I will be attending ICLR 2025 in Singapore to give an oral presentation on our work developing a foundation model for phylogenetics at the LMRL Workshop!

Hi, my name is Andrew! I’m an incoming PhD student in Biomedical Data Science at Stanford University and a current Research Associate at Harvard Medical School working with Marinka Zitnik. I also work with Joshua Glaser at Northwestern University where I completed my Masters in Artificial Intelligence. I completed my undergraduate education at UC San Diego in Bioinformatics and Computer Science.

I am broadly interested in solving problems at the intersection of AI and science, but particularly in the areas of biology and medicine. Some of my current research endeavors consist of biologically inspired foundation models for proteins and interpretable methods for neural decoding.

I have also been involved with other labs and have been fortunate to work with Heather Moss at Stanford Health Care, Melissa Gymrek at UC San Diego, and Kavita Sarin at Stanford Health Care.

Feel free to reach out to connect at andrew7shen@gmail.com!

Publications

1. Phyla: Towards a Foundation Model for Phylogenetic Inference
   A Shen*, Y Ektefaie*, L Jain, MR Farhat, M Zitnik. ICLR 2025 LMRL Workshop.
2. Mixtures of decoders for interpreting dynamic neural-behavioral mappings
   Andrew Shen, Xuan Ma, David Xing, Xinyue An, Andrew Miri, Lee Miller, Joshua Glaser. Computational and Systems Neuroscience Conference.
3. Evaluating generalizability of artificial intelligence models for molecular datasets
   Y Ektefaie, A Shen, D Bykova, M Marin, M Zitnik, M Farhat. Nature Machine Intelligence, 1-13.
4. Evolution of Disparities in Outpatient Ophthalmic Care at a Tertiary Care Center in California at the Beginning of and One Year into the COVID-19 Public Health Emergency
   AA Shen, KG Gutierrez, NC Villegas, HE Moss. Ophthalmic Epidemiology 31 (1), 21-30.
5. Genome-wide detection of somatic mosaicism at short tandem repeats
   A Sehgal, H Ziaei-Jam, A Shen, M Gymrek. Bioinformatics 40 (8), btae485.
6. Fitzpatrick phototype disparities in identification of cutaneous malignancies by Google Reverse Image
   JL Jia, JY Wang, DE Mills, A Shen, KY Sarin. Journal of the American Academy of Dermatology 84 (5), 1415-1417.
7. Gamification improves melanoma visual identification among high school students: results from a randomized study.
   JL Jia*, A Shen*, MM Tabata, KY Sarin. Pediatric Dermatology 37 (4), 752-753.

* Co-first Author

Awards

1. NSF GRFP Honorable Mention (2025)
2. Harvard Medical School Summer Institute in Biomedical Informatics Fellow (2023)
3. National Merit Finalist (2019)