Machine Learning and Systems Biology Research Department

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116 repositories

CellPick
Public
An interactive cell selection tool for spatial omics
proteomics single-cell
Python
•
BSD 3-Clause "New" or "Revised" License
•0•2•0•0•Updated Dec 12, 2025Dec 12, 2025
bioverse
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•0•1•0•0•Updated Dec 10, 2025Dec 10, 2025
graph-kernels
Public
Graph kernels
C++
•
GNU General Public License v2.0
•26•55•0•0•Updated Dec 3, 2025Dec 3, 2025
RECOMB2026Cosmo
Public
Python
•0•0•0•0•Updated Nov 29, 2025Nov 29, 2025
Cosmo
Public
Python
•0•0•0•0•Updated Nov 29, 2025Nov 29, 2025
AutoGraph
Public
Official code for "Flatten Graphs as Sequences: Transformers are scalable graph generators" (NeurIPS 2025)
molecular-generation autoregressive-models graph-generative-models neurips-2025
Python
•
BSD 3-Clause "New" or "Revised" License
•1•11•1•0•Updated Oct 17, 2025Oct 17, 2025
polygraph-benchmark
Public
Benchmarking framework for graph generative models
benchmarking graph-generation graph-neural-networks
Python
•
BSD 3-Clause "New" or "Revised" License
•0•5•0•0•Updated Oct 14, 2025Oct 14, 2025
orbit-count
Public
Python bindings for ORCA (ORbit Counting Algorithm)
C++
•
GNU General Public License v3.0
•0•2•0•0•Updated Oct 12, 2025Oct 12, 2025
rnaglib-experiments
Public
Python
•0•2•0•0•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 architecture"
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•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
•0•0•0•0•Updated Jul 31, 2025Jul 31, 2025
PCR-bias
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•0•3•0•0•Updated Jul 28, 2025Jul 28, 2025
NeuralWalker
Public
Official Pytorch implementation of NeuralWalker (ICLR 2025)
random-walk state-space-models graph-neural-networks graph-representation-learning graph-transformer
Python
•
BSD 3-Clause "New" or "Revised" License
•2•38•0•0•Updated Jun 25, 2025Jun 25, 2025
MLDEEP
Public
Data-driven Protease Engineering by DNA-Recording and Epistasis-aware Machine Learning
Python
•0•0•0•0•Updated May 5, 2025May 5, 2025
proteinshake
Public
Protein structure datasets for machine learning.
Python
•
BSD 3-Clause "New" or "Revised" License
•11•112•1•0•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
•1•5•0•0•Updated Apr 16, 2025Apr 16, 2025
GNNsCanCountSubstructures
Public
Code and Data for the paper: "Graph Neural Networks Can (Often) Count Substructures" (ICLR 2025 Spotlight)
subgraph-isomorphism gnns iclr2025
GLSL
•
MIT License
•0•4•0•0•Updated Feb 27, 2025Feb 27, 2025
autoregressive-noisy-filtration-modeling
Public
Official implementation of the ANFM graph generative model
generative-model graph-generation graph-neural-networks graph-generative-model
Python
•
MIT License
•0•4•0•0•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-networks neurips-2024
Python
•
MIT License
•0•1•0•0•Updated Oct 29, 2024Oct 29, 2024
PST
Public
Protein Structure Transformer (PST): Endowing pretrained protein language models with structural knowledge
protein-structure protein-representation-learning graph-transformer evolutionary-scale-modeling
Python
•
BSD 3-Clause "New" or "Revised" License
•3•46•0•0•Updated Oct 17, 2024Oct 17, 2024
WWL
Public
Wasserstein Weisfeiler-Lehman Graph Kernels
Python
•
BSD 3-Clause "New" or "Revised" License
•20•86•4•0•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 Everything Workshop)
graph-matching substitution-matrices recomb2024 icml-2024
Python
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MIT License
•0•3•0•0•Updated Jul 28, 2024Jul 28, 2024
WTK
Public
A Wasserstein Subsequence Kernel for Time Series.
machine-learning data-mining optimal-transport time-series-classification
Python
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MIT License
•7•21•0•1•Updated Jun 17, 2024Jun 17, 2024
CARPE
Public
Jupyter Notebook
•
Other
•0•2•0•0•Updated Jun 15, 2024Jun 15, 2024
MultimodalAMR
Public
Python
•1•2•0•0•Updated May 30, 2024May 30, 2024
DeepEST
Public
protein-structure protein-function-prediction multimodal-deep-learning expression-location
Python
•
Other
•1•6•0•0•Updated Feb 9, 2024Feb 9, 2024
HOGImine
Public
Higher-order genetic interaction discovery with network-based biological priors.
bioinformatics pattern-mining gwas-tools ismb2023
C++
•
GNU General Public License v3.0
•1•13•0•0•Updated Feb 8, 2024Feb 8, 2024
LongCOVID
Public
Prediction of long COVID from proteomic and clinical data
Python
•
MIT License
•0•1•0•0•Updated Feb 8, 2024Feb 8, 2024
FindComb
Public
Scientifica app for finding the most significant combinations of features
Python
•3•3•1•1•Updated Feb 7, 2024Feb 7, 2024
JointMDS
Public
Official implementation of Joint Multidimensional Scaling
Python
•
BSD 3-Clause "New" or "Revised" License
•3•23•1•1•Updated Nov 19, 2023Nov 19, 2023