The Long Cut

Category: life

  • What have I been up to?

    Hello from the Land of Enchantment! In October, our family moved to Albuquerque, New Mexico – our fourth state in two years. Understandably, blogging has been a bit slower, but we’re finally getting settled, so I’m going to start with some basics before doing research updates and then expanding on some of these things.

    The day after the election my then-fianceé Emily got offered a fellowship at the National Academies of Science. We packed up and left for DC, for what we thought was just 6 months. In order to keep us afloat, I took full-time work at the Internet Archive. We got married in May and when she was offered a (semi-)permanent position, we moved to suburban Maryland.

    The Archive does heroic work for preservation and access, but was not a good fit for me, so in January 2018 I started a new position at Cornell University, working on the arXiv Next Generation (arXiv-NG) publishing platform. I’ve gotten a kick out of the fact that I moved to an organization with the exact same URL pronunciation (archive.org → arxiv.org), and the work we do has tremendous impact on scientific communications, with over 22 million monthly article downloads.

    Skipping ahead to June 2018, our son Javier was born. With expenses already at their limit before adding a child and the challenges of employment in Trump’s Washington, we had to relocate in October. After triangulating what was important to us in a home – a bilingual blue state with sunny weather, low cost of living, and a lack of anti-vaxers – New Meixco was our choice. It’s definitely delivered on the promise: not a day goes by where I wish we were back East. There’s something exciting about being on the frontier, somewhere no one in my family history has ever lived.

    tl;dr: moved 3 times, got married, had a baby, archive.org → arxiv.org

    Sunset at Volcanoes Day Use Area, Petroglyph National Monument, Albuquerque, NM

  • Granddad’s Indonesian Career

    The Granddad had two tenures in Indonesia at the Bogor Agricultural School (Institut Pertanian Bogor – IPB) from 1968-1970 and 1980-1985. IPB became independent from the University of Indonesia in 1963, and Granddad’s work was instrumental in its reorganization as the first degree-granting agricultural school in Indonesia. In his first term, he created the 4-year undergraduate curriculum and set general education requirements, helping the university exceed its goal of 20,000 graduates by the year 2000. In his second term, he served as Director of the Graduate Education Project and began issuing doctoral degrees.

    IPB was founded on a “tri-darma” of teaching, research, and extension, which matched the educational philosophy of the American land grant universities that trained Granddad. His design for the flagship Darmaga Campus was located on a Dutch rubber plantation and recognized that a university hosted not only research and faculty, but also students and their families. Therefore, it included classroom buildings, research and teaching fields, extension offices, residence halls and chapels. On a tour of the campus on Christmas Eve 2013, he was especially proud that the church and the mosque were located on the same courtyard sharing the same playground, that actual rubber, banana, rice, and corn fields for the students had been preserved, and that the library had been vastly expanded. He visited his IPB colleagues every year from his retirement at UW-Madison through his death in 2014 (pictured laughing in 2006, below).

    Granddad talking about his career on our way to the IPB Darmaga Campus (December 2013)
    December 2006 gathering of Granddad and IPB colleagues at Aunt Cindy's house
    Gathering of The Granddad and IPB colleagues at Aunt Cindy’s house (December 2006)

  • Debut Album: “We are the 123s!”

    On November 21st, The 123s will release our debut album “We are the 123s!” Recorded on June 10, 2014 at Russian Recording in Bloomington, IN, the album features 7 tracks and is available for streaming at http://wearethe123s.com/

    Additionally, we’ll be having a FREE release show:

    “We are the 123s!” Release Show
    November 21, 2014 10 pm
    Max’s on the Square
    106 W 6th St, Bloomington, IN

    Finally, we’ve released a full set of music videos from the live recording:

    A lot of hard work went into this album, and I’m very excited to share it with everyone! Physical copies on a “vinyl” CD are available as well, message me for more details.

