Friday, January 31, 2014

"Ottoman Art" and Movies

Here are a bunch of famous moves scenes cast in the style of "Ottoman art". I can't vouch for the accuracy of the artistic style (in particular, whether it is "Ottoman" per se), but these are still very cool.

(Tip of the cap to Craig Montuori.)

Beach Art

For some really awesome geometric art created on beach sand, take a look at this website.

(Tip of the cap to Greg Stolerman and Susan Schaeffer.)

Thursday, January 30, 2014

The Social Status of British Cows

Patrick Stewart explains the different types of moos from cattle based on their social status. As Sir Patrick explains, bovine dialects also depend on political, environmental, and cultural conditioning.

(Tip of the cap to Meredith Alden.)

Data Availability

As Aaron Clauset writes thoughtfully (as usual), PLoS journals have a new policy on the public availability of data sets for papers published in their journals.

I have written a comment on his entry that should appear in a while (once Aaron has a chance to take a look at confirm that I'm not a robot spammer, etc.).

Long, Very Long, and ... What the Hell are You Doing?

Well, I guess I have a well-deserved reputation for writing very long papers.

Ernie Barreto wanted to make sure that I saw this article. I really like the terse commentary that likely ended a certain debate. It's key words are priceless. The others are excellent as well, though I had seen those before. In one of them, Michael Berry told me that his abstract of "Probably not." was "No." at some point but that he and his coauthors wanted to leave some possibility that their conclusions were wrong.

Fun Fact: Version 1 of my thesis was about 400 pages. My committee was (very understandably) not very happy with this --- among other things --- and demanded that I write version 2.0 (rather than 1.1) and that it be less than 200 pages. This was not fun at the time.

Fun Fact 2: One version of one of my papers --- the published version was much terser at 20 pages + 20 pages SOM (mostly a table) --- had a 100-page SOM at one reasonably final point, but then we decided the referees would kill us. So the version (which was desk-rejected, of course) that we sent to Nature had an SOM that was in the 60s or so, though that was regular typefacing and spacing rather than in journal-page format. [Acronym: SOM = Supplementary Online Material]

In progress now: a revision of a now 42-journal-page paper (though a review article), and new papers: a 40+ pager, a 35-pager, a pair of 32-pagers, and a few of them currently in the 20s.

(Tip of the cap to Ernie Barreto.)

Tuesday, January 28, 2014

"Cross-Linked Structure of Network Evolution"

A new paper of mine was published in final form today. In this paper, my coauthors and I use a structure called a "cross-link" that connects a pair of time-dependent edges based on the similarity of their temporal evolution. In our study, the time-dependent edges arise from similarity of temporal dynamics of different nodes. The basic idea is to try to tease out when sets of edges evolve separately and when there is co-evolution. In this paper, we consider time-dependent networks that we construct from time series from functional brain networks and from output of coupled Kuramoto oscillators. Here are the details of the paper.

Title: Cross-Linked Structure of Network Evolution

Authors: Danielle S. Bassett, Nicholas F. Wymbs, Mason A. Porter, Peter J. Mucha, and Scott T. Grafton

Abstract: We study the temporal co-variation of network co-evolution via the cross-link structure of networks, for which we take advantage of the formalism of hypergraphs to map cross-link structures back to network nodes. We investigate two sets of temporal network data in detail. In a network of coupled nonlinear oscillators, hyperedges that consist of network edges with temporally co-varying weights uncover the driving co-evolution patterns of edge weight dynamics both within and between oscillator communities. In the human brain, networks that represent temporal changes in brain activity during learning exhibit early co-evolution that then settles down with practice. Subsequent decreases in hyperedge size are consistent with emergence of an autonomous subgraph whose dynamics no longer depends on other parts of the network. Our results on real and synthetic networks give a poignant demonstration of the ability of cross-link structure to uncover unexpected co-evolution attributes in both real and synthetic dynamical systems. This, in turn, illustrates the utility of analyzing cross-links for investigating the structure of temporal networks.

