The Long Cut

Author: Jaimie Murdock

  • Farewell to a Friend

    Today is the memorial service for Helga Keller, a dear friend who has changed so many lives. Since the first weekend in Bloomington, Helga has been a surrogate grandmother for me. We met after church the first weekend I was here and had an instant bond: A German immigrant, her first home in America was my hometown – Murray, Kentucky – and she knew many friends from home. She also was the administrative assistant for Douglas Hofstadter, one of the major inspirations for coming to Indiana. These common bonds of faith, people, and place brought us together throughout the years.

    There are so many things for which I am extremely grateful to her. One day I sent her an e-mail inquiring about the CopyCat program and where I could find articles about it. She responded with a three-page e-mail, with the article attached, links  to all subsequent research, contact information for all of the authors, an offer to introduce me to them, and an invitation to the CRCC lab meetings. As if that weren’t enough, the next time I encountered her she gave me an autographed copy of the book the study appeared in, along with photocopies of the articles mentioned in the e-mail.

    This is but one of many stories of her overwhelming kindness and dedication. May she rest in peace.

  • 2010 in Music

    A year ago, I reflected upon my musical evolution during 2009. As another year passes us by, it’s time to dive into my last.fm data once again for an empirical reality-check on what I’m listening to:

    ‘10 Artist ‘09 Change
    1 The Avett Brothers 3 (+2)
    2 John Mayer 29 (+27)
    3 Radiohead 2 (-1)
    4 The Black Keys 40 (+36)
    5 The Beatles 5
    6 Laura Veirs 52 (+46)
    7 Wilco 1 (-6)
    8 Say Hi 6 (-2)
    9 Kings of Leon 22 (+13)
    10 Nada Surf 10

    All in all, this year was a transition year for music, and I feel it’s continuing to move. Whereas 2009 was largely a solidification of 2008’s favorites, 2010 saw dramatic shifts, with 4 bands making double digit jumps, and 5 bands falling off the top 10 entirely. The only music from last year’s top 10 which became more popular was The Avett Brothers, who leaped to a commanding first place lead on the strength of I and Love and You and a belated discovery of Four Theives Gone.

    As a whole, this year was a move towards a stronger rock influence, as opposed to a folk influence. John Mayer, The Black Keys, Kings of Leon, and the Gaslight Anthem have all landed in my favorite artist lists. In particular, three albums have stood out as essential listening: The Black Keys’ Brothers, The Gaslight Anthem’s The ’59 Sound, and Kings of Leon’s Because of the Times.

    This year I turned 21, which opened up some new opportunities for concerts. Electric Six, Regina Spector, Guster, The Avett Brothers, John Mayer, The Tallest Man on Earth, Joe Pug, and Sufjan Stevens were all particularly memorable nights. Sufjan’s concert was mind-blowingly amazing, both in terms of on-stage production and overall musicianship. I had not heard Age of Adz until that night, but the epic 25-minute “Impossible Soul” is one of the coolest experiments ever. (Sufjan ranked 12th in 2010.)

  • Gentoo: Subversion not permanently accepting SSL certs

    Today I had a rather frustrating issue, as svn would not allow me to permanently accept an SSL Cert under Gentoo, rather just offering me the option to reject or accept temporarily.

    Error validating server certificate for \'xxxxxxxx\':
 - The certificate is not issued by a trusted authority. Use the
   fingerprint to validate the certificate manually!
 - The certificate has an unknown error.
Certificate information:
 - Hostname: xxxxxxxx
 - Valid: from xxxxxxxx until xxxxxxxx
 - Issuer: xxxxxxxx
 - Fingerprint: xxxxxxxx
(R)eject or accept (t)emporarily?

    After some Googling, I found Bug 295617: subversion won’t save bad certificates permanently with Neon 0.29. By this point Neon 0.28 had left the portage tree, so downgrading was not an easy option. However, a comment on Bug 238529 hinted at a workaround: build Neon without GnuTLS.

    To fix this issue, the easy fix is:

    echo \'net-libs/neon -gnutls\' >> /etc/portage/package.use
emerge -DN subversion

    Neon should rebuild and all will be well!

    Error validating server certificate for \'xxxxxxxx\':
 - The certificate is not issued by a trusted authority. Use the
   fingerprint to validate the certificate manually!
 - The certificate has an unknown error.
Certificate information:
 - Hostname: xxxxxxxx
 - Valid: from xxxxxxxx until xxxxxxxx
 - Issuer: xxxxxxxx
 - Fingerprint: xxxxxxxx
(R)eject, accept (t)emporarily or accept (p)ermanently?

  • Graduation

    Final grades are in, so I can finally announce that on December 17, 2010, I graduated from Indiana University with dual degrees and honors in Cognitive Science and Computer Science after 7 semesters.