  • Granddad

    On August 29, Granddad passed away suddenly at 86 in his home on Terrapin Creek. As the public obituary shows, Granddad was a legendary man: a Professor of Soil Science for 39 years at University of Wisconsin – Madison, he led the green revolution in Indonesia and Brazil (for which he received doctorates in 1985 and 2014, respectively). As President of the Midwest Universities Consortium on International Activities (MUCIA), he helped many other institutions and countries coordinate humanitarian aid. After retirement, Granddad still traveled to Indonesia every year and worked on the Ponderosa through his last day.

    At his funeral, all his grandchildren were given the opportunity to speak and my eulogy is below.

    After Grandma passed away, Granddad started a new tradition of writing his grandchildren a Christmas letter every year. In them, he told us his life’s story – from childhood on Terrapin Creek to finding the love of his life to moving away for school and then his first job. Throughout everything Granddad’s letters were filled with love and his profound sense of finding home, wherever he was.

    In the past two years, Granddad and I recognized that I was following in part of his footsteps by becoming a PhD student. This Christmas, I made plans to see him in Indonesia. Granddad and I arrived in Jakarta within an hour of each other. He had just come back from the mission field in Sulawesi, and was undeniably sick. Granddad’s health was never a complaint, it was just a statement. When his lung stopped working almost a decade ago, he didn’t. When he visited the doctor in Indonesia, the doctor asked to take a picture of him. Granddad asked why and the doctor said “My dad is 84 and giving up on life, you’re 86 and your life is just beginning!”

    Granddad’s life always was just beginning – he started every day in gratitude and as his letters showed us, even recollections of the past started with thankfulness for the day he was given and the future he had created for his family and the world.

    Granddad and I at IPB on Christmas Eve 2014 As he was feeling better, he started whistling again as he was in the house. One morning I asked him to take me to IPB – the Bogor Agricultural School – that he worked at for 7 years. Twenty minutes later, in a moment that was very Granddad, he said “car’s out front, let’s go.” Now, I was expecting him to take a few days to make arrangements, so I hurried off to get shoes. When we got in the car he started telling me all about the work he had done there restructuring the curriculum and I hadn’t realized he literally designed the university – from the library to offices to fields to chapels. They had set a goal of 20,000 graduates by the year 2000, which they met early!

    Granddad made an immediate impact on so many lives, but the life and work he created was built to last. We each saw that first-hand as he mentored so many of us. Now, as his letters stop, we are left to find our own path, but the lessons he gave us of love and dedication will live on forever.

  • 2013 in Review

    As 2013 comes to an end, I’ve found myself in Indonesia again. With Granddad turning 86 and deciding to take an extended 2 month trip, it seemed like an important time to go and events in my own life lined up well — no finals, no school until January 13th, and no particular attachments in Bloomington. I’m spending 10 days with family, then off to Bali for 5 days, the beach for 4 days, 2 more days in Bogor, and then back to America. As in 1990 and 2007, I will leave on January 8th, 2014, which is apparently my Indonesian expiration date.

    The opportunity to explore Bogor and just unplug from my normal life has given me time for reflection and pause on what has been an eventful and fantastic year. I summarized much of the first half of the year earlier, but since then I’ve been moving swiftly.

    In July, I returned to DC to give a talk at the International Association for Computing and Philosophy, came back to Indy to give a poster at the Joint Conference on Digital Libraries, and then left for a 2 week vacation in the Bay. The vacation was amazing: I saw The Postal Service reunion, went on a road trip down California 1, checked out a music festival in Santa Cruz, then headed to Outside Lands in SF. When I got back, I ran off to Illinois to give a presentation and then moved down the hall to a new 2-bedroom apartment with a loft and 2-story ceilings. September and October were a blur of shows, homework, and settling into my new place.

    Perhaps November is the most emblematic of all the ways I’ve grown: I ran my first half-marathon (2:03!), organized my first retreat, hosted Friendsgiving, played with The 123s at The Bishop, gave presentations for all my classes, and hosted Mom’s Thanksgiving. None of these things would’ve been possible at the start of the year.

    For the first time in years, I feel caught up on life and comfortable in my own skin. While I still get overwhelmed, I’m starting to recognize that it’s going to work out. 2013 was a rediscovery of my values, and it feels like 2014 was the destination. I can’t wait to see what’s next.