Monday, January 27, 2014

A New Rejection Record!

Fastest. Rejection. Ever. (I wonder if this is a new world record?)

Today, Nature Communications desk-rejected our paper 2 hours and 1 minute after we submitted it.


Sunday, January 26, 2014

Pictures and Vampires in Paris

Here are my initial pictures from Paris from today and last night. (Most of them are from today.)

Notice the Theatre du Chaos on Rue Henri Poincaré. I approve! The street is a dinky little residential street, and I was very pleased indeed to see this local theatre in one of its corner. It made me really happy.

I just noticed on Google Maps that Paris has a Vampire Museum not far from Rue Henri Poincaré. Too bad I only noticed that after walking all the way back instead of when I was there a couple of hours ago... I think there is a decent chance it's not open today anyway, but let's see if I can figure out from here when it's open. You can also find some information on another page from the Atlas Obscura website

And here is how to make an appointment to visit the museum (it's by appointment only). I have to admit that I am very tempted to do try to make one, but I would rather look around in there without talking to someone while I am doing it, so I'm likely not going to do it. This is the type of thing I'd like to go and do with a friend. :)

Saturday, January 25, 2014

What Happens in Paris Stays in Paris

I am making my first ever trip to France (aside from a few hours in an airport for a layover). I am adding a new country early in 2014, and I have at least one more new country for me on the docket for this year.

I am going to Paris to visit Vittoria Colizza at EPIcx Lab.

Friday, January 24, 2014

Wednesday, January 22, 2014

LinkedIn Fail

LinkedIn Fail: Today I got an e-mail notice suggesting that I should congratulate one of my connections on a professional milestone: "[first name] [last name] is celebrating 7 years at [Institution of Higher Learning]"

Dear LinkedIn: You do realize that that means that this person is still a graduate student at that place, right?

For what it's worth, I would laugh at this out of sheer perversity even if that anniversary were mine.

Tuesday, January 21, 2014

Saturday, January 18, 2014

Additional Translation Fails

Translating can be hard, and sometimes things don't quite go right. You can find many of the signs from the above website in one of my previous posts. However, many of the "new" ones are also glorious. It's hard to say which are my favorites in the new list, because several of them are awesome. For example, 'soup for sluts' and a fire extinguisher being labeled as hand grenades are simply excellent! (Those are both on the other list as well.)

(Tip of the cap to Iain Macmillan.)

Friday, January 17, 2014

Pictures of a Bubble Freezing

Here are some pictures of a bubble as it freezes. Awesome!

(Tip of the cap to I Fucking Love Science.)

20 Years Ago Today

Today is the 20th anniversary of the Northridge earthquake, which occurred during my senior year in high school.

It was early morning. I heard the neighborhood dogs all go nuts, then felt everything and saw a wall-covering bookshelf spew many of its books, and was very happy that it occurred while I was in bed instead of next to the bookshelf.

Then I went back to bed.

It's All in the Name

Some scientists have names that reflect what they study. A recent one to make a public appearance is K. Cheeseman, who just published a paper on cheese-making fungi. In this vein, I should also point out that one of my Somerville College colleagues is Charlotte Potts, who studies Etruscan and Italic archaeology and art.

Thursday, January 16, 2014

1981 News Report on The Internet

Long before the internet was for porn, the "two to three thousand" residents of San Francisco who owned home computers had the chance to download text from newspapers.

Anyway, watch this old news report from 1981 on electronic newspapers. It is awesome in several respects.

(Tip of the cap to Elizabeth Leicht.)

RIP Russell Johnson (1924-2014)

Russell Johnson, who starred as The Professor on Gilligan's Island, has died at the age of 89.

I briefly tried to find via Google a commercial that Johnson did a couple of decades ago in the guise of The Professor. (At some point in the commercial, he becomes rather indignant: "First they take me out of the theme song and now this!")

Claymation Video for "Re: Your Brains"

Here is a really cool claymation video to go along with the song "Re: Your Brains".

