Cataloging a sparse year of blogging: IMO workshop and preprints

Happy 2018!

With 2017 finally behind us, TheEGG enters its 8th calendar year. This past year has been a slow one for the blog, with only 10 new articles and two posts cataloguing 2016 (on cancer and on more theoretical aspects of evolution and general modelling). Half the months were barren: I posted nothing in March, April, May, July, August, September; and only October and November saw more than one post. But those two months of activity were good. We saw the list of TheEGG authors joined by David Robert Grimes, Vincent Cannataro, and Matthew Wicker; plus the return of Robert Vander Velde.

If you’re keeping score at home, this means that I only wrote six new articles last year.

As in the past, I want to start the new year by summarizing the old.

The extra collaborative mood of the blog this past year was inspired by the Integrated Mathematical Oncology workshop. Although I attended the workshop in many prior years (see my posts on our work on CML in 2013, gastric cancer in 2014, ALL in 2015, and CMML in 2016), I did not attend in 2017. As part of my penance for skipping this year, I wrote a post outlining mathematical oncology and the spirit behind this fun workshop:

  1. Hackathons and a brief history of mathematical oncology (October 28th)
  2. This article was an extended form of a piece I wrote for the Oxford computer science department’s InSPIREd Research newsletter. It allowed me to share some history of mathematical oncology. I think a history is important for a field to write. Next step might be a Wikipedia page.

    But just because I didn’t attend the IMO Workshop, doesn’t mean that I completely skipped out on visiting Moffitt last year. I visited in September, as Hurricane Irma was bearing down on Tampa. The primary purpose was to work with Andriy Marusyk and David Basanta in fleshing out our winning project from the 2016 IMO Workshop on dark selection for ruxolitinib resistance in myeloid neoplasms. A big part of this was soliciting our group members to write a number of guest posts on their aspects of the project:

  3. Oxygen fueling dark selection in the bone marrow (October 24th) by David Robert Grimes
  4. Ratcheting and the Gillespie algorithm for dark selection (November 14th) by Robert Vander Velde
  5. Dark selection from spatial cytokine signaling networks (November 30th) by Vincent Cannataro
  6. My job was then simply to add a bit more writing and combine these posts into a preprint on our project. We were happy to release this on BioRxiv on Oxtober 30th, just in time for the 2017 workshop:

    Kaznatcheev, A., Grimes, D. R., Vander Velde, R., Cannataro, V. L., Baratchart, E., Dhawan, A., Liu, L., Myroshnychenko, D., Taylor-King, J.P., Yoon, N., Padron, E., Marusyk, A., & Basanta, D. (2017). Dark selection for JAK/STAT-inhibitor resistance in chronic myelomonocytic leukemia. bioRxiv, 211151.

    During my Tampa visit, Matthew Wicker — a visiting student that I had the privilege of supervising during the summer in Oxford — was able to come down from the University of Georgia to give a talk about some of our ongoing work. He was so happy with Moffitt, that he returned for the workshop to work on ovarian cancer:

  7. Identifying therapy targets & evolutionary potentials in ovarian cancer (November 8th) by Matthew Wicker
  8. In his first post for TheEGG, Matthew recounted his experience at Moffitt and the models that his team built for the workshop. I am very impressed by their visualizations.

    As part of the prep for my other summer student, I wrote a tutorial on a useful technique in evolutionary game theory:

  9. Spatializing the Go-vs-Grow game with the Ohtsuki-Nowak transform (June 30th)
  10. Here I got to revisit the Ohtsuki-Nowak transform and my first mathonco paper: edge-effects in solid tumours. During her two week in2science UK placement, my student learned both how to apply the ON-transform and classify three strategy games. She then worked on extending the INV-AG spatialization to the INV-AG-GLY game.

    After the summer, I was finalizing a number of preprints. Apart from the above one on dark selection, I released three more in August, September, and December:

    Kaznatcheev, A., Peacock, J., Basanta, D., Marusyk, A., & Scott, J.G. (2017). Fibroblasts and alectinib switch the evolutionary games that non-small cell lung cancer plays. bioRxiv: 179259.

    Kaznatcheev, A. (2017). Complexity of evolutionary equilibria in static fitness landscapes. bioRxiv: 187682

    Kaznatcheev, A. (2017). Two conceptions of evolutionary games: reductive vs effective. bioRxiv: 231993.

    Given this much preprint prep, I ended up reflecting on the role of and arguments for preprints in science:

  11. Preprints and a problem with academic publishing (October 14th)
  12. Poor reasons for preprints & post-publication peer-review (October 21st)
  13. It was these reflections that got me back into a burst of blogging for October and November.

    This burst fed a positive feedback loop.

    For example, the last preprint was generated by ideas (including the ON-transform) that I’ve been exploring for a number of years in TheEGG. The final ingredient that crystallized this paper was my recent realization about the ontology of games:

  14. Ontology of player & evolutionary game in reductive vs effective theory (November 4th)
  15. Replicator dynamics and the simplex as a vector space (December 1st)

This realization would not have been possible without the blog. In a forthcoming post, I’ll discuss effective games more closely and create a linkdex of the blog posts that went into the paper. I think it is one of the notable successes of the blog.

Even though my posting this year has been sparse, the blog and community of readers and contributors have continued to improve my science. And although views were lower this year (only 35.3k) that the previous five (high was in 2014 at 151.5k), the blog still attracted general recognition as one of the top 12 science blogs in Canada.

For this and all your helpful feedback and support: thank you, dear reader.

I look forward to a more active 2018.


About Artem Kaznatcheev
From the Department of Computer Science at Oxford University and Department of Translational Hematology & Oncology Research at Cleveland Clinic, I marvel at the world through algorithmic lenses. My mind is drawn to evolutionary dynamics, theoretical computer science, mathematical oncology, computational learning theory, and philosophy of science. Previously I was at the Department of Integrated Mathematical Oncology at Moffitt Cancer Center, and the School of Computer Science and Department of Psychology at McGill University. In a past life, I worried about quantum queries at the Institute for Quantum Computing and Department of Combinatorics & Optimization at University of Waterloo and as a visitor to the Centre for Quantum Technologies at National University of Singapore. Meander with me on Google+ and Twitter.

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