  • One down, N to go

    This has been a very intense year, but the end has been worth it. In August, I started graduate school at Indiana University in the Computer Science Program. By October, I started having my first round of grad school anxieties – was a PhD worth it? Was I just doing more of the same by staying at IU? Was I going to grow? Several job offers and much discernment later, I realized that I truly wanted my doctorate, but that I had not positioned myself in the right programs — my interests are intensely interdisciplinary and more cognitive than computational. So, after some negotiations, I transferred from Computer Science to the Complex Systems Group in Informatics, which is a much better fit for my research goals.

    After this academic identity crisis, I came down with mono in December. Since I was the AI for the 75-student Data Structures course, I had to take incompletes in my coursework to focus my much-diminished energy on teaching. Despite the setback, mono was a very positive catalyst for me. I finally got to a doctor, which woke me up to the reality of what I had done to my body over the past 6 years: I was 23 and my blood pressure was in the hypertension range. For some reason the nurses weren’t freaked out about this, the doctor just said to check it out in a few months, but I knew something was wrong. So while recovering from mono, I decided to change things. I quit drinking to focus on my incompletes, started hitting the gym 5 times a week, picked up running, and have lost 40 pounds since January. I have collarbones, wristbones, and an Adam’s apple. It’s fucking awesome. Plus, I finished my first year of graduate school with a 3.83 GPA! 😀

    Research-wise, I’ve been distilling a new research area and imagining what my committee will look like. Right now, I’m diving into a literature review on what Colin is calling “biographically-plausible corpora”. The general intuition is that while “big data” approaches can create excellent recommendations, humans gain expertise from much smaller datasets. Thus, instead of training semantic models on 50 million books, what happens if you train them only on 50 or 500 books? I’ll be presenting this work at a symposia at IACAP 2013 in July.

    I’ve also had two side projects. The first is a return to Polyworld to examine correlations between TSE complexity and social behavior — an ALife approach to the social brain hypothesis. The second is an examination of the information flow between science and the humanities using the PhilPapers index and the UCSD Map of Science. Preliminary results are being presented as a poster at the Joint Conference on Digital Libraries (JCDL) and we’re aiming for a journal article by the end of the summer.

    Outside of school, I’ve been really enjoying myself musically. In January, I joined The 123s, playing alto sax on early rock, blues, and soul covers (stuff like Ray Charles, Aretha Franklin, Little Richard, Smokey Robinson, and Chuck Berry). This month Afro-Hoosier got a new trombone player, which has allowed me to switch to bari full-time. I’m playing gigs every other week, and on May 17th I’ll be playing my first gig in another town – a fundraiser out in Lafayette. On May 23rd, I’ll be headlining at the Bishop with The 123s. In the next 3 months I’ll be seeing Of Monsters and Men, Cold War Kids, Portugal. the Man, Todd Snider, The Wailers, The Postal Service, and all the bands at Outside Lands. Life has been good to my ears.

    So, all in all, I feel pretty great about where I’ve come this year. It took a bit of soul-searching to realize how much I wanted my PhD, and a lot of work to get my body ready for it, but I’m ready now and extremely satisfied with my position.

  • Grad School: The Right Place

    If you like where you live, if you like what you do,
    If you like what you’re seein, when you’re lookin at you,
    If you like what you’re sayin, when you open your face,
    Then you got the right feeling, you’re in the right place.
    Monsters of Folk – “The Right Place”

    In November, I delivered two lectures to student organizations on campus and realized that I really miss teaching. Despite the amazing flexibility of a career in research and development, I won’t be able to find fulfillment until I am working with students. The only way to realize that goal is to become a professor, and in order to realize that I need a PhD, so I applied to graduate schools in December.

    After visiting the available options, I’ve decided to continue my studies at Indiana University, pursuing the Joint PhD In Cognitive Science and Computer Science. All in all, IU just feels like the right place. I’m well-positioned to make a lasting impact, both in my own studies and in the community, and there’s no break for moving to a new city and building a new professional network. Plus, there is a large amount of social and financial stability in Bloomington, which helps maintain my sanity.

