Update Dec 2012: ResearchGate still keeps on sending me their spam. Most of the colleagues I had that tried out RG now deleted their account there, apparently, so the invitation mails become fewer. Please do not try to push this link on Wikipedia just because you are also annoyed by their emails. My blog is not a "reliable source" by Wikipedia standards. It solely reflects my personal view of that web site, not journalistic or scientific research. The reason why I call ResearchGate spam is the weasel words they use to trick authors into sending the invitation spam. Here's the text coming with the checkbox you need to uncheck (from the ResearchGate "blog")

Add my co-authors that are already using ResearchGate as contacts and invite those who are not yet members.

See how it is worded so it sounds much more like "link my colleagues that are already on researchgate" instead of "send invitation emails to my colleagues"? It deliberately avoids the mentioning of "email", too. And according to the researchgate news post, this is hidden in "Edit Settings", too (I never bothered to try it -- I do not see any benefit to me in their offers, so why should I?). Original post below:

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If you are in science, you probably already received a couple of copies of the ResearchGate spam. They are trying to build a "Facebook for scienctists", and so far, their main strategy seems to be aggressive inivitation spam. So far, I've received around 5 of their "inivitations", which essentially sound like "Claim your papers now!" (without actually getting any benefit). When I asked my colleagues about these invitations none actually meant to invite me! This is why I consider this behaviour of ResearchGate to be spam. Plus, at least one of these messages was a reminder, not triggered by user interaction. Right now, they claim to have 1.9 million users. They also claim "20% interact at least once a month". However, they have around 4000 Twitter followers and Facebook fans, and their top topics on their network are at like 10000-50000 users. That is probably a much more real user count estimation: 4k-40k. And these "20%" that interact, might just be those 20% the site grew in this timeframe and that happened to click on the sign up link. For a "social networking" site, these numbers are pointless anyway. That is probably even less than MySpace. Because I do not see any benefit in their offers! Before going on an extremely aggressive marketing campaign like this, they really should consider to actually have something to offer... And the science community is a lot about not wasting their time. It is a dangerous game that ResearchGate is playing here. It may appeal to their techies and investors to artificially inflate their user numbers in the millions. But if you pay for the user numbers with your reputation, that is a bad deal! Once you have the reputation as being a spammer (and mind it, every scientist I've talked to so far complained about the spam and "I clicked on it only to make it stop sending me emails") it's hard to be taken serious again. The scientific community is a lot about reputation, and ResearchGate is screwing up badly on this. In particular, according to researchgate founder on quora, the invitations are opt-out on "claiming" a paper. Sorry, this is wrong. Don't make users annoy other users by sending them unwanted invitations to a worthless service! And after all, there are alternatives such as Academia and Mendeley that do offer much more benefit. (I do not use these either, though. In my opinion, they also do not offer enough benefit to bother going to their website. I've mentioned the inaccuracy of Mendeleys data - and the lack of an option to get them corrected - before in an earlier blog post. Don't rely on Mendeley as citation manager! Their citation data is unreviewed. I'm considering to send ResearchGate (they're Berlin based, but there maybe also is a US office you could direct this to) a cease and desist letter, denying them to store personal information on me, and to use my name on their websites to promote their "services". They may have visions of a more connected and more collaborative science, but they actually don't have new solutions. You can't solve everything by creating yet another web forum and "web2.0izing" everything. Although many of the web 2.0 bubble boys don't want to hear it: you won't solve world hunger and AIDS by doing another website. And there is a life outside the web.

Thanks to Erich Schubert s blog posting on Planet Debian I became aware of the 2012 GNOME User Survey at Phoronix. Like back in 2006 I still use some GNOME applications, so I do consider myself as GNOME user in the widest sense and hence I filled out that survey. Additionally I have to live with GNOME 3 as a system administrator of workstations, and that s some kind of usage, too. ;-) The last question in the survey was Do you have any comments or suggestions for the GNOME team? Sure I have. And since I tried to give constructive feedback instead of only ranting, here s my answer to that question as I submitted it in the survey, too, just spiced up with some hyperlinks and highlighting:

