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blengerich/README.md

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.

GoogleScholar
### 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
📈 Stats
My Github Stats

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  1. cnellington/Contextualized cnellington/Contextualized Public

    An SKLearn-style toolbox for estimating and analyzing models, distributions, and functions with context-specific parameters.

    Python 74 12

  2. AdaptInfer/CompBioDatasetsForMachineLearning AdaptInfer/CompBioDatasetsForMachineLearning Public

    A Curated List of Computational Biology Datasets Suitable for Machine Learning

    177 25

  3. AdaptInfer/ConferenceCountdown AdaptInfer/ConferenceCountdown Public

    Webpage used to countdown time until ML/Compbio conference deadlines

    JavaScript 5

  4. AdaptInfer/Dropout_Interactions AdaptInfer/Dropout_Interactions Public

    Code for "Dropout as a Regularizer of Interaction Effects"

    Jupyter Notebook 1

  5. interpretml/interpret interpretml/interpret Public

    Fit interpretable models. Explain blackbox machine learning.

    C++ 6.6k 758

  6. AdaptInfer/DeathByRoundNumbers AdaptInfer/DeathByRoundNumbers Public

    Glass-box ML reveals biases in medical practice at round number thresholds

    Jupyter Notebook 2 1

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