Yi Li, Ph.D.

Associate Director of Machine Learning & Imaging Services

Genetic component dissection for complex human diseases via integrative analysis of diverse genetic and genomic data; method development for data analysis; machine learning

I pursued my PhD study in Computer Science (specifically, statistical machine learning) from 1997-2000 at National University of Singapore. During this period of time, I not only worked in machine learning theory, but also designed and implemented a new family of online learning algorithms to recognize the handwriting digits in MNIST dataset, and obtained the state-of-art performance that could be achieved by online learning algorithms at that time.

From 2001-2003, I worked on microarray gene expression data. The methods I explored included supervised classifications via relevance vector machines and unsupervised class discovery. Since 2004, I have been working in statistical genetics -- dissecting genetic bases for complex human diseases by analysis of genome-wide linkage and association data, exome-wide sequencing data, RNA-sequencing data. Since the genetic variants far out-numbered the sample size, various statistical methods, including data imputation, regularized regression, generalized linear mixed models, pathway analysis, fine mapping and evidence combination from heterogeneous data sources, have been explored and developed.

I have published more than 40 peer-reviewed papers in various journals, including first or co-first author publications in Nature Genetics, American Journal of Human Genetics, Machine Learning, Journal of Computer and System Sciences, and IEEE Transactions on Information Theory.

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Yi Li on Google Scholar

Education and experience


  • 1997– 2000: National Univ. of Singapore, Singapore
    Awarded degree: PhD in Computer Science. (awarded IDA gold medal and prize for being the PhD student with the best thesis in 2001)
    Thesis title: “From support vector machines to large margin classifiers” (Supervisor: Prof. Phil Long)
  • 1990– 1993: Xi’an Jiaotong Univ., P R China. Computer Science.
    Awarded Degree: M. Eng.
  • 1986– 1990; Xi’an Jiaotong Univ., P R China. Computer Science.
    Awarded Degree: B. Sci. (top 5%) (admitted to the university without taking the national university entrance examinations)

Work Experience:

  • Jun 2007 – now: senior computational scientist at Computational Sciences, The Jackson Laboratory, Farmington, CT, US
  • Jan 2007 – Jun 2017: staff scientist at Human Genetics, Genome Institute of Singapore, Singapore.
  • Apr 2002 – Dec 2006: Postdoc at Information & Mathematical Sciences, Genome Institute of Singapore, Singapore
  • Jan 2001 – Apr 2002: Research assistant at Dept. of Engineering Mathematics, Univ. of Bristol. U.K.