FundScience Blog

Here it is:

https://sourceforge.net/p/workingwiki/code/1000/

handle \psfig dependencies
(bug #296)

clutter the make logs less

What is that in (sort of) English?

1. When including graphical images in a LaTeX document, you're not supposed to use the psfig package any more, because graphics and/or graphicx do everything it does, but better. Nonetheless, there are lots of documents that use the psfig package, and even more that still use the old \psfig{} command, because the new packages support that command for compatibility reasons. WorkingWiki needs to understand these commands, just a little, because it infers what images and other files a document includes so that it can remake the document if one of the images or other files has changed. It does fine with the \includegraphics{} command, which is what people generally use these days, but it wasn't working right with \psfig{}, because \psfig{} takes the filename in a different place, and I didn't realize it (I never used \psfig{} myself...).
2. It keeps track of these dependencies between documents and their components by creating a little "dependency file", created by running a fairly complicated series of Unix shell commands at the beginning of the process of making a typeset document. In addition to fixing the above problem with old-style graphics commands, I also changed a few lines of code so that instead of echoing all those shell commands into the log file that you sometimes need to read through, it just says one line, "Creating (name of dependency file)". That should make things a little easier for people.

I am accepting suggestions on ways to celebrate this milestone.

We've just uploaded a new paper to arXiv.org:

Effects of mixing in threshold models of social behavior
Andrei R. Akhmetzhanov, Lee Worden, Jonathan Dushoff
We consider the dynamics of an extension of the influential Granovetter model of social behavior, where individuals are affected by their personal preferences and observation of the neighbors' behavior. Individuals are arranged in a network (usually, the square lattice) and each has a state and a fixed threshold for behavior changes. We simulate the system asynchronously either by picking a random individual and either update its state or exchange it with another randomly chosen individual (mixing). We describe the dynamics analytically in the fast-mixing limit by using the mean-field approximation and investigate it mainly numerically in case of a finite mixing. We show that the dynamics converge to a manifold in state space, which determines the possible equilibria, and show how to estimate the projection of manifold by using simulated trajectories, emitted from different initial points.
We show that the effects of considering the network can be decomposed into finite-neighborhood effects, and finite-mixing-rate effects, which have qualitatively similar effects. Both of these effects increase the tendency of the system to move from a less-desired equilibrium to the "ground state". Our findings can be used to probe shifts in behavioral norms and have implications for the role of information flow in determining when social norms that have become unpopular (such as foot binding or female genital cutting) persist or vanish.

Submitted to Physical Review E.

Biomathematics and Biostatistics Seminar, University of Guelph, Guelph, Ontario, Canada
Tuesday, Mar. 26, 2:00 - 3:00 pm
SCIE, rm. 1511

In Defense of Information Cascades

Lee Worden

The Information Cascade model (Bikhchandani et al., 1992) is widely cited as an explanation for failure of the "wisdom of crowds", that is, suboptimal collective behavior among rational agents. Upon relaxing the model's premises by restricting agents' influences to local contacts, rather than fragile, contingent outcomes on the whole-population level we see robust integration of agents' private information, and the crowd's wisdom is not undermined.

Bikhchandani, Hirshleifer and Welch, 1992. "A Theory of Fads, Fashion, Custom, and Cultural Change as Informational Cascades", Journal of Political Economy, Vol. 100, No. 5 (Oct., 1992), pp. 992-1026. http://www.jstor.org/stable/10.2307/2138632

Open research links:
* The talk's slides
* The draft paper

Biomathematics and Biostatistics Seminar, University of Guelph, Guelph, Ontario, Canada
Tuesday, Mar. 26, 2:00 - 3:00 pm
SCIE, rm. 1511

In Defense of Information Cascades

Lee Worden

The Information Cascade model (Bikhchandani et al., 1992) is widely cited as an explanation for failure of the "wisdom of crowds", that is, suboptimal collective behavior among rational agents. Upon relaxing the model's premises by restricting agents' influences to local contacts, rather than fragile, contingent outcomes on the whole-population level we see robust integration of agents' private information, and the crowd's wisdom is not undermined.

