Retro school children University of Washington Department of Computer Science & Engineering
 527: Computational Biology, Email Log
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Below is a log of all email sent to the class mailing list cse527@cs.washington.edu. Feel free to use it to ask questions, post information, or initiate discussions of general interest to the class.

Administrative requests concerning the mailing list itself, such as add/delete/address change requests, should be addressed to majordomo@cs.washington.edu.

Index of Messages

(Latest message Friday, 11-Jan-2002 19:16:05 PST.)

 

Messages


Date: Fri, 12 Oct 2001 13:31:13 -0700 (PDT) From: Jochen Jaeger <jj@cs.washington.edu> To: cse527@cs.washington.edu, baek@u.washington.edu, lkim@u.washington.edu, pmork@cs.washington.edu, shefner@u.washington.edu, Saurabh Sinha <saurabh@cs.washington.edu>, tjaden@cs.washington.edu, yanhan@u.washington.edu, yzizhen@u.washington.edu Subject: CSE527 TA Hello, finally CSE527 has a TA, yeah ;) My name is JJ and I am a 2nd year CSE (computer science and engineering) and CMB (computational molecular biology) student. The office hours will be on Thursdays at 2:30 in 429 Sieg Hall or in one of the cubicles on the 4th floor in Sieg Hall. If this is not a good time please email me and I will move it. Bu we can of course also make other appointments by email. It would be great if all of you could subscribe to our mailing list. Simply write mail to: majordomo@cs.washington.edu with the body: subscribe cse527 Future emails will only be on that list but you can always access our list online at: http://www.cs.washington.edu/education/courses/527/01au/bboard.html I thought about putting up the lecture notes on the web but would need some help from your side. If you can provide me with TeX, Word or other electronic notes from the lectures I will do my best, format it and put it online. So please email me, the more we have the better it will be ;) cu, Jj
Date: Wed, 07 Nov 2001 17:50:09 -0800 From: "Walter L. Ruzzo" <ruzzo@cs.washington.edu> To: cse527@cs.washington.edu Subject: Re: Today's lecture (11/6) References: <20011107070841.45072.qmail@web14205.mail.yahoo.com> > Okay, I was pretty much lost in the > math in today's lecture. I'm not sure > if this was due to a general insufficient > stats background or the specifics of > the lecture. Did you present from a paper > or were these just your notes? If > it's the former, can you send me the > reference? I'm sure you weren't alone. that was the most technical lecture so far. Unfortunately, it was drawn from several sources: * basics on sample spaces, conditional probability, Bayes rule, "prior" vs "posterior" probabilities via Bayes rule, expectation, linearity of expectation, basics of the maximum likelihood method of parameter estimation -- I happened to draw from a book called something like intro to mathematical stats by Hogg & Craig, but most any good stats book will have this. * plain max-likelihood estimation (mle) lets you answer a question like "given X1, X2, ..., a sample from a normal (say) distribution with unknown parameters like mean and/or variance, what values of those parameters maximize the likelihood that I would observe the data I actually did observe." E.g., in the model-based clustering context, *IF* you knew which clusters each point belonged to, it gives a way to estimate the parameters defining each cluster. * The Bayes rule stuff is used to answer a complementary question: *IF* you knew the parameters for each cluster, what are the odds that each given data point belongs to each cluster. * This suggests a heuristic algorithm for clustering (or, more generally, for max likelihood parameter estimation in the face of hidden data): alternate the above two steps, (called the M step and E step, resp.) and hope it converges to a good estimate. That's the EM algorithm. For the particular case of 2 normals in one dimension with common variance, I was following the development in Mitchell's book on Machine Learning. * It's not obvious that this is a good idea -- do the parameter estimates get better with every step, or usually, or sometimes? So the last 10-15 minutes of what I talked about was a proof that the EM algorithm has the property that the revised parameter estimates after an E-step/M-step