Up-to-date information is at http://cse.unl.edu/~sscott/teach/Classes/cse471S15
| INSTRUCTOR: |
| Stephen Scott |
| 268 Avery |
| 472-6994 |
| sscott AT cse |
| Office Hours: 10:30–11:30 Mon, 11:00–12:00 Tue, or by appointment in Avery 268 |
PREREQUISITES: CSCE 310 (Data Structures & Algorithms) or 311 (Data Structures & Algorithms for Informatics); MATH/STAT 380/880 (Statistics and Applications) or equivalent
TIME: 9:30–10:45am Tuesday, Thursday
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
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.
EXAMSThere will be no exams in this course.
PROJECTIn 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 27–May 1), and if necessary, during the week prior to Dead Week (April 20–24). You will submit your written report to me no later than 11:59 p.m. on April 29; the homework late policy applies to the written reports as well. In accordance with UNL 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.
GRADINGThe above items will be weighted as follows:
| hwks: 35% | proj. report: 35% | proj. presentation: 30% |
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.
All submitted work must be your own. No direct collaboration with fellow students, past or current, is allowed unless otherwise stated. The Computer Science & Engineering Department has an Academic Integrity Policy. All students enrolled in any computer science course are bound by this policy. You are expected to read, understand, and follow this policy. Violations will be dealt with on a case by case basis and may result in a failing assignment or a failing grade for the course itself.
Students with disabilities are encouraged to contact the TA or me for a confidential discussion of their individual needs for academic accommodation. It is the policy of the University of Nebraska-Lincoln to provide flexible and individualized accommodations to students with documented disabilities that may affect their ability to fully participate in course activities or to meet course requirements. To receive accommodation services, students must be registered with the Services for Students with Disabilities (SSD) office, 132 Canfield Administration, 472-3787 voice or TTY.
The CSE Department has an anonymous suggestion box at http://cse.unl.edu/department/suggestion.php that you may use to voice your concerns about any problems in the course or department if you do not wish to be identified.
All CSE GTA office hours are held in the CSE Student Resource Center in Avery 12.
It is CSE Department policy that all students in CSE courses are expected to regularly check their email so they do not miss important announcements.
UNL has received federal funding to continue the design and implementation of Creative Competency Exercises designed to improve computational and creative thinking in courses at the University of Nebraska. This semester evaluation will be done in the class to help understand how doing these exercises impacts student learning and student attitudes and motivation for science, engineering, technology and math courses. Faculty from CSCE and Educational Psychology will be coming to class or lab to proctor surveys that will aid in this evaluation. You will be getting more information from them during the first or second week of the semester. Thank you in advance for your help with this important project.