Epistasis Lab at Cedars Sinai (@EpistasisLab)
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EpistasisLab

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Top repositories

1

tpot

A Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming.
Python
9,545
star
2

pmlb

PMLB: A large, curated repository of benchmark datasets for evaluating supervised machine learning algorithms.
Python
790
star
3

KRAGEN

Software to implement GoT with a weviate vectorized database
Python
459
star
4

scikit-rebate

A scikit-learn-compatible Python implementation of ReBATE, a suite of Relief-based feature selection algorithms for Machine Learning.
Python
401
star
5

Aliro

Aliro: AI-Driven Data Science
JavaScript
222
star
6

ClinicalDataSources

Open or Easy Access Clinical Data Sources for Biomedical Research
167
star
7

tpot2

A Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming.
Jupyter Notebook
156
star
8

scikit-mdr

A sklearn-compatible Python implementation of Multifactor Dimensionality Reduction (MDR) for feature construction.
Python
125
star
9

ReBATE

Relief Based Algorithms of ReBATE implemented in Python with Cython optimization. This repository is no longer being updated. Please see scikit-rebate.
Python
32
star
10

MIMIC_trajectories

Jupyter Notebook
30
star
11

digen

Diverse and generative ML benchmarks
Jupyter Notebook
14
star
12

ml-analyst

Analysis pipeline for quick ML analyses.
Python
11
star
13

interpret_ehr

Interpretation of machine learning predictions for patient outcomes in electronic health records
Jupyter Notebook
9
star
14

imputation

https://www.biorxiv.org/content/early/2017/07/24/167858
Jupyter Notebook
9
star
15

3DHeatmap

3D Heatmap tool in Unity3D. Inst. for Biomed. Informatics, Univ. of PA
C#
9
star
16

hibachi

Data simulation software that creates data sets with particular characteristics
Python
8
star
17

autoqtl

Automated Quantitative Trait Locus Analysis (AutoQTL)
Python
7
star
18

EBIC.jl

EBIC - a biclustering algorithm in Julia
Julia
7
star
19

EpistasisLab.github.io

Identifying the complex genetic architectures of disease
6
star
20

qsar-gnn

TeX
6
star
21

SAFE

The SAFE Algorithm: Solution and Fitness Evolution
Python
4
star
22

DTox

A knowledge-guided deep learning model for prediction and interpretation of drug toxicity
HTML
4
star
23

AlzKB

Python
4
star
24

regens

Recombines real genomic segments to simulate whole genomes
Python
4
star
25

rebate-benchmark

A centralized repository to benchmark ReBATE performance across a variety of parameter settings and datasets.
Jupyter Notebook
4
star
26

gecco2017-new-benchmarking-standards

Pages for workshops run by Epistasis Lab members
3
star
27

evolved-stats

A research project using genetic programming to discover and optimize statistical tests.
Jupyter Notebook
3
star
28

penn-lpc-scripts

Scripts that I wrote for use on the Penn LPC
Python
2
star
29

LPC

Documentation and informational resources for LPC use
2
star
30

tpot-kaggle

tpot applications on kaggle datasets
Jupyter Notebook
2
star
31

OMNIREP

The OMNIREP algorithm: Coevolving encodings and representations
Python
2
star
32

SimpleModelView

A Unity package for a simplified model-view system to help with code<->UI management.
ShaderLab
2
star
33

GPT4_and_Review

Using GPT-4 to write a scientific review article: a pilot evaluation study
Python
2
star
34

regens-analysis

Shell
1
star
35

PICV

Proportional instance cross validation
1
star
36

PennAI-Ed

Materials for PennAI-Ed - an initiative to enhance AI and data science education built on PennAI
Shell
1
star
37

TINY

Tiny Genetic Algorithm (GA) and Tiny Genetic Programming (GP)
Python
1
star
38

EVE

ENSEMBL VEP on EC2
1
star
39

pennai-arm64-deps

Pre-compiled dependencies for building PennAI Docker images on 64-bit ARM OSs (e.g., raspberry pi)
1
star
40

Conservation-Machine-Learning

Conservation Machine Learning
Python
1
star
41

latent_phenotype_project

Python
1
star
42

PAGER

Python
1
star
43

epistasis_detection

Implementation of an efficient algorithm to compute linear regression models for epistasis that permit varied genetic encodings (penetrance functions) of the interactions of loci and provide statistical evidence for epistasis.
Jupyter Notebook
1
star
44

VEPDB_populator

Population utilities for the VEPDB distributed annotation database, with an annotator written in Python
Python
1
star