Wednesday, January 15, 2014

Dodgers Sign Kershaw to 7-Year Contract Extension!

The Dodgers have signed Clayton Kershaw to a very lucrative 7-year contract extension. Yay! Kershaw is the best pitcher in Major League Baseball, and I am very glad that he'll be ours for quite a while. (Given how long-term contracts --- especially to pitchers --- can blow up in a team's face, check back with me on this in a few years. For now, though, I am happy.)

Wednesday, January 08, 2014

New 2014 Hall of Famers

The Baseball Hall of Fame announcement has now occurred, and Greg Maddux, Tom Glavine, and Frank Thomas have made it to the Hall! They are richly deserving, and they join the richly deserving trio of managers (Bobby Cox, Tony La Russa, and Joe Torre). Also note the distinctively Braves-themed set of inductees, and it is nice to see Cox, Maddux, and Glavine go in together.

It looks like Biggio didn't quite make it this year (despite estimates based on 'exit polls' that he would be just over the 75% bar). Lame. Incredibly lame. We'll see what the percentages look like once those are out. From the exit polls, I know that at least one person didn't vote for Maddux, which is also incredibly lame.

A couple of hours ago, I wrote the following comments on Buster Olney's most recent article that focuses on the Hall of Fame, performance-enhancing drugs (PEDs), etc.

(1) The big increase for Bagwell (and others) from year 1 on the ballot to year 2 presumably includes a significant effect of many people distinguishing between a "first-ballot HOFer" and merely "an HOFer". People can argue about whether there should be such a distinction --- I think it's a reasonable one --- but many writers do seem to vote that way, so that is an important factor when considering subsequent increases in vote percentages. That effect can only occur once.

(2) I am fine with known PED users being in the Hall, but I would like a statement of it (if there is hard evidence) on their plaques. For example, McGwire's case (which would admittedly be more clear cut than most in this respect) could include a sentence "Admitted to using ... in [year he admitted it." That way, these people are in the Hall as part of history, and the uglier part of their history is _also_ being documented. Visitors to the Hall will read this and can judge the player for themselves. The Hall can --- and should --- be used to inform.

Update: As reported in this article, Biggio fell only 0.2% shy of being elected. Given the number of voters, this should imply that he missed by only 1 or 2 votes. I guess he'll get in next year, but (a) ouch and (b) he should already have been elected in his first year of eligibility. After Biggio, it looks like the next highest candidate was Mike Piazza with 62.2% of the vote (though he was projected to be in the high 60s based on an exit poll that had tabulated just over 1/3 of the estimated HOF ballots). Jack Morris was at 61.5% in his 15th and final year on the ballot. I'm glad he didn't make it, as he doesn't deserve to be in the HOF, and his tally presumably went down because the HOF ballot is exceptionally crowded this year. A crowded ballot is a continuing theme of HOF elections that won't go away any time soon.

Update 2: The website above now has the vote totals. It looks like there were 571 ballots in total. Based on that, Biggio missed by 2 votes. Jeff Bagwell, Tom Raines, and many others unfortunately saw their percentages go down (presumably due to the crowded ballot). Rafael Palmeiro failed to achieve the 5% mark to remain on the ballot next year. Sammy Sosa received enough votes to remain on the ballot in 2015. Next year will be Don Mattingly's 15th and final year on the ballot. I believe that his largest vote total was in his 1st year, and his support has been going down since then. He did have a few brilliant years, but injuries curtailed his performance and cut his career very short, and he doesn't deserve to be enshrined in the Hall.

One Does Not Simply Walk Into Los Angeles

Not only does nobody walk in LA, but it also seems that one does not simply walk into Los Angeles: a climate model applied to Middle Earth has found that Mordor's climate is basically like that of Los Angeles.

(Tip of the cap to Physics Today.)

It's Official: Hell Has Frozen Over

Yup, that's right: Hell has frozen over because of the polar vortex that is sweeping (part of) the nation. Perhaps that's because it's in Michigan?

