Archive for life

Spring 2011

With the passing of another semester comes another life update post. Even though I am no longer a student, being embedded in academia means progress is still measured by semesters.

Recently, I was awarded the Provost’s Award for Undergraduate Research and Creative Activity, which was a really nice capstone on my undergraduate experience. Since I did not walk at graduation, the Honors Convocation was a good opportunity to give my family closure on this chapter of my life.

Throughout these few months, I’ve been busy writing up a storm – one week in April saw 30 pages of manuscripts submitted. My previous post details the accepted poster summary on "Genetic Clustering for Species Identification" and the accepted book chapter on "Evaluating Dynamic Ontologies". There are two more papers in review and preparation right now. One is an expansion of the speciation work for a (hopeful) full-paper presentation. The other details work on taxonomy alignment carried out this semester.

I’ve still been travelling a ton. In December, I headed to Berkeley for my first California Christmas with Dad and Justin and my first non-business trip in 4 months. Three weeks later, I went back to California for a site visit at the Stanford Encyclopedia of Philosophy, Big Data Camp, and the O’Reilly Strata Conference. Strata was amazing – learned a ton, and met some really great people. Definitely planning to go again next year. I was scheduled to go to the Digital Humanities API Workshop but snow delays forced me to cancel, and last minute logistics chagnes made PyCon and ThatCamp SE impossible to attend. These three were certainly disappointments, but after being in an airport every month for 8 months, it was kind of nice to stay rooted for a while. Earlier this week, I visited Princeton University and Beth Mardutho: The Syriac Institute, as part of my work with the Syriac Reference Portal.

On a more personal note, the diaspora of friends has been steadily widening since graduation, including my roommate of 3 years. This has been disturbed, however, by just as many friends changing their plans to either stay in Bloomington or move back. While we will no longer have a single house to hang out in all the time, I’m excited about the social continuity next year.

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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.

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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!

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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

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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!

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Spring Break in DC

For 2010, I’ve decided that the adventure part of my identity needs some attention, so I’m going somewhere for Spring Break. I’ve decided to go to Washington DC, as I’ve never been and have really grown to appreciate our political process and common history. Here’s what I’ve got scrapped together so far:

When: March 11-16, 2010
Where: Washington DC

  • Depart Thursday, March 11 around 9pm to catch the midnight Amtrak Cardinal from Indy to Union Station. Spend the night on the train and the next day observing the beauty of the Appalachian Mountains from railcar. Arrive on Friday at 6pm. – $59 for coach, 18-hours in transit including 1 night.
  • Check in at Hosteling International – Washington DC, which is 4 blocks from the National Mall. Set up home base for the next 4 days, find some grub and walk around for a while. – $30/night in the dorm.
  • Saturday-Tuesday are pretty open- I would be content to spend hours in the Smithsonian and the National Archives. Of course, there’s all the monuments, and I suspect I’ll spend plenty of time just chilling in the Mall.
  • Gilberto Gil (, the former cultural minister of Brazil and Creative Commons advocate, will be performing a concert on Saturday night at George Washington University – this would be super awesome. Seats start at $35, but I think it would be an awesome experience.
  • Leave DC around 5pm Tuesday, March 16. Catch plane from Baltimore to Indy. $9 for Amtrak to Baltimore, $78 for BWI->IND direct flight. Arrive around 10pm.

Overall, I think the plans look good. I’m very excited about travelling by train. The hostel is insanely convenient and includes free breakfast. A cheaper place would likely end up costing more due to transportation and lost time. I chose a flight back because the train would cause me to lose two days – it departs on Wednesday at 11am and arrives Thursday at 5am, after which I would just sleep all day. It seems the base for this is around $270, including lodging, transportation and breakfast. Most of the monuments and museums are free, so lunch and dinner would be the major incidental costs.

Does anyone have any tips for DC? Any places that you would or wouldn’t see? General critiques?

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Hymn #101

Yeah I’ve come to know the wishlist of my father.
I’ve come to know the shipwrecks where he wished.
I’ve come to wish aloud among the overdressed crowd.
Come to witness now the sinking of the ship.
Throwing pennies from the seatop next to it.

And I’ve come to roam the forest past the village
With a dozen lazy horses in my cart.
I’ve come here to get eyed
To do more than just get by
I’ve come to test the timber of my heart.
Oh I’ve come to test the timber of my heart.

And I’ve come to be untroubled in my seeking.
And I’ve come to see that nothing is for naught.
I’ve come to reach out blind
To reach forward and behind
For the more I seek the more I’m sought
Yeah, the more I seek the more I’m sought.

And I’ve come to meet the sheriff and his posse,
To offer him the broad side of my jaw.
I’ve come here to get broke,
Then maybe bum a smoke.
We’ll go drinking two towns over after all.
Well, we’ll go drinking two towns over after all.

And I’ve come to meet the legendary takers.
I’ve only come to ask them for a lot.
Oh they say I come with less than I should rightfully possess.
I say the more I buy the more I’m bought.
And the more I’m bought the less I cost.

And I’ve come to take their servants and their surplus.
And I’ve come to take their raincoats and their speed.
I’ve come to get my fill
To ransack and spill.
I’ve come to take the harvest for the seed.
I’ve come to take the harvest for the seed.

And I’ve come to know the manger that you sleep in.
I’ve come to be the stranger that you keep.
I’ve come from down the road,
And my footsteps never slowed.
Before we met I knew we’d meet.
Before we met I knew we’d meet.

