Hello and welcome! I’m Trang Le. I’m a postdoctoral fellow with Jason Moore at the Computational Genetics Lab, University of Pennsylvania. I enjoy developing machine learning methods for analyses of biomedical data, including neuroimage (functional/structural MRI), transcriptomics and genotypes. Most of the datasets I work with are high dimensional (i.e., have many predictors/features), so I spend most of my time building feature selection algorithms for these data. I trade my bias toward the nearest-neighbor concept for lower variance of my methods and better generalizability. When I’m not knee deep in data, I run, dance and seasonally ski.

Explorations

Earlier this month, I had a blast leading a machine learning workshop at an R Ladies Philly meetup. After an introduction to machine learning, we used a beer review dataset to predict the alcohol concentration of beer using the caret R package. We even dabbled in text analysis. Everyone was awesome and asked many excellent questions throughout! I used RStudio Cloud to facilitate this workshop to …

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The Quaker Strong challenge

November 27 2019

In the last Quaker Strong challenge in the spring (March Madness edition), I was competing with several friends and enjoyed seeing how they were doing with the challenge. However, this time, with 46 registered participants, I figured it might be fun to write a few lines of code and make some fun visualization out of the logged progress. Code and details can be found here. To protect the …

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TPOT: Where do I start?

November 5 2019

Tree-based Pipeline Optimization Tool (TPOT) is an automated machine learning tool that helps the data scientist find the optimal model pipeline for their prediction problem. Using genetic programming (GP), TPOT explores different pipelines (sequences of feature selectors, model classifiers, etc.) and recommends one with optimal cross-validated score after a specified number of generations. Here …

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Last week, I got to attend a series of presentations followed by a panel discussion on open science at Penn Van Pelt-Dietrich library during the Open Access week. The panel featured (from left to right) Ted Satterthwaite, Jennifer Sisto, Daniel Himmelstein – all initiated enlightening discussions around different aspects of open science. ⊕ Photo credit: Rebecca Miller Jennifer Stiso …

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Recent Works

  • npdr: Select features with nearest-neighbor concepts (2019)      
  • Necibe Tuncer and Trang T. Le (2018) Structural and practical identifiability analysis of outbreak models. doi:10.1016/j.mbs.2018.02.004
  • TPOT: Overview and live demonstration, Clinical Research Informatics Core, University of Pennsylvania, Mar 13, 2019      
  • Trang T Lê, Zach Osman, D K Watson, Martin Dunn and B A McKinney (2019) Generalization of the Fermi pseudopotential. doi:10.1088/1402-4896/ab0811
  • Trang T. Le, Rayus Kuplicki, Brett A. McKinney, Hung-wen Yeh, Wesley K. Thompson, Martin P. Paulus and NA NA (2018, preprint) A nonlinear simulation framework supports adjusting for age when analyzing BrainAGE. doi:10.1101/377648
  • STIR feature selection, Pacific Symposium on Biocomputing, Jan 5, 2019      
  • stir: ReliefF on steroid (2018)      
  • Sahib S. Khalsa, ..., Trang T Le, ... and Nancy Zucker (2017) Interoception and Mental Health: A Roadmap. doi:10.1016/j.bpsc.2017.12.004