Repositories list

• Gelato

  Public
  Code and Data for the paper: "Gelato: Graph Edit Distance via Autoregressive Neural Combinatorial Optimization" (ICLR 2026)

  gnnsgraph-edit-distanceiclr2026

  gnnsgraph-edit-distanceiclr2026

  Python

  •

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Apr 17, 2026Apr 17, 2026

• polygraph-benchmark

  Public
  Benchmarking framework for graph generative models (ICLR 2026)

  benchmarkinggraph-generationgraph-neural-networks

  benchmarkinggraph-generationgraph-neural-networks

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•99 stars•00 issues•00 pull requests•Updated Mar 26, 2026Mar 26, 2026

• CellPick

  Public

  BorgwardtLab/CellPick’s past year of commit activity
  An interactive cell selection tool for spatial omics

  proteomicssingle-cell

  proteomicssingle-cell

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•33 stars•00 issues•00 pull requests•Updated Feb 20, 2026Feb 20, 2026

• DeepEST

  Public
  protein-structureprotein-function-predictionmultimodal-deep-learning+ 1

  protein-structureprotein-function-predictionmultimodal-deep-learningexpression-location

  Python

  •

  Other

  •22 forks•77 stars•00 issues•00 pull requests•Updated Feb 19, 2026Feb 19, 2026

• ed_outcome_prediction_benchmark

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 13, 2026Feb 13, 2026

• Human_scDVP_Analysis

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 30, 2025Dec 30, 2025

• bioverse

  Public

  BorgwardtLab/bioverse’s past year of commit activity
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•11 star•00 issues•00 pull requests•Updated Dec 10, 2025Dec 10, 2025

• graph-kernels

  Public
  Graph kernels

  C++

  •

  GNU General Public License v2.0

  •2424 forks•5656 stars•00 issues•00 pull requests•Updated Dec 3, 2025Dec 3, 2025

• RECOMB2026Cosmo

  Public

  BorgwardtLab/RECOMB2026Cosmo’s past year of commit activity
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 29, 2025Nov 29, 2025

• Cosmo

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 29, 2025Nov 29, 2025

• AutoGraph

  Public
  Official code for "Flatten Graphs as Sequences: Transformers are scalable graph generators" (NeurIPS 2025)

  molecular-generationautoregressive-modelsgraph-generative-models+ 1

  molecular-generationautoregressive-modelsgraph-generative-modelsneurips-2025

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •11 fork•1515 stars•11 issue•00 pull requests•Updated Oct 17, 2025Oct 17, 2025

• orbit-count

  Public
  Python bindings for ORCA (ORbit Counting Algorithm)

  C++

  •

  GNU General Public License v3.0

  •00 forks•22 stars•00 issues•00 pull requests•Updated Oct 12, 2025Oct 12, 2025

• rnaglib-experiments

  Public
  Python

  •00 forks•33 stars•00 issues•00 pull requests•Updated Oct 7, 2025Oct 7, 2025

• Human_scDVP_data_dashboard

  Public
  Data dashboard accompanying the manuscript "Single cell spatial proteomics maps human liver zonation patterns and their vulnerability to disruption in tissue ar…

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 1, 2025Oct 1, 2025

• esm3_on_raven

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

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 31, 2025Jul 31, 2025

• PCR-bias

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•55 stars•00 issues•00 pull requests•Updated Jul 28, 2025Jul 28, 2025

• NeuralWalker

  Public
  Official Pytorch implementation of NeuralWalker (ICLR 2025)

  random-walkstate-space-modelsgraph-neural-networks+ 2

  random-walkstate-space-modelsgraph-neural-networksgraph-representation-learninggraph-transformer

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •55 forks•3939 stars•00 issues•00 pull requests•Updated Jun 25, 2025Jun 25, 2025

• MLDEEP

  Public
  Data-driven Protease Engineering by DNA-Recording and Epistasis-aware Machine Learning

  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 5, 2025May 5, 2025

• proteinshake

  Public
  Protein structure datasets for machine learning.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1111 forks•114114 stars•11 issue•00 pull requests•Updated Apr 22, 2025Apr 22, 2025

• ConformalAMR

  Public
  Main repository for "Detecting antimicrobial resistance through MALDI-TOF mass spectrometry with statistical guarantees using conformal prediction".

  Python

  •11 fork•55 stars•00 issues•00 pull requests•Updated Apr 16, 2025Apr 16, 2025

• Human_scDVP_CellSelection

  Public
  Pipeline for automated cell selection along a gradient with conservation of spatial information

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 7, 2025Apr 7, 2025

• GNNsCanCountSubstructures

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

  subgraph-isomorphismgnnsiclr2025

  subgraph-isomorphismgnnsiclr2025

  GLSL

  •

  MIT License

  •00 forks•55 stars•00 issues•00 pull requests•Updated Feb 27, 2025Feb 27, 2025

• autoregressive-noisy-filtration-modeling

  Public
  Official implementation of the ANFM graph generative model (TMLR, 2026)

  generative-modelgraph-generationgraph-neural-networks+ 1

  generative-modelgraph-generationgraph-neural-networksgraph-generative-model

  Python

  •

  MIT License

  •00 forks•66 stars•00 issues•00 pull requests•Updated Feb 7, 2025Feb 7, 2025

• NodeIndividualizedGNNs

  Public
  Code and Data for the paper: On the Expressivity and Sample Complexity of Node-Individualized Graph Neural Networks (NeurIPS 2024)

  graph-neural-networksneurips-2024

  graph-neural-networksneurips-2024

  Python

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Oct 29, 2024Oct 29, 2024

• PST

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

  protein-structureprotein-representation-learninggraph-transformer+ 1

  protein-structureprotein-representation-learninggraph-transformerevolutionary-scale-modeling

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •33 forks•4646 stars•00 issues•00 pull requests•Updated Oct 17, 2024Oct 17, 2024

• WWL

  Public
  Wasserstein Weisfeiler-Lehman Graph Kernels

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •2020 forks•8888 stars•44 issues•00 pull requests•Updated Sep 1, 2024Sep 1, 2024

• GraphMatchingSubstitutionMatrices

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

  graph-matchingsubstitution-matricesrecomb2024+ 1

  graph-matchingsubstitution-matricesrecomb2024icml-2024

  Python

  •

  MIT License

  •00 forks•33 stars•00 issues•00 pull requests•Updated Jul 28, 2024Jul 28, 2024

• WTK

  Public
  A Wasserstein Subsequence Kernel for Time Series.

  machine-learningdata-miningoptimal-transport+ 1

  machine-learningdata-miningoptimal-transporttime-series-classification

  Python

  •

  MIT License

  •77 forks•2121 stars•00 issues•11 pull request•Updated Jun 17, 2024Jun 17, 2024

• CARPE

  Public
  Jupyter Notebook

  •

  Other

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jun 15, 2024Jun 15, 2024

• MultimodalAMR

  Public
  Python

  •11 fork•11 star•00 issues•00 pull requests•Updated May 30, 2024May 30, 2024