(Tip of the cap to Andy Sayer.)

Tuesday, January 07, 2014

Rodman Vs. Kim: One on One

The java mini-gam, Rodman Vs. Kim: One on One is just too funny. It has a combination of snarky commentary and allusion to a game from bygone times that I simply love. (I never did like that old game or its sequel, but I am highly amused by the reference to it amidst the current basketball diplomacy. I just find this whole thing to be bizarre more than anything else.)

(Tip of the cap to Travis Hime.)

Epigenetics and Enhanced Brain Connectivity from Reading a Good Book

These are actually from two separate series of studies --- and the former technically is referring to a single study --- but they have in common that they're both really interesting and both with strong connections to neuroscience (which of course has tons of cool things up its sleeves).

Epigenetics sounds like science fiction, and it includes behavioral epigenetics, which refers to genetic experiences that an animal (including humans) can have based on experiences of their ancestors. (You may be interested in the wikipedia entry on epigenetics.) It is also easy to see why this is a controversial subject.

Meanwhile, it was demonstrated in a recent study that brain connectivity (in the resting state) can increase for 5 days after reading an engaging novel. The popular article to which I have linked indicates that "function" increases, but it is a leap to go from the conclusion of increasing connectivity (which one can measure, e.g., using tools from network analysis) to that of increasing function. I only looked at the paper very briefly, but from a scientific perspective I am currently much more comfortable claiming the former than the latter. Note, however, that this is very consistent with loads of anecdotal evidence and what many people have claimed about their own reading experiences for a very long time. I view it as somewhat akin to exercise and do think the strong form of the big-picture conclusion to be pretty damn likely (and the result is both sensible and intuitive), but the bar for scientific comfort naturally must be very high (and obviously is much higher than what intuitively I believe to be valid).

(Tip of the cap to Stephen Heise for neurological tips on reading a good book and to Susan Baldry Dole --- Stephen's friend on Facebook --- for posting the link to the popular article on behavioral epigenetics.)

Weighed Random-Number Generators, Sports Commentary, and Dungeons & Dragons

Yup, there is a lot of truth to this xkcd.

I probably blogged about this xkcd panel before, but anyway here it is again. On a slightly related note, take a look at Slate's coverage of Aaron Clauset's (and collaborators) recent work on sports.

(Tip of the cap to MoMath [The Museum of Mathematics].)

Demotivational Poster... Now With Actual Demotivation

This Demotivational Poster is not only brilliant, but (unlike most posters on the Demotivational Poster site) it includes actual demotivation.

Caltech Strikes the Rose Bowl... Again

Caltech has struck the Rose Bowl again in a prank that also harkens back to the classic Hollywood sign prank of 1987.

On this website, Caltech highlighted several of the most famous pranks in its history (as compiled by the Legends I, II, and III books).

Monday, January 06, 2014

What Happens in the Bay Area Stays in the Bay Area

I have made it to Sunnyvale, where I am staying with friends. I'll be hanging out with several of my peeps who live in various parts of the Bay Area! (And there will also be gaming!) Huzzah!

Charmin: Always an Asgardian

I love this ad for Charmin toilet paper. Too bad it got pulled so quickly...

(Tip of the cap to the Demotivational Poster blog.)

A Fun Scientific Name (And Other Similarly Fun Names)

Death match: Macaca fuscata fuscata versus Yo Yo Ma versus Boutros Boutros Ghali. And, yes, I am thinking of a certain Seinfeld soundbite right now. A certain album by The Police also came to mind.

Some scientific disciplines get so many of the fun names...

My Undergraduate Lecture Course on Networks

My lecture course on networks makes its debut as an undergraduate course in our new term (Hilary Term 2014).

I have some more information to include, but I am going to try to ignore such things for another week or so, but I have included a hyperlink to the official course synopsis. Normally, I would use a title like "Useful Links" for relevant websites, but for this course it's going to have to be "Useful Out-Edges". That's just the way it is.

