Lectures for CS 581, Fall 2023
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.
Starting sometime in October,
each student will be assigned to present a paper and
lead a discussion. All students
will be required to read the papers that are
presented, and submit homework
based on the papers.
- August 22, 2023
(Overview of course)
-
August 24, 2023 (Newick strings, additive matrices,
Naive Quartet Method, distance-based tree estimation)
-
August 29, 2023 (constructing rooted trees)
-
August 31 - September 5, 2023 (constructing unrooted trees from subtrees and
maximum parsimony).
Note: Sept 5 lecture will be by zoom (see Moodle for link),
and will start from slide 40
-
September 7, 2023 (maximum likelihood and Bayesian estimation).
Note: Sept 7 lecture will be by zoom (see Moodle for link)
-
September 12-19 2023 (species tree estimation)
-
Sept 21, 2023
(Introduction to Phylogenetic Networks)
(PPTX)
(PDF)
-
September 26: Multiple sequence alignment
-
Introduction to Multiple Sequence Alignment
(PDF)
-
Needleman-Wunsch (PDF)
-
September 28: Profile Hidden Markov Models and MSAs
- October 3:
What we learn from data
about MSA methods.
- October 5: Discussing papers that were
assigned and read. Handing out the midterm.
- Oct 10: Discussing midterm and HW 6.
- Oct 12: Phylogenetics for language families, part I
(PDF)
- Oct 17: Phylogenetics for language families, part II
(PDF)
(PPTX)
- Oct 19: Supertrees
(PDF)
- Oct 24: Divide and conquer tree estimation
(PDF)
(PPTX)
- Oct 26: Chengze Shen will give a talk on his multiple
sequence alignment methods, by zoom (see Moodle for link)
(PPTX)
- Oct 31: Student presentations of papers on machine learning.
Papers: (1) Azouri et al. "Harnessing machine learning to guide phylogenetic-tree search algorithms." Presented by Bo and Daniel, see (PDF) and
Zou et al. "Deep residual neural networks resolve quartet molecular phylogenies" (Jiaheng and Griffen) (PPTX)
- Nov 2: Student presentations of remaining papers on machine learning (see Moodle for
assignments).
-
Daniel and Jiaheng will present the Azouri et al. paper (Game)
(PDF)
- Mitali and Bo will present Smith and Hahn (PDF)
- Nov 7: Student presentations.
- Griffen and Mitali will present DEPP (PDF)
- Nov 9: Student presentations of papers related to their projcts.
-
Bo will present "M-Coffee: combining multiple sequence alignment
methods with T-Coffee."
(PDF)
-
Jiaheng will present "ProbCons: Probabilistic consistency-based multiple sequence alignment."
(PDF)
-
Mitali will present "GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters."
(PDF)
- Nov 14: Student presentations of papers related to their projects.
-
Griffen will present a paper by
Sviatopolk-Mirsky Pais et al.,
"Assessing the efficiency of multiple sequence alignment programs"
(PDF)
-
Daniel will present a paper by Criscuolo and Gascuel, "Fast NJ-like
algorithms to deal with incomplete distance matrices"
(PDF)
- Nov 16:
- Minhyuk Park will talk about UPP2 (paper) and HMM-based
methods for multiple sequence alignment more generally
- Tandy will talk about clustering methods in large networks
(PPTX)
- Nov 21 and 23: UIUC holiday
- Nov 28: Mohammed El-Kebir, guest lecture (cancer phylogeny)
(PDF)
- Nov 30: Leah Weber, PhD student of Mohammed El-Kebir, guest lecture
(BCR phylogenetics)(PDF)
- Dec 4: Last day of class (what we do will be decided later).
Meet in the classroom, not on zoom.