Syllabus for CSCE 471/871 (Spring 2008)

Up-to-date information is at http://csce.unl.edu/~sscott/teach/Classes/cse471S08

CONTENTS

• COURSE INFORMATION
• COURSE OBJECTIVES
• COURSE ELEMENTS

COURSE INFORMATION

PREREQUISITES: CSCE 310 (Data Structures & Algorithms), STAT 380/880 (Prob. and Stats.) or equivalent

TIME: 10:30–11:20am Monday, Wednesday, Friday

CLASSROOM: Avery 112

TEXTBOOKS:
Required:
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, by Richard Durbin, Sean Eddy, Anders Krogh, and Graeme Mitchison. Cambridge University Press, 1998. ISBN 0-521-62971-3.

Optional:
Introduction to Mathematical Methods in Bioinformatics, by Alexander Isaev. Springer, 2004. ISBN 3540219730.
Problems and Solutions in Biological Sequence Analysis, by Mark Borodovsky and Svetlana Ekisheva. Cambridge University Press, 2006. ISBN 0521612306.

These books are on reserve at Love Library.

COURSE OBJECTIVES

In this course you will learn several fundamentals and current trends in bioinformatics. As such, this course will not show you how to use existing computational biology tools, though you will probably learn some of that on your own as a side effect. Instead you will acquire a deep understanding of how they work, to the point where you can adapt existing tools to new problems and create new tools.

The biological problems we will study include sequence alignments, protein family modeling, and phylogeny. The approach we will focus on is hidden Markov models, though time permitting we will also discuss dynamic programming as well as machine learning models like decision trees and artificial neural networks.

COURSE ELEMENTS

There will be 2–4 homework assignments, each due by 11:59 p.m. on its due date. (cse's system clock, which timestamps your submissions, is the official clock for this course. Do not assume that just because the handin program allows you to submit that the deadline has not passed; you are responsible for ensuring that your files are submitted and timestamped before the deadline.) Late homework submissions will be penalized exponentially: if your submission is m minutes late, your final score will be multiplied by 2^–m/60. Thus you will lose 16% of your points if you submit 15 minutes late, 29.3% of your points if you submit 30 minutes late, 50% if you submit 60 minutes late, etc. (amount of lateness is measured by the time stamp given by cse's web-based handin). Thus unless you are making very significant improvements to your submission, it is better to submit a partially completed homework assignment than a late one. If you have a valid excuse for a late submission (e.g. illness), contact the instructor as soon as possible.

You may consult each other for assistance on the homework, but you must write up your results in your own words and indicate whom you consulted. You must use some document processing package (e.g. LaTeX) to write your homework submissions, and you must submit your reports electronically in pdf format (see "Help on Creating pdf Files" and "Help with LaTeX, etc."). You must also write as clearly and concisely as possible. Presentation of your results is as important as the results themselves, and will be heavily weighted in grading. If I cannot understand what you wrote due to poor writing, etc., then I cannot award full credit, even if your answers are correct. Thus I recommend that you ask someone to proofread your write-ups before you submit them, to check for clarity, typographical errors, etc. If English is not your native language, then I strongly recommend this!

Finally, ensure that all your files (e.g. program code, homework write-ups) are reasonably well-protected. You will be held responsible if someone copies your files and submits them as homework solutions.

There will be no exams in this course except for the prerequisite test, which will evaluate your understanding of this course's necessary background material as well as your writing ability.

Each of you will be assigned one lecture to summarize in the course wiki. After we complete your assigned topic in lecture, you will summarize that topic in the course wiki within one week of when we finish covering that topic in class (the due time is 11:59 p.m.; the homework late penalty applies here as well). No collaboration is allowed! Your summary will be based on the lecture, relevant readings from the text, and any other supplementary material that I distribute in class. You are also strongly encouraged to refer to other resources (e.g. published papers) and cite these in your summary. This summary must be in your own words! If you merely copy material from the textbook or the papers, you will be severely downgraded. Finally, as with the homeworks and projects, quality of writing and brevity will be heavily weighted in the grading. See the CSCE 970 Spring 2007 course wiki for example writeups.

After you finish your wiki, please notify the entire class at cse471-ml AT cse to notify everyone that you are finished.

You will also edit three other students' wikis this semester. You are to make substantive changes to each wiki you edit. I.e. while you should fix typos, you cannot limit your edits to that: you also need to make significant enhancements to each one you edit (additional depth on existing topics, broadening it into new topics, etc.). After you complete each edit, please notify me at sscott AT cse with a summary of changes you made so I can grade them.

In this course you will do a substantial project. This project can be: (1) a very extensive literature search and summary on a relevant topic, (2) a good implementation and evaluation of a relevant known result, or (3) a small (but nontrivial) amount of original, relevant research. You may work on these projects individually or in small groups, though if you work in a group, my expectations will be much higher when I grade your project.

You will summarize your project results in a written report and an oral presentation. If your project involves an implementation, then you may be asked to also give a brief demonstration. The written report must use a professional writing style similar to that found in an ACM or IEEE journal, including abstract, introduction, summary of related work, your contribution, references, and an appendix (if necessary). The oral presentation will be to the entire class at the end of the semester: during Dead Week (April 28–May 2), and if necessary, during the week prior to Dead Week (April 21–25). You will submit your written report to me no later than 11:59 p.m. on May 2. In accordance with UNL 15th week policies, you have now been informed in writing of the nature and scope of this project prior to the eighth week of classes.

Later this semester (around February 18) I will set a deadline for submission of 1–3 paragraph proposals on your projects. You must do this in order to get full credit for your project, and you must get my approval on it before starting work on your project. I will provide a list of possible topics later this semester, but you may propose your own topic as well. To be a valid topic, it must go beyond the scope of the course. So your project could be on a topic we did not cover in class at all, or could more deeply explore a topic we covered in class.

The above items will be weighted as follows:

In computing your letter grade I will start with the following base scale, where s is your final score:

You will receive a "+" with your grade if the last digit of your score is ≥ 7, and a "–" if the last digit is < 3. I will scale up from this base scale if necessary. So if you get an 87% in this course you are guaranteed a B+ (similarly, an 82% guarantees a B–), but your grade might be higher depending on your performance relative to the rest of the class and your level of class participation. Note that for students registered for CSCE 871, a B is required to pass the course; a B– is insufficient.

In general, students registered for CSCE 871 will be graded more stringently on everything and will have more problems to solve on the homework assignments.

Academic dishonesty of any kind will be dealt with in a manner consistent with the CS&E Department's Policy on Academic Integrity. You are expected to know and abide by this policy.