Month: July 2011

Norwegian terror

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A terrible act happened yesterday in Norway with at least 17 dead.

Several terror experts were keen to speculate that the perpetrator was associated with islamism. Why on earth? Why would a islamic terrorist first blow up a bomb in central Oslo and then travel a fairly long distance to a small island? Wouldn’t it be easier to “stick” to Oslo? The people on the island was socialdemocrats. It should have seemed more likely that it was a rightwing lunatic.

In the DR program Deadline former manager in Danish intelligence Hans Jørgen Bonnichsen put up a much more balance comment mentioning rightwing terrorism and Oklahoma City.

…And after midnight the public finally got to know the person the police suspected. If the media and the police are correct the perpetrator is an armed nationalistic christian conservative who likes hunting and World of Warcraft among other things.

The Christian Science Monitor had around 4:00 my local time 23. july still a “related stories” infobox in connection with an article about the Utøya shooting. The infobox mentioned “Terrorism * Islamism * Shootings”. I wonder if they will correct that tomorrow to “Terrorism * Christianity * Shootings”?

The youth organisation of the Norwegian social democrates has had their worst experience. The bomb alone is the worst in Scandinavia. How can we avoid it? Apparently, the perpetrator owned a firm that grew vegetables where he had easy access to fertilizers. Is it possible to better track and control the use of fertilizers? Better gun control?


Correction: Just after I submitted this I saw that “least 17 dead” was a gross understatement. The police now says at least 80 killed on Utøya!

Did Ward Cunningham invent linkify prior to Apple’s patent?

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Through my The Tweeted Times I was alerted to the recent issue of Apple’s patent attack
on HTC and Google Android described in Adrian Kingsley-Hughes’ ZDNet article as a “massive patent blow”. Here in July 2011 HTC was found to have infringed two of Apples patents, according to Bloomberg.

One of the two patents in question is U.S Patent 5,946,647 (see also at Google patents). I found a good detailed introduction to the patent and case at FOSS Patents. The patent is filed February 1st, 1996 and has the date August 31st, 1999.

The particular software patent deals with identifying structured elements in a text so it can be linked to “actions” – if I understand the patent correctly. These structured elements could be “a phone number, post-office address, e-mail address, and name.” Identifying the phone number could result in a program implementing an action such as “dialing a number identified by the telephone number grammar or placing the number in an electronic telephone book”. With my quick scan of the patent I couldn’t see that identification of Web links was mentioned.

In Android a related functionality seems to be implemented with the so-called Linkify. As far as I can see the functionality allows you to identify email addresses, street addresses, phone numbers and web links.

It occurred to me that wikis do identification of structured elements: weblinks and CamelCase, – but usually wikis do not identify phone numbers, names and street addresses. Identification of web links are associated with clickable links (well, of course). CamelCase are either associated with links to an existing page or construction of a new page. Ward Cunningham‘s wiki goes back to March 25, 1995. I was not familiar with that early system, but I suppose it had link extraction with regular expressions. So hasn’t Cunningham come up with a linkify functionality for web links already in 1995?

When I was visiting NEC Research Center in Princeton in 1999-2000 several researchers were working with extracting structured elements from texts such as emails, scientific papers and web pages. Andries Kruger constructed a system that would identify names and dates from scientific call for papers. The system is described in DEADLINER: Building a new niche search engine. Kurt Bollacker, Steve Lawrence and C. Lee Giles were working on the CiteSeer system that extracted authors, titles and years among other things from scientific papers. This is described in CiteSeer: an autonous Web agent for automatic retrieval and identification of interesting publications. I also had a go on regular expressions for extraction of structured elements. Most recently I have been working on extracting brain coordinates from neuroscience papers. If you press the “Extract: Talairach coordinates from linked PDF” link on a Brede Wiki page there is a regular expression going over the text in a PDF so individual brain coordinates can be linked up to specialized neuroscientific searches. Similar extraction is happening in large-scale in Tal Yarkoni’s NeuroSynth database, see this entry for an example extraction rendered nicely on a MRI brain scan.

The 2000th article on the Brede Wiki became ‘Left dorsal anterior cingulate cortex’

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The article on Left dorsal anterior cingulate cortex on the Brede Wiki became number 2000. There are presently 360 other pages on the wiki about brain regions.
The left dorsal anterior cingulate area corresponds to the left part of Brodmann area 32.
When you search PubMed on left dorsal anterior cingulate reviews you only find one: Increased Anterior Cingulate and Caudate Activity in Bipolar Mania which is actually an original study with an added table summarizing previous neuroimaging studies on mania in bipolar disorder. Searching more broadly on dorsal anterior cingulate reviews neuroimaging finds that, e.g., it is apparently associated
with cognitive demand.

Brave new world: Japanese popstar is just computer graphics

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The story has been around for some weeks in the international media such
as Daily Telegraphy, but now apparently just reached mainstream Danish news: Aimi Eguchi, member of the Japanese girlband AKB48, is a computer graphics creation amalgamated from six other members of the band.