And I’ve come here to ignore your cries and heartaches.
I’ve come to closely listen to you sing.
I’ve come here to insist
That I leave here with a kiss.
I’ve come to say exactly what I mean.
And I mean so many things.

And you’ve come to know me stubborn as a butcher.
And you’ve come to know me thankless as a guest.
But will you recognize my face
When God’s awful grace
Strips me of my jacket and my vest,
And reveals all the treasure in my chest?

Joe Pug – Hymn #101
Buy the EP on Amazon

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Most Influential

What is your biggest influence?

It’s an open question – the {noun} that most influenced your calling/work/studies/career/purpose/etc to date: book, article, movie, paper, film, photo, story, person, relative, musician, artist, website, event, gadget, activity, anything! What’s the one thing that got you into what you’re into?

For me it’s the Towards 2020 Science Report (2.3MB PDF). The buzz I had after reading this report was incredible. We are standing literally on the precipice of scientific revolution – just as the discovery of algebra and calculus prompted the scientific revolutions of ages past, the development of computation is completely changing how we can look at the universe. Everything can be modeled. We can create “artificial scientists”. This awesomeness is why I do artificial intelligence.

Right now – what is that thing? What is your biggest influence? What sparks your fire?

Edit: Had to republish and refocus on school/career/interests – in the grand scheme of things there are other influences of greater or equal stature. 🙂

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Just went to Bloomington Bone and Joint for another appointment with the doctor and therapist and they declared my elbow healed, with full motion and no restrictions! I’m extremely ecstatic as this was supposed to be a 6 week process, and I’ve done it in 3.

deCycles 2009 seems to have gone really well – Patti/Signe, Stacey, and Andrew got back on Sunday. The prevailing sentiment is that the trip brings you to overwhelming highs and lows, but it’s a completely different mental state – one of those “you have to experience it” things. They all seem to have grown through the experience, especially in “get-up-and-go”-ness.

Of course I’m bummed that I couldn’t finish the trip, and it sucks that I’m in every article as “one of the two who couldn’t make it”. I still made something out of the past two weeks though:

  • Put in over 30 hours, which turns into a lot of money.
  • Earnestly started on the InPhO paper.
  • Enjoyed some time reflecting and set two (reasonably) ambitious goals for the next year:
    1. Establish an emergency fund of $1,000 and leave debt behind by January.
    2. Publish/present at least 3 times by next May.

Also, I have to get back on the bike and get really serious about training. Sure, I put in 650 miles before deCycles, but they were sporadic – 150 miles one week, 0 the next two. In order for it to become a lifestyle, I need to be consistent. There’s still 3 1/2 months before winter and next semester has a lot of free time for group rides. I’m thinking short 20-25 mile rides on MTWR (2 hours tops) and then longer 50+ mile rides over the weekend (mornings at 9). Let me know if you’re interested! Company for the weekend rides would be especially awesome 🙂

This year’s deCycles is going to nag at me for a long time. There’s not much of a silver lining, but dwelling on “might-have-beens” isn’t gonna do anything. There’s still the Hilly Hundred, a return trip to Wisconsin (potential route – Bike 4 Trails, Great River Road, Wisconsin River Valley, Madison) and maybe deCycles 2010. Things happen, so I’ll take solace in only being down for 3 weeks.

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Some Thoughts

So this blog is getting updated a little more frequently – hopefully, you are finding some useful tips. At this stage, I’m still a mere squidling (undergraduate), so you’re getting a lot of redirects to other awesome things instead of novel ideas, but that’s how life works. Hopefully I’m guiding you to the right places.

My elbow is healing up gradually – I can rotate my wrist almost entirely and my arm can almost straighten. Twisting my arm remains difficult. The progress is promising, but I still can’t lift more than two pounds. Perhaps in two weeks I can meet up with deCycles in Lexington and finish the last 3 days of the ride.

It’s not too bad being back in Bloomington. This weekend I started earnest work on the paper for InPhO. Right now I’m articulating how AI should be used to augment human feedback, without superseding it. I’ve also been working on some user interfaces and came across a really good Google Tech Talk, “Don’t Make Me Click“. Aza Raskin does a great job of emphasizing the importance of minimalist design and of doing as much as possible for your users. I found it worth the hour.

I’ve also been researching polyphasic sleep. Basically instead of sleeping 8 hours in a row, you have a shorter period of “core sleep” and then take 20 minute naps throughout the day. There are variations ranging from 6 hours of core sleep with a 30 minute nap in the day (Biphasic) to no core sleep and 6 20 minute naps throughout the day (Uberman) and a bunch of middle ground (Everyman). The less extreme versions are more pretentious ways of explaining what people do anyways, but the uberman concept is a fascinating extreme. Steve Pavlina has an interesting journal on adopting the uberman (day 30) (day 120) (going back). My roommate seems to have accidentally adopted the everyman system last year.

This month, I’m going to adopt biphasic sleep as my “thing” (although it seems this is how I naturally react to the school year). My only concern with adopting a true polyphasic sleep schedule is physical activity. No reports seem to have a regular exercise routine, and with 150+ miles of biking per week, I think core sleep may play a larger role in muscle recovery. For more findings on sleep, monitor my sleep tag on Delicious.

Some (public domain) visualizations of sleep patterns from Wikipedia:

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