Link communities R package

A while ago, I wrote about Rob Spencer over at Scaled Innovation‘s implementation of the algorithm for detecting link communities. Today, I am happy to report on another exciting development for the alorithm. Alex Kalinka from the Tomancak lab at the Max Plank Institute (MPI-CBG) has written a great implementation in R, called linkcomm. It is now up on CRAN:

http://cran.r-project.org/web/packages/linkcomm/index.html

While everything is excellent, the graphics are particularly beautiful – much prettier than our own visualizations – check out the colored link dendrogram plot (from the CRAN website)

And the spatial network layout options are great as well; the various community visualizations are simple, elegant, and very pretty:

The panel on the left shows a 'Spencer circle' layout, while the panel on the right shows a Fruchterman-Reingold layout. From the linkcomm documentation.

In addition, there are many neat features. For example, linkcomm allows you to visualize sub-communities by themselves. Alex has also published an Application Note in Bioinformatics about the implementation, so take a look if you’re interested:

http://bioinformatics.oxfordjournals.org/content/early/2011/05/19/bioinformatics.btr311.abstract (open access).

We also link to the package from our link communities download page.

Tu Vuò Fà L’Americano

I’m excited to leave Boston for a bit to participate in ARS’11: The Third International Workshop on Social Network Analysis, Collaboration Networks and Knowledge diffusion: Theory, Data and Methods. It takes place in Naples, Italy this week, and the speaker line-up looks exciting (despite the fact that they invited me) [1].

Here’s a bit of text from the official description:

ARS’11 International Workshop is a follow up to two very successful previous editions ( ARS’07 and ARS’09) and will be held on June 23-25, 2011 in Naples (Italy).
Collaboration networks attract a lot of attention in many fields and are considered a key element in the advancement and dissemination of knowledge in scientific as well as in socio-economic domains. The workshop has the objective of presenting the most relevant results and recent developments in the areas of Collaboration Networks, Innovation Networks and Knowledge Diffusion.

The workshop also aims to deepen existing scientific cooperation between Social network analysts, to establish new cooperation between researchers, and to provide a forum for exchange of ideas among them.

The workshop topics include:

  • Collaboration theory
  • Analysis of innovation networks in economics environments
  • Sources of collaboration data
  • Social Network Analysis methods for collaboration data

Notes:

[1] I stole the idea for this elegant, faux self deprecating plug from Aaron Clauset’s blog.

Back in the USA

I’m delighted to report that I’m back in Boston for the summer. The next couple of days (May 31st and June 1st), I’ll be attending the Interdisciplinary Workshop on Information and Decision in Social Networks, which looks to be really exciting.

And for the next couple of months I’ll primarily be at the Center for Complex Network Research at Northeastern University. So do look me up if you’re in town.

Whitman

I recently came across the following Whitman poem:

When I Heard the Learn’d Astronomer

When I heard the learn’d astronomer,
When the proofs, the figures, were ranged in columns before me,
When I was shown the charts and diagrams, to add, divide, and measure them,
When I sitting heard the astronomer where he lectured with much applause in the lecture-room,
How soon unaccountable I became tired and sick,
Till rising and gliding out I wander’d off by myself,
In the mystical moist night-air, and from time to time,
Look’d up in perfect silence at the stars.

This poem beautifully captures the feeling that when you quantitatively analyze something (be it Nature or literature), it often feels like some of the initial beauty and magic of the phenomenon disappears [1].

As a scientist, the position that a scientific viewpoint somehow diminishes ‘beauty and magic’, is something you run into once in a while, so it’s good to have an answer. My own reply is that while it’s true that analysis tends to strip many phenomena of some kind of immediate (and often trivial) appeal, digging deeper almost always reveals new layers of beauty.

I had developed some examples to go along with this argument, based on my own experiences, but a couple of years ago, I watched an interview with Richard Feynman [2], and his answer is so much better than mine that I’ll leave the rebuttal of Whitman to him:

Postscript

After writing the above, I googled the poem – I guess I should have done that before writing – and found a lot of fun/interesting discussions. One commenter pointed to a modern version of Whitman’s standpoint courtesy of the Insane Clown Posse (from Miracles, 2009):

Water, fire, air and dirt
Fucking magnets, how do they work?
And I don’t wanna talk to a scientist
Y’all motherfuckers lying, and getting me pissed.

