Curriculum Vitae for Luke A. D. Hutchison
PhD in computer science and computational biology,
MIT CSAIL (in collaboration with Harvard Medical School)
TED Fellow, Long Beach 2011
MIT CSAIL (in collaboration with Harvard Medical School)
TED Fellow, Long Beach 2011
See also my LinkedIn public profile.
I completed a PhD in Computer Science and Computational Biology at MIT CSAIL in collaboration with Harvard Medical School. For my thesis research I searched for genomic regulators of cell phenotype. I am passionate about algorithms, machine learning, both computer and human languages, and the power of information to change society. I have been programming and/or building circuits and gadgets my whole life. I am a TED Fellow.
Senior Research Scientist / Deep Learning Researcher, Google Accelerated Science; Google Machine Intelligence, Oct 2012 - Oct 2016
- On the Google Accelerated Science team, applied novel deep learning techniques to accelerate computational chemistry. I was able to accelerate quantum chemistry calculations by up to 7 orders of magnitude with high accuracy using a trained machine learning model, which will allow chemists and material scientists to explore a much larger area of the chemical space for compounds with interesting properties.
- Also worked as Tech Lead on Ray Kurzweil's Artificial Intelligence project; was recruited directly by Ray to found his AI team. Responsibilities included meeting with heads of major product areas throughout Google to determine how to optimally add AI capabilities to current and future Google products, and growing the team from scratch to 30+ engineers. Also led an effort to apply unsupervised learning to the problem of inferring the structure of language from the statistical patterns of language usage across all text on the Web. Involved technical design of Natural Language Processing technologies, implementation of novel algorithms for parsing and semantic modeling, reverse-engineering of human cognition and experimentation to reconstruct human cognition in software.
- Statistical analysis and publication of large civic housing datasets from New York City for easy access (including complaints, violations and litigation data sources) to disrupt slumlord corruption in the housing rental market, by providing data transparency to tenants.
- Biometric signal processing; code optimization for embedded systems; designing population-level data analysis strategy
- Integrative genomics study of cell division and tissue differentiation in C. elegans
- Integrative genomics study of cell division and tissue differentiation in C. elegans
- Responsibilities: Development of a large distributed Naïve Bayes clustering algorithm in C++ that predicted subject code from metadata and content of millions of books.
- Responsibilities: Development of new software algorithms for population genetics and analysis of DNA and genealogical data, including phylogeny, clustering, fuzzy matching of genealogical data, data mining, pattern recognition, DNA sequence processing, measurement of linkage disequilibrium, calculation of time to most recent common ancestor, and data conversion/manipulation. Significant extension of the smgf.org website. Architecture and implementation of core package hierarchy in Java, JSP, SQL and HTML.
- Skills used: algorithm and data structure design, discrete mathematics, statistics, combinatorics, parallel programming, optimization, technical writing.
- Leadership: Technical leadership for a team of 7 other people, including four other bioinformaticists. Advising of mathematical/statistical aspects of all research projects.
- Responsibilities: Software development and support for a large call-center and job-tracking application used by the Automobile Association of New Zealand and the Royal Automobile Club of Queensland
- Responsibilities: Developed software tools to transform SGML documents between different schemata
- Responsibilities: Wrote extensive libraries for rapid development of interactive educational software
Postdoctoral Research, Harvard Medical School, June 2011 - August 2012
- Continuation of PhD research
- PhD thesis: Whole-organism integrative expressome for C. elegans enables in silico study of developmental regulation. [recent poster summarizing research]
Short abstract: The C. elegans nematode has been extensively studied as a model organism since the 1970s, and is the only organism for which the complete cell division tree and the genome are both available. These two datasets were integrated with a number of other datasets available at WormBase.org, such as the anatomy ontology, gene expression profiles extracted from 8000 peer-reviewed papers, and metadata about each gene, to produce the first ever whole-organism, cell-resolution map of gene expression across the entire developmental timeline of the organism, with the goal to find genomic features that regulate cell division and tissue differentiation. Contingency testing was performed to find correlations between thousands of gene attributes (e.g. the presence or absence of a specific 8-mer in the 3' UTR, the GC-content of the sequence upstream of the transcriptional start site, etc.) and thousands of cell attributes (e.g. whether cells that express specific genes die through apoptosis, whether cells become neurons or not, whether cells move in the anterior or posterior direction after division). The resulting database of contingency test scores allow us to quickly ask a large number of biologically-interesting questions, like, "Does the length of introns of expressed genes increase across the developmental timeline?"; "Across what period of development and in which cell types is this specific gene most active?"; "Do regulatory motifs exist that switch on or off genes in whole subtrees of the cell pedigree?"; "Which genes are most strongly implicated in apoptosis?", etc. This whole-organism expressome enables direct and powerful in silico analysis of development.