Bikhchandani, Hirshleifer and Welch, 1992. "A Theory of Fads, Fashion, Custom, and Cultural Change as Informational Cascades", Journal of Political Economy, Vol. 100, No. 5 (Oct., 1992), pp. 992-1026. http://www.jstor.org/stable/10.2307/2138632

Open research links:
* The draft paper
* The talk's slides, in progress

From N. N. Taleb, Antifragility:

Gigerenzer and Brighton (2009) bust the following myth, as presented in The Selfish Gene by Richard Dawkins, in which we find the following about how a baseball outfielder catches a ball: "[H]e behaves as if he had solved a set of differential equations in predicting the trajectory of the ball. . . . At some subconscious level, something functionally equivalent to the mathematical calculations is going on."

Not quite, Professor Dawkins. Gerd Gigerenzer et al. counter by saying that none of that is done. They write the following:

Instead, experiments have shown that players rely on several heuristics. The gaze heuristic is the simplest one and works if the ball is already high up in the air: fix your gaze on the ball, start running, and adjust your running speed so that the angle of gaze remains constant. A player who relies on the gaze heuristic can ignore all causal variables necessary to compute the trajectory of the ball— the initial distance, velocity, angle, air resistance, speed and direction of wind, and spin, among others. By paying attention to only one variable, the player will end up where the ball comes down without computing the exact spot.

The same heuristic is also used by animal species for catching prey and for intercepting potential mates. In pursuit and predation, bats, birds, and dragonflies maintain a constant optical angle between themselves and their prey, as do dogs when catching a Frisbee.

Additional examples:

To choose a mate, a peahen uses a heuristic: Rather than investigating all peacocks posing and displaying in a lek eager to get her attention or weighting and adding all male features to calculate the one with the highest expected utility, she investigates only three or four, and chooses the one with the largest number of eyespots.

Just like humans. Another example:

To measure the area of a nest cavity, a narrow crack in a rock, an ant has no yardstick but a rule of thumb: Run around on an irregular path for a fixed period while laying down a pheromone trail, and then leave. Return, move around on a different irregular path, and estimate the size of the cavity by the frequency of encountering the old trail. This heuristic is remarkably precise.

I'm a big fan of heuristics, especially ones I wouldn't think of.

PDFs of my papers are at http://leeworden.net/lw/publications.

(See http://pdftribute.net/ for context. RIP Aaron Swartz.)

I just created an API for uploading source files into WorkingWiki. I also created an R script that uses it to upload a file into a WorkingWiki project, as a proof of concept, and as a starting point for our users who want to use R to develop code and publish it to the wikis, in the same way that you can develop things and publish them on Rpubs.com.

The sample script is at http://lalashan.mcmaster.ca/theobio/projects/index.php/WorkingWiki/Docum....

Soon enough we may have a fuller Rpubs-like system for publishing R and knitr documents to our wikis. A fully free-software and DIY system - no need to have someone else, like Rpubs, publish your documents for you...

I didn't mean it as a demo - I did it to get some work done. But now I have a wiki page that demonstrates using Sage to do symbolic mathematics in a WorkingWiki page.

It also demonstrates how awesome Sage is - in a remarkably short few bursts of code I've managed to create differential equation objects that can evaluate and plot themselves, have Sage do the timescale separation to construct the MacArthur-Levins competition model from a resource-uptake model, and use Sage's differentiation chops to construct the adaptive dynamics of the Mac-Lev model from the model itself. That's right - it generates the adaptive dynamics from the population dynamics, not me!

It then confirms that evolution reduces competition (in the one case I tried), not increases it.

Here's the link, by the way: http://lalashan.mcmaster.ca/theobio/worden/index.php/Selection_Gradients...

Experimenting with displaying PDFs directly in the wiki page using Mozilla's pdf.js. It looks great to me! If this works well enough, it would make our lives a lot simpler, not having to make a separate HTML version of each paper for display in the wiki page.

Created by wordle.com using the full text of my dissertation.

After Caroline Farrior.