Check out the pages below for more. Particularly the comment thread for the first post is a treasure trove:

References

[1] My own favorite example is that – when conditions are good – there are 9110 stars visible to unaided human eye. I’m pretty sure that bringing up this factoid could ruin a romantic evening under the stars. Anyway, I’m rambling.

[2] From the BBC program Horizon. Interview recorded in 1981 – the whole thing is highly recommended.

NetSci 2013: Venue and Dates

It’s time to get out your pencils and mark your 2013 calendars:

NetSci 2013 will take place June 3rd – 7th at the new The Royal Library (the Black Diamond) in Copenhagen, Denmark.

Along with fellow organizing committee members Petter Holme, Sebastian Bernhardsson, and Alan Mislove, I’m excited to announce that we’ve secured an incredible venue for NetSci 2013.

In order to provide non-Copenhageners with a sense of how amazing this space is going to be, I’ve included a few photos:

And the interior is spectacular as well:

And the venue is, of course, just the beginning – we have many more pleasant surprises planned for NetSci 2013. Stay tuned for updates.

Image credits (in order of appearance):

  • http://www.flickr.com/photos/snorri/158763944/
  • http://www.flickr.com/photos/heilemann/6506528/
  • http://www.photosight.org/photo.php?photoid=92235
  • http://www.flickr.com/photos/16nine/2679547688/
  • http://www.photosight.org/photo.php?photoid=81798
  • http://www.flickr.com/photos/janlykke/3973906292/

Conference: Applications of Network Theory

Just a quick advertisement for an exciting European conference co-organized by my fellow NetSci 2013 organizer Petter Holme. It takes place in Stockholm, Sweden in early April. The speaker line-up looks pretty good, despite the fact that they invited me [1].

Conference on Applications of Network Theory

Date & Location: 7 – 9 April 2011 at AlbaNova in Stockholm Sweden

Organizers: Peter Minnhagen (Umeå) and Petter Holme (Umeå)

Invited speakers:
Lada Adamic, University of Michigan
Albert-Laszlo Barabási, Northeastern University
Jordi Bascompte, Consejo Superior de Investigaciones Cientificas
Sebastian Bernhardsson, Niels Bohr Institute
Vincent Blondel, University of Louvain
Aaron Clauset, University of Colorado
Sergey Dorogovtsev, University of Aveiro
Birgitte Freiesleben de Blasio, University of Oslo
Thilo Gross, MPI Dresden
Kimmo Kaski, Aalto University
Beom Jun Kim, Sungkyunkwan University
Renaud Lambiotte, FUNDP
Vito Latora, Catania University
Sune Lehmann, Technical University of Denmark
Fredrik Liljeros, Stockholm University
Jukka-Pekka Onnela, Harvard University
Juyong Park, Kyung-Hee University
Veronica Ramenzoni, MPI Nijmegen
Martin Rosvall, Umeå University
Jari Saramäki, Aalto University
Bo Söderberg, Lund University
Brian Uzzi, Northwestern University
Jevin West, University of Washington

Description: The main idea is to convene key world-class researchers on complex networks and let them interact freely with the Nordic groups interested in the area. The program will be divided into four thematic areas: biological networks, general network theory, technological networks, and social networks. Many of the intended participants are interested in several of these points. Much progress in network theory has been made by analogies from different fields, and complex-network researchers value this, therefore we believe such a schedule will not seem unattractive to participants. In addition to the regular schedule during the Nordita program, of one or two talks per day, we will arrange a more intense, three day workshop April 7-9. One purpose of this workshop, is to attract researchers not able to stay the extended time required by the program.

This workshop is being organized as part of a long-program on networks at NORDITA.

Registration deadline: 15 March 2011 or when 70 participants have registered.

Footnote

[1] I stole this last charming and self deprecating sentence from Aaron Clauset’s blog.

Tell a Story!

Although I’m trying to cut down on my podcasts use — to see if a bit of mind-wandering might be good for my brain [1] — I still allow myself to listen to podcasts to alleviate the pain of some of the dreariest of chores (e.g. cleaning the bathroom). On those occasions I’m currently working my way though the podcast RadioLab‘s excellent back catalog [2].