- Selected as one of 40 in inaugural class from among 1200 applicants
Graduate of HBA (Harvard Beijing Academy) intensive summer Chinese language training program in 3rd year Chinese, summer 2008
- Completed 4.5 years of Harvard Chinese syllabus "on the side" in 2.5 years, including HBA summer program, while working on my PhD in CS at MIT
- Achievement: 1st Class Honors
- Research: Neural networks; successful construction of a hierarchical network-of-networks for online handwriting recognition.
- Research: Optimization of computer graphics algorithms; finding heuristic approximations to NP-hard and NP-complete problems. (Found fast heuristics for Traveling Salesman and Hamilton Cycle problems.)
- TED Fellowship, TED 2011 ("The Rediscovery of Wonder"), Long Beach, CA, USA. [Press release] [Fast Company interview] [Directory] [Profile] "Founded in January 2009, the TED Fellows program handpicks world-changing innovators from around the globe, and brings them to the TED stage – literally and figuratively – to raise international awareness of their remarkable work... The Fellows program helps amplify the impact of each Fellow's eye-opening ideas, and we're thrilled to welcome these innovators to the TED community."
- First in Auckland, South Pacific solo programming contest (1998)
- First in New Zealand, ACM programming competition (1994). Took first place in this university-level competition as a high school student with two friends the same age.
- Feast Fellowship, The Feast Conference 2013 (http://feastongood.com). [Blog post] "The Feast convenes the most remarkable entrepreneurs, radicals, doers and thinkers who are revolutionizing the way things work for the betterment of humanity."
- $25,000 scholarship and selection for the inaugural class of Singularity University (GSP-09) "Our mission is to educate, inspire and empower leaders to apply exponential technologies to address humanity’s grand challenges."
- Inaugural inductee into the Rangitoto College "Summit Academy -- Distinguished Alumni Hall of Fame" (2011).
- Best Student Paper Award. RootsTech 2011, Salt Lake City, UT.
- Best App Idea in Developer Challenge. RootsTech 2011, Salt Lake City, UT.
- Language awards: Third prize, Chinese speech competition, Harvard 2nd Year Chinese (2008); First prize, Korean Speech Competition, BYUP (2003); First prize, Korean Speech Competition, University of Auckland (1998); Third in Auckland, French Speech Competition, Alliance Française (1994)
- University of Auckland Science Faculty Postgraduate Study Award (1999)
- Senior Prize in Computer Science, University of Auckland (1998)
- Information Technology scholarship, RHE and Associates Ltd. Auckland (1998)
- Coca-Cola/SPANZ national Bachelor's degree full tuition scholarship (1995)
Selected Publications / Talks
- Luke A. D. Hutchison, Systems and methods for parallelization of program code, interactive data visualization, and graphically-augmented code editing. US Patent #9411558, 2012-10-20.
- Taught a 2-hour workshop at TEDSummit 2016, “Can we re-create intelligence in machines?”
- Invited speaker, Machine Intelligence and the Future of Work, Institute for the Future (IFTF), Palo Alto, April 2014.
- Luke Hutchison. [PhD thesis]: Whole-organism integrative expressome for C. elegans enables in silico study of developmental regulation. MIT EECS / CSAIL, June 2011.
- Luke Hutchison. [Talk]: "How can 100 trillion cells in your body be encoded in only 3.2 billion base pairs of DNA in your genome?". Renaissance Weekend, Monterey, CA, July 2012.
- Luke Hutchison. [Invited talk]: DNA to Cell to Organism. TED Fellows Pre-Conference, Long Beach, California, March 2012.
- Luke Hutchison. [Invited Paper, Invited Talk, Best Student Paper Award]: "Go forwards and not Backwards: Dramatically Accelerating the Rate of Innovation in Family History Technology Research via Lessons Learned From Genomics and the Space Race". RootsTech, 2011. A modified excerpt is published in this blog post on the commoditization of technology.
- Luke Hutchison. [Invited Talk.] OneGlobalVoice: SMS applications infrastructure for the developing world. World Future Society Annual Meeting 2010, Boston.
- Luke A. D. Hutchison, Bonnie A. Berger, Isaac S. Kohane. Whole-organism integrative expressome for C. elegans enables in silico study of developmental regulation. [Abstract.] RECOMB 2010, Lisbon, Portugal.
- Luke Hutchison. Secrets of the Nexus One Screen Ars Technica, April 2010.
- Luke A. D. Hutchison, Natalie M. Myres, Jayne E. Ekins, Ugo A. Perego, Kathleen H. Ritchie, Bonnie Berger, and Scott R. Woodward. Optimal analysis of duplicated Y chromosome STR loci. (In progress.)
- N.M. Myres, S.R. Woodward, L.A.D. Hutchison. Method and System for Displaying Genetic and Genealogical Information. US Patent #8855935, 2006-10-02.
