Jaimie Murdock

Jaimie Murdock

A Joint PhD Student in Cognitive Science and Informatics at Indiana University, I study the dynamics of expertise and innovation through the lenses of history and philosophy of science, machine learning, and cognitive science. A prolific programmer of both web and data processing interfaces, with ten years of research experience in digital humanities as lead developer of the InPhO Project.

Education

Indiana University Bloomington, IN

School of Informatics, Computing, and Engineering

Joint Ph.D. in Cognitive Science and Informatics May 2019
Master of Science, InformaticsDecember 2018
Bachelor of Science, Computer ScienceDecember 2010
  • Graduated with departmental honors.
  • Concentrations in programming languages and artificial intelligence.
  • President and Founder of the Computer Science Club, September 2010 – May 2011.

College of Arts and Sciences

Bachelor of Science, Cognitive ScienceDecember 2010
  • College of Arts and Sciences Direct Admit.
  • Chair of the inaugural 2009 and 2010 Midwest Undergraduate Cognitive Science Conferences (MUCSC). Created sustainable organization, with the 10th annual meeting in 2018.
  • President of the Student Organization for Cognitive Science (SOCS), January 2009 – August 2010.

Additional Coursework

  • Science Mapping Standards Workshop November 2013
  • Principles of Functional Programming in Scala September – November 2013
  • North American Summer School on Logic, Language, and Information (NASSLLI) June 2012
  • Indiana University School of Continuing Studies January 2012 – May 2012
    • MATH-S303 Honors Linear Algebra
  • IEEE Summer School on Semantic Computing July 2010
  • North American Summer School on Logic, Language, and Information (NASSLLI) June 2010
    • Served on organizing committee, responsible for opening celebration arrangements.
  • NSF/JSMF Workshop on Mapping the History and Philosophy of Science June 2009

Positions Held

Cornell University - arXiv.org Ithaca, NY

Web Applications Engineer January 2018 – Present

Internet Archive San Francisco, CA

Web Crawl Engineer March 2017 – January 2018

Publications

  1. Designates representative publications

Journal Articles

  1. Jaimie Murdock, Colin Allen, and Simon DeDeo. (2018) Quantitative and Qualitative Approache to the Development of Darwin's Origin of Species. Current Research in Digital History. doi:10.31835/crdh.2018.14.
  2. Colin Allen, Hongliang Luo, Jaimie Murdock, Jianghuai Pu, Xiaohong Wang, Yanjie Zhai, Zhao Kun. (2017) Topic Modeling the Hàn diăn Ancient Classics (汉典古籍). Journal of Cultural Analytics. doi:10.22148/16.016. Data: doi:10.7910/DVN/3QXX29
  3. Jaimie Murdock, Colin Allen, Katy Börner, Robert Light, Simon McAlister, Robert Rose, Doori Rose, Jun Otsuka, David Bourget, John Lawrence, Andrew Ravenscroft and Chris Reed. (2017) Multi-level Computational Methods for Interdisciplinary Research in the HathiTrust Digital Library. PLoSone. 12(9): e0184188.doi:10.1371/journal.pone.0184188. Pre-print: arXiv:1702.01090. Data: doi:10.5967/K8251GBZ.
  4. Jaimie Murdock, Colin Allen, and Simon DeDeo. (2017) Exploration and Exploitation of Victorian Science in Darwin's Reading Notebooks. Cognition. 159: 117-126. doi:10.1016/j.cognition.2016.11.012. Pre-print: arxiv:1509.07175 [cs.CL]
  5. Jared Lorince, Sam Zorowitz, Jaimie Murdock, and Peter Todd. (2015) Wisdom of the Few? "Supertaggers" in Collaborative Tagging Systems. Journal of Web Science 1:1. Now Publishers. doi:10.1561/106.00000002.

