Workshops, Tutorials and Classes
Referent Tracking for Biomedical Informatics. Lecture for the 2023 Biomedical Informatics Bootcamp, July 5 - August 21, University at Buffalo, August 14, 2023. (slides)
Mutualistic integration of Referent Tracking and BFO2020-style FOL axiomatization. Buffalo Ontology Day, October 24, 2022. (slides)
Tutorial: An introduction to Referent Tracking, ICBO 2019, July 30, 2019.
Referent tracking Tuples. Lecture for BMI714: Principles of Referent Tracking. University at Buffalo, March 26, 2019. (slides)
The Essence of Referent Tracking. Lecture for BMI714: Principles of Referent Tracking. University at Buffalo, February 5, 2019. (slides)
Using Referent Tracking for ontology development and use. Lecture for BMI508: Biomedical Ontology. University at Buffalo, November 5, 2018. (slides)
Representing negative findings in Referent Tracking. Lecture for PhD course BMI714, Principles of Referent Tracking in Biomedical Informatics, University at Buffalo, March 2, 2018. (slides)
Building Referent Tracking Systems. Lecture for PhD course BMI714, Principles of Referent Tracking in Biomedical Informatics, University at Buffalo, February 20, 2018. (slides)
The Ontological Basis of Referent Tracking. Lecture for PhD course BMI714, Principles of Referent Tracking in Biomedical Informatics, University at Buffalo, February 6, 2018. (slides)
Referent Tracking. Lecture for BMI508/PHI548: Biomedical Ontology, University at Buffalo, October 24, 2016. (slides)
What can Ontological Realism and Referent Tracking contribute to computer vision?Keynote presentation at the 1st International Workshop on Computer vision + ONTology Applied Cross-disciplinary Technologies (CONTACT 2014), Zurich, Switzerland, Sept 7th, 2014. (slides)
Referent Tracking: Use of Ontologies in Tracking Systems. Lecture part of the course Ontological Engineering, Dept of Industrial and Systems Engineering IE 500, Dept of Computer Science CSE510, and Dept of Philosophy PHI 598. SUNY at Buffalo, Sept. 22, 2014. (slides)
Referent Tracking: Use of Ontologies in Tracking Systems. Lecture part of the course Ontological Engineering, Department of Industrial and Systems Engineering IE 500 and Department of Philosophy: PHI 598. SUNY at Buffalo, Sept. 23, 2013. (slides, without videos, lecture audio and video)
A common framework for representing data and what they are about. Ontology seminar, April 1, 2013, Dept. of Philosophy, University at Buffalo, Buffalo, NY. (abstract, slides)
Biomedical Ontology and Referent Tracking: Introduction to Basic Principles. IADR Satellite Workshop on Orofacial Pain, March 20, 2013, Seattle, WA. (slides)
Ontological Perspectives on Data. Informatics sessions for year-3 medical students, University at Buffalo, Jan. 11, 2013. (slides)
Referent Tracking: focus on particulars. Guest lecture for PHI 531 Problems in Ontology, class 23893, University at Buffalo, Sept 10, 2012. (slides)
Realism-Based Ontology for Integrating Individually Compiled Biomedical Data Repositories. 3-Hour tutorial as part of the Medical Informatics Europe Conference (MIE 2012), Pisa, Italy, August 26-29, 2012. (Tutorial outline, slides)
Ontologies for the bio-science industry: development and use.. Short course at the Molecular Medicine Tri-Con 2012 conference, San Francisco, CA, February 20, 2012. (slides)
Ontological Realism for Biomedical Ontologies and Electronic Health Records. Tutorial as part of the Medical Informatics Europe Conference, MIE 2011, Oslo, Norway, August 28-31, 2011.
Improving Structured Electronic Health Record Data through Ontological Realism. Tutorial as part of the International Conference on Biomedical Ontology, ICBO 2011, Buffalo NY, July 26-30, 2011. (slides)
Introduction to Referent Tracking. Tutorial co-located with the International Conference on Biomedical Ontology (ICBO), Buffalo NY and part of the 2-day class From Basic Formal Ontology to the Information Artifact Ontology - July 22, 2009. slides
Solving Crimes using Referent Tracking.
Referent Tracking (RT) is a new methodology to build digital copies of the parts of the world we are interested in. These copies, when running inside a computer, should mimic what is happening in reality. RT was originally designed to solve problems in healthcare, but has shown to be applicable to other fields. In this seminar, we will apply RT to reconstruct histories of criminal activities and demonstrate how the paradigm can cope with facts, beliefs, and mistakes, keeping track of information that is sometimes accurate, sometimes misleading, and often contradictory. We will look specifically at a well-known case in which a man was wrongly sentenced to death for a rape and murder he didn’t commit, although all evidence was against him.
This class has been offered in:
Difficult Problems, Easy Solutions: Referent Tracking in Biomedicine. UB Discovery Seminar Program – Fall 2007.
