Résumé. Updated April 2020.

David Soergel, Ph.D.

28 Mountain Laurel Path
•Northampton, MA 01062
(650) 303-5324 (c)
•(413) 282-9961 (h)

david@davidsoergel.com
•http://www.davidsoergel.com

Computing Skills

Summary

Software engineer and research scientist with recent experience in machine learning infrastructure. Previous experience in computational biology, metagenomics, natural language processing, bibliometrics, open access advocacy, and reproducible research. Expert in large-scale data management, database design, and distributed computing. Experienced in project management and system administration. Proficient with a wide variety of computing technologies and platforms. Effective team player; also able independently to complete entire projects from conception through launch.

Objective

Transitively move many needles, by building tools to support research in machine learning and natural sciences. I like to design and build software systems that enable researchers and developers to solve hard problems quickly and confidently. I strive to design intuitive APIs and visualizations, so that users can focus on their own interests, not on framework friction.

Education and Experience

2015 -
Software Engineer, Google AI.
2013 - 2015
Software Engineer, Google Maps.
  • Google My Maps and Google Maps Gallery.
2012 - 2013
Founding project lead, OpenReview.net.
  • Scoped, designed, and built system for open peer review of academic papers, housed in the lab of Andrew McCallum at UMass Amherst.
  • OpenReview.net has now been used for dozens of high-profile computer science conferences over many years.
2011 - 2013
Research Scientist and Software Engineer, School of Computer Science, University of Massachusetts Amherst.
  • Laboratory of Andrew McCallum.
  • Large-scale machine learning for natural language processing.
2011
University of Colorado, Boulder and University of California, Berkeley
  • Joint postdoctoral position with Rob Knight and Steven Brenner.
  • Topic: New Tools for Understanding the Composition and Dynamics of Microbial Communities in Human Body Habitats.
2003 - 2010
Ph.D. in Biophysics, University of California, Berkeley
2001 - 2003
Lead Bioinformatics Developer, The Molecular Sciences Institute, Berkeley, CA.
  • Databases and web applications supporting basic research in biology.
1998 - 2001
Silicon Valley startups (cofounder, etc.).

1999 - 2000

Research Associate, Department of Genetics, Stanford University School of Medicine.

  • Laboratory of L. Luca Cavalli-Sforza.
  • Databases and software for analyzing the geographic distributions of human genes.
1995 - 1998
B.S., Stanford University.
1992 - 1996
Student researcher in physics and computing.
  • San Onofre/Palo Verde Neutrino-Oscillation Experiment, Caltech.
  • H1 collaboration, Deutsches Elektronen-Synchrotron (DESY).
  • Institute for Scientific Computing Research, Lawrence Livermore National Laboratory.
1993 - 1995
California Institute of Technology.

Publications

Smilkov D, Thorat N, Assogba Y, Yuan A, Kreeger N, Yu P, Zhang K, Cai S, Nielsen E, Soergel D, Bileschi S, Terry M, Nicholson C, Gupta SN, Sirajuddin S, Sculley D, Monga R, Corrado G, Viegas FB, Wattenberg M. (2019). TensorFlow.js: Machine Learning for the Web and Beyond. Proceedings of the 2nd SysML Conference, Palo Alto, CA, USA. PDF

Xia D, Mewald D, Sculley D, Soergel DAW, Roumpos G, Cheng H, Polosukhin I, Smith JA, Xie J, Hong L, Wicke M, Ispir M, Tucker PD, Tang Y, Haque Z. (2017). TensorFlow Estimators: Managing Simplicity vs. Flexibility in High-Level Machine Learning Frameworks. Proceedings of the 23th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Halifax, Canada. PDF

Soergel DAW. (2015). Rampant software errors may undermine scientific results. F1000Research 3: 303. Full Text, PDF, Reviews and Discussion

Soergel DAW, Saunders AC, McCallum A. (2013). Open Scholarship and Peer Review: a Time for Experimentation. ICML Workshop on Peer Reviewing and Publishing Models (PEER). PDF, Discussion

Dey N, Soergel DAW, Repo S, Brenner SE. (2013). Association of gut microbiota with post-operative clinical course in Crohn's disease. BMC Gastroenterology 13: 131. Full text, PDF

F1000 Recommended

Soergel DAW, Dey N, Knight R, Brenner SE. (2012). Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. The ISME Journal 6: 1440-1444. Full text, PDF

Yooseph S, Sutton G, Rusch DB, ... Soergel DAW, ... Venter, JC. (2007). The Sorcerer II global ocean sampling expedition: expanding the universe of protein families. PLoS Biology 5: e16. Full text

Lareau LF, Brooks AN, Soergel DAW, Meng Q, Brenner SE. (2007). The coupling of alternative splicing and nonsense-mediated mRNA decay. In Blencowe B and Graveley B, ed., Alternative splicing in the post-genomic era (pp. 190-211), Landes Bioscience. PDF

Soergel DAW, Lareau LF, Brenner SE. (2006). Regulation of gene expression by the coupling of alternative splicing and nonsense-mediated mRNA decay. In Maquat L, ed., Nonsense-mediated mRNA decay (pp. 175-196), Landes Bioscience. PDF

Soergel DAW, Choi K, Thomson T, Doane J, George B, Morgan-Linial R, Brent R, Endy D. (2004). MONOD, a collaborative tool for manipulating biological knowledge. Working paper

Grants and Awards

Chang-Lin Tien Scholar in Environmental Sciences and Biodiversity, UC Berkeley. (2008-2010)

Contributing author to a successful NIH R01 grant to Rob Knight. (2011)

Predoctoral Fellow, Howard Hughes Medical Institute. (2003-2008)

National Defense Science and Engineering Graduate Fellowship. (2003, declined)

Caltech and Stanford Summer Undergraduate Research Fellowships. (1994, 1995, 1997)

Caltech Merit Awards. (1994, 1995)

Robert Andrews Millikan Scholar, Caltech. (1993)

Teaching and Mentoring

Research Mentor for graduate rotation students, undergraduate research assistants, and software developers. (5 total, 2005-2010)

Graduate Student Instructor for Microbial Genetics and Genomics, U.C. Berkeley (2007)