Data Science & AI Development

The Laboratory for Innovation Science at Harvard (LISH) is conducting a number of different crowdsourcing challenges and field research aimed at using the tools of data science and artificial intelligence to provide innovative solutions. LISH is working to help its partner organizations understand the value of data collection and the power of data analysis to drive problem solving. Browse LISH’s Data Science & Artificial Intelligence projects and papers below.

Publications

Karim R. Lakhani, Andrew Hill, Po-Ru Loh, Ragu B. Bharadwaj, Pascal Pons, Jingbo Shang, Eva C. Guinan, Iain Kilty, and Scott Jelinsky. 2017. “Stepwise Distributed Open Innovation Contests for Software Development: Acceleration of Genome-Wide Association Analysis.” GigaScience, 6, 5, Pp. 1-10. Publisher's VersionAbstract

BACKGROUND: The association of differing genotypes with disease-related phenotypic traits offers great potential to both help identify new therapeutic targets and support stratification of patients who would gain the greatest benefit from specific drug classes. Development of low-cost genotyping and sequencing has made collecting large-scale genotyping data routine in population and therapeutic intervention studies. In addition, a range of new technologies is being used to capture numerous new and complex phenotypic descriptors. As a result, genotype and phenotype datasets have grown exponentially. Genome-wide association studies associate genotypes and phenotypes using methods such as logistic regression. As existing tools for association analysis limit the efficiency by which value can be extracted from increasing volumes of data, there is a pressing need for new software tools that can accelerate association analyses on large genotype-phenotype datasets.

RESULTS: Using open innovation (OI) and contest-based crowdsourcing, the logistic regression analysis in a leading, community-standard genetics software package (PLINK 1.07) was substantially accelerated. OI allowed us to do this in <6 months by providing rapid access to highly skilled programmers with specialized, difficult-to-find skill sets. Through a crowd-based contest a combination of computational, numeric, and algorithmic approaches was identified that accelerated the logistic regression in PLINK 1.07 by 18- to 45-fold. Combining contest-derived logistic regression code with coarse-grained parallelization, multithreading, and associated changes to data initialization code further developed through distributed innovation, we achieved an end-to-end speedup of 591-fold for a data set size of 6678 subjects by 645 863 variants, compared to PLINK 1.07's logistic regression. This represents a reduction in run time from 4.8 hours to 29 seconds. Accelerated logistic regression code developed in this project has been incorporated into the PLINK2 project.

CONCLUSIONS: Using iterative competition-based OI, we have developed a new, faster implementation of logistic regression for genome-wide association studies analysis. We present lessons learned and recommendations on running a successful OI process for bioinformatics.

Christoph Riedl, Richard Zanibbi, Marti A. Hearst, Siyu Zhu, Michael Menietti, Jason Crusan, Ivan Metelsky, and Karim R. Lakhani. 2016. “Detecting Figures and Part Labels in Patents: Competition-Based Development of Image Processing Algorithms.” International Journal on Document Analysis and Recognition (IJDAR), 19, 2, Pp. 155-172. Publisher's VersionAbstract

Most United States Patent and Trademark Office (USPTO) patent documents contain drawing pages which describe inventions graphically. By convention and by rule, these drawings contain figures and parts that are annotated with numbered labels but not with text. As a result, readers must scan the document to find the description of a given part label. To make progress toward automatic creation of ‘tool-tips’ and hyperlinks from part labels to their associated descriptions, the USPTO hosted a monthlong online competition in which participants developed algorithms to detect figures and diagram part labels. The challenge drew 232 teams of two, of which 70 teams (30 %) submitted solutions. An unusual feature was that each patent was represented by a 300-dpi page scan along with an HTML file containing patent text, allowing integration of text processing and graphics recognition in participant algorithms. The design and performance of the top-5 systems are presented along with a system developed after the competition, illustrating that the winning teams produced near state-of-the-art results under strict time and computation constraints. The first place system used the provided HTML text, obtaining a harmonic mean of recall and precision (F-measure) of 88.57 % for figure region detection, 78.81 % for figure regions with correctly recognized figure titles, and 70.98 % for part label detection and recognition. Data and source code for the top-5 systems are available through the online UCI Machine Learning Repository to support follow-on work by others in the document recognition community.