    I’m extraordinarilly excited to finally be done with coursework so I can focus entirely on research. I’ll be continuing work with Prof. Colin Allen and the Indiana Philosophy Ontology Project (InPhO), completing our integration with the Stanford Encyclpedia of Philosophy (SEP) and working on further refinements of the dynamic ontology methodology, generalizing our methods for use in other disciplines. Starting in January, I’ll be working with Prof. David Michelson at the University of Alabama to redeploy the InPhO for the Syriac Reference Portal (SRP). This will hopefully lead to extended collaborations in the digital humanities.

    Additionally, I’m planning to continue contributing to Prof. Larry Yaeger‘s Polyworld Project, which is an Artificial Life simulation that provides a framework for replicable studies in evolution, genetics, and neural networks. I’ve been working on methods of species identification, using information-theoretic measures of genetic distance. This has led to a series of complexity improvements to a popular clustering algorithm used in bio-informatics. I’ve also built a data-access library in Python to facilitate analysis and visualization of experimental data.

    Sometime last year I started travelling all the time. My work was presented in Valencia, Evansville, and Chicago, and I further went to DC, Berkeley, Palo Alto, Louisville, Nashville, and Madrid. So far I’ve got three big trips planned for 2011: Santa Clara in January for the O’Reilly Strata Conference, DC and Philadelphia in February, and Atlanta in March for PyCon. Over the summer, I’ll hopefully be headed to conferences in Ireland and San Fransisco, but we’ll see how that goes.

    Past that, my future plans are predicated on the results of my Fulbright proposal. If this comes through, I’ll head to Karlsruhe, Germany in July to spend a year as a research assistant, developing methods for ontology-driven machine translation and sentiment analysis in collaboratively-generated corpora. Either way, 2011 should be a great year!

  • Published!

    In June, my paper "Two Methods for Evaluating Dynamic Ontologies" was accepted to the 2nd Knowledge Engineering and Ontology Development (KEOD) Conference in Valencia, Spain on October 25-28. The paper was co-authored with Cameron Buckner, a graduate student in Philosophy, and Colin Allen, a Professor in Cognitive Science and History & Philosophy of Science, and details some of our work with the Indiana Philosophy Ontology (InPhO) Project.

    This paper is the culmination of two summers of research on knowledge representation. If you’re interested in the InPhO project, section 3 of the paper is a reasonably accessible summary. The paper as a whole deals with a subproblem in ontologies – how do you quantify the quality of a candidate knowledge representation? We hypothesize that the structure of a domain corpus should be reflected in the structure of a taxonomy of that domain, and that a better taxonomy will better match the corpus statistics.

    I’ll be headed to Valencia October 22-31, and the Hutton Honors College has generously approved a travel grant to cover expenses for the week. I’ve set up my flights to and from Madrid, and I’ll have 2 days before and 3 days after the conference to wander around Spain — I’ve never been to Europe before, so I’m extremely excited!

    The abstract is below:

    Ontology evaluation poses a number of difficult challenges requiring different evaluation methodologies, particularly for a "dynamic ontology" representing a complex set of concepts and generated by a combination of automatic and semi-automatic methods. We review evaluation methods that focus solely on syntactic (formal) correctness, on the preservation of semantic structure, or on pragmatic utility. We propose two novel methods for dynamic ontology evaluation and describe the use of these methods for evaluating the different taxonomic representations that are generated at different times or with different amounts of expert feedback. The proposed "volatility" and "violation" scores represent an attempt to merge syntactic and semantic considerations. Volatility calculates the stability of the methods for ontology generation and extension. Violation measures the degree of "ontological fit" to a text corpus representative of the domain. Combined, they support estimation of convergence towards a stable representation of the domain. No method of evaluation can avoid making substantive normative assumptions about what constitutes "correct" representation, but rendering those assumptions explicit can help with the decision about which methods are appropriate for selecting amongst a set of available ontologies or for tuning the design of methods used to generate a hierarchically organized representation of a domain.

  • virtualbox-bin in Gentoo

    Some non-Linux-dork posts are in the pipe, but today I had issues getting VirtualBox up and running on Gentoo. Here’s some proper install instructions to work around Bug 283617. I’ll get to fixing the ebuild later this weekend.

    emerge virtualbox-bin
chmod 4750 /opt/VirtualBox/VBoxNetAdpCtl
chmod 4510 /opt/VirtualBox/VBoxSDL /opt/VirtualBox/VBoxHeadless /opt/VirtualBox/VirtualBox
gpasswd -a youruser vboxusers

    After a logout/login, VirtualBox should appear in your Applications menu, and can be run from the command line with VirtualBox.