Don t try to change the users. Give the users more possibilities to change GNOME if they don t agree with your own preferences and decisions. (The trend to castrate the user was already starting with GNOME 2 and GNOME 3 made that worse IMHO.) If you really think that you need less configurability because some non-power-users are confused or challenged by too many choices, then please give the other users at least the chance to enable more configuration options. A very good example in that hindsight was Kazehakase (RIP) who offered several user interfaces (novice, intermediate and power user or such). The popular text-mode web browser Lynx does the same, too, btw. GNOME lost me mostly with the change to GNOME 2. The switch from Galeon 1.2 to 1.3/2.0 was horrible and the later switch to Epiphany made things even worse on the browser side. My short trip to GNOME as desktop environment ended with moving back to FVWM (configurable without tons of clicking, especially after moving to some other computer) and for the browser I moved on to Kazehakase back then. Nowadays I m living very well with Awesome and Ratpoison as window managers, Conkeror as web browser (which are all very configurable) and a few selected GNOME applications like Liferea (luckily still quite configurable despite I miss Gecko s about:config since the switch to WebKit), GUCharmap and Gnumeric. For people switching from Windows I nowadays recommend XFCE or maybe LXDE on low-end computers. I likely would recommend GNOME 2, too, if it still would exist. With regards to MATE I m skeptical about its persistance and future, but I m glad it exists as it solves a lot of problems and brings in just a few new ones. Cinnamon as well as SolusOS are based on the current GNOME libraries and are very likely the more persistent projects, but also very likely have the very same multi-head issues we re all barfing about at work with Ubuntu Precise. (Heck, am I glad that I use Awesome at work, too, and all four screens work perfectly as they did with FVWM before.)

Thanks to Dirk Deimeke for his (German written) pointer to Marcus Moeller s interview with Ikey Doherty (in German, too) about his Debian-/GNOME-based distribution SolusOS.

$ gsettings set \
org.gnome.desktop.interface gtk-color-scheme '
os_chrome_fg_color:black;
os_chrome_bg_color:#FED;
os_chrome_selected_fg_color:black;
os_chrome_selected_bg_color:#f5a089;
selected_fg_color:white;
selected_bg_color:#c50039;
theme_selected_fg_color:black;
theme_selected_bg_color:#c50039;
tooltip_fg_color:black;
tooltip_bg_color:#FFC;
'

ELKI is a data mining software project that I have been working on for the last years as part of my PhD research. It is open source (AGPL-3 licensed) and avilable as both a Debian package and Ubuntu package in the official repositories. So a simple aptitude install elki should get you going and give you a menu entry for ELKI. These packages come with the scripts elki to launch the MiniGUI and elki-cli to run from command line. The key feature that sets ELKI apart from existing open source tools used in data mining (e.g. Weka and R) is that it has support for index structures to speed up algorithms, and a very modular architecture that allows various combinations of data types, distance functions, index structures and algorithms. When looking for performance regressions and optimization potential in ELKI, I recently ran some benchmarks on a data set with 110250 images described by 8 dimensional color histograms. This is a decently sized dataset: it takes long enough (usually in the range of 1-10 minutes) to measure true hotspots. When including Weka and R in the comarison I was quite surprised: our k-means implementation runs at the same speed as Rs implementation in C (and around twice that of the more flexible "flexclus" version). For some of the key agorithms (DBSCAN, OPTICS, LOF) we are an order of magnitude faster than Weka and R, and adding index support speeds up the computation by another factor of 5-10x. In the most extreme case - DBSCAN in Weka vs. DBSCAN with R-tree in ELKI - the speedup was a factor of 330x, or 2 minutes (ELKI) as opposed to 11 hours (Weka).
The reason why I was suprised is that I expected ELKI to perform much worse. It is written in Java (as opposed to R's kmeans, which is in C), uses a very flexible architecture which for example does not assume distances to be of type double and just has a lot of glue code inbetween. However, obviously, the Java Hotspot compiler actually lives up to its expectations and manages to inline the whole distance computations into k-means, and then compiles it at a level comparable to C. R executes vectorized operations quite fast, but on non-native code as in the LOF example it can become quite slow, too. (I would not take Weka as reference, in particular with DBSCAN and OPTICS there seems to be something seriously broken. Judging from a quick look at it, the OPTICS implementation actually is not even complete, and both implementations actually copy all data out of Weka into a custom linear database, process it there, then feed back the result into Weka. They should just drop that "extension" altogether. The much newer and Weka-like LOF module is much more comparable.) Note that we also have a different focus than Weka. Weka is really popular for machine learning, in particular for classification. In ELKI, we do not have a single classification algorithm because there is Weka for that. Instead, ELKI focuses on cluster analysis and outlier detection. And ELKI has a lot of algorithms in this domain, I dare to say the largest collection. In particular, they are all in the same framework, so they can be easily compared. R does of course have an impressive collection in CRAN, but in the end they do not really fit together. Anyway, ELKI is a cool research project. It keeps on growing, we have a number of students writing extensions as part of their thesis. It has been extremely helpful for me in my own research, as I could quickly prototype some algorithms, then try different combinations and use my existing evaluation and benchmarking. You need some time to get started (largely because of the modular architecture, Java generics and such hurdles), but then it is a very powerful research tool. But there are just many more algorithms, published sometime, somewhere, but barely with source code available. We'd love to get all these published algorithms into ELKI, so researchers can try them out. And enhance them. And use them for their actual data. So far, ELKI was mostly used for algorithmic research, but it's starting to move out into the "real" world. More and more people that are not computer scientists start using ELKI to analyze their data. Because it has algorithms that no other tools have. I tried to get ELKI into the "Google Summer of Code", but it was not accepted. But I'd really like to see it gain more traction outside the university world. There are a number of cool projects associated with ELKI that I will not be able to do myself the next years, unfortunately.

