SCS
Student
Seminar
Series
|
|
|
|
|
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.
| Tue, Jan 17 | GHC 4303 | Severin Hacker | |
| Fri, Jan 20 | GHC 4303 | ||
| Tue, Jan 24 | GHC 4303 | ||
| Fri, Jan 27 | GHC 4303 | ||
| Tue, Jan 31 | GHC 4303 | B. Aditya Prakash | |
| Fri, Feb 3 | GHC 4303 | Wittawat Tantisiriroj | |
| Tue, Feb 7 | GHC 4303 | Severin Hacker | |
| Fri, Feb 10 | GHC 4303 | ||
| Tue, Feb 14 | GHC 4303 | ||
| Fri, Feb 17 | GHC 4303 | ||
| Tue, Feb 21 | GHC 4303 | ||
| Fri, Feb 24 | GHC 4303 | ||
| Tue, Feb 28 | GHC 4303 | Karl Naden | |
| Fri, Mar 2 | GHC 4303 | ||
| Tue, Mar 6 | GHC 4303 | ||
| Fri, Mar 9 | GHC 4303 | Midsemester Break | |
| Tue, Mar 13 | GHC 4303 | Spring Break | |
| Fri, Mar 16 | GHC 4303 | Spring Break | |
| Tue, Mar 20 | GHC 4303 | ||
| Fri, Mar 23 | GHC 4303 | Julian Shun | |
| Tue, Mar 27 | GHC 4303 | ||
| Fri, Mar 30 | GHC 4303 | Luke Zarko | |
| Tue, Apr 3 | GHC 4303 | Ligia Nistor | |
| Fri, Apr 6 | GHC 4303 | ||
| Tue, Apr 10 | GHC 4303 | ||
| Fri, Apr 13 | GHC 4303 | ||
| Tue, Apr 17 | GHC 4303 | ||
| Fri, Apr 20 | GHC 4303 | Spring Carnival | |
| Tue, Apr 24 | GHC 4303 | ||
| Fri, Apr 27 | GHC 4303 | Ligia Nistor | |
| Tue, May 1 | GHC 4303 | ||
| Fri, May 4 | GHC 4303 | Seunghak Lee | |
| Tue, May 8 | GHC 4303 | ||
| Fri, May 11 | GHC 4303 | Elie Krevat |
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.
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:
- 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.
- 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.
- On the day of your talk, make sure you print Speakers Club evaluation forms for your evaluators to use.
Armaghan Naik, Computational Biology
Lin Xiao, CSD