The computer graphics is awfully well-done. It is difficult to spot the
artificial creation from the video.

Clown: reflection on and a Bayesian analysis of a Danish comedy

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In December 2010 the Danish pseudo cinéma vérité sitcom Klovn (English: Clown) made the transition to silver screen with the å-movie Klovn: The movie, and with great success ticket-, award– and critical-wise, – and one American(?) blogger even referring to the Klovn-duo as part of The Danish cinema trinity – the two others being Susanne von Bier and Lars Trier. Now the movie is scheduled to have its North American premiere in Montreal July 22th 2011 at the Fantasia International Film Festival, and we have, what I believe, the first longer non-Danish English review by one Simon Howell. Previously the movie has also roamed other Nordic countries: Iceland, Norway and Finland (Swedes, I am told, have no humor so it hasn’t been running there apparently).

In Klovn we get embarrasment comedy coupled with a half-serious story on maturation with the issue of harrassment and a realistic dialogue, nakedness and setting in camp school and nature, – some elements reminding me of Nils Malmros 1981 film “The Tree of Knowledge“. In Malmros’ case the realism is gained by closely directing amateur actors and paying particular attention to the Aarhus prosody. In Klovn the realism comes from the Curb Your enthusiasm-inspired improvised dialog and perhaps a Riget-inspired non-imposing discontinuous editing and handheld camerawork. Reviewer Simon Howell further tells us that Klovn shows elements of Apatow‘s manchild maturation movies (which I haven’t seen or heard of before) as well as “the debauched bro humor of 2009 film The Hangover” (another one that I didn’t know of). I had to look up what “debauched bro” meant: I think it might mean something like Danish drengerøv.

I wonder how the self-exposuring de-tabooing humor sits with an American audience? Could this disinhibited piece start a new crisis as Muhammed Cartoons did or scale the Lars Trier nazi Cannes controversy? The “south of the waist line” and “expose everything” Freudian tsunami comedy in this “drengerøvs”-movie portraying self-promoting immature males can generate some mixed attitudes. Although Danes have generally been positive, negative response are found here and there, e.g., in the conservative news Berlingske comment section where one woman stated she had never seen more pervert entertainment. Care for a taste the American blogger suggests one (I would say) very innocuous (for the audience!) clip from the TV-series.

Are we dealing with a movie only for males? IMDb rating voters for the Klovn TV-series shows a much larger proportion of male compared to female voters (7% female of total). The same pattern occures for the movie (8% female votes). The Shawshank Redemption reaches 13% female voters and Amélie 23%. I theorized that female reviewers rate the movie lower than males.

So with the help of a small poster on Odense train station listing many reviews I tracked and I went through the movie reviews noting the gender of the reviewer and the number of stars given. In Denmark you can usually give up to six stars. However, comedies are not allowed to get six stars unless they get special permission, so for Klovn all reviewers either gave the movie 4 or 5 stars. That is, we have a two-by-two problem: female/male-times-four/five. And what is then more natural than to use the Bayesian version of test with the hypergeometric statistical distribution on the two-by-two categorical contigency table to examine if female reviewers on average give Klovn a lower score than male reviewers. How do we do that? Luckily, prominent statistician Andrew Gelman has suggested using two parallel binomial distributions and one of his blog readers Bob Carpenter implemented a simulation in R. Below are some of the data listed after I lost the original data:

Review Publication Gender Rate Link
Iben Albinus Sabroe Berlingske F 4 link
Birgitte Grue BT F 4 link
Morten Dürr Børsen M 4  
Frederik A. Vandrup M 4 link
Henrik Jonsen Citylife M 5 link
Per Juul Carlsen DR P1 Filmland M 5 link
Kristian Ditlev Jensen Ekko M 4 link
Henrik Queitsch Ekstra Bladet M 5 link
Rikke Rottensten Femina M 5 link
Bjørn Kryger Larsen M 5 link
Søren Ildved Filmz M 4 link
Simon Staun Fyens M 5 link
Holger Madsen Jydske Vestkysten M 5 link
Palle Schantz Lauridsen Kristeligt Dagblad F 5 link, (star link)
Nanna Frank Rasmussen F 5 link
Christoffer Dvinge Onfilm M 4 link
Sofie Rosendahl Q F 5 link
Erik Jensen Politiken/iByen M 5 link
Jonas Varsted Kirkegaard Information M ? link
Nikolaj Mangurten Lassen Weekendavisen M ?  

Several bloggers have reviewed the movie: A woman giving 3/6, male giving 1/4, woman giving 4/5, male giving 5/5 and a blogger of too me unknown gender giving 6/6. We will ignore these.

In the main data set I find 8 out a total 13 male reviewers gave ‘5’, while 3 out of a total 5 female reviews gave ‘5’. The Bayesian analysis results in a fairly symmetric distribution, where males are not very much more likely to give a higher rating than females: There is only a 50-51% change that males are more likely to rate the movie higher than females using the hyperprior 0 for the beta distribution.