- J.E. Ekins, J.B. Ekins, L. Layton, L.A.D. Hutchison, N.M. Myres, S.R. Woodward. Inference of ancestry: Constructing hierarchical reference populations and assigning unknown individuals. Human Genomics. 2006 Jan; 2(4):212-35.
- L.A.D. Hutchison, N.M. Myres, K.H. Ritchie, B.Berger, S.R. Woodward. Formalization of Matching strategies for duplicated Y chromosome loci. The American Society of Human Genetics Annual Meeting, 2006.
- L.A.D. Hutchison and W.A. Barrett. [Invited Paper; special journal issue.] Fourier-Mellin registration of line-delineated tabular document images. International Journal on Document Analysis and Recognition (IJDAR), 8(2):87-110, 2006.
- L.A.D. Hutchison, N.M. Myres, K.H. Ritchie, J.E. Ekins, J.B. Ekins, L. Layton, M.L. Lunt, S.S. Maesek, A.A. Nelson, M.E. Nelson, K.L. Pennington, U.A. Perego, J.L. Peterson, T. Tolley, S.R. Woodward. Formalization of matching strategies for duplicated loci. The American Society of Human Genetics Annual Meeting, 2005.
- J.L. Peterson, J.E. Ekins, K.L. Pennington, K.H. Ritchie, L.A.D. Hutchison, N.M. Myres, J.B. Ekins, J.E. Gomez, A.A. Nelson, M.E. Nelson, L. Layton, M.L. Lunt, T.A. Tolley, S.S. Masek, U.A. Perego, S.R. Woodward. Characterization of a novel private allele for East Asia and Oceania. The American Society of Human Genetics Annual Meeting, 2005.
- K.L. Pennington, K.H. Ritchie, J.E. Ekins, J.L. Peterson, N.M. Myres, J.B. Ekins, L.A.D. Hutchison, L. Layton, M. Lunt, S. Masek, A.A. Nelson, M.E. Nelson, U.A. Perego, T.A. Tolley, S.R. Woodward. Characterization of family-specific LD patterns in Sorenson Molecular Genealogy Foundation dataset. The American Society of Human Genetics Annual Meeting, 2005.
- B.L. Hutchison, Luke A.D. Hutchison, J.M.D. Thompson and E.A Mitchell. Quantification of plagiocephaly and brachycephaly in infants using a digital photographic technique.
The Cleft Palate-Craniofacial Journal, September 2005, Vol. 42, No. 5, pp. 539-547.
- L.A.D. Hutchison et al. Direct determination of mutation characteristics of Y chromosome STR loci. The American Society of Human Genetics Annual Meeting, Toronto, Canada, Oct 2004.
- L.A.D. Hutchison, N.M.Myres and S.R. Woodward. Growing the Family Tree: The Power of DNA in Reconstructing Family Relationships. Proceedings of the First Symposium on Bioinformatics and Biotechnology (BIOT-04), Sept. 2004, pp. 42-49. Also presented at Family History Technology Workshop 2005 [Slides]
- W. Barrett, L.A.D. Hutchison, D. Quass, H. Nielson, D. Kennard. Digital mountain: from granite archive to global access. Proceedings, Document Image Analysis for Libraries, 2004, 104-121.
- L.A.D. Hutchison, W. Barrett. Fast Registration of Tabular Document Images Using the Fourier-Mellin Transform. Proceedings, Document Image Analysis for Libraries, 2004, 253-267.
- B.L. Hutchison, Luke A.D. Hutchison, J.M.D. Thompson, E.A. Mitchell. Plagiocephaly and Brachycephaly in the First Two Years of Life: A Prospective Cohort Study. Pediatrics, Vol. 114 No. 4 October 2004, pp. 970-980.
- Luke A. D. Hutchison, Natalie M. Myres, Jacob E. Ekins, Ugo A. Perego, Jayne B. Ekins, Katie Hadley, Lara Layton, Mindy L. Lunt, Sacha S. Masek, Alison A. Nelson, Mary E. Nelson, Katie L. Pennington, Jenny L. Peterson, Amanda Sims, Trish Tolley, Alison Welch, Scott R. Woodward. Direct determination of mutation characteristics of Y chromosome STR loci. American Society of Human Genetics Annual Meeting, 2004.
- J.B. Ekins, L.A.D. Hutchison, J.E. Ekins, N.M. Myres, K.Hadley, L. Layton, M. L. Lunt, S.S. Masek, A.A. Nelson, M.E. Nelson, K.L. Pennington, U.A. Perego, J.L. Peterson, A. Sims, T. Tolley, A. Welch, S.R. Woodward. Methods for improved reconstruction of haplotypes of highly polymorphic loci. American Society of Human Genetics Annual Meeting, 2004.
