Math 612 Class Project

The goal of the class project is for you to engage in research. Starting from a paper (or
collection of papers on a coherent topic) present the ideas to the class, propose an interesting
line for future work, and take a first step in that direction.

Timeline

1. The first component of the project will be a short Project Proposal. Send me your project
proposal by 11/6. Put “M612 Project Proposal” in the email subject.
2. The second component of the project will be a 30 to 40 minute in-class presentation.
Schedule your presentation for between Nov 17 and Dec 3. Each class will contain 2-3
presenters. Sign up for a presentation date on the scribe googledoc. You may work on
the project in pairs.
3. Written report due on December 10. About 3 pages. Based on feedback from from class
presentation.

Project Proposal (120 words max)

Write a short description of your first choice presentation topic, and a few words on your
second choice presentation topic. Explain why you find the topic interesting, and what
your goals are for the project.

Presentation (30 to 40 minutes)

Each class will contain 2 presenters. Don’t use up the time of the second presenter.

Project topics:
I started putting together a list of papers that can serve as jumping off points for class projects. I
may add to this over the next week or so. You are also encouraged to pick your own topic! If you
are interested in a topic, write your name in parenthesis. For some of these, it will be ok to have
multiple people on a similar topic. But do check with me about this.

1. MEASURE-VALUED SPLINE CURVES: AN OPTIMAL TRANSPORT VIEWPOINT

https://arxiv.org/pdf/1801.03186.pdf
Interested:
Your name here

2. DNA Microscopy: Optics-free Spatio-genetic Imaging by a Stand-Alone Chemical

Reaction (write your name here if interested)
https://www.sciencedirect.com/science/article/pii/S0092867419305471
Interested:
Liam Yih
3. Uncovering axes of variation among single-cell cancer specimens
https://www.nature.com/articles/s41592-019-0689-z
Interested:
Your name here

4. MAGIC: A diffusion-based imputation method reveals gene-gene interactions in

single-cell RNA-sequencing data
https://www.biorxiv.org/content/10.1101/111591v1
Interested:
Naila

5. Charting a tissue from single cell transcriptomics

https://www.biorxiv.org/content/10.1101/456350v1
Interested:
(Matt Budd), Jordan

6. Near-linear time approximation algorithms for optimal transport via Sinkhorn iteration
https://arxiv.org/abs/1705.09634
Interested:
Your name here

7. Stochastic Optimization for Large-scale Optimal Transport

https://papers.nips.cc/paper/6566-stochastic-optimization-for-large-scale-optimal-
transport.pdf
Interested:
Merlin, Tim

8. Autoencoder and Optimal Transport to Infer Single-Cell Trajectories of Biological

Processes
https://www.biorxiv.org/content/10.1101/455469v1
Interested:
Tim, Jordan

9. Batch effects in single-cell RNA-sequencing data are corrected by matching mutual

nearest neighbors.
https://europepmc.org/abstract/MED/29608177
Can we use optimal transport for this instead?
Interested:
Jalal Khouhak, Jordan

10. RNA velocity and acceleration:

https://www.nature.com/articles/s41586-018-0414-6
 Can we incorporate growth into this model? Can we incorporate RNA velocity
information into the cost function for optimal transport?
Compare to scVELO: https://www.biorxiv.org/content/10.1101/820936v1

Acceleration:
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1945-3
Interested:
Sierra

11. Learning Generative Models with Sinkhorn Divergences

https://arxiv.org/abs/1706.00292
Interested:
Tim

12. Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during
mammalian germ layer specification
https://www.biorxiv.org/content/10.1101/519207v1
How would you analyze this data differently?
Interested:
Your name here

13. Dynamic Cell Imaging in PET with Optimal Transport Regularization

https://arxiv.org/abs/1902.07521
Interested:
Your name here

14. Unbalanced optimal transport

https://arxiv.org/abs/1607.05816
Interested:
Your name here

15. A reconstruction of the initial conditions of the Universe by optimal mass transportation
https://arxiv.org/abs/astro-ph/0109483
Interested:
Jordan

16. The single-cell transcriptional landscape of mammalian organogenesis.

https://shendure-web.gs.washington.edu/documents/cao_nature_2019.pdf

Interested:
Your name here
17. A unified framework for lineage tracing and trajectory inference
https://www.biorxiv.org/content/10.1101/2020.07.31.231621v1
Interested:
(Matt Budd) (Sierra)(Becca)

18. The Data-Driven Schrodinger Bridge

https://math.nyu.edu/faculty/tabak/publications/Pavon_Tabak_Trigila.pdf
Interested:
Merlin

19. Multi-Marginal Schrodinger Bridges

https://arxiv.org/abs/1902.08319
Interested:
Becca

20. Deep generative modeling for single-cell transcriptomics

https://pubmed.ncbi.nlm.nih.gov/30504886/
https://academic.oup.com/bioinformatics/article/36/11/3418/5807606
Interested:
(Matt Budd)

21. DNA-based memory devices for recording cellular events

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6492567/
Nozomu Yachie (UBC) has some work on this. Not sure if it’s published yet.
Interested:
Liam Yih, Jordan

22. Fundamental limits on dynamic inference from single-cell snapshots

https://www.pnas.org/content/115/10/E2467
Interested:
Liam Yih

23. To find your own topic, look at papers by John Marioni, Oliver Stegle, Dana Pe’er, Smita
Krishnaswamy, Fabian Theis, Aviv Regev, Eric Lander, Allon Klein, … Or pick a topic
from the Computational Optimal Transport Textbook that we haven’t covered yet.