduction to Machine Learning for Biology (Workshop @ D-BSSE Retreat 2019)

latex-document machine-learning machine-learning-tutorials slides

Last synced: 10 Jun 2025

https://github.com/borgwardtlab/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).

Last synced: 17 Aug 2025

https://github.com/borgwardtlab/significant-subgraph-mining

Finding statistically significant subgraphs while correcting for multiple testing

Last synced: 29 Oct 2025

https://github.com/borgwardtlab/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

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/kernel-conditional-clustering

Kernel Conditional Clustering

Last synced: 15 Jul 2025

https://github.com/borgwardtlab/hogimine

Higher-order genetic interaction discovery with network-based biological priors.

bioinformatics gwas-tools ismb2023 pattern-mining

Last synced: 24 Oct 2025

https://github.com/borgwardtlab/graphhopper-kernels

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

Last synced: 13 Jun 2025

https://github.com/borgwardtlab/uea_ucr_datasets

A small package for loading and handling UEA UCR time series classification datasets.

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/lsh-wtk

Locality-Sensitive Hashing for the Wasserstein Time Series Kernel.

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/gp-pom

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/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

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/ardiss

Automatic Relevance Determination for Imputation of Summary Statistics

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/gnnscancountsubstructures

Code and Data for the paper: "Graph Neural Networks Can (Often) Count Substructures" (ICLR 2025 Spotlight)

gnns iclr2025 subgraph-isomorphism

Last synced: 11 Feb 2026

https://github.com/borgwardtlab/findcomb

Scientifica app for finding the most significant combinations of features

Last synced: 18 Jul 2025

https://github.com/borgwardtlab/simbsig

The official implementation for the SIMBSIG package

Last synced: 11 Jul 2025

https://github.com/borgwardtlab/multi-scones

Multi-task feature selection coupled with multiple network regularizers

Last synced: 13 Jul 2025

https://github.com/borgwardtlab/graphmatchingsubstitutionmatrices

Code and Data for the paper: Structure- and Function-Aware Substitution Matrices via Learnable Graph Matching (RECOMB 2024 & ICML 2024 Differentiable Almost Everything Workshop)

graph-matching icml-2024 recomb2024 substitution-matrices

Last synced: 19 Jan 2026

https://github.com/borgwardtlab/mods-recovery

Codes for prediction of the recovery of pediatric sepsis patients with MODS

Last synced: 15 Mar 2025

https://github.com/borgwardtlab/epistasis-lightbulb

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

Last synced: 30 Jul 2025

https://github.com/borgwardtlab/batchcorrectionpublicdata

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

Last synced: 06 Oct 2025

https://github.com/borgwardtlab/sc-autoencoding

student internship of Simon Streib to reduce single cell data

Last synced: 21 Jul 2025

https://github.com/borgwardtlab/significantpatternminingfdr

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

Last synced: 30 Aug 2025

https://github.com/borgwardtlab/ccsvm

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

Last synced: 01 Sep 2025

https://github.com/borgwardtlab/moproembeddings

Implementation of moment propagation embeddings.

Last synced: 08 Aug 2025

https://github.com/borgwardtlab/longcovid

Prediction of long COVID from proteomic and clinical data

Last synced: 15 Mar 2025

https://github.com/borgwardtlab/homebrew-mlcb

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

homebrew homebrew-tap

Last synced: 21 May 2026

https://github.com/borgwardtlab/gene-representations-in-networks

A systematic evaluation of gene representations in network based genetic analysis

Last synced: 11 Oct 2025

https://github.com/borgwardtlab/glide-scripts

Companion scripts to the GLIDE software

Last synced: 15 Mar 2025

https://github.com/borgwardtlab/tda-cnn-ad

Model combining topological descriptors with patch based MR imaging features

Last synced: 15 Mar 2025

https://github.com/borgwardtlab/spss

Code for pediatric sepsis study

Last synced: 15 Mar 2025

https://github.com/borgwardtlab/baselepi

SEIR model framework used to describe the spread of the first SARS-CoV-2 wave within Basel-City

Last synced: 15 Mar 2025

https://github.com/borgwardtlab/alloimmunity-kinetics

Code for "Pre-transplant kinetics of anti-HLA antibodies in patients on the kidney transplant waiting list."

Last synced: 15 Mar 2025

https://github.com/borgwardtlab/carpe

Last synced: 15 Mar 2025

https://github.com/borgwardtlab/conformalamr

Main repository for "Antimicrobial drug recommendation from MALDI-TOF MS with statistical guarantees using conformal prediction"

Last synced: 15 Mar 2025

https://github.com/borgwardtlab/spinoptmmd

This is the official repository for our paper

Last synced: 01 Jan 2026

https://github.com/borgwardtlab/esm3_on_raven

Code and guide for distributed embedding generation using ESM‑3 on the MPCDF Raven GPUs.

Last synced: 21 Jun 2025

https://github.com/borgwardtlab/cofi

Visualization and analysis of data sets containing time series with history information

Last synced: 24 Sep 2025

https://github.com/borgwardtlab/scones

Selecting CONected Explanatory SNPs

Last synced: 15 Mar 2025

https://github.com/borgwardtlab/deepgwas-genereps

Set learning for obtaining gene representations for deep GWAS approaches

Last synced: 15 Mar 2025