- J.E. Ekins, J.B. Ekins, L. Layton, N. Myres, L.A.D. Hutchison, K. Hadley, U.A. Perego, J.L. Peterson, M.L. Lunt, S.S. Masek, A.A. Nelson, M.E. Nelson, K.L. Pennington, A. Sims, T. Tolley, A. Welch, S.R. Woodward. Empirical Evaluation of Inferred Population Structure from Y-chromosomal Haplotypes. American Society of Human Genetics Annual Meeting, 2004.
- K. Hadley, N.M. Myres, J.B. Ekins, J.E. Ekins, L.A.D. Hutchison, L. Layton, M.L. Lunt, S.S. Masek, A.A. Nelson, M.E. Nelson, K.L. Pennington, U.A. Perego, J.L. Peterson, A. Sims, T.Tolley, A. Welch, S. Woodward. Non-Paternity and Locus Specific Mutation Rates of 36 Y Chromosome STRs. American Society of Human Genetics Annual Meeting, 2004.
- N.M. Myres, J.B. Ekins, K. Hadley, U.A. Perego, J.E. Ekins, L.A.D. Hutchison, L.Layton, M.L. Lunt, S.S. Masek, A.A. Nelson, M.E. Nelson, K.L. Pennington, J.L.Peterson, A. Sims, T. Tolley, A. Welch, S.R. Woodward. Database characterization of Y-chromosomal 39-locus haplotypes. American Society of Human Genetics Annual Meeting, 2004.
- L.A.D. Hutchison, W.A. Barrett. Tabular Document Image Registration Using the Fourier-Mellin Transform. [Slides] Family History Technology Workshop, 2004.
- L.A.D. Hutchison, W.A. Barrett. Handwriting Recognition for Genealogical Records. Family History Technology Workshop, 2003.
- S.R. Woodward, N. Myres, J.B. Ekins, J.E. Ekins, K. Hadley, L. Hutchison, L. Layton, U. Perego, A. Sims, A. Nelson, M. Nelson, A. Welch. Large Scale DNA Variation as an Aid to Reconstruction of Extended Human Pedigrees. American Society of Human Genetics Annual Meeting, 2003.
- L.A.D. Hutchison, S.R. Woodward. DNA analysis techniques for Molecular Genealogy. [Slides] Family History Technology Workshop, 2002.
- L.A.D. Hutchison, S.R. Woodward. Handwriting Recognition for Genealogical Records. Family History Technology Workshop, 2002.
- Leonid M. Mestetskii, Ivan A. Reyer, Thomas W. Sederberg, Luke A.D. Hutchison. A Continuous Approach to the Segmentation of Handwritten Text. International Workshop on the Foundations of Handwriting Recognition, 2001.
- Luke Hutchison, A New Algorithm for the Fast Scan-Conversion and Rasterization of Lines. Usenet comp.graphics.algorithms . 19 Jan 1994.
- [Older:] Luke Hutchison and Tony Garnock-Jones. Braitenberg Vehicles: An Electronic Model of Neural Behavior. CREST report, 1993. [109-page project for the CREST Award in Science and Technology, consisting of software and hardware simulations of neurally-controlled robot vehicles, re-creation of Boolean logic gates, flip-flops, adders etc. in neurons, and more.]
Program Committees / Peer Review
- Invited to Program Committee, HILT 2014 (High Integrity Language Technology), Portland, OR, USA, Oct 2014; HILT 2013 (High Integrity Language Technology), Pittsburgh, PA, USA, Nov 2013.
- Peer reviewer, ISMB 2012 (International Society for Computational Biology), Long Beach, CA, USA, July 2012.
- Peer reviewer, RECOMB 2011 (Annual International Conference on Research in Computational Molecular Biology), Vancouver, BC, Canada, March 2011; RECOMB 2008, Singapore, April 2008.
- Invited to Program committee, RootsTech 2011, FHTW (Family History Technology Workshop), Salt Lake City, February 2011.
- Invited to Program committee, FHTW (Family History Technology Workshop), Provo, UT, USA, for many years: 2010, 2009, 2008, 2005, 2004, 2003, 2002.
- Invited peer reviewer, International Journal on Document Analysis and Recognition (IJDAR) special issue, 8(2), 2006.
Open Source Software
Selected blog posts
- The Turing test and Artificial Stupidity
- Machine intelligence: the earthmoving equipment of the information age, and the future of meaning
- The commoditization of technology, and when to open the source
- On hierarchical learning and building a brain
- Watson's Jeopardy win, and a reality check on the future of AI
- Life, Intelligence and the Second Law of Thermodynamics
- On Intel 3D chips and human 4D brains. (And flying cars.)
- Why NDAs are usually pointless and counterproductive
English, Korean, French and Chinese (all to professional level)
New Zealand citizen; US permanent resident / green card holder (obtained via O-1 / EB-1A)
See an extensive list of recommendations here.