• A web browser frontend would be cool. Maybe even connected to Google Refine, using Refine for preprocessing the data, then migrating it into ELKI for analysis. The current visualization engine of ELKI is using SVG - this should be fairly easy to port into the web browser. Likely, the web browers will even be faster than the current Apache Batik renderer.
• Visual programming frontend. Weka, RapidMiner, Orange: they all have visual programming style UIs. This seems to work quite well to model the data flow within the analysis. I'd love to see this for ELKI, too.
• Cluster/Cloud backend. ELKI can already handle fairly large data sets on a big enough system. If someone spends extra effort on the index structures, the data won't even need to fit into main memory anymore. Yet, everybody now wants "big data", and parallel computation probably is the future. I'm currently working on some first Hadoop YARN based experiments with ELKI. But this is a huge field, turning this into true "elk yarn". I will likely only lay some foundations (unless I get funding to continue as a PostDoc on this project. I sure hope to get to do at least a few years of postdoc somewhere, as I really enjoy working with students on this kind of project)
• New visualization engine. The current visualization engine, based on Apache Batik and SVG is quite okay. It does what I need, which is to get a quick glance at the results and the ability to export them for publications in print quality. (in particular, I can easily edit the SVG files with Inkscape) But it is not really something fancy (although we have a lot of cool visualizations). And it is slow. I havn't found a portable and fast graphics toolkit for Java yet that can produce SVG files. There is a lot of hype around processing, for example, but it seems to be too much about art for me. In fact, I'd love to use either something like Clutter or Cairo. But getting them to work for Windows and Mac OSX will likely be a pain.
• Human Computer Interaction (HCI). This is in my opinion the biggest challenge we are facing with all the "big data" stuff. If you really go into big data (and not just run Hadoop and Mahout on a single system; yes - a lot of people seem to do this), you will at some point need to go beyond just crunching the numbers. So far, the challenges that we are tackling are largely data summarization and selection. TeraSort is a cool project, and a challenge. Yet, what do you actually get from sorting this large amount of data? What do you get from running k-means on a terabyte? When doing data mining on a small data set, you quickly learn that the main challenge actually is preprocessing the data and choosing parameters the right way so that your result is not bogus. Unless you are doing simple prediction tasks, you often don't have a clearly defined objective. Sure, when predicting churn rates, you can hope to just throw all the data into a big cloud and hope you get some enlightement out. But when you are doing cluster analysis or outlier detection - unsupervised methods - the actual objective by definition cannot be hardcoded into a computer. The key objective then is learn something new on the data set. But if you want to have your user learn something on the data set, you will have to have the user guide the whole process, and you will have to present results to the user. Which gets immensely more difficult with larger data. Big data just does no longer look like this. And neither are the algorithms as simple as k-means or hierarchical clustering. Hierarchical clustering is good for teaching the basic ideas of clustering. But you will not be using a dendrogram for a huge data set. Plus, it has a naive complexity of O(n^3) and for some special cases O(n^2) - too slow for truly big data.
  For the "big data future" once we get over all the excitement of being able to just somehow crunch these numbers we will need to seriously look into what to do with the results (in particular, how to present them to the user), and how to make the algorithms accessible and usable for non-techies. Right now, you cannot expect a social sciences researcher to be able to use a Hadoop cluster. Yet to make sense of the results. But if you are a smart guy to actually solve this, and open up "big data processing" to the average non-IT user, this will be big.
• Oh, and of course there are just hundreds of algorithms not yet available (accessible) as open source. Not in ELKI, and usually not anywhere else either. Just to name a few from my wishlist (I could probably implement many of them in a few hours in ELKI, but I don't have the time to do so myself, plus they are good student or starter project to get used to ELKI): BIRCH, CLARA, CLARANS, CLINK, COBWEB, CURE, DOC, DUSC, EDSC, INSCY, MAFIA, P3C, SCHISM, STATPC, SURFING, ... just to name a few.