  • Installing a Brother Printer on Gentoo

    I’ve been migrating over to Gentoo from Ubuntu (more on this later) and today had the lovely experience of installing a printer. Since at least 2 other computers will be needing these instructions, here we are:

    Install CUPS

    1. emerge cups
    2. /etc/init.d/cupsd start
    3. rc-update add cupsd default

    Install Driver

    1. Download the LPD and PPD RPM drivers from Brother’s Linux driver site.
    2. emerge rpm tcsh
    3. rpm  -ihv  --nodeps  (lpr-drivername)
    4. rpm  -ihv  --nodeps  (cupswrapper)
    5. Verify the drivers installed correctly: rpm  -qa  |  grep  -e (lpr-drivername)  -e  (cupswrapper-drivername) (if this is your only rpm package, just use rpm -qa)
    6. Create a symlink to the filter: ln -s /usr/lib/cups/filter/brlpdwrapper[printer name] /usr/libexec/cups/filter/brlpdwrapper[printer name]

    Add printer

    1. In a browser, go to the CUPS server at http://localhost:631/
    2. Click Add Printer and enter a name. Location and description are optional, but user-friendly.
    3. On the next page select: Device: AppSocket/HP JetDirect
    4. On the next page enter: Device URI: socket://192.168.1.11 (substitute with the IP address of your printer)
    5. The final page has a list of printer manufacturers. Skip that and click Choose File. Select the proper PPD file at /usr/share/cups/model/(printermodel).ppd. Click next.
    6. Print a test page and enjoy!

    As an aside, I did stumble upon the Brother PPD source code, however there were no make files for my printer, nor were there any LPD drivers. It is unfortunate to have rpm or dpkg as a dependency for my printer drivers, but so be it – they’re lightweight packages on their own.

  • Ahead of the Curve

    Another perfect day
    They keep pilin’ up
    I got happiness that I can maintain
    So beginner’s luck

    I had shoes to fill
    Walkin’ barefoot now
    Can’t tell north from south
    But no split hair’s gonna get me down

    Stayin’ above the flat line
    I’m ahead of the curve
    Take a piece of the sunshine with me
    On a redeye flight to another world

    It isn’t any trouble
    If you wanna come with me
    I know it’s out of the question, honey
    But I sure could use the company
    And a place to be

    Now the sky is pink
    Rooftop swimmin’ pool
    I’m not carefree, no
    I’m free to care
    I just never do

    All the bags are checked
    And the reasons why
    Yesterday lingers on
    That’s the piece you keep when you say goodbye

    You can get what you want now
    Knock it out of the park
    Bury it by the river, easy
    There’s a search party but it’s getting dark

    I won’t hold you to nothin’
    I wanna make that plain
    Probably end up a stranger and crazy
    But I’m still hopin’ there’s another way
    And a place to stay

    What the scene has got too sentimental
    When the night comes
    When the night comes loose
    All the things you put upon the mantle
    What a shame
    What a shame
    It’s old news

    I’m stayin’ above the flatline
    I’m ahead of the curve
    Take a piece of the sunshine with me
    On an all-night drive to another world

    You can get what you want now
    Knock it out of the park
    Probably end up a drifter and lonely
    But I’m still hoping for a change of heart
    And a place
    A place
    A place
    To start

    Monsters of Folk – Ahead of the Curve

  • Spring Semester

    Spring semester is over! All in all, this was an extremely exciting semester. A very brief, concise recap:

    It’s been super busy, but also incredibly stimulating. My grades are coming back, finances are under control and sleep is finally consistent. Can’t wait to keep things moving and get back on the bike this summer!

  • Dealing with ATi’s Linux Drivers

    ATi has gotten much better Linux support, but there is still much to be desired. Kernel upgrades pushed through the update manager tend to destroy the ATI kernel module. I’ve found the quickest, most painless way is to simply uninstall and then reinstall the drivers:

    sudo /usr/share/ati/fglrx-uninstall.sh

    Download the latest drivers from the ATI site: 32-bit and 64-bit <http://support.amd.com/us/gpudownload/linux/Pages/radeon_linux.aspx>.

    Open a terminal in the directory with the downloaded file (note: your exact file name may be different):

    sudo chmod +x ati-driver-installer-10-2-x86.x86_64.run
sudo ./ati-driver-installer-10-2-x86.x86_64.run

    Install the drivers, restart the computer and type the following into a terminal:

    sudo aticonfig -f --initial

    Then restart X (Ctrl+Alt+Backspace) or restart the computer and all will be well!

    Update: If you experience black or grey screen artifacts in Firefox/Thunderbird using Catalyst 10.6 or higher, it may be due to the new 2D rendering system. To force use of the old XAA system run the following command after the initial aticonfig setup:

    sudo aticonfig --set-pcs-str=DDX,ForceXAA,TRUE

    Restart X, and all should be well!