While always interesting and informative, the RadioLab podcast I listened to yesterday is worth a special shout-out. The podcast featured a simple recoding of the speech co-host Robert Krulwich was invited to give at CalTech’s commencement back in 2008 (you can listen to it here). During the passionate (and funny) speech, Krulwich argues for the value of science communication; not just in general, but also when people ask you about your work:

But because this is your day, and because this person loves you, or because he can’t think of anything to say after “hi,” he asks about your work. And to make it still more interesting, let’s assume that if you explain to this person what you’ve been working on, you might have to use certain words like “protein” or “quark” or “differential” or maybe “hypotenuse.” And if you do, he is going to listen to you very, very politely, but upstairs, those words are going to mean not a whole lot. [...] So … here’s my question: When you are asked, “What are you working on?” should you think, “There’s no way I can talk about my science with this guy, because I don’t have the talent, or the words, or the patience to do it—it’s too hard, and anyway, what’s the point?” [3]

Now, Krulwich argues (and I wholeheartedly agree) that it’s important to come up with a good answer to this question.

The ‘science story’ is a weapon against the ‘nut-case story’

So the podcast is great, and you should be listening to it, rather than reading this. But just in case you’re not convinced, I’ll highlight a few of the elements I think are most important. First of all, Krulwich has a good argument as to why science communication is important. It’s not because there’s an intrinsic value in enlightening the spirit of man. It’s because reason is at war with all sorts of irrational/crazy causes:

[E]ven if it’s hard to explain, even if you know they don’t really want to hear it, not really, I urge you to give it a try. Because talking about science, telling science stories to regular folks, is important. In a way, it’s crucial. Scientists need to tell stories to nonscientists, because science stories—and you know this—have to compete with other stories about how the universe works, and how it came to be. And some of those other stories—Bible stories, movie stories, myths—can be very beautiful and very compelling. But to protect science and scientists—and this is not a gentle competition—you’ve got to get in there and tell your version of how things are, and why things came to be.

So Krulwich makes the excellent point that to most people a story is just a story. And a science-story is no different from a religion-story. The only way to defend science is to tell better stories; to tell stories that are more compelling — also on an emotional level.

Are metaphors bad?

The other element in the talk that I wanted to highlight is the Krulwich’s discussion of the use of metaphor and (potential) lack of precision in science communication:

And yet many scientists remain wary of metaphors, of adjectives [...] But the job we face is to put more stories out there about nature that are true and complex—not dumbed down—and that still have the power to enthrall, to excite, and to remind people that there’s a deep beauty, a many-leveled beauty in the world. What scientists say is hard-won information, carefully hewn from the world. It’s not the offhand opinions of a tribe of privileged intellectuals who look down on everybody. It’s my sense that if more scientists wanted to, they could learn how to tell their stories with words and pictures and metaphors, and people would hear and remember those stories and not be as willing to accept the other folks’ stories. Or at least there’ll be a tug of war, and I think that the science stories will, surprisingly, very often win.

To me, the key words here are ‘true and complex’ coupled with ‘a deep beauty’. It’s true that you can’t really explain measurement in quantum mechanics to someone who doesn’t know what an eigenvalue is, etc. But you can still convey the absolute weirdness and wonder of the laws that govern all things quantum.

Science itself should not be dominated by metaphor or vagueness; science is about incremental discovery of complex relations. This process of discovery is built on the precision and clarity of scientific colleagues and the giants on whose shoulders we stand [4]. But that doesn’t mean that you shouldn’t spin an entertaining yarn to explain and motivate your research. So tell a story! Just remember to stay clear of condescension and to stay true to the complex reality that underlies your work.

Notes

[1] Steven Johnson’s excellent new book Where Good Ideas Come From suggests that a bit of mind-wandering is one way allow ideas to ‘bubble’ to the surface (if I remember correctly). I’m not sure that it works, but I guess that a break from the usual near-constant stream of input can’t be a bad thing.

[2] In case someone’s interested, my other favorite podcasts are (1) the absolutely unmissable Mark Kermode and Simon Mayo’s Film Reviews which features the best film reviews in the universe (sorry @ebertchicago), (2) NYT’s Book Review, and (3) the classic This American Life.

[3] Text here and in the following was copied from the official transcript. Download it here [pdf].

[4] Some attentive readers may have noticed my subtle reference to Newton’s famous metaphor (which, according to Wikipedia, doesn’t really originate from a Newton quote).