Archive for PCI Evol Biol

PCI Math Comp Biol gets live!

Posted in Books, Statistics, University life with tags , , , , , on March 5, 2020 by xi'an

A new Peer Community (PCI) preprint and postprint server is about to get live, with Mathematical & Computational Biology as its core interest. Thanks to the efforts of Amaury Lambert, Céline Scornavacca, and Eric Tannier. Following the earlier PCI Evol Biol (and my aborted attempt to start a PCI Comput Stats…). Although the funding and the core team are mostly French, the target is obviously international and editors from all backgrounds and specialties are most welcome to join as authors and reviewers!

troubling trends in machine learning

Posted in Books, pictures, Running, Statistics, University life with tags , , , , , , , , , , , , , on July 25, 2018 by xi'an

This morning, in Coventry, while having an n-th cup of tea after a very early morning run (light comes early at this time of the year!), I spotted an intriguing title in the arXivals of the day, by Zachary Lipton and Jacob Steinhard. Addressing the academic shortcomings of machine learning papers. While I first thought little of the attempt to address poor scholarship in the machine learning literature, I read it with growing interest and, although I am pessimistic at the chances of inverting the trend, considering the relentless pace and massive production of the community, I consider the exercise worth conducting, if only to launch a debate on the excesses found in the literature.

“…desirable characteristics:  (i) provide intuition to aid the reader’s understanding, but clearly distinguish it from stronger conclusions supported by evidence; (ii) describe empirical investigations that consider and rule out alternative hypotheses; (iii) make clear the relationship between theoretical analysis and intuitive or empirical claims; and (iv) use language to empower the reader, choosing terminology to avoid misleading or unproven connotations, collisions with other definitions, or conflation with other related but distinct concepts”

The points made by the authors are (p.1)

  1. Failure to distinguish between explanation and speculation
  2. Failure to identify the sources of empirical gains
  3. Mathiness
  4. Misuse of language

Again, I had misgiving about point 3., but this is not an anti-maths argument, rather about the recourse to vaguely connected or oversold mathematical results as a way to support a method.

Most interestingly (and living dangerously!), the authors select specific papers to illustrate their point, picking from well-established authors and from their own papers, rather than from junior authors. And also include counter-examples of papers going the(ir) right way. Among the recommendations for emerging from the morass of poor scholarship papers, they suggest favouring critical writing and retrospective surveys (provided authors can be found for these!). And mention open reviews before I can mention these myself. One would think that published anonymous reviews are a step in the right direction, I would actually say that this should be the norm (plus or minus anonymity) for all journals or successors of journals (PCis coming strongly to mind). But requiring more work from the referees implies rewards for said referees, as done in some biology and hydrology journals I refereed for (and PCIs of course).

machine learning methods are useful for ABC [or my first PCI Evol Biol!]

Posted in Books, Kids, pictures, Statistics, University life with tags , , , , , , on November 23, 2017 by xi'an

While I am still working on setting a PCI [peer community in] Comput Stats, having secure sponsorship of some societies (ASA, KSS, RSS, SFdS, and hopefully ISBA), my coauthors Jean-Michel Marin and Louis Raynal submitted our paper ABC random forests for Bayesian parameter inference to PCI Evol Biol. And after a few months of review, including a revision accounting for the reviewers’ requests, our paper stood the test and the recommendation by Michael Blum and Dennis Prangle got published there. Great news, and hopefully helpful for our submission within the coming days!

and the travelling salesman is…

Posted in Books, pictures, Statistics, University life with tags , , , on July 21, 2017 by xi'an

Here is another attempt at using StippleGen on… Alan Turing‘s picture. My reason for attempting a travelling salesman rendering of this well-known picture towards creating a logo for PCI Comput Stats, the peer community project I am working on this summer. With the help of the originators of PCI Evol Biol.

exciting week[s]

Posted in Mountains, pictures, Running, Statistics with tags , , , , , , , , , , , , , , on June 27, 2017 by xi'an

The past week was quite exciting, despite the heat wave that hit Paris and kept me from sleeping and running! First, I made a two-day visit to Jean-Michel Marin in Montpellier, where we discussed the potential Peer Community In Computational Statistics (PCI Comput Stats) with the people behind PCI Evol Biol at INRA, Hopefully taking shape in the coming months! And went one evening through a few vineyards in Saint Christol with Jean-Michel and Arnaud. Including a long chat with the owner of Domaine Coste Moynier. [Whose domain includes the above parcel with views of Pic Saint-Loup.] And last but not least! some work planning about approximate MCMC.

On top of this, we submitted our paper on ABC with Wasserstein distances [to be arXived in an extended version in the coming weeks], our revised paper on ABC consistency thanks to highly constructive and comments from the editorial board, which induced a much improved version in my opinion, and we received a very positive return from JCGS for our paper on weak priors for mixtures! Next week should be exciting as well, with BNP 11 taking place in downtown Paris, at École Normale!!!