Book Chapters

  1. Jaimie Murdock (2019) Computational Discovery in The Dynamics of Science: Computational Frontiers in History and Philosophy of Science, Grant Ramsay and Andreas De Block (eds.). Pittsburgh: University of Pittsburgh Press.
  2. Jaimie Murdock, Colin Allen, and Simon DeDeo (2019) Darwin's Semantic Voyage in The Dynamics of Science: Computational Frontiers in History and Philosophy of Science, Grant Ramsay and Andreas De Block (eds.). Pittsburgh: Univeristy of Pittsburgh Press
  3. Jaimie Murdock, Cameron Buckner and Colin Allen. (2013) Evaluating Dynamic Ontologies. in Knowledge Discovery, Knowledge Engineering, and Knowledge Management: Second International Joint Conference, IC3K 2010, Valencia, Spain, October 25-28, 2010, Revised Selected Papers. (Communications in Computer and Information Science, Lecture Notes, vol. 272). Springer-Verlag. doi:10.1007/978-3-642-29764-9_18.

Conference Proceedings

  1. Jaimie Murdock, Jacob Jett, Tim Cole, Yu Ma, J. Stephen Downie, and Beth Plale. (2017) Towards Publishing Secure Capsule-based Analysis. Proceedings of the 2017 Joint Conference on Digital Libraries (JCDL). Toronto, Ontario, Canada, June 19-23, 2017.
  2. Jared Lorince, Sam Zorowitz, Jaimie Murdock, and Peter Todd. (2014) "Supertagger" Behavior in Building Folksonomies. in Web Science 2014, Bloomington, Indiana, USA, June 23-26, 2014. ACM Press. doi:10.1145/2615569.2615686.
  3. Jaimie Murdock and Larry Yaeger. (2011) Identifying Species by Genetic Clustering. In Proceedings of the 2011 European Conference on Artificial Life (ECAL). Paris, France, MIT Press, 2011, 565-572.
  4. Jaimie Murdock and Colin Allen. (2011) InPhO for All: Why APIs Matter. Journal of the Chicago Colloquium on Digital Humanities and Computer Science (JDHCS). Evanston, Illinois, 2011.
  5. Jaimie Murdock, Cameron Buckner and Colin Allen. (2010) Two Methods for Evaluating Dynamic Ontologies. In Proceedings of the 2nd International Conference on Knowledge Engineering and Ontology Development (KEOD). Valencia, Spain, 2010, 110-122. doi:10.5220/0003101601100122
  6. Mathias Niepert, Cameron Buckner, Jaimie Murdock and Colin Allen. (2008) InPhO: A System for Collaboratively Populating and Extending a Dynamic Ontology. in JCDL '08: Proceedings of the 8th ACM/IEEE-CS Joint Conference on Digital Libraries. doi:10.1145/1378889.1378976.

Demos, Workshops, Tutorials, and Posters

  1. James Pustejovsky, Marc Verhagen, Keigh Rim, Yu Ma, Liang Ran, Samitha Liyanage, Jaimie Murdock and Beth Plale (2017). Enhancing Access to Digital Media: The Language Application Grid in the HTRC Data Capsule in Proceedings of the 2017 Practice & Experience in Advanced Research Computing Conference (PEARC'17).
  2. Jaimie Murdock, Jiaan Zeng, and Robert McDonald (2015). Topic Exploration with the HTRC Data Capsule for Non-Consumptive Research [tutorial] Proceedings of the 2015 Joint Conference on Digital Libraries (JCDL). Knoxville, Tennessee, June 21-25, 2015. doi:10.1145/2756406.2756929.
  3. Jaimie Murdock and Colin Allen. (2015) Visualization Techniques for Topic Model Checking [demo track] in Proceedings of the 29th AAAI Conference (AAAI-15). Austin, Texas, USA, January 25-29, 2015.
  4. Jakob Huber, Timo Sztyler, Jan Noessner, Jaimie Murdock, Colin Allen, and Mathias Niepert. (2014) LODE: Linking Digital Humanities Content to the Web of Data. [demo track] Proceedings of the 2014 Joint Conference on Digital Libraries (JCDL). London, United Kingdom, ACM Press, 2014.
  5. Jaimie Murdock, Robert Light, Colin Allen and Katy Börner. (2013) Mapping the Intersection of Science & Philosophy. in Proceedings of the 2013 Joint Conference on Digital Libraries (JCDL). Indianapolis, Indiana, ACM Press, 2013. doi:10.1145/2467696.2467777.
  6. Jaimie Murdock, Cameron Buckner and Colin Allen. (2012) Containing the Semantic Explosion. In Proceedings of the Philoweb Workshop at the World Wide Web Conference 2012 (WWW2012).
  7. Jaimie Murdock and Larry Yaeger. (2011) Genetic Clustering for Species Identification. In Proceedings of the 13th Genetic and Ecolutionary Computation Conference (GECCO '11). Dublin, Ireland, ACM Press, 2011, 29-30. doi:10.1145/2001858.2001875

