MIDAS Special Seminar: Qianying Lin – MIDAS Data Science Fellow

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Qianying Lin

Michigan Institute for Data Science – Data Science Fellow

VIEW RECORDING

COVID-19 outbreak in Wuhan, China: in retrospect and in prospect

Since first confirmation in December 2019, the novel coronavirus diseases (COVID-19) infected more than 50,000 people and claimed over 2000 lives in Wuhan, China. It was transmitted across the whole country shortly, and now swept the world by causing more 20,000 infections in countries other than China. Using official reported cases and assuming changing reporting ratio, we investigated the early stage of the epidemic of COVID-19 in Wuhan and analysed its transmissibility. We then built up a conceptual model and incorporated the zoonotic introduction, emigration, individual reaction, and governmental action to simulate the trends of the outbreak in Wuhan and predicted the disease would be completely controlled by the end of April under current policies. These studies provide insights into not only the characteristics of COVID-19 itself, but the impact of governmental actions.

Read Global Reach’s article here. Read full transcript here.

For more information on MIDAS or the Seminar Series, please contact midas-contact@umich.edu.

U-M, MIDAS researchers supported by Chan Zuckerberg Initiative

By | General Interest, Happenings, News, Research

Several University of Michigan researchers, including faculty affiliated with MIDAS, recently received support from the Chan Zuckerberg Initiative under its Human Cell Atlas project.

The project seeks to create a shared, open reference atlas of all cells in the healthy human body as a resource for studies of health and disease. The project is funding a variety of software tools and analytic methods. The U-M projects are listed below:

Identifying genetic markers: dimension reduction and feature selection for sparse data
Investigator: Anna Gilbert, Department of Mathematics, MIDAS Core Faculty Member
Description: One of the modalities that scientists participating in the Human Cell Atlas will use to gather data is single cell RNA sequencing (scRNA-seq). The analysis, however, of scRNA-seq data poses novel biological and algorithmic challenges. The data are high dimensional and not necessarily in distinct clusters (indeed, some cell types are exist along a continuum or developmental trajectory). In addition, data values are missing. To analyze this data, we must adjust our dimension reduction algorithms accordingly and either fill in the values or determine quantitatively the impact of the missing values. Furthermore, none of these steps is performed in isolation; they are part of a principled data analysis pipeline. This work will leverage over a decade of modern, sparsity-based machine learning methods and apply them to dimension reduction, marker selection, and data imputation for scRNA-seq data. In one of our two feature selection methods, we adapt a 1-bit compressed sensing algorithm (1CS) introduced by Genzel and Conrad. In order to select markers, the algorithm finds optimal hyperplanes that separate the given clusters of cells and that depend only on a small number of genes. The second method is based on the mutual information (MI) framework developed in. This algorithm greedily builds a set of markers out of a set of statistically significant genes that maximizes information about the target clusters and minimizes redundancy between markers. The imputation algorithms use sparse data models to impute missing values and are tailored to integer counts.

Computational tools for integrating single-cell RNA sequencing studies with genome-wide association studies
Investigator: Xiang Zhou, Biostatistics
Description: Single cell RNA sequencing (scRNAseq) has emerged as a powerful tool in genomics. Unlike previous bulk RNAseq that measures average expression levels across many cells, scRNAseq can measure gene expression at the single cell level. The high resolution of scRNAseq has thus far transformed genomics: scRNAseq has been applied to classify novel cell-subpopulations and states, quantify progressive gene expression, perform spatial mapping, identify differentially expressed genes, and investigate the genetic basis of expression variation. While many computational tools have been developed for analyzing scRNAseq data, tools for effective integrative analysis of scRNAseq with other existing genetic/genomic data types are underdeveloped. Here, we propose to extend our previous integrative methods and develop novel computational tools for integrating scRNAseq data with genome-wide association studies (GWASs). Our proposed tools will identify cell-subpopulations relevant to GWAS diseases or traits, facilitate the interpretation of association results, catalyze more powerful future association studies, and help understand disease etiology and the genetic basis of phenotypic variation. The proposed tools will be applied to integrate summary statistics from various GWASs with fine-scale cell-subpopulations identified from the Human Cell Atlas (HCA) project, to maximize the impact of HCA and facilitate our understanding of the genetic architecture of various human traits and diseases — a question of central importance to human health.

