🔥 Medical Image Analysis 2025: Towards Cardiac MRI Foundation Models: Comprehensive Visual-Tabular Representations for Whole-Heart Assessment and Beyond

BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data

easyPheno: a model agnostic phenotype prediction framework

Microbial Phenotype Prediction, successor to PICA, implemented with Python 3.7 and scikit-learn

Package to serve public and freely-available data from rare disease patients.

Create binary traits for UKbio using ICD/OPER/medication/self reports/age of diagnosis/visit-dates etc). The current output includes variables on history, study visit, future, time-to-first-event, episode-duration. this is a starting point to construct your favorite trait in ukb. The code was written on the go, so not super clean code..

Apply AI-based trait prediction from BacDive to your own genomes.

A physics-inspired R package for robust Euclidean embedding of sparse, non-metric dissimilarity data. Particularly powerful for antigenic cartography and viral evolution tracking, but applicable to any domain with incomplete similarity measurements. Published in *Bioinformatics* (2025).

A comparison of classical and machine learning-based phenotype prediction methods on simulated data and three plant species

IDeRare Phenotype Analysis suite : Convert Indonesia SATUSEHAT terminology (SNOMED-CT, LOINC, ICD-10) to Rare Disease Terminology / Ontology (HPO, OMIM) and find the likelihood differential gene and disease explaining patient phenotype

Relative adiponectin score (RAS) model

Indonesia Exome Rare Disease Variant Discovery Pipeline. Phenotype analysis part available on Streamlit and PyPi

Using machine learning to predict E. coli phenotypes

A class based on COBRApy to handle quantitative mutations on metabolic models.

Bayesian Network Model Predicting Personal Phenotypes using Genome-Sequencing Data

Comp Bio fall 2017 project

PHEMALE-Bacteria: tool for prediction of bacterial phenotypes based on its genome

Joint Repository of GR Metrics Regression and Kinase Interaction Network (KIN) Clustering

Phenotype prediction pipeline