Lectures for CS 581, Fall 2021
The lectures in the first part of course (up to the take-home midterm)
cover the basis of the material. The second part of the course will
be decided based on student interests, and will include presentations
by students and some guest lectures.
- August 24, 2021
(Overview of course)
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August 26, 2021
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August 31, 2021 (constructing trees from subtrees)
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September 2-7, 2021 (maximum parsimony)
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September 9, 2021 (maximum likelihood)
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September 14-21, 2021 (species tree estimation)
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September 23 to October 5, 2021
(Eleanor Wedell lectures on September 28)
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Introduction to Multiple Sequence Alignment
(PDF)
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Needleman-Wunsch (PDF)
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Introduction to Profile Hidden Markov Models
(PDF)
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What we learn from data
(PPTX)
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October 7: Take-home midterm presented and discussed.
- Midterm submission deadline: Sunday October 10, 10 PM (Moodle).
If your homework includes any handwritten material, then you are
required to provide the hardcopy midterm
(identical to what you upload in Moodle) by
11:45 AM on
Monday October 11, to
either Samantha Smith or
Candice Steidinger in 3234 Siebel.
- October 14.
- October 19.
-
Yasamin will present the paper about
Rooting Species Trees under the MSC.
and Sarthak will present the paper on
Triplets MaxCut.
You should send a one paragraph summary and 3 questions to both students (cc to me and Eleanor) 24 hours before their talks.
- October 21.
- October 26: two student presentations:
Greg and Akhil.
Greg will present a paper about parsimony heuristcs in TNT software at this page.
Akhil will present this paper on quartet amalgamation.
All students should send a one paragraph summary and 3 questions to both students (cc to me and Eleanor) 24 hours before their talks.
- October 28: two student presentations:
Mingye and Kowshika.
Mingye's paper and
Kowshika's paper.
All students should send a one paragraph summary and 3 questions to both students (cc to me and Eleanor) 24 hours before their talks.
- November 2:
one student presentation: Yutong.
Her paper is on alignment-free tree estimation, here.
You should send a one paragraph summary and 3 questions to Yutong (cc to me and Eleanor) 24 hours before her talk.
We will begin with a talk by Paul Zaharias, who will present
his paper on Alignment Merging (HTML), which will be presented in
ALCOB 2021 next week
- November 4: Research project reports (7 presentations, 5 minutes each)
- November 9: Guest lectures (practice talks for ALCOB 2021: Eleanor and
James Willson
- November 11: Historical linguistics, see
(PDF)
- Nov 16: Luay Nakhleh, guest lecturer. Talking about phylogenetic networks
- Nov 18: Mohammed El-Kebir, guest lecturer. Talking about motif finding and gene finding in coronavirus genomes, using a variant of Smith-Waterman
- November 23, 26: Fall break
- November 30: Constrained optimization (PDF)
- Dec 2: Mohammed El-Kebir, guest lecturer. (He will finish his presentation from Nov 18.) Also, Melissa and Homa will present their course projects.
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December 7, last day. The remaining students will present their course projects.