Joint analysis of single cell and bulk RNA data via matrix factorization
Investigator: Clayton Scott, Electrical Engineering and Computer Science, MIDAS Affiliated Faculty
Description: Single cell RNA sequence (ssRNAseq) data is a recently developed platform that enables the measurement of thousands of gene expression levels across individual cells in a tissue sample of interest. The ability to quantify gene expression at the cell level has great potential for advancing our understanding of the cellular processes that characterize a broad range of biological phenomena. However, compared with older bulk RNA technology, which measures expression levels of large numbers of cells in aggregate, ssRNAseq data has higher levels of measurement noise, which complicates its analysis. Furthermore, the problem of inferring cell type from ssRNAseq data is an unsupervised machine learning problem, an already difficult problem even without high measurement noise. To address these issues, we propose a mathematical and algorithmic framework to infer cellular characteristics by analyzing single cell and bulk RNA data simultaneously, via an approach grounded in matrix factorization. The developed algorithms will be evaluated on real data gathered by researchers at the University of Michigan who study breast cancer and spermatogenesis.

Integrating single cell profiles across modalities using manifold alignment
Investigator: Joshua Welch, Computational Medicine and Bioinformatics
Description: Integrating the variation underlying different types of single cell measurements is a critical step toward a comprehensive catalog of human cell types. The ideal approach to construct a cell type atlas would use high-throughput single cell multi-omic profiling to simultaneously measure all cellular modalities of interest within each cell. Although this approach is currently out of reach, it is possible to separately perform high-throughput transcriptomic, epigenomic, and proteomic measurements at the single cell level. Computationally integrating multiple data modalities measured on different individual cells can circumvent the experimental challenges of multi-omic profiling. If different types of single cell measurements are performed on distinct single cells from a common population, each modality will sample a similar set of cells. Matching up similar cells to infer multimodal profiles enables some analyses for which multi-omic profiling is desirable, including multimodal cell type definition and studying covariance among different data types. Manifold alignment is a powerful computational technique for integrating multiple sources of data that describe the same set of events by discovering the common manifold (general geometric shape) that underlies them. Previously, we showed that transcriptomic and epigenomic measurements performed on distinct single cells share underlying sources of variation. We developed a computational method, MATCHER, which uses manifold alignment to integrate cell trajectories constructed from these measurements and infer single cell multi-omic profiles. Here, we will extend this approach to match multimodal single cell profiles sampled from an entire tissue.

Computational methods to enable robust and cost-effective multiplexing of single cell rna-seq experiments in population-scale
Investigator: Hyun Min Kang, Biostatistics
Description: With the advent of single-cell genomic technologies, Human Cell Atlas (HCA) seeks to create a reference maps of each individual cell type and to understand how they develop and maintain their functions, how they interact with each other, and which environmental and/or genetic changes trigger molecular dysfunction that leads to disease. To achieve these goals, it becomes increasingly important to creatively integrate single-cell genomic technologies with novel computational methods to maximize the potential of the new technological advances. Recently, our group has developed a computational tool demuxlet that enable population- scale multiplexing of droplet-based single-cell RNA-seq (dscRNA-seq) experiments. Our approach harnesses natural genetic variation carried within dscRNA-seq reads to multiplex cells from many samples in a single library prep, and statistically deconvolute the sample identity of each barcoded droplet while filtering out multiplets (droplets that contain two or more cells). In this proposal, we aim to further extend our method to increase the accuracy by harnessing cell-specific expression levels, and to eliminate the constraint requiring external genotype data. We will enable application of these methods through production, distribution, and support of efficient, well-documented, open-source software; and test these tools through analysis of simulated data and of real dscRNA-seq data.

 

Video available from MIDAS Research Forum

By | General Interest, Happenings, News, Research

Video is now available from the MIDAS Research Forum held Dec. 1 in the Michigan League at http://myumi.ch/6vA3V

The forum featured U-M students and faculty showcasing their data science research; a workshop on how to work with industry; presentations from student groups; and a summary of the data science consulting and infrastructure services available to the U-M research community.