pair as above never result in a decrease in likelihood. (I.e., it's a "hill climbing" method. If you always go up hill, you'll eventually find a hilltop, but maybe not the highest hilltop around.) This (non-decreasing likelihood from an E/M pair) is true in general, i.e. for most any sort parameter estimation problem with hidden variables, not just the clustering problem we've been looking at. The proof I showed came from the comp bio book by Durbin, Eddy, Krogh & Michison; I forget the title. EM is usually attributed to Dempster, Laird, & Rubin, 1977 (online at http://links.jstor.org/sici?sici=0035-9246%281977%2939%3C1%3AMLFIDV%3E2.0.CO%3B2-X ), but seemingly had appeared many times in various forms, at least as early as the 1890's, where I understanbd it was used for some form of "model-based clustering" of astronomical data. I don't know how readable the Dempster paper is, but again this is a technique taht's widely used, so probably there are other texts that describe it. If any of you know of other good expositions, please let us know. I hope this helps. Ask more questions if not.
Date: Wed, 28 Nov 2001 08:55:52 -0800 From: "Walter L. Ruzzo" <ruzzo@cs.washington.edu> To: cse527@cs.washington.edu Subject: [Fwd: viterbi.xls] This is a multi-part message in MIME format. --------------45B1E7C2AACD2C6B0815203D Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit for your amusement, there's a (not very pretty) excel spreadsheet attached that does the Viterbi calculation for the loaded dice example I gave yesterday. --------------45B1E7C2AACD2C6B0815203D Content-Type: message/rfc822 Content-Transfer-Encoding: 7bit Content-Disposition: inline Return-Path: <ruzzo@cs.washington.edu> Received: from cs.washington.edu (ruzzo-pc.cs.washington.edu [128.95.3.251]) (authenticated bits=0) by june.cs.washington.edu (8.12.1/8.12.1/0.5) with ESMTP id fARNR44Y096863 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for <ruzzo@cs.washington.edu>; Tue, 27 Nov 2001 15:27:04 -0800 (PST) Message-ID: <3C042148.C724F220@cs.washington.edu> Date: Tue, 27 Nov 2001 15:27:04 -0800 From: "Walter L. Ruzzo" <ruzzo@cs.washington.edu> X-Mailer: Mozilla 4.78 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: ruzzo@cs.washington.edu Subject: viterbi.xls Content-Type: multipart/mixed; boundary="------------2A8253DE1FDB961D2B7FB857" This is a multi-part message in MIME format. --------------2A8253DE1FDB961D2B7FB857 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit --------------2A8253DE1FDB961D2B7FB857 Content-Type: application/msexcel; name="viterbi.xls" Content-Transfer-Encoding: base64 Content-Disposition: inline; filename="viterbi.xls" 0M8R4KGxGuEAAAAAAAAAAAAAAAAAAAAAPgADAP7/CQAGAAAAAAAAAAAAAAABAAAAKQAAAAAA AAAAEAAA/v///wAAAAD+////AAAAACgAAAD///////////////////////////////////// //////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////// 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Date: Tue, 04 Dec 2001 16:08:01 -0800 From: "Walter L. Ruzzo" <ruzzo@cs.washington.edu> To: cse527@cs.washington.edu Subject: 527 presentations/finals/grades [Apologies if you got this already; I had some mailer trouble.] I think a few people missed my discussion of class projects/grading/etc. a couple weeks ago. The gist is that I'm going to grade based on the lecture notes you've written, and an informal project, consisting of either reading and reporting on a paper or two on a computational bio-related topic of interest to you, or doing some data analysis (e.g. trying some of the clustering algorithms we discussed on real or synthetic data). There will be NO final exam. The Project FAQ: > If I choose to read a paper and give presentation, when will > I give it? Do I need to submit a written report? I'd slightly prefer an oral report, so I can ask questions, but a written report is fine if you prefer; no need for both. In either case, nothing elaborate is required. Oral: just come tell me about what you read, perhaps relate it to class material, and/or suggest what sort of computational tools would be needed to make further progress on the problem. Written: 4-5 pages should be fine, similar content. I'm flexible as to timing, but would prefer to have them finished by, say, the Wednesday of finals week (12/19). Send me an email when you're ready to schedule a meeting. > I'm actually interested in doing some data analysis with a > {biology|computing} student, ... Great! > ... but I doubt if there is enough time considering I have > another project due. When is the deadline for that? If you have a project in mind that will stretch past finals, talk to me. Also, feel free to use this mailing list to find a partner and/or toss around project ideas.
