Syllabus for CSCE 471/871 (Spring 2011)

Up-to-date information is at



Stephen Scott
268 Avery
sscott AT cse
Office Hours:
1:30–2:30 Mon,
2:30–3:30 Tue,
or by appointment

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

TIME: 12:30–1:20pm Monday, Wednesday, Friday

CLASSROOM: Avery 110

TEXTBOOK (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.


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 may 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 other machine learning modeling techniques.



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 2m/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.


After we complete each topic in lecture, you will submit a brief (3–5 pages) summary of that topic. This is due one week (at 11:59 p.m.; the homework late penalty applies here as well) after we finish covering that topic in class (as with the homeworks, all submissions must be electronic in pdf format). 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. Your summary should include at least the following: (a) an overview of the "big picture" of that topic; (b) a description of what you feel are the most and least interesting results related to that topic; (c) 2–3 questions on material that you did not understand from the readings and lectures; (d) 2–3 interesting research ideas related to this topic; and (e) a detailed description of one subtopic. 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 this small set of sample topic summaries to use as guides in writing your own.

Each of you will be expected to grade 10–12 other students' submissions of one topic summary. For that topic summary, you will receive a perfect score so long as you grade according to the above guidelines. So if you grade students' submissions for e.g. the topic summary on pairwise alignment, then you need not submit your own summary on that topic.


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. 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 25–29), and if necessary, during the week prior to Dead Week (April 18–22). You will submit your written report to me no later than 11:59 p.m. on April 27. 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 (mid-February) 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:

hwks: 30% proj. report: 25% proj. presentation: 25% topic summaries: 20%

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

s ≥ 90% ⇒ A 80% ≤ s < 90% ⇒ B 70% ≤ s < 80% ⇒ C 60% ≤ s < 70% ⇒ D s < 60% ⇒ F

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.

Last modified 07 January 2011; please report problems to sscott.