Tag Archives: Open science

SciPost

Recently, I was invited to sign up for SciPost, an online platform similar to the arXiv. However, the major difference is that SciPost is creating a suite of free and open-access peer-reviewed online journals. Moreover, copyrights will be held by the authors of the papers, and not by publishers.

Publications will be free for both authors and readers. The journal articles will be completely open to everyone.

To be honest, such a platform has probably been a long time coming for our community. The FAQ page on the website states that SciPost is launching because:

The publishing landscape is evolving rapidly, and it is not clear that the best interests of science and scientists are being represented. SciPost offers a grassroots solution to the problem of scientific publishing, designed and implemented by scientists in the best interests of science itself.

SciPost is open for submissions starting June 2016. I sincerely hope that those in charge of SciPost have it running smoothly by then and that it reaches the critical mass to be successful. Good luck to the team and particularly J.-S. Caux, the condensed matter theorist who started this endeavor.

Open-Access Publications

Imagine that taxes are collected from the public by the government, then the government uses some of that money to fund scientific research. Then imagine that after the scientific research is carried out, the scientists write up their results and submit their manuscript to a journal for peer review. The publisher of that journal selects the reviewers (who are not paid for these services). Soon after, the publisher hears back from the reviewers, forwards their comments to the papers’ authors and after some adjustments, publishes this paper.

This paper is then not available to the public, who has funded the research, and not even necessarily available to the government, unless the government agency has a subscription to the journal. In fact, the authors themselves are barred for a period of time from sharing their own work online. The work is owned by a third-party, the publisher.

Though this may seem absurd and overly-simplistic, this is not too much unlike how the current system of publishing in scientific journals actually works. I have argued previously, in Data and Plots for the Public, that it is important for the public to have access to data, plots and articles. It is also necessary for science journalists to be able to reprint these plots for articles that are more accessible to the public.

I am not alone in this point of view as it seems like open-access journals are becoming more popular in many fields, as reported recently in The Guardian. However, I do see a problem occurring with many of the current open-access journal models. These journals work by charging authors a fee for publication. It is easy for this model to become corrupted, as the more a journal publishes, the higher its revenue. Therefore, scientific quality will easily fade when faced with higher potential profits.

One way to rectify this situation is by charging the authors a fee for peer-review even if the paper may not be published. This method also has its drawbacks, however, as it may end up preventing some authors from submitting results to a journal altogether for fear of rejection.

There are a few ideas on how to solve these problems, but I think one thing is clear: the current model is unsustainable, unfair to the public and opposes scientific principles of openness. One wonders if public opinion would have been swayed sooner on the topics of climate change or nicotine addiction had the public been given access to the data and plots from scientific journals rather than having to intuit such information from secondary and tertiary sources. The current model of scientific publication is in need of reform.

Sign problems, Terry Tau, and open science

Recently a colleague of mine had a pretty amazing experience in open science. In brief, an outstanding conjecture in determinant quantum Monte Carlo about the sign problem was posed and answered by Terrance Tao and others on mathoverflow. The total turnaround time was approximately 3 days from beginning to finish, making it a wonderful example of the power of open science.

First some background. Pretty much any Monte Carlo simulation of fermions suffers from the notorious sign problem. In essence, because the exchange of two Fermi particle contributes a negative weight, any stochastic sampling of a Fermi distribution will result in approximately equal positive and negative parts. In fact, if one measures the sign weight throughout a Monte Carlo simulation, it can be seen to decay to zero exponentially with the number of states/particles and projection time/inverse temperature. There’s been some work by Troyer and Wiese that showed the sign problem in some specific instances falls into the NP-complete complexity class (http://arxiv.org/abs/cond-mat/0408370), though this deserves a blog post of its own. The upshot is it’s a HUGE hindrance to studying fermions and any progress on this front is generally considered very important.

Determinant quantum Monte Carlo (DQMC) is a specific breed of QMC that stochastically samples determinants representing all permutations of single particle fermion states. It was first introduced by some heavy hitters in the QMC committee to study the 2D Fermi Hubbard model (http://journals.aps.org/prb/abstract/10.1103/PhysRevB.80.075116), where they found that for the spin unpolarized system (equal spin-up and spin-down) there was no sign problem! Essentially the spin-up and spin-down signs could cancel each other. Later, Wu and Zhang extended the space of models that were sign problem free in DQMC (http://journals.aps.org/prb/abstract/10.1103/PhysRevB.71.155115). In both these works, however, the lack of a sign problem was found empirically without any hard proof.

Now, my friend and colleague Lei Wang wanted to know exactly why this true, and possibly if more models could fall under this category of sign problem free. Empirically, people see the following:

If Ai=(0 B_i^{T} // B_i 0), where B_i are real matrices and i=1,2,,N, then det(I+exp(A_1)exp(A_2)exp(A_N))0

For spin unpolarized systems it’s pretty clear why each A_i is of this form, but for others systems it’s not as clear. Anyways, this was the question he posed to mathoverflow. Amazingly people jumped on it, and it wasn’t long before Fields Medalist Terrance Tao got involved! It was then only a matter of 3 days before the conjecture was proven to be true in a mathematically rigorous way. For a full writeup of the proof, you can check out Tao’s blog.

When I found out about this, I was super excited to see the open science model working so incredibly well. Tao really is a leader on this front (though perhaps it’s much easier for him to command a crowd-sourced legion as well). At any rate, I would love to see more of this in the future, and I think we can take this instance as an excellent example of success.