Machine Learning and Systems Biology Research Department

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111 repositories

PCR-bias
Public
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Jul 22, 2025Jul 22, 2025
CellPick
Public
An interactive cell selection tool for spatial omics
Python
•0•2•0•0•Updated Jul 21, 2025Jul 21, 2025
rnaglib-experiments
Public
Python
•0•1•0•0•Updated Jul 18, 2025Jul 18, 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 Jun 26, 2025Jun 26, 2025
NeuralWalker
Public
Official Pytorch implementation of NeuralWalker (ICLR 2025)
random-walk state-space-models graph-neural-networks graph-representation-learning graph-transformer
Python
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BSD 3-Clause "New" or "Revised" License
•2•34•0•0•Updated Jun 25, 2025Jun 25, 2025
bioverse
Public
Python
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BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Jun 24, 2025Jun 24, 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
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BSD 3-Clause "New" or "Revised" License
•11•111•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
•0•2•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
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MIT License
•0•4•0•0•Updated Feb 27, 2025Feb 27, 2025
orbit-count
Public
Python bindings for ORCA (ORbit Counting Algorithm)
C++
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GNU General Public License v3.0
•0•1•0•0•Updated Feb 26, 2025Feb 26, 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
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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
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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
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BSD 3-Clause "New" or "Revised" License
•2•43•0•0•Updated Oct 17, 2024Oct 17, 2024
WWL
Public
Wasserstein Weisfeiler-Lehman Graph Kernels
Python
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BSD 3-Clause "New" or "Revised" License
•19•83•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
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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
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Other
•0•4•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++
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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
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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
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BSD 3-Clause "New" or "Revised" License
•3•22•1•1•Updated Nov 19, 2023Nov 19, 2023
motifiesta_models
Public
Python
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BSD 3-Clause "New" or "Revised" License
•2•0•0•0•Updated Oct 16, 2023Oct 16, 2023
proteinshake_models
Public
Python
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BSD 3-Clause "New" or "Revised" License
•2•9•0•0•Updated Oct 13, 2023Oct 13, 2023
SignificantPatternMiningFDR
Public
Code and Data for the paper: FASM and FAST-YB: Significant Pattern Mining with False Discovery Rate Control (ICDM 2023).
C
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BSD 3-Clause "New" or "Revised" License
•0•2•0•0•Updated Oct 13, 2023Oct 13, 2023
multicenter-sepsis
Public
Python
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Apache License 2.0
•4•17•0•0•Updated Oct 9, 2023Oct 9, 2023
spinoptmmd
Public
This is the official repository for our paper
Python
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BSD 3-Clause "New" or "Revised" License
•0•1•0•0•Updated Sep 29, 2023Sep 29, 2023
scikit-learn
Public
scikit-learn: machine learning in Python
Python
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BSD 3-Clause "New" or "Revised" License
•26k•0•0•0•Updated Aug 23, 2023Aug 23, 2023