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Ben Lengerich

📖 Asst Professor @ UW-Madison
💡 Let's chat about ML, precision medicine, and computational omics.
🚀 Check out our group website for ongoing projects and open positions.

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### Open-Source Research Projects
Libraries and Utilities
Library Description
Contextualized.ML PyPi Heterogeneous ML models for context-specific inference PyTorch
scContextualized.ML Tools for applying Contextualized.ML to single-cell analysis
clEHRity PyPi Automated deconfounding for EHRs
gam_purification PyPi Utilities for Purifying Generalized Additive Models
ebm_utils PyPi 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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