Michael Bobak
Ontology / Knowledge Engineer / Research Programmer / Analyst
linkedin.com/in/michaelbobak @Mbstream MBcode.github.io
Summary:
Research-Programmer starting with (bio)physical-science simulation, adding AI study and years of Knowledge Engineering work as well (in: edu/gov/com).
Focus on Knowledge-Based aids, for process improvement to teaching. AI: Ontology, Knowledge-Representation and Reasoning, Rules, Kn-Acq, NLP, ML
University of Illinois, Urbana-Champaign
MS Biophysics & Comp-Biology with AI, Research Assistant /Research Programmer 1990 - 1993
BS Physics, BS Biophysics, Dept. distinction Research Programmer(1⁄2 time w/local lab) 1983 - 1988
Professional Organizations:
AAAI (Association for the Advancement of Artificial Intelligence) life-member.
IEEE (Institute of Electrical and Electronics Engineers) & Computer Society 10 years
Other Groups: meetup.com, linkedin-groups
ID: orcid.org/0000-0003-2357-5918 wikidata.org/wiki/Q104512704
Papers: scholar.google.com/&q=michael+bobak
Sr Semantic Web Engineer panaceadirect/IMOhealth(Remote) 2026 – present
Similar to the vertex work, but more healthcare focused and at a larger scale
SubjectMatterExpert Pivot Path Solutions (Remote) 2026
SME for a DARPA digital-twin pitch & suggested a general path fwd incl semantics
Ontology Data Developer/Analyst (Integrations) xendat.com/vrtx.com (Remote) 2023 - 2025
Contract to a pharma’s Ontology Group using: Python, SPARQL, Triple-Stores, (web)Protege, Semantic-Web-Libs
Wrote new libs used for both a Semantic-ETL and for an automated QA/QC, aiding Ontologist & BizDev, incl several apps
Sr Research Software Engineer National Center for Supercomputing Applications, Urbana, IL 2019 - 2023
Bringing my background to earthcube.org and other grants.
Focus on semantics/metadata search, with some NLP & sim. EarthCube's GeoCODES: Crawl data repositories json-ld for extended schema.org,and provide faceted search, related datasets, and transition to notebooks. Built up related semantic-web python libs, use of triple-stores.. FAIR data principles
Sr Knowledge-Engineering AlohaHealthNet (Remote) 2017 - 2025
Advising early-stage startup built on the topic of my UCSF.edu research. Matching EHR to get people into clinical trails
Sr Software Engineer Agrible/Nutrien Champaign IL 2017 - 2018
Planned & guided reworking the main simulation, documentation, & ML/verification which helped with it's acquisition
Working as an ontologist for osthus.com on aligning bio/pharma ontologies to BFO to annotate masses of data in HDF5 files, for the allotrope.org
Worked with the Siemens Web of Things research group on use of SemWeb+IoT for adaptable manufacturing
Worked with IDEO on their systems integration issues that could be aided by Knowledge-Graph for info refine/cleanup
Advised with a variety of start-ups in understanding AI tech, including Fashion start-up that would track unstructured blog info to surface trends - Sports startup thewhytehousegroup.com needed dbpedia search ability
Developed ideas to take my UCSF research and fuse it with the Patient Data Mining Cluster that was developed by the UCSF Head of Research Computing and a PhD student, which has now been submitted for a patent
Worked with UCSF in Psychology Department understand how to apply NLP and graph relation insights into an app they developed called Prime for schizophrenic young adults, with application to depression management as well
Help with an assisted eco-sim/modeling environment in Lisp.
Continued to build skills around ML, Semantic-Web/Linked-Data, and Knowledge-Engineering:
Coursera courses: Data Analysis, Data Science (with distinction), Machine Learning (with distinction), Discrete Optimization (audit) – open-HPI courses: Semantic Web, Knowledge Engineering, Knowledge-Engineering with Semantic Web technology, Linked-Data-Engineering - Stanford courses: Design Thinking
Architect, Adaptive Learning Platform Apollo Education Group, San Francisco, CA Oct 2010 - Jul 2011
Conceptually annotate study material and tests for automated remediation, instrument classroom to learn from using: Hadoop, Lisp, KM
Medical-Informatics research (relating to clinical-trails) in Lisp/KM, and Natural Language Processing in Java; paper with Stanford group; ontology dev/using: Lisp, KM, Match conceptually annotated patient EMR against a concept based in/ex-clusion criteria annotated from ClinicalTrials.gov to see which trials they might be eligible for, via semantic-search
Freelance Knowledge Engineer/ Research-Programmer Feb 2001 - Sep 2007
mindbox.com 3/02-10/02. (used Art*Enterprise) See: Ocwen_Mindbox
Worked up to half-time for cas.dis.anl.gov 5/03-5/04 (Java Simulation)
Worked full-time 8/03-~05(verizon)labs.gte.com, Model-Based-Diagnosis on a national scale. (Art *Enterprise) See: aaai.org/Papers/IAAI/1996/IAAI96-287.pdf
Bioinformatics/control contract 11/04-12/05 (CLIPS&Protege.stanford.edu/Java/DB) Control of perfusion pumps on light microscope sample, monitoring incl. Machine-vision, Bio-ontology/reasoning/Kn-mngt for the experiment setup. & Grant proposal work.
Worked for CME.com 2/06-06/06 (re)organizing trade-data validation code. (CLIPS/Jess)
Signal-Processing/Machine-Learning (startup) 06/06-(Lisp/etc)
Hospital Informatics/Machine-Learning ghx.com 02/07-05/07-(Lisp),
MachineLearning speedup for financial-scientific (Lisp)
Senior Research Programmer UIUC Knowledge Based Systems Lab, Urbana, IL Jun 1998 - Feb 2001
Organized many levels of a very large knowledge-based simulation projects. Brought over 18 programmers together to deliver a coherent product. Ran weekly group meetings, down to help solving any problem.
Hiring, demo, design, install trips, prototyping to lead project direction. Taught group of 6 how to use a Rule-Based-shell for a reasoner-rewrite in Art*Enterprise.
Projects included: Simulation-based, Intelligent Tutoring System (ITS) & Real- Time control system. Being used in classroom, real life testing, presented at IAAI99 'Automated Instructor Assistant for Ship Damage Control' - The system teaches Navy officers how to save a simulated ship in crisis. A variant was developed to catch real-time crisis conditions and suggest solutions www.dwilkins.org/members.htm
Helped develop and install their very first product (intelligent email reply). Worked between development and consulting. Helped on several Knowledge-Based business applications. Helped with several deployed Knowledge-Based business applications (i.e. financial: mortgage, web based job finder). w/Art*Enterprise See: www.brightware.com/eservice_solutions &later 1/2 year for the new version of the company: Mindbox.
Wrote Lisp code (mainly GUI) for Qualitative Research Group. Learned more about Qualitative/Quantitative Simulation, Model-Based Reasoning, Intelligent-Tutoring-Systems, and general Lisp programming.
See: www.qrg.northwestern.edu/projects/NSF/Cyclepad/aboutcp.htm