Paper presentations for CS 581, Fall 2020
Policies
Brief summary: The paper presentation and the Q&A counts towards
your course participation, and the write-ups you do count towards
your homework grade. You do need to do the write-up for the papers you
present as well as the ones you are just in the audience for.
Due dates:
-
If you are presenting the paper, then
the PPTX or PDF for the presentation should be emailed to Tandy two days
before the presentation (i.e., Sunday night for Tuesday, Tuesday night
for Thursday), and these will be uploaded to the class website.
This counts towards your class participation.
-
If you
are an audience member, you will submit 2 questions for each paper
via email to the speaker, with a cc to
Vlad (smirnov3@illinois.edu) and Tandy.
These are due by
10 PM on
the day before (Monday night for Tuesday, Wednesday night for Thursday).
You will ask these questions at the end of the talk during the Q&A session.
This counts towards your class participation.
-
All students are expected to also do the associated homework (see
below), which is due Monday at 10 PM of the week before the talks,
in Moodle.
Homework for each paper:
You are expected to obtain the paper (use the university library)
and
read each paper.
Each day, two papers will be presented by students
(some weeks will have four papers presented, and some
weeks will only have two papers presented).
Pick one of the two papers for each day that week
and write up a 1-2 page
critique of the paper.
Note: These are due the Monday that the talks are presented.
Use the following structure (in PDF):
-
Identify the paper (full bibliography item)
-
Summarize the paper: what problem does it address, and what does it
contribute?
-
Critique the paper: what is good, what is not good, and do you agree with the
conclusions?
How does the paper relate to other papers on the same topic?
-
If relevant, comment in particular
on reproducibility.
-
If the paper has supplementary materials, read them.
Collaboration policy:
If you are presenting this paper with another student, you should split the
presentation into two parts, with each of you having responsibility for
one part.
Grading policy:
The paper presentation and Q&A after the talk counts toward the class participation.
Paper Presentation schedule
- Oct 27:
-
C Zhang, C Scornavacca, EK Molloy, S Mirarab, ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy, Molecular Biology and Evolution, msaa139, https://doi.org/10.1093/molbev/msaa139
(James and Mrinmoy will present)
-
S Snir and S Rao. "Quartets MaxCut: a divide and conquer quartets algorithm." IEEE/ACM Transactions on Computational Biology and Bioinformatics 7.4 (2008): 704-718.
(Baqiao will present)
- Oct 29:
-
FA Matsen, RB Kodner, EV Armbrust. "pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree." BMC bioinformatics 11.1 (2010): 538.
(Kathie and Eleanor will present)
-
P Barbera, AM Kozlov, L Czech, B Morel, D Darriba, T Flouri,
and A Stamatakis. "EPA-ng: massively parallel evolutionary placement of genetic sequences." Systematic biology 68, no. 2 (2019): 365-369.
(Grant and Vishal will present)
- Nov 5:
-
M Balaban, S Sarmashghi, and S Mirarab. "APPLES: scalable distance-based phylogenetic placement with or without alignments." Systematic Biology 69.3 (2020): 566-578.
(Elizabeth and Malachi will present)
-
E Garriga, P Di Tommaso, C Magis, C. et al. Large multiple sequence alignments with a root-to-leaf regressive method. Nat Biotechnol 37, 1466-1470 (2019). https://doi.org/10.1038/s41587-019-0333-6 (Qikai will present)
- Nov 10::
-
M Bordewich, O Gascuel, KT Huber, V Moulton. Consistency of topological moves based on the balanced minimum evolution principle of phylogenetic inference. IEEE/ACM transactions on computational biology and bioinformatics. 2008 Apr 25;6(1):110-7.
(Gillian will present)
-
J Söding. "Protein homology detection by HMM--HMM comparison." Bioinformatics 21.7 (2005): 951-960.
(Chengze and Qinghui will present)
Schedule for presentation
- Tuesday October 27:
(1) James and Mrinmoy and (2) Baqiao
- Thursday October 29:
(1) Grant and Vishal and (2) Kathie and Eleanor
- Tuesday November 5:
(1) Elizabeth and Malachi and (2) Qikai
- Thursday November 10:
(1) Gillian and (2) Chengze and Qinghui