Michael Bobak

Knowledge-Engineer / Research-Programmer

Summary

Research-Programmer starting with (bio)physical-science simulation, adding AI study and years of Knowledge-Engineering work

Knowledge-Based aids, for process improvement to teaching. AI: Knowledge-Representation&Reasoning, Rules, Kn-Acq, NLP, ML, ...

Work Experience

Xendat/Vertex remote

Ontology Data Developer/Analyst (Integrations)

Present

Contract ontology engineer through a shop serving a large pharma using: Python, SPARQL, Triple-Stores, (web)Protege, SemanticWeb-Libs
Wrote new libs used for both a Semantic-ETL and for an automated QA/QC, aiding Ontologist & BizDev, incl several apps

AlohaHealth remote

Sr AI Research-Engineer

2025

Part of a startup built on the topic of my UCSF research. Semantic search for clinical trials. (graph store/s)
pivot incl: Intelligent document processing, of pharma CofAs etc, automation that also allows for better analytics

Freelance San-Francisco, CA

consultant

Jul 2018

- 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 IDEO on their systems integration issues that could be aided by Knowledge-Graph for information refinement and cleanup
- Worked with the Siemens Web of Things research group on use of SemWeb+IoT for adaptable manufacturing
-Advised start-ups in AI: fashion blog to trends, sport dbpedia info, work chatbot
- 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, to help with metal health management
- Continued to build skills around ML, Semantic-Web/Linked-Data, and Knowledge-Engineering, with these courses, from:
  - Coursera: Data Analysis, Data Science (with distinction), Machine Learning (with distinction), Discrete Optimization (audit)
  - openHPI: Semantic Web, Knowledge Engineering, Kn Eng w/Semantic Web technology, LinkedDataEngineering
  - Stanford: Design Thinking

ApolloGrp.edu San-Francisco, CA

Architect , Adaptive Learning Platform

Conceptually annotate study material & tests for automated remediation, instrument classroom to learn from use (Hadoop, Lisp, KM)

UCSF.edu San-Francisco, CA

Programmar/Analyst III

Medical-Informatics research (relating to clinical-trails) in Lisp/KM, and Natural-Language-Processing in Java/etc; paper with Stanford group; ontology dev/use (Protege, Lisp, KM, ..)

Freelance Chicago/Boston

Knowledge-Engineer/ Research-Programmer

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)

kbs.ai.UIUC.edu Urbana, IL

(Senior) Research Programmer (Knowledge Based Systems Lab)

University of Illinois Urbana-Champaign, IL Organize many levels of a very large knowledge based simulation projects. Brought over 18 programmers together to deliver a coherent product. Ran weekly (sub)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

Brightware out of Chicago, IL

Knowledge-Engineer

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 (ie. financial: mortgage, web based job finder). (Art*Enterprise)See: http://www.brightware.com/eservice_solutions/ More recently I worked 1/2year for the new version of the company: Mindbox.

Argonne National Lab Argonne, IL

Software Engineer (EAD then DIS groups)

Wrote fielded Expert System by myself at the end of grad-school. (in Lisp rule-shell then CLIPS) Prototyped communication & control of distributed simulation. (in CLIPS PVM etc) Agent wrapping of simulations with CLIPS+PVM, to describe then mix and match them. Also used C++/Smalltalk/FORTRAN with PVM; Other work as needed. Algo/Viz/Etc. Written up in a book about innovative distributed object application. See: http://www.dis.anl.gov/DEEM HLAsim http://www.dis.anl.gov/DEEM/DIAS diaswp.pdf _More recently I worked part-time for the new subgroup of dis: cas.dis.anl.gov.

UIUC.edu Urbana, IL

Graduate Research Assistant /Research Programmer

Wrote molecular graphics package used in classes & for publications. (in C) Used machine-learning techniques for protein structure prediction.
Wrote thesis on Knowledge-Based Simulation Environment. (Lisp/OPS5/C) Overseen by heads of the NCSA CompBio group and head of Biophysics at the time. see: web.bilkent.edu.tr/ncsa/Apps/CBdir.html

Shearson Lehman Hutton London, England

Programmer (Research Computing)

Maintained financial databases & daily report information. Organized worldwide mailing system. Wrote statistics code for stock predictions. (MUMPS and Maths-package)

US Army Corp. of Eng. Research Lab Champaign, IL

Research Programmer (Modeling then Acoustics teams)

Provided research support from start to finish. (FORTRAN) Wrote and ran computer simulation code, compared output with field data. Did field measurements to back up predictions. (Team/Self; Local/US/World-wide) My work went into several published papers. GRASS: grass.osgeo.org

Education

University of Ilinois, Urbana-Champaign

MS Biophysics & Computational Biology with AI, 1990-93

BS Physics, BS Biophysics, 1983-88, dept. distinction

Professional Organizations:

Skills & Expertise

AI
Artificial Intelligence
Adaptive Systems
Business Rules
Case-Based_Reasoning
Composite Applications
Computational Intelligence
Conceptual Modeling
Controlled Vocabularies
Causal Inference
Data Analysis
Data Quality
Data Mining
Decision Modeling
Expert Systems
Information Access
Information Extraction
Information Retrieval
Intelligent Agents
Intelligent Systems
Intelligent Tutoring Systems
Knowledge Acquisition
Knowledge-based Systems
Knowledge Engineering
Knowledge Representation
Logic Programming
Mathematical Logic
Mathematical Programming
Machine Learning
Metadata standards
Model-based_reasoning
Natural Language Processing
Natural Language Understanding
Ontology Development
Ontology Engineering
Recommender-Systems
Rules
Rules Engines
Semantics
Semantic Search
Semantic Technologies
Semantic Web
SNOMED
Taxonomy Development
Text Classification
Science
Research
Scientific Software
Scientific Computing
Scientific Visualization
Simulation
Computational Mathematics
Biophysics
Computational Biology
Physics
Others
Cloud Computing
MapReduce
Hadoop
Dynamic Languages
Exploratory_programming
Common Lisp
other Languages

Programming Languages/...:

25+ years overall

Object Orientated 14+yr

Rule-Based KnRep&
Reasoning:10+yrs

Libs:

Databases:

Operating-Systems:

C 6+yrs FORTRAN 6+yrs

Smalltalk(1yr),C++ 1+yr

 OPS5, Prolog,GoldWorks 1yr

Viz: OpenGL 3+yrs

MS-Jet/SQL, MySQL

NeXTSTEP, MS(NT..XP) (8+yr)

Scheme ~1 yr MUMPS 1/2yr..

Python 8+yrs

 CLIPS 4+yrs,ART 4+yrs,

HPC: PVM 1+yr

PostgreSQL, ORDB

UNIX/.GNULinux 25+yrs
CommonLisp 7+yrs

CLOS(CL -Object-System)

Knowledge-Machine 3+yrs

WS:Tomcat/Axis SOAP/REST

Graph&triple 8+yrs

OS-X.Darwin 20+yrs

other Lisps 10+yrs

Java/Scala 2+yrs

 JESS1yr,Protege 8+yrs persistance&NoSQL



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