Miscellaneous

  1. Jaimie Murdock, Jiaan Zeng, Colin Allen. (2015) Towards Cultural-Scale Models of Full Text HTRC ACS Technical Report. arXiv:1512.05004 [cs.DL]
  2. Jakob Huber, Timo Sztyler, Jan Noessner, Jaimie Murdock, Colin Allen, and Mathias Niepert. (2013, submitted) LODE: Linking Digital Humanities Content to the Web of Data.. arXiv:1406.0216 [cs.DL]
  3. Colin Allen, Jaimie Murdock, Cameron Buckner, and Robert Rose. (2013) Computational Philosophy and the Examined Text: A Tale of Two Encyclopedias. in American Philosophical Association Newsletter on Philosophy and Computers, 12:2, p28-30.
  4. Colin Allen and The InPhO Group. (2013) Cross-Cutting Categorization Schemes in the Digital Humanities. Isis 104: 573-583.

Projects

HathiTrust Research Center http://analytics.hathitrust.org/

Research Assistant July 2016 – Present

Topic Explorer https://inphodata.cogs.indiana.edu/

Lead Developer August 2014 – Present

InPhO Project https://inpho.cogs.indiana.edu/

Graduate Research Assistant August 2012 – August 2016

  • Created the InPhO Topic Explorer for visualizing large text corpora.
  • Enhanced bibliography parser and the document ontology. Completed SKOS migration of concept ontology. Developed administrative tools for thinker ontology crowdsourcing data.
  • Mentored 5 undergraduate students, managed 12 member research team.

Visiting Research Associate August 2011 – August 2012

  • Presented research program at the Philoweb Workshop of the WWW2012 Conference.
  • Led web portal redesign using Twitter's Bootstrap library, adding an AJAX administrative interface and enhanced crowdsourcing capabilities.
  • Managed development team of 4 undergraduate programmers.

Lead Developer October 2007 – August 2011

  • Drafted system architecture and implemented a RESTful HTTP API supporting JSON, XML, RDF, and HTML output using the Pylons web framework, SQLAlchemy ORM, and Mako templating engine.
  • Migrated the development environment from a closed-source model utilizing PHP, Perl, static HTML forms, and SVN to an open-source, agile development model using Python, AJAX, and Git.
  • Developed two novel ontology evaluation methods, culminating in the forthcoming publication of a book chapter in Springer-Verlag's Communications in Computer and Information Science series.
  • Created a cross-reference suggestion engine for the Stanford Encyclopedia of Philosophy (SEP) using statistical methods derived from the computational ontology.

Stanford Encyclopedia of Philosophy http://plato.stanford.edu/

Stanford, CA

Programming Consultant June 2014 – August 2014

Polyworld https://github.com/polyworld

Bloomington, IN

Open-source Contributor April 2010 – Present

  • Developed memory-efficient, lazy-loading, parallelized Python data-access library using the NumPy, SciPy, and Multiprocessing libraries.
  • Created several data visualization and parallel analytics tools using Python's matplotlib library.
  • Researched the use of clustering algorithms for high-dimensionality data discovery problem. Discovered algorithmic improvements amortizing the cost of QT-Clust algorithm and published results at two international conferences. Implemented using C, with OpenMP for parallelization.
  • Investigated the use of GPU programming for data clustering, using the OpenCL framework and AMD/ATI hardware. Exploring code portability for nVidia hardware.

Syriac Reference Portal http://www.syriaca.org/

Tuscaloosa, AL

Lead DeveloperOctober 2010 – August 2011

  • Designed and implemented data architecture for international digital humanities initiative.
  • Deployed Semantic MediaWiki (SMW) environment with full RDF support. Explored the use of quad stores and triple stores for historical data.
  • Developed a bibliography parsing engine, with an interface for Semantic MediaWiki's sources engine.

Power of Logic Web Tutor http://www.poweroflogic.com/

Programming Consultant October 2008 – May 2009

Teaching

History and Philosophy of Science http://www.indiana.edu/~hpscdept/

Bloomington, IN

HPSC-X420/X521 Computational Methods for HPS January 2016 – May 2016

  • Course Assistant — Assisted with classroom deployment of the InPhO Topic Explorer and provided support for student final projects.

