Machine Learning and Systems Biology Research Department

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104 repositories

ConformalAMR
Public
Main repository for "Antimicrobial drug recommendation from MALDI-TOF MS with statistical guarantees using conformal prediction"
Python
•0•0•0•0•Updated Nov 5, 2024Nov 5, 2024
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•0•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
•1•32•0•1•Updated Oct 17, 2024Oct 17, 2024
PCR-bias
Public
Jupyter Notebook
•0•0•0•0•Updated Sep 9, 2024Sep 9, 2024
WWL
Public
Wasserstein Weisfeiler-Lehman Graph Kernels
Python
•
BSD 3-Clause "New" or "Revised" License
•18•77•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
•
MIT License
•0•2•0•0•Updated Jul 28, 2024Jul 28, 2024
proteinshake
Public
Protein structure datasets for machine learning.
Python
•
BSD 3-Clause "New" or "Revised" License
•9•101•84•2•Updated Jul 3, 2024Jul 3, 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•0•0•0•Updated Jun 15, 2024Jun 15, 2024
NeuralWalker
Public
Official Pytorch implementation of NeuralWalker
random-walk state-space-models graph-neural-networks graph-representation-learning graph-transformer
Python
•
BSD 3-Clause "New" or "Revised" License
•3•21•0•0•Updated Jun 6, 2024Jun 6, 2024
MultimodalAMR
Public
Python
•1•2•0•0•Updated May 30, 2024May 30, 2024
proteinshake-v1
Public
Protein structure datasets for machine learning.
Python
•
BSD 3-Clause "New" or "Revised" License
•9•0•17•0•Updated Apr 29, 2024Apr 29, 2024
DeepEST
Public
protein-structure protein-function-prediction multimodal-deep-learning expression-location
Python
•
Other
•0•3•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•21•1•1•Updated Nov 19, 2023Nov 19, 2023
motifiesta_models
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•2•0•0•0•Updated Oct 16, 2023Oct 16, 2023
proteinshake_models
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•2•8•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
•
BSD 3-Clause "New" or "Revised" License
•0•2•0•0•Updated Oct 13, 2023Oct 13, 2023
multicenter-sepsis
Public
Python
•
Apache License 2.0
•3•12•0•0•Updated Oct 9, 2023Oct 9, 2023
spinoptmmd
Public
This is the official repository for our paper
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Sep 29, 2023Sep 29, 2023
scikit-learn
Public
scikit-learn: machine learning in Python
Python
•
BSD 3-Clause "New" or "Revised" License
•25k•0•0•0•Updated Aug 23, 2023Aug 23, 2023
filtration_curves
Public
Code for the KDD 2021 paper 'Filtration Curves for Graph Representation'
topological-data-analysis graph-representation graph-classification kdd2021
Python
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BSD 3-Clause "New" or "Revised" License
•9•18•0•0•Updated Aug 8, 2023Aug 8, 2023
MotiFiesta
Public
Approximate subgraph motif mining through learnable edge contraction.
Python
•
GNU General Public License v3.0
•2•12•0•0•Updated Aug 3, 2023Aug 3, 2023
GraphKernels
Public
A package for computing Graph Kernels
kernels python-package graph-kernels graph-classification graph-comparison
C++
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MIT License
•55•102•4•2•Updated Jul 21, 2023Jul 21, 2023
reComBat
Public
reComBat package to correct batch effects
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•2•10•5•0•Updated Jul 17, 2023Jul 17, 2023
batchCorrectionPublicData
Public
Summary of the code published in 'reComBat: Batch effect removal in large-scale, multi-source omics data integration'.
Python
•1•1•0•0•Updated Jul 17, 2023Jul 17, 2023
networkGWAS
Public
Method for performing genome-wide association like studies on neighborhoods identified on biological networks relevant for the phenotype of interest.
Python
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Other
•3•14•0•0•Updated Jun 28, 2023Jun 28, 2023
proteinshake_release
Public
Python
•
GNU General Public License v3.0
•1•2•6•0•Updated Jun 21, 2023Jun 21, 2023