Date: Thu, 06 Dec 2001 09:22:29 -0800 From: "Walter L. Ruzzo" <ruzzo@cs.washington.edu> To: cse527@cs.washington.edu Subject: re: presentation > Also, did you have in mind that we would prepare > slides, or something more informal? Informal. slides are unnecessary, but fine if they help you.
Date: Thu, 06 Dec 2001 09:24:50 -0800 From: "Walter L. Ruzzo" <ruzzo@cs.washington.edu> To: cse527@cs.washington.edu Subject: Re: presentation References: <3C0FA955.1DF04DB0@cs.washington.edu> PS: I'm expecting everyone to take about half an hour to describe what they read, including some time for me to ask dumb questions. "Walter L. Ruzzo" wrote: > > > Also, did you have in mind that we would prepare > > slides, or something more informal? > > Informal. slides are unnecessary, but fine if they help > you.
Date: Thu, 06 Dec 2001 10:25:11 -0800 From: "Walter L. Ruzzo" <ruzzo@cs.washington.edu> To: compbio-seminars@cs.washington.edu, cse527@cs.washington.edu Subject: Phil Green talk today Phil's talk today in the Biostats seminar may be of interest to many of you. Speaker: Philip P. Green Professor of Molecular Biotechnology Adjunct Professor of Computer Science University of Washington Subject: Analyzing Genome Sequences Date: Thursday, December 6, 2001 Time: 3:30PM-5:00PM Place: T-639 Health Sciences Building ABSTRACT: Our ability to determine the genome sequences of organisms now greatly outpaces our ability to extract the biological information contained in those sequences. I will briefly survey existing methods for identifying and delineating one important kind of genomic sequence feature, the protein-coding genes, and then describe our own work in developing a computational approach to gene identification. Probalistic models of gene and genome structure play a key role in this work.
Date: Thu, 06 Dec 2001 10:28:34 -0800 From: "Walter L. Ruzzo" <ruzzo@cs.washington.edu> To: cse527@cs.washington.edu Subject: another gene finding talk > Date: Wed, 28 Nov 2001 11:16:19 -0800 > From: "Walter L. Ruzzo" <ruzzo@cs.washington.edu> > To: cse590cb@cs.washington.edu, compbio-seminars@cs.washington.edu > Subject: CSE 590CB 12/7: mRNA Secondary Structure vs Splicing > And lest I forget, here's yet another talk related to gene finding. > > We'll use the last session of 590cb this quarter for Don to give > a warm-up to his talk at PSB in January. Usual time/place: > 10:30AM, EE 045, Friday 12/7. > > Pre-mRNA Secondary Structure Prediction Aids Splice Site > Prediction > > Donald J. Patterson, Ken Yasuhara and Walter L. Ruzzo > > To appear: Pacific Symposium on Biocomputing, Kauai, Hawaii, > Jan., 2002. > > Abstract: Accurate splice site prediction is a critical > component of any computational approach to gene prediction in > higher organisms. Existing approaches generally use > sequence-based models that capture local dependencies among > nucleotides in a small window around the splice site. We present > evidence that computationally predicted secondary structure of > moderate length pre-mRNA subsequences contains information that > can be exploited to improve acceptor splice site prediction > beyond that possible with conventional sequence-based > approaches. Both decision tree and support vector machine > classifiers, using folding energy and structure metrics > characterizing helix formation near the splice site, achieve a > 5--10% reduction in error rate with a human data set. Based on > our data, we hypothesize that acceptors preferentially exhibit > short helices at the splice site. > > Download: > http://www.cs.washington.edu/homes/ruzzo/papers/splice.pdf
Date: Fri, 14 Dec 2001 14:20:50 -0800 (PST) From: Jochen Jaeger <jj@cs.washington.edu> To: cse527 <cse527@cs.washington.edu> Subject: lecture notes Hi, just wanted to tell you that all of the lecture notes are now up on the web. If anything is terribly wrong with it please email me so that I can fix it. Thanks, Jj


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