Foundations in Science and Mathematics http://www.indiana.edu/~fsm/

Bloomington, IN

Introduction to Computer Science June 2015, 2016

  • Instructor — Taught 2-week high school course in computational thinking using Python.

Cognitive Science Program http://cogs.indiana.edu/

Bloomington, IN

COGS-Q260 – Programming for the Cognitive and Info. Sciences January 2016 – March 2016

COGS-Q320 – Computation in the Cognitive and Info. Sciences March 2016 – May 2016

  • Instructor of Record — Taught computational thinking and artificial intelligence using Python. Led weekly lab section of 21 students, responsible for grading.

COGS-Q260 – Programming for the Cognitive and Info. Sciences January 2015 – March 2015

COGS-Q320 – Computation in the Cognitive and Info. Sciences March 2015 – May 2015

  • Associate Instructor — Taught computational thinking and artificial intelligence using Python. Led weekly lab section of 23 students, responsible for grading.

Computer Science Program http://soic.indiana.edu/

Bloomington, IN

INFO-I399 – Research Methods August 2013 – December 2013

  • Graduate Mentor — Supervised 4 undergraduate students in research Project.

CSCI-Y390 – Independent Study January 2013 – May 2013

  • Graduate Mentor — Supervised 2 students in the Undergraduate Research Opportunities in Computing Program (UROC @ SOIC).

CSCI-C343 – Data Structures August 2012 – December 2012

  • Associate Instructor — Assumed full responsibility for course logistics, including assignment creation and instructor management for 66 student course. Led two weekly lab sections of 19 and 27 students.

CSCI-C343 – Data Structures August 2010 – December 2010

  • Undergraduate Instructor — Led weekly lab section of 20 students for a 43 student course.

Lectures

  1. The Development of Darwin's Origin of Species March 17, 2018
    Current Research in Digital History 2018
  2. Towards Publishing Secure Capsule-based Analysis June 20, 2017
    JCDL 2017
  3. HTRC Data Capsule - faster, bigger, better March 2, 2017
    HTRC User Group Meeting
  4. Darwin's Semantic Voyage November 4, 2016
    Philosophy of Science Association (PSA) 2016 Meeting
  5. From Texts to InPhO (and back!)November 3, 2016
    Guest lecture in ILS-Z657 Digital Humanities
  6. The Cognitive Science of Darwin's Delay August 4, 2016
    International Conference on Thinking 2016
  7. From Texts to InPhO (and back!) May 13, 2016
    HASTAC 2016 Workshop
  8. Darwin's Semantic Voyage May 12, 2016
    HASTAC 2016
  9. Darwin's Semantic Voyage Apirl 19, 2016
    Maryland Insitute for Technology in the Humanities (MITH) Staff Talk
  10. From Texts to InPhO (and back!)April 13, 2016
    IU CCCP Lab Meeting
  11. Darwin's Semantic Voyage March 23, 2016
    IU Intelligent and Interactive Systems Seminar
  12. Topic Modeling: A Practical Introduction March 4, 2016
    Pestilli Research Laboratory
  13. Visualizing Scientific Data February 26, 2016
    IU Speech and Hearing Science Graduate Seminar
  14. Topic Modeling: A Practical Introduction February 18, 2016
    Guest Lecture in HPSC-X521 Digital Methods for History and Philosophy of Science
  15. Topic Modeling: A Practical Introduction February 10, 2016
    IU CCCP Lab Meeting
  16. Charles Darwin, Information Foraging, and Non-consumptive Research November 11, 2015
    HathiTrust Research Center User Group
  17. Darwin's Semantic Voyage October 27, 2015
    Student Organization for Cognitive Science
  18. Darwin's Semantic Voyage October 23, 2015
    CLingDing: IU Computational Linguistics Discussion Group
  19. Darwin's Semantic Voyage October 2, 2015
    2015 Conference on Complex Systems (CCS'15)
  20. Exploration and Exploitation of Darwin's Reading Notebooks September 11, 2015
    Guest Lecture in STAT-S675 Statistical Learning
  21. Polymathic and Polygraphic: Thomas Jefferson's Mind June 4, 2015
    International Center for Jefferson Studies Fellows' Forum
  22. Visualization Techniques for LDA April 17, 2015
    IU Cognitive Science Program 25th Anniversary Interactive Cognitive Systems Open House
  23. Topic-Driven Foraging April 10, 2015
    Goldstone, Landy, Todd Lab
  24. Darwin's Semantic Voyage April 8, 2015
    IU SoIC Informatics PhD Un-poster Session
  25. Comparing Topic Models of Digital Philosophy Resources April 4, 2015
    APA Pacific Division Invited Symposia
  26. Topic Modeling with the HTRC Data Capsule March 30, 2015
    HathiTrust Research Center Uncamp
  27. Topics Over Time: Into Darwin's Mind March 9, 2015
    Network Science Talks @ IU
  28. Making Pretty Pictures w/Topic Models November 5, 2014
    IU Cognitive Computing Lab
  29. InPhO and HathiTrust: Digging for Philosophy in the Sciences September 9, 2013
    HathiTrust Research Center Uncamp
  30. Simulating Expertise through Subcorpus Modeling July 17, 2013
    International Association for Computing and Philosophy (IACAP) Annual Meeting
  31. A Tale of Two Encyclopedias August 7, 2012
    Berkeley Insitute of Design Lunch Series
  32. Containing the Semantic Explosion April 17, 2012
    WWW2012 Philoweb Workshop
  33. Practical Parallelism November 17, 2011
    IU Computer Science Club Tech Talk
  34. Categorization November 15, 2011
    IU Student Organization for Cognitive Science (SOCS)
  35. Two Methods for Evaluating Dynamic Ontologies October 26, 2010
    2nd International Conference on Knowledge Engineering and Ontology Development (KEOD)