If you are a researcher in cluster analysis or outlier detection, consider contributing your algorithms to ELKI. Spend some time optimizing them, adding some documentation. Because, if ELKI keeps on growing and gaining popularity, it will be the future benchmark platform. And this can give you citations, which are somewhat the currency of science these days. Algorithms available in the major toolkits just do get cited more, because people compare to them. See this list for an overview of work cited by ELKI - scientific work that we reimplemented at least to some extend for ELKI. It is one of the services that we provide with ELKI for researchers: not only the algorithm, but also the appropriate citation.

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Vijay Kumar gave an interesting TED talk about autonomous UAVs [1]. His research is based on helicopters with 4 sets of blades and his group has developed software to allow them to develop maps, fly in formation, and more. Hadiyah wrote an interesting post about networking at TED 2012 [2]. It seems that giving every delegate the opportunity to have their bio posted is a good conference feature that others could copy. Bruce Schneier wrote a good summary of the harm that post-911 airport security has caused [3]. Chris Neugebauer wrote an insightful post about the drinking culture in conferences, how it excludes people and distracts everyone from the educational purpose of the conference [4]. Matthew Wright wrote an informative article for Beyond Zero Emissions comparing current options for renewable power with the unproven plans for new nuclear and fossil fuel power plants [5]. The Free Universal Construction Kit is a set of design files to allow 3D printing of connectors between different types of construction kits (Lego, Fischer Technic, etc) [6]. Jay Bradner gave an interesting TED talk about the use of Open Source principles in cancer research [7]. He described his research into drugs which block cancer by converting certain types of cancer cell into normal cells and how he shared that research to allow the drugs to be developed for clinical use as fast as possible. Christopher Priest wrote an epic blog post roasting everyone currently associated with the Arthur C. Clarke awards, he took particular care to flame Charles Stross who celebrated The Prestige of such a great flaming by releasing a t-shirt [8]. For a while I ve been hoping that an author like Charles Stross would manage to make more money from t-shirt sales than from book sales, Charles is already publishing some of his work for free on the Internet and it would be good if he could publish it all for free. Erich Schubert wrote an interesting post about the utility and evolution of Favebook likes [9]. Richard Hartmann wrote an interesting summary of the problems with Google products that annoy him the most [10]. Sam Varghese wrote an insightful article about the political situation in China [11]. The part about the downside of allowing poorly educated people to vote seems to apply to the US as well. Sociological Images has an article about the increased rate of Autism diagnosis as social contagion [12]. People who get their children diagnosed encourage others with similar children to do the same. Vivek wrote a great little post about setting up WPA on Debian [13]. It was much easier than expected once I followed that post. Of course I probably could have read the documentation for ifupdown, but who reads docs when Google is available?