NOTE: The keynote presentation from Christopher Rozell of the Georgia Institute of Technology will be available in the near future.

2017 U-M Data Science Research Forum

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Forum Highlights

  • Oral and poster presentations on
    • Theoretical foundations of data science
    • Data science methodology
    • Data science applications in any research domain
    • Social impact of data science research
  • Networking Reception

All presentations will come from submissions in response to our call for abstracts.
Oral presentations are closed. Posters are welcome and encouraged. 

Abstract Submission – Posters Only – Deadline: November 15, 2017

We welcome submission from all U-M data science researchers (faculty, staff, trainees)

Please register for this event.  Please also see the call for abstracts for instruction, and submit through the Abstract Submission Form.

Preliminary Schedule

Downloadable Flyer

Research Poster Printing options.

Call for Proposals: Amazon Research Awards, deadline 9/15/17

By | Data, Educational, Funding Opportunities, News, Research

The Amazon Research Awards (ARA) program offers awards of up to $80,000 in cash and $20,000 in AWS promotional credits to faculty members at academic institutions in North America and Europe for research in these areas:

  • Computer vision
  • General AI
  • Knowledge management and data quality
  • Machine learning
  • Machine translation
  • Natural language understanding
  • Personalization
  • Robotics
  • Search and information retrieval
  • Security, privacy and abuse prevention
  • Speech

The ARA program funds projects conducted primarily by PhD students or post docs, under the supervision of the faculty member awarded the funds. To encourage collaboration and the sharing of insights, each funded proposal team is assigned an appropriate Amazon research contact. Amazon invites ARA recipients to speak at Amazon offices worldwide about their work, meet with Amazon research groups face-to-face, and encourages ARA recipients to publish their research outcome and commit related code to open-source code repositories.

Submissions are to be made online and details including rules and who may apply are located here.

Data science institutes at University of Michigan and University College London sign academic cooperation agreement

By | Al Hero, Educational, General Interest, News
From left, Al Hero, U-M; Patrick Wolfe, UCL; and Brian Athey, U-M signed an agreement for research and educational cooperation between the University of Michigan and University College London.

From left, Al Hero, U-M; Patrick Wolfe, UCL; and Brian Athey, U-M signed an agreement for research and educational cooperation between the University of Michigan and University College London.

ANN ARBOR, MI and LONDON — The Michigan Institute of Data Science (MIDAS) at the University of Michigan and the Centre for Data Science and Big Data Institute at UCL (University College London) have signed a five-year agreement of scientific and academic cooperation.

The agreement sets the stage for collaborative research projects between faculty of both institutions; student exchange opportunities; and visiting scholar arrangements, among other potential partnerships.

“There is a lot of common ground in what we do,” said Patrick Wolfe, Executive Director of UCL’s Centre for Data Science and Big Data Institute. “Both MIDAS and UCL cover the full spectrum of data science domains, from smart cities to healthcare to transportation to financial services, and both promote cross-cutting collaboration between scientific disciplines.”

Alfred Hero, co-director of MIDAS and professor of Electrical Engineering and Computer Science at U-M, said that one of the original goals of the institute when it was founded in 2015 under U-M’s $100 million Data Science Initiative was to reach out to U.S. and international partners.

“It seemed very natural that this would be the next step,” Hero said, adding that it would complement MIDAS’s recent partnership with the Shenzhen Research Institute of Big Data in China. “UCL epitomizes the collaboration, multi-disciplinarity and multi-institutional involvement that we’re trying to establish in our international partnerships.”

Wolfe visited Ann Arbor in early January to sign a memorandum of understanding along with Hero and Brian Athey, professor of bioinformatics and the other MIDAS co-director.

The agreement lists several potential areas of cooperation, including:

  • joint research projects
  • exchange of academic publications and reports
  • sharing of teaching methods and course design
  • joint symposia, workshops and conferences
  • faculty development and exchange
  • student exchange
  • exchange of visiting research scholars.

Links:

MIDAS at U-M

UCL Big Data Institute

Follow UCL’s data science activities @uclbdi

Follow MIDAS at @ARC_UM