EpistasisLab/regens-analysis

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EpistasisLab/regens-analysis

EpistasisLab

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tpot

A Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming.

pmlb

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

KRAGEN

Software to implement GoT with a weviate vectorized database

scikit-rebate

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

Aliro

Aliro: AI-Driven Data Science

tpot2

A Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming.

Jupyter Notebook

ClinicalDataSources

Open or Easy Access Clinical Data Sources for Biomedical Research

scikit-mdr

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

ReBATE

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 This repository is no longer being updated.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

MIMIC_trajectories

Jupyter Notebook

digen

Diverse and generative ML benchmarks

Jupyter Notebook

ml-analyst

Analysis pipeline for quick ML analyses.

3DHeatmap

3D Heatmap tool in Unity3D. Inst. for Biomed. Informatics, Univ. of PA

imputation

https://www.biorxiv.org/content/early/2017/07/24/167858

Jupyter Notebook

interpret_ehr

Interpretation of machine learning predictions for patient outcomes in electronic health records

Jupyter Notebook

AlzKB

hibachi

Data simulation software that creates data sets with particular characteristics

autoqtl

Automated Quantitative Trait Locus Analysis (AutoQTL)

EBIC.jl

EBIC - a biclustering algorithm in Julia

EpistasisLab.github.io

Identifying the complex genetic architectures of disease

qsar-gnn

SAFE

The SAFE Algorithm: Solution and Fitness Evolution

DTox

A knowledge-guided deep learning model for prediction and interpretation of drug toxicity

regens

Recombines real genomic segments to simulate whole genomes

rebate-benchmark

A centralized repository to benchmark ReBATE performance across a variety of parameter settings and datasets.

Jupyter Notebook

gecco2017-new-benchmarking-standards

Pages for workshops run by Epistasis Lab members

evolved-stats

A research project using genetic programming to discover and optimize statistical tests.

Jupyter Notebook

penn-lpc-scripts

Scripts that I wrote for use on the Penn LPC

LPC

Documentation and informational resources for LPC use

tpot-kaggle

tpot applications on kaggle datasets

Jupyter Notebook

OMNIREP

The OMNIREP algorithm: Coevolving encodings and representations

SimpleModelView

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

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

GPT4_and_Review

Using GPT-4 to write a scientific review article: a pilot evaluation study

STAR_outliers

PICV

Proportional instance cross validation

PennAI-Ed

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

TINY

Tiny Genetic Algorithm (GA) and Tiny Genetic Programming (GP)

escargot

AlzKB-updates

Jupyter Notebook

EVE

ENSEMBL VEP on EC2

Conservation-Machine-Learning

Conservation Machine Learning

pennai-arm64-deps

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

latent_phenotype_project

PAGER

VEPDB_populator

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