Awards

  • Designates high-profile awards
  • International Center for Jefferson Studies (ICJS) Fellowship $2,000 May 2015
  • Cognitive Science Program Supplemental Research Grant $4,550 January 2015
  • Provost's Award for Undergraduate Research and Creative Activity $1,000 April 2011
  • School of Informatics and Computing CHIP Scholarship $1,000 August 2010
  • School of Informatics and Computing Cerner Scholarship $1,000 August 2009
  • Hutton Honors College Research Grant $2,000 May 2009
  • Cognitive Science Program Undergraduate Research Scholarship $1,000 May 2009
  • Cognitive Science Program Outstanding Contribution Award April 2009
  • Hutton Honors College Research Partnership Grant $1,500 May 2008
  • Cognitive Science Program Undergraduate Research Scholarship $800 May 2008
  • Arthur Metz Scholar $24,000 August 2007
  • Hutton Honors College Faculty Award $28,000 August 2007
  • Woodcock Foundation Scholarship $7,400 August 2007

Skills

Serious projects in several programming paradigms: functional (Scheme, Haskell), imperative (C), logic (Prolog, miniKanren), object-oriented (Python, Java), and scripting (Python, Perl, Bash). Skilled in database management, architecture, SQL, and object relational mapping (ORM). Experience with web applications architecture, including RESTful design, the HTTP protocol, AJAX, and semantic web technologies (RDF, OWL, SKOS).

Organizations

  • Association for Computing Machinery (ACM) January 2009 – Present
    • Program committee, 2014 ACM Web Science Conference.
  • International Association for Computing and Philosophy (IACAP) January 2009 – Present
    • Program committee, IACAP 2013 Computing in Philosophy track.
    • Local volunteer, IACAP 2009 Annual Meeting.
  • Cognitive Science Society January 2009 – Present
  • Psychonomic Society January 2015 – Present
    • Reviewer, Behavioral Research Methods
  • Association for the Advancement of Artificial Intelligence (AAAI) January 2015 – Present
  • Leibniz Institute for the Social Sciences
    • Program committeee, 2017 International Conference on Computational Social Science (IC2S2)

References

  • Colin Allen colallen

    Provost's Professor of Cognitive Science and History & Philosophy of Science InPhO

  • Simon DeDeo sdedeo

    Assistant Professor of Cognitive Science and Informatics InPhO

  • Peter Todd pmtodd

    Provost's Professor of Cognitive Science, Informatics, and Psychology Tagging

  • Katy Börner katy

    Victor H. Yngve Professor of Information Science InPhO

  • Beth Plale plale

    Professor of Informatics HathiTrust