    As for now, I’m off to Lyon, France to give a presentation titled “Containing the Semantic Explosion”, covering work with the Indiana Philosophy Ontology Project. An abstract and slides will follow later this week.

  • A New Chapter

    In July, the Indiana Philosophy Ontology (InPhO) Project was awarded a new NEH-DFG Bi-lateral Digital Humanities Program grant with the University of Mannheim for linking and populating digital humanities databases. Our current grant ends in December, so this brought tons of relief, injecting $172,215 into the project. The DFG’s contribution of €126,400 allows InPhO co-founder Mathias Niepert to return to the project, along with his team at the University of Mannheim. All in all, the project will be able to continue for another two years.

    As a result of the grant, I was offered a full-time, salaried faculty position as a Visiting Research Associate with the IU Cognitive Science Program, continuing work on the InPhO Project. During this time, I will be working on new methods of knowledge representation and machine learning with applications in document classification, ontology evaluation, and taxonomy alignment, bringing the digital humanities into the Linked Open Data initiative. I’ll also be working on a new bibliography management system for the Stanford Encyclopedia of Philosophy, using a tool developed for Cognitive Science Program faculty publication records.

    I started the new position on August 16th. The new full-time job, plus the move to a my own 1-bedroom apartment, along with joining the band, have me falling more and more in love with Bloomington. For the first time in a long, long time, I’m satisfied with where I am. Looking forward to this new chapter of post-college life.

  • Summer 2011

    Figured it’s been another 4 months, so it’s time for another life update. This was an incredibly productive summer with the open-sourcing of the InPhO Project, an extremely successful refactoring, and two publications hitting press. It was also fun, as I started gigging with Afro-Hoosier International and took a road trip up California 1 with my brothers. All in all, a great bookend on this past chapter of life.

    Work

    All of the InPhO code has been open-sourced and uploaded to GitHub in two repos. The inpho repo contains our data mining code, while the inphosite repo contains our API and website. Most of the code in the inpho repo was newly ported from Java so that we could use NLTK and integrate with the ORM. We hired a new undergraduate, Evan Boggs, to help refactor the code, and after a long summer, were able to cut 10,000 lines form the code base.

    In July, I quit the Syriac Reference Portal (SRP), after several months of work deploying Semantic MediaWiki and the new COGS Bibliography Engine. I learned a lot about generalizability of the InPhO code, and what the humanities side of digital humanities needs, but ultimately the data provenance goals of the historical community are still an open question for semantic web research and standardization, and I want to focus my research efforts elsewhere. I hope the project finds success and will continue to support it through work on the COGS Bibliography Engine.

    Publications-wise, the work on speciation and clustering was accepted as a full paper at the European Conference on Artificial Life (ECAL). I’m really pleased with the biological narrative we were able to weave, and am working on some further work with Larry Yaeger and Sean Dougherty on adapting the clustering tool to larger datasets. Also, Colin and I’s paper on the InPhO API from last year’s Chicago Colloquium on Digital Humanities and Computer Science was finally published.

    Play

    In May, I joined Afro-Hoosier International, a local afropop and world music dance band. Five gigs in, it’s been crazy fun to play sax with other people again. We’re an 11-piece band, with three horns, three vocalists, keyboard, guitar, bass, kit, and auxillary, and we groove. We’ll be hitting the studio sometime soon to put togehter an album — I’m really pumped. This is a recording from my second gig with the band in Bryan Park:

    At the end of July, I finally got to take a little vacation from the grind. For the first time ever, both of my brothers and I headed out to California at the same time to visit my Dad. While we were there, we took a road trip up the North Coast on California 1 to the Avenue of the Giants, the Black Sands, and Arcata in Humboldt County. We managed to make no plans at all, and took things at a completely leisurely pace, stopping and going as we pleased. I kept my cell phone and e-mail turned off for a record 5 days.

  • 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.