By the way, I previously taught this module as an ad hoc course (2 years ago) and also for Masters students (last year). This term marks its debut as part of the undergraduate curriculum. 38 students are enrolled in my course, which is quite a strong debut (most debut courses only have a handful of students). I'll try not to ruin their lives.

Sunday, January 05, 2014

The Importance of Being Curious

One of the attendees of Dynamics Days 2014 (I am not at the conference) posted a picture of one of the speaker's slides. This slide is paraphrasing Richard Hamming and has the following three questions: (1) What are the important problems in your field?; (2) What important problems are you working on?; and (3) Why are the answers to (1) and (2) different?

I reject what appears to be intended by the speaker's take-home message on that slide.

Here is my two-part answer to question (3):

(a) You should work on what damn well interests you --- forget about whether it's important. If both are true, great! But you work on whatever interests you.

(b) From a practical perspective, you make progress where you have ideas of how to make progress. If that includes what you consider to be the most important problems, so much the better.

Grants can fund important problems, but not every problem one works on is funded by a grant. To me, science is about pursuing things for curiosity, and I need no other reason for choosing what problems I work on.

Friday, January 03, 2014

"A Method Based on Total Variation for Network Modularity Optimization Using the MBO Scheme"

One of my papers just came out in final form. Here are the details.

Title: A Method Based on Total Variation for Network Modularity Optimization Using the MBO Scheme

Authors: Huiyi Hu, Thomas Laurent, Mason A. Porter, and Andrea L. Bertozzi

Abstract: The study of network structure is pervasive in sociology, biology, computer science, and many other disciplines. One of the most important areas of network science is the algorithmic detection of cohesive groups of nodes called "communities." One popular approach to finding communities is to maximize a quality function known as modularity to achieve some sort of optimal clustering of nodes. In this paper, we interpret the modularity function from a novel perspective: we reformulate modularity optimization as a minimization problem of an energy functional that consists of a total variation term and an l_2 balance term. By employing numerical techniques from image processing and l_1 compressive sensing --- such as convex splitting and the Merriman-Bence-Osher (MBO) scheme --- we develop a variational algorithm for the minimization problem. We present our computational results using both synthetic benchmark networks and real data.

The really cool thing about this paper is what it does for "technology translation". We reformulate the modularity quality function in a way that relates it to compressive-sensing-like problems. One can thereby adapt methods from the latter to use for modularity optimization. One of the best compliments that we have received about this paper thus far occurred right after posting it on the arXiv: Somebody from the image-processing community told us that our paper was written in a language such that he could finally understand what people were doing with graphs. Given the goals of the paper, that was exactly what I wanted to hear!

My Research is Magically Delicious!

One of these years, I am going to have the opportunity to include something like this in one of my papers:

"In Fig. 1, we show plots for parameter values a = 1 (pink hearts), a = 2 (yellow moons), a = 3 (orange stars), a = 4 (green clovers), a = 5 (blue moons), and a = 6 (purple horseshoes)."

And rest assured that I will do this.

(For those of you not in the know, this comes from the cereal Lucky Charms.)

Update: As Rachel Gray points out, I swapped the ordering of orange and yellow. As John Baker points out, the blue marshmallows at the time were diamonds rather than moons. It's good to get things straight now so that the published version is accurate. :)

Wednesday, January 01, 2014

Dogs Have a Preferred Pooping Orientation

Yup, you read that correctly: apparently, dogs prefer to take a dump in roughly a north-south orientation. It's science --- and also a strong contender for an Ig Nobel Prize.

(Tip of the cap to Julius Su.)

Isaac Asimov's 1964 Essay on Life in 2014

In 1964, Isaac Asimov wrote about life in 2014 via a visit to the 2014 World's Fair. His predictions were rather good on several counts.

(Tip of the cap to Maria Satterwhite.)

Happy 2015!

I hope that you and yours have a happy and healthy 2015!

Oh wait... is it too soon? ;)