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A Curated List of Computational Biology Datasets Suitable for Machine Learning

datasets curated-list machine-learning computational-biology dataset computational-biology-datasets biomedical-data-science

compbiodatasetsformachinelearning's Introduction

📖 Postdoc at MIT
💡 Happy to chat about ML, precision medicine, and computational omics.

Open-Source Research Projects

Libraries and Utilities

Library	Description
Contextualized.ML	Heterogeneous ML models for context-specific inference
scContextualized.ML	Tools for applying Contextualized.ML to single-cell analysis
clEHRity	Automated deconfounding for EHRs
gam_purification	Utilities for Purifying Generalized Additive Models
ebm_utils	Utilities for Explainable Boosting Machines
my_twilio	Simple utility to text myself when ML training is finished
GO_Translator	Simple utiltiy for handling GO Terms in Python

Compilations and Resources

Title	Description
CompBio Datasets for ML	A list of compbio datasets for ML
ConferenceCountdown	Webpage used to countdown time until ML/Compbio conference deadlines
SnareSeq	A preprocessed version of Snare-seq data
Best Practices	A collection of best practices for CS/ML phd students
Basic Python Repo	A basic repo for Python projects

Papers and Experiments

Title	Paper(s)	Repo
Death by Round Numbers and Sharp Thresholds	[Medrxiv 2022]	Code
Automated interpretable discovery of heterogeneous treatment...	[JBI 2022]	Code
Dropout as a Regularizer of Interaction Effects	[AISTATS 2022]	Code
Neural Additive Models: Interpretable ML with Neural Nets	[NeurIPS 2021]	Code
NOTMAD: Estimating Bayesian Networks with Sample-Specific Structures...	[Arxiv 2021]	Code
Purifying Interaction Effects with the Functional ANOVA	[AISTATS 2020]	Code
Disentangling Increased Testing from Covid-19 Epidemic Spread	[Medrxiv 2020]	Code
Discriminative Subtyping of Lung Cancers from Histopathology Images...	[Medrxiv 2020]	Code
Differential Principal Components Analysis	[Biorxiv 2019]	Code
Precision Lasso: Accounting for Correlations and Linear Dependencies...	[Bioinformatics 2018]	Code
Retrofitting Distributional Embedding to Knowledge Graphs...	[COLING 2018]	Code
Personalized Regression	[NeurIPS 2019], [ISMB 2018]	Code

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