• [1] http://www.ted.com/talks/vijay_kumar_robots_that_fly_and_cooperate.html
• [2] http://hadiyahdotme.wordpress.com/2012/03/08/ted2012-and-why-conferences-will-never-be-the-same/
• [3] http://www.schneier.com/blog/archives/2012/03/harms_of_post-9.html
• [4] http://chris.neugebauer.id.au/2012/04/06/do-australian-tech-conferences-suffer-from-a-culture-of-exclusion-how-do-we-avoid-it/
• [5] http://beyondzeroemissions.org/media/newswire/clean-fossils-future-how-about-ready-renewables-120404
• [6] http://fffff.at/free-universal-construction-kit/
• [7] http://www.ted.com/talks/jay_bradner_open_source_cancer_research.html
• [8] http://www.antipope.org/charlie/blog-static/2012/03/buy-the-tee-shirt.html
• [9] http://www.vitavonni.de/blog/201204/2012041101-are-likes-still-worth-anything.html
• [10] http://richardhartmann.de/blog/posts/2012/04/13-woegle-is-me/
• [11] http://wildcard.gnubies.com/?p=1940
• [12] http://thesocietypages.org/socimages/2012/03/21/the-rise-of-autism-social-contagion-or-environmental-causation/
• [13] http://www.cyberciti.biz/faq/debian-linux-wpa-wpa2-wireless-wifi-networking/

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Since my last SE Linux in Debian status report [1] there have been some significant changes. Policy Last year I reported that the policy wasn t very usable, on the 18th of January I uploaded version 2:2.20110726-2 of the policy packages that fixes many bugs. The policy should now be usable by most people for desktop operations and as a server. Part of the delay was that I wanted to include support for systemd, but as my work on systemd proceeded slowly and others didn t contribute policy I could use I gave up and just released it. Systemd is still a priority for me and I plan to use it on all my systems when Wheezy is released. Kernel Some time between Debian kernel 3.0.0-2 and 3.1.0-1 support for an upstream change to the security module configuration was incorporated. Instead of using selinux=1 on the kernel command line to enable SE Linux support the kernel option is security=selinux. This change allows people to boot with security=tomoyo or security=apparmor if they wish. No support for Smack though. As the kernel silently ignores command line parameters that it doesn t understand so there is no harm in having both selinux=1 and security=selinux on both older and newer kernels. So version 0.5.0 of selinux-basics now adds both kernel command-line options to GRUB configuration when selinux-activate is run. Also when the package is upgraded it will search for selinux=1 in the GRUB configuration and if it s there it will add security=selinux. This will give users the functionality that they expect, systems which have SE Linux activated will keep running SE Linux after a kernel upgrade or downgrade! Prior to updating selinux-basics systems running Debian/Unstable won t work with SE Linux. As an aside the postinst file for selinux-basics was last changed in 2006 (thanks Erich Schubert). This package is part of the new design of SE Linux in Debian and some bits of it haven t needed to be changed for 6 years! SE Linux isn t a new thing, it s been in production for a long time. Audit While the audit daemon isn t strictly a part of SE Linux (each can be used without the other) it seems that most of the time they are used together (in Debian at least). I have prepared a NMU of the new upstream version of audit and uploaded it to delayed/7. I want to get everything related to SE Linux up to date or at least with comparable versions to Fedora. Also I sent some of the Debian patches for the auditd upstream which should reduce the maintenance effort in future. Libraries There have been some NMUs of libraries that are part of SE Linux. Due to a combination of having confidence in the people doing the NMUs and not having much spare time I have let them go through without review. I m sure that I will notice soon enough if they don t work, my test systems exercise enough SE Linux functionality that it would be difficult to break things without me noticing. Play Machine I am now preparing a new SE Linux Play Machine running Debian/Unstable. I wore my Play Machine shirt at LCA so I ve got to get one going again soon. This is a good exercise of the strict features of SE Linux policy, I ve found some bugs which need to be fixed. Running Play Machines really helps improve the overall quality of SE Linux.

• [1] http://etbe.coker.com.au/2011/10/31/selinux-status-2011-10/

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