If you care to read more about the Klovn-phenomenon there is a Danish research article hypothesizing Klovn to be inspired from ideas of Goffman, Zizek and Sloterdijk and introducing the article with (my translation attempt):

“‘Klovn’ is read as a portrait of a radical postmodern condition,
characterized partly by the porous construction of identity of the agents through fragmented social games, partly by the dissolving of the reality-references of the series, where distinctions between true/false, good/evil, masculine/feminine are substituted by a reflexion over the aesthetic seduction effects of the signs. ‘Klovn’ shows these elements in the postmodern with a satirical, ironic distance.”

Auch! I have misunderstood it then. I thought the Klovn-phenomenon was a sincere self-satire on a post-postmodern wannabee.

(conflict of interest: I received a free movie ticket)

(Ups 14 December 2011: The alert reader would have discovered that I mislabeled “Palle” from Kristeligt Dagblad as a female. He is indeed a male person, and since he gives 5 a rerun of the analysis changes the results. It now shows that it is around 70% likely that a male gives a higher grade than a female! I am sorry, Palle)

Kempton is out and Brede Wiki is down

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Matthew Kempton‘s and his coauthors’ article with a large meta-analysis of structural neuroimaging in Major Depressive Disorder is out in the current issue of Archives of General Psychiatry. It is called Structural Neuroimaging Studies in Major Depressive Disorder: Meta-analysis and Comparison With Bipolar Disorder.

The data from the paper is available from the Google Sites Major Depressive Disorder Neuroimaging Database (MaND). Now you will see on this page there is a link to the Brede Wiki’s MaND page as we have been setting up the data on the Brede Wiki with a suitable real-time meta-analysis. Unfortunately the server with the Brede Wiki and the online meta-analysis of Kempton’s data crashed yesterday with a nasty SCSI error after a reboot: “Wide Negotiation failed. Please check your SCSI cable.” So you cannot see the data on the Brede Wiki. It will take me several days to get a new server set up.

The server has been running for around 10 years with no hardware problems. Either it is the recent Lyngby rain storm with thundering that got it into troubles or the server acquired an acute stage fright in front of the prominent Archives of General Psychiatry audience.

ReaderMeter: readership analytics for scientists

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For those up to social web metrics here is yet another one: ReaderMeter! It is based on bookmark data from the research paper sharing social web site Mendeley and ReaderMeter computes a bookmark-based h-index to evaluate one’s readership impact. Thus it is mostly for scientists.

The ReaderMeter service is constructed by Dario Taraborelli who also co-organized the altmetrics workshop recently held in Koblenz. He is now at the Wikimedia Foundation and furthermore co-organizes the WikiViz Wikipedia visualization challenge.

As with Google Scholar and Microsoft Academic Search ReaderMeter has problems with name variations and disambiguation. I am found under Finn A Nielsen and Finn Arup Nielsen and Finn Nielsen and Finn Aarup Nielsen. Taraborelli assures us that “Spelling variants will be addressed in the next major upgrade.” My “Finn Nielsen” clashes with another “Finn Nielsen”. As with Google Scholar and the Microsoft service there are also identification issues for individual papers. There are two listed items (1 and 2) with the same DOI in ReaderMeter.

Below I have tried to aggregate my papers across naming variations:

# Article Readership/Bookmarks
1 Nielsen 2006 23
2 Nielsen 2009 16
3 Frokjaer 2008 14
4 Nielsen 2007 14
5 Hansen 2011 13
6 Balslev 2006 13
7 Kalbitzer 2009 12
8 Balslev 2005 12
9 Pennock 2001 11
10 Kalbitzer 2010 11
11 Nielsen 2009 11
12 Nielsen 2005 9
13 Balslev 2002 8

So the metrics seems to be somewhat skewed and independent of the Google Scholar citations… Or what? Where is my co-author Cyril Goutte, who wrote highly cited papers 10 years ago?

Goutte’s Modeling the hemodynamic response in fMRI using smooth FIR filters amasses 92 Google Scholar citations but only 1 Mendeley bookmark according to ReaderMeter! But there are two entries for the article on Mendeley: one with one reader and another with 21 readers.

I cannot find On clustering fMRI time series in ReaderMeter. It got 44 “Readers on Mendeley” and 217 Google Scholar citations.

ReaderMeter is interesting, but its present version seems to suffer from a few “child diseases” for it to be a full fledged recommendable service (at least for the papers I examined). Microsoft Academic Search has an ‘Edit’ button where you can merge authors, merge publications and do a few other things (you need to sign in with Live ID to gain this functionality). ReaderMeter may very well improve if it implements similar functions. It is unclear for me how open Microsoft Academic Search is. Taraborelli’s ReaderMeter is on CC-by-sa so users may be more willing to spend time on merging and disambiguating authors and papers on ReaderMeter.


(Update 6 July 2011: When I wrote this blog post I was lazy and didn’t look on the good blogs that have already touched upon the same issues that I mentions.Taraborelli himself has a nice blog post and Rod Page also has a good one. Apart from author name normalization, article deduplication and author disambiguation Taraborelli also mentions a possible readership selection bias.)