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The Next Talk Sp'12 Talks General Info Speaking Req't

Leveraging Input and Output Structures For Joint Mapping of Epistatic and Marginal eQTLs

Friday, May 4th, 2012 from 12-1 pm in GHC 4303.

Seunghak Lee, CSD

Since many complex disease and expression phenotypes are the outcome of intricate perturbation of molecular networks underlying gene regulation resulted from interdependent genome variations, association mapping of causal QTLs or eQTLs must consider both additive and epistatic effects of multiple candidate genotypes. This problem poses a significant challenge to contemporary genome-wide-association (GWA) mapping technologies because of its computational complexity. Fortunately, a plethora of recent developments in biological network community, especially the availability of genetic interaction networks, make it possible to construct informative priors of complex interactions between genotypes, which can substantially reduce the complexity and increase the statistical power of GWA inference.

In this paper, we consider the problem of learning a multi-task regression model while taking advantage of the prior information on structures on both the inputs (genetic variations) and outputs (expression levels). We propose a novel regularization scheme over multi-task regression called structured jointly input/output lasso based on an L1/L2 norm, which allows shared sparsity patterns for related inputs and outputs to be optimally estimated. Such patterns capture multiple related SNPs that jointly influence multiple related expression traits. In addition, we generalize this new multi-task regression to structurally regularized polynomial regression to detect epistatic interactions with manageable complexity by exploiting the prior knowledge on candidate epistatic SNPs from biological experiments. We demonstrate our method on simulated and yeast eQTL datasets.

This is joint work with Eric Xing.

Presented in Partial Fulfillment of the CSD Speaking Skills Requirement.


Spring 2012 Schedule
Tue, Jan 17 GHC 4303 Severin Hacker Duolingo
Fri, Jan 20 GHC 4303 Expired
Tue, Jan 24 GHC 4303 Expired
Fri, Jan 27 GHC 4303 Expired
Tue, Jan 31 GHC 4303 B. Aditya Prakash Influence Propagation in Large Graphs
Fri, Feb 3 GHC 4303 Wittawat Tantisiriroj On the Duality of Data-intensive File System Design: Reconciling HDFS and PVFS
Tue, Feb 7 GHC 4303 Severin Hacker Duolingo
Fri, Feb 10 GHC 4303 Expired
Tue, Feb 14 GHC 4303 Expired
Fri, Feb 17 GHC 4303 Expired
Tue, Feb 21 GHC 4303 AVAILABLE
Fri, Feb 24 GHC 4303 AVAILABLE
Tue, Feb 28 GHC 4303 Karl Naden A Type System for Borrowing Permissions
Fri, Mar 2 GHC 4303 AVAILABLE
Tue, Mar 6 GHC 4303 AVAILABLE
Fri, Mar 9 GHC 4303 Midsemester Break By request only
Tue, Mar 13 GHC 4303 Spring Break By request only
Fri, Mar 16 GHC 4303 Spring Break By request only
Tue, Mar 20 GHC 4303 AVAILABLE
Fri, Mar 23 GHC 4303 Julian Shun Internally Deterministic Parallel Algorithms Can Be Fast
Tue, Mar 27 GHC 4303 AVAILABLE
Fri, Mar 30 GHC 4303 Luke Zarko ConcertOS, or: How I Learned to Stop Worrying and Love x64
Tue, Apr 3 GHC 4303 Ligia Nistor Verifying Object-Oriented Code Using Object Propositions
Fri, Apr 6 GHC 4303 AVAILABLE
Tue, Apr 10 GHC 4303 AVAILABLE
Fri, Apr 13 GHC 4303 AVAILABLE
Tue, Apr 17 GHC 4303 AVAILABLE
Fri, Apr 20 GHC 4303 Spring Carnival By request only
Tue, Apr 24 GHC 4303 AVAILABLE
Fri, Apr 27 GHC 4303 Ligia Nistor Verifying Object-Oriented Code Using Object Propositions
Tue, May 1 GHC 4303 AVAILABLE
Fri, May 4 GHC 4303 Seunghak Lee Leveraging Input and Output Structures For Joint Mapping of Epistatic and Marginal eQTLs
Tue, May 8 GHC 4303 AVAILABLE
Fri, May 11 GHC 4303 Elie Krevat Exploring an Automated Resource-efficient Approach to Meeting Service Deadlines


General Info

The Student Seminar Series is an informal research seminar by and for SCS graduate students from noon to 1 pm on Tuesdays and Fridays. Lunch is provided by the Computer Science Department (personal thanks to Sharon Burks and Debbie Cavlovich!). At each meeting, a different student speaker will give an informal, 40-minute talk about his/her research, followed by questions/suggestions/brainstorming. We try to attract people with a diverse set of interests, and encourage speakers to present at a very general, accessible level.

So why are we doing this and why take part? In the best case scenario, this will lead to some interesting cross-disciplinary work among people in different fields and people may get some new ideas about their research. In the worst case scenario, a few people will practice their public speaking and the rest get together for a free lunch.


Guideline & Speaking Requirement Need-to-Know

Note: Step #1 below are applicable to all SSS speakers. You can schedule AT MOST THREE talks per semester.

SSS is an ideal forum for SCS students to give presentations that count toward fulfilling their speaking requirements. The specifics, though, vary with each department. For instance, students in CSD will need to be familiar with the notes in Section 8 of the Ph.D. document and follow the instructions outlined on the Speakers Club homepage. Roughly speaking, these are the steps:

  1. Schedule a talk with SSS by sending your talk title, abstract, additional info (like "Joint work with..." or "In Partial Fulfillment of the Speaking Requirement"), and a picture of yourself (preferably jpeg) to sss@cs at least TWO WEEKS before your scheduled talk.
  2. After you are confirmed with your SSS slot, go to the Speakers Club Calendar and schedule your talk at least THREE WEEKS in advance of the talk date.
  3. On the day of your talk, make sure you print Speakers Club evaluation forms for your evaluators to use.
Students outside of CSD will need to check with their respective departments regarding the procedure. As another example, ISRI students fulfill their speaking requirements by attending a semesterly Software Research Seminar and giving X number of presentations per school year. If you have experience with your department that might help others in your department, please feel free to contribute your knowledge by emailing us. Thank you!


SSS Coordinators

Armaghan Naik, Computational Biology
Lin Xiao, CSD

 


Web contact: sss+www@cs