Princeton beehive

Statistical Genetics and Machine Learning Research at Princeton

[Princeton beehive @PrincetonHive]

Ari Gewirtz defended her impressive thesis today: "Exploring Context-Specific Expression Variation and Distal Gene Regulation via Latent Variable Models." I can't wait for her to share the last chapter on QTL mapping w/single cell data -- preprint soon! We will miss you, Ari!

[Princeton beehive @PrincetonHive]

@sunny_ccui, with Liz Yoo, @DidongLi, and collaborators from @PennMedicine, presented her paper 'Hierarchical Gaussian Processes and Mixtures of Experts to Model COVID-19 Patient Trajectories' last week at @PacSymBiocomp https://t.co/1ir6UrAK00

[Princeton beehive @PrincetonHive]

Congratulations to Guillaume Martinet, PhD who successfully defended his thesis: "Invariant Mechanisms in Transfer Learning and Causal Inference: Some Theoretical Perspectives and Algorithms" on Tuesday! Great presentation, and exciting work! 🌟

[Sunny Cui @sunny_ccui]

Our paper “Hierarchical Gaussian Processes and Mixtures of Experts in Predicting COVID Patient Trajectories” has been accepted accepted for publication in the proceedings AND oral presentation at PSB 2022! Can’t wait to share our results with you on the Big Island 🏝️ #PSB22

[Princeton beehive @PrincetonHive]

Great work from @hotarcheetos in leading the project with @ras_trophysics and in the Toettcher lab members/collaborators @kazuhiroaokilab and @danielle_isakov!

[Princeton beehive @PrincetonHive]

Do you have time-series fluorescence data in which you would like to quantify signaling? Our cellular point process paper is out: https://t.co/FYrKANnJrU

[Princeton beehive @PrincetonHive]

Amazing collaboration with @toettch and @ras_trophysics -- can't wait for the next one!

[Princeton beehive @PrincetonHive]

Wonderful work on best practices EHR data processing and some cool vignettes by @Aishwarya_R_M, Liz Yoo, and Jeff Soules (Flatiron), and a great collaboration with Dr. Krzysztof Laudanski (HUP).

Try out COP-E-CAT if you build AI/ML methods for EHR data!

[Princeton beehive @PrincetonHive]

Our COP-E-CAT paper and software are available! COP-E-CAT allows you to access, regularize, filter, impute, and chunk the MIMIC-IV data into regular time slices. Then you can use this EHR dataset easily in ML downstream analyses: prediction, dimension reduction, RL, etc.

[Princeton beehive @PrincetonHive]

COP-E-CAT paper: https://t.co/TPXmMxwnLF

COP-E-CAT software:
https://t.co/JRidfwwI9E

MIMIC-IV data:
https://t.co/Br89chMMEQ

[Princeton beehive @PrincetonHive]

@Brian_SungJoon successfully defended his thesis on Tuesday: "Analysis of Distal eQTLs across Multiple Human Tissues and Methods to Improve Their Quality" -- incredible work on trans-eQTLs and methods for discovery in the GTEx data. Congratulations, Brian!

[Princeton beehive @PrincetonHive]

Incredible Greg Gundersen defended his thesis today "Practical Algorithms for Latent Variable Models." His curiosity, determination, & the gradient of his trajectory will not be matched soon. The blog he wrote for his own understanding is an ML treasure: https://t.co/yqYkKOH9Rj

[Princeton beehive @PrincetonHive]

.@hotarcheetos Archit Verma, PhD successfully defended his thesis "Bayesian modeling of single cell data" last week. His work on models to study single cell data is phenomenal! We will miss him so much, but hope he will join us for future group retreats! Best of luck, Archit!

[Princeton beehive @PrincetonHive]

PhD student @andy_c_jones did so well on his generals exam on contrastive latent variable models for case-control study data. I love his collaborator slide because it shows the breadth of his work & collaborations, and also the mentoring he's involved in with amazing undergrads!

[Princeton beehive @PrincetonHive]

This is the work of @jordan_t_ash, Greg Darnell, and @danbmunro -- all code available at https://t.co/RVRJJ71F2V

[Princeton beehive @PrincetonHive]

The ImageCCA paper is out! Seven years in the making, this work uses a convolutional autoencoder plus CCA to
find associations between histopathological images and bulk gene expression data across tissues. In GTEx v6 data, we find image morphology QTLs.
https://t.co/3gaqDoES5q

[Princeton beehive @PrincetonHive]

The scGeneFit paper is out! Amazing collaboration with @SoledadVillar5 and @bidumit -- and an easy-to-use Python package available for marker discovery in single cell data! https://t.co/6RChE4B3SZ

[Princeton beehive @PrincetonHive]

Barbara was selected for the ISCB Overton Prize! She will give the Overton lecture this July at ISMB. https://t.co/CVppYUXOLk

[Princeton beehive @PrincetonHive]

Out in PLoS Comp Bio: Causal network inference from gene transcription time series data. Super excited about this work with (then) undergrad @JonathanLu11, @bidumit, and @timreddy's Lab! https://t.co/j5TN6chhJx