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46 repositories

confounding-strength-estimation
Public
Snapshot of the modified implementation from the paper "Sensitivity Analysis to Unobserved Confounders: A Comparative Review to Estimate Confounding Strength in Sensitivity Models", Baitairian et al. (2025).
sensitivity-analysis causal-inference confounding-variables confounding-strength-calibration unobserved-confounder
R
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Other
•0•0•0•0•Updated Oct 17, 2025Oct 17, 2025
RiboNN
Public
RiboNN: predicting translation efficiencies from mRNA sequences
deep-learning mrna-translation-efficiency
Python
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Other
•11•39•0•0•Updated Oct 3, 2025Oct 3, 2025
saemixPBPK
Public
The 'saemixPBPK' package allows the use of the SAEM algorithm to perform estimations with PBPK/QSP models developped with the OSP Suite
R
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GNU General Public License v2.0
•0•1•0•0•Updated Sep 26, 2025Sep 26, 2025
MIPHEI-ViT
Public
MIPHEI-ViT: Repository to train Image-to-Image H&E to Immunofluorescence models
Jupyter Notebook
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Other
•3•17•0•0•Updated Sep 19, 2025Sep 19, 2025
GNN-Timeseries
Public
Jupyter Notebook
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Other
•0•0•0•0•Updated Sep 4, 2025Sep 4, 2025
SNAC-DB
Public
Repository containing pipelines developed for the SNAC-DB (Structural NANOBODY® VHH and Antibody Complex Database). SNAC-DB is ML-ready curation of the Protein Data Bank (PDB) for NANOBODY® VHH and antibody complex structures.
ai protein-structure ml antibody structure-prediction nanobody nanobody-antigen-interaction antibody-antigen-interaction
Python
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Other
•0•6•1•0•Updated Jul 31, 2025Jul 31, 2025
Clinical-BERT-Explainability
Public
To explain clinical BERT model predictions, we present an approach which leverages integrated gradients to attribute events in medical records that lead to an outcome prediction.
bert clinical-data explainable-ai integrated-gradients bert-fine-tuning
Python
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Other
•1•10•0•0•Updated Jul 30, 2025Jul 30, 2025
risk.assessr
Public
Define quality variables for evaluating the risk associated with R packages.
R
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GNU General Public License v2.0
•2•27•3•0•Updated Jul 28, 2025Jul 28, 2025
prodigyprotein
Public
Protein Diversification and Generation through Yielded mutations (Prodigy) Protein is an end-to-end platform for plug and play protein engineering
zero-shot protein-engineering protein-language-models
Python
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Other
•0•1•0•0•Updated Jul 27, 2025Jul 27, 2025
CImpact
Public
Causal inference library for timeseries analysis
machine-learning ai time-series solutions impact causal-inference advanced-analytics
Python
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Other
•1•17•2•1•Updated Jul 23, 2025Jul 23, 2025
RetroDMTA
Public
Code for the paper "Back to the Future of Lead Optimization: Benchmarking Compound Prioritization Strategies"
Python
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Other
•0•0•0•0•Updated Jul 4, 2025Jul 4, 2025
Clinical-BERT-Training
Public
Python
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Other
•0•2•0•0•Updated Jul 3, 2025Jul 3, 2025
causal_survival_analysis
Public
Causal survival analysis
R
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GNU General Public License v3.0
•0•1•0•0•Updated Jun 26, 2025Jun 26, 2025
enact-pipeline
Public
Repository for ENACT pipeline for end-to-end analysis of Visium HD data
Python
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Other
•15•65•9•1•Updated Jun 13, 2025Jun 13, 2025
teal.builder.checks
Public
R
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GNU General Public License v2.0
•0•2•0•0•Updated Jun 3, 2025Jun 3, 2025
sharp-bounds-for-continuous-treatment-effects
Public
Snapshot of the implementation used to generate figures and numerical results from the paper "Sharp Bounds for Continuous-Valued Treatment Effects with Unobserved Confounders", Baitairian et al. (2024).
sensitivity-analysis causal-inference confounder continuous-treatment average-potential-outcome
R
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Other
•0•0•0•0•Updated May 28, 2025May 28, 2025
PMX-CovEval
Public
AMPL
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MIT License
•0•1•0•0•Updated May 28, 2025May 28, 2025
CLM-LER
Public
Train, and fine-tune transformer models on huggingface for tasks involving electronic health records (EHR) and laboratory data
bert clinical-nlp ehr-data
Python
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Other
•0•2•0•0•Updated May 13, 2025May 13, 2025
MolQuery
Public
Python
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Other
•0•0•0•0•Updated Apr 16, 2025Apr 16, 2025
CAP-PLM
Public
Jupyter Notebook
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Other
•1•0•0•0•Updated Apr 4, 2025Apr 4, 2025
Alien
Public
Python
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Other
•3•14•0•0•Updated Apr 1, 2025Apr 1, 2025
PyEvoCell
Public
Python
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Other
•0•3•0•0•Updated Mar 31, 2025Mar 31, 2025
IDD-papers-generative-applicability-domains
Public
Repository for the code associated with the paper Impact of applicability domains by Maxime Langevin et al.
cc-f40ccl2041
Jupyter Notebook
•5•13•1•0•Updated Feb 19, 2025Feb 19, 2025
IDD-papers-avoiding_failure_modes
Public
Repository for the code associated with the paper Avoiding Failure Modes by Maxime Langevin et al.
Jupyter Notebook
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Other
•4•2•0•0•Updated Feb 18, 2025Feb 18, 2025
PMCB-scGFT
Public
A single-cell RNA-seq data generative model
R
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Other
•2•16•0•0•Updated Jan 11, 2025Jan 11, 2025
SKAI
Public
SKAI is a toolbox for analyzing reaction kinetics mechanisms. It includes a reaction network generator and Bayesian inference modeling. Ideal for researchers in chemical kinetics.
Jupyter Notebook
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Other
•0•5•0•0•Updated Jan 11, 2025Jan 11, 2025
CD-spectra-classification
Public
Python
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Other
•0•0•0•0•Updated Dec 19, 2024Dec 19, 2024
RWD-Proxy-Endpoint-Models
Public
Jupyter Notebook
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Other
•1•2•0•0•Updated Dec 16, 2024Dec 16, 2024
mRNA-LM
Public
Python
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Other
•9•14•3•1•Updated Dec 5, 2024Dec 5, 2024
spatialone-pipeline
Public
Spatial One
python bioinformatics spatialomics spatial-biology
Python
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Other
•4•29•0•0•Updated Oct 31, 2024Oct 31, 2024