In laboratories throughout the world, researchers are making strides towards improving the way we live through amazing advances in biomedical science. From discovering cures for diseases to developing innovative new drugs, to testing safety and efficacy, biomedical research depends on computer technology to progress. But for this, all of the data produced, at all of the stages of discovery – including patient data collected in patient records - needs to be capable of being integrated and computer applications need to be able to understand each other. This seminar will uncover the role of Referent Tracking in Biomedicine, an innovative technique combining the distinct disciplines of biomedicine, philosophy, and informatics. It will be shown how common sense and logical thinking can lead to solutions that give software agents the capacity to know what natural language terms refer to. By allowing many different types of information resources to be exchanged, life-saving scientific research can be shared across disciplines.
Class materials
Mutualistic integration of Referent Tracking and BFO2020-style FOL axiomatization. Buffalo Ontology Day, October 24, 2022. (slides)
Tutorial: An introduction to Referent Tracking, ICBO 2019, July 30, 2019.
- Ceusters W.: Introduction to Referent Tracking Theory. (slides)
- Hogan W.: Introduction to Referent Tracking Applications.(slides)
- Limbaugh D.: Advanced Referent Tracking: Application to Diagnosis.(slides)
Referent tracking Tuples. Lecture for BMI714: Principles of Referent Tracking. University at Buffalo, March 26, 2019. (slides)
The Essence of Referent Tracking. Lecture for BMI714: Principles of Referent Tracking. University at Buffalo, February 5, 2019. (slides)
Using Referent Tracking for ontology development and use. Lecture for BMI508: Biomedical Ontology. University at Buffalo, November 5, 2018. (slides)
Representing negative findings in Referent Tracking. Lecture for PhD course BMI714, Principles of Referent Tracking in Biomedical Informatics, University at Buffalo, March 2, 2018. (slides)
Building Referent Tracking Systems. Lecture for PhD course BMI714, Principles of Referent Tracking in Biomedical Informatics, University at Buffalo, February 20, 2018. (slides)
The Ontological Basis of Referent Tracking. Lecture for PhD course BMI714, Principles of Referent Tracking in Biomedical Informatics, University at Buffalo, February 6, 2018. (slides)
Referent Tracking. Lecture for BMI508/PHI548: Biomedical Ontology, University at Buffalo, October 24, 2016. (slides)
What can Ontological Realism and Referent Tracking contribute to computer vision?Keynote presentation at the 1st International Workshop on Computer vision + ONTology Applied Cross-disciplinary Technologies (CONTACT 2014), Zurich, Switzerland, Sept 7th, 2014. (slides)
Referent Tracking: Use of Ontologies in Tracking Systems. Lecture part of the course Ontological Engineering, Dept of Industrial and Systems Engineering IE 500, Dept of Computer Science CSE510, and Dept of Philosophy PHI 598. SUNY at Buffalo, Sept. 22, 2014. (slides)
Referent Tracking: Use of Ontologies in Tracking Systems. Lecture part of the course Ontological Engineering, Department of Industrial and Systems Engineering IE 500 and Department of Philosophy: PHI 598. SUNY at Buffalo, Sept. 23, 2013. (slides, without videos, lecture audio and video)
A common framework for representing data and what they are about. Ontology seminar, April 1, 2013, Dept. of Philosophy, University at Buffalo, Buffalo, NY. (abstract, slides)
Biomedical Ontology and Referent Tracking: Introduction to Basic Principles. IADR Satellite Workshop on Orofacial Pain, March 20, 2013, Seattle, WA. (slides)
Ontological Perspectives on Data. Informatics sessions for year-3 medical students, University at Buffalo, Jan. 11, 2013. (slides)
Referent Tracking: focus on particulars. Guest lecture for PHI 531 Problems in Ontology, class 23893, University at Buffalo, Sept 10, 2012. (slides)
Realism-Based Ontology for Integrating Individually Compiled Biomedical Data Repositories. 3-Hour tutorial as part of the Medical Informatics Europe Conference (MIE 2012), Pisa, Italy, August 26-29, 2012. (Tutorial outline, slides)
Ontologies for the bio-science industry: development and use.. Short course at the Molecular Medicine Tri-Con 2012 conference, San Francisco, CA, February 20, 2012. (slides)
Ontological Realism for Biomedical Ontologies and Electronic Health Records. Tutorial as part of the Medical Informatics Europe Conference, MIE 2011, Oslo, Norway, August 28-31, 2011.
Improving Structured Electronic Health Record Data through Ontological Realism. Tutorial as part of the International Conference on Biomedical Ontology, ICBO 2011, Buffalo NY, July 26-30, 2011. (slides)
Introduction to Referent Tracking. Tutorial co-located with the International Conference on Biomedical Ontology (ICBO), Buffalo NY and part of the 2-day class From Basic Formal Ontology to the Information Artifact Ontology - July 22, 2009. slides
Solving Crimes using Referent Tracking.
Referent Tracking (RT) is a new methodology to build digital copies of the parts of the world we are interested in. These copies, when running inside a computer, should mimic what is happening in reality. RT was originally designed to solve problems in healthcare, but has shown to be applicable to other fields. In this seminar, we will apply RT to reconstruct histories of criminal activities and demonstrate how the paradigm can cope with facts, beliefs, and mistakes, keeping track of information that is sometimes accurate, sometimes misleading, and often contradictory. We will look specifically at a well-known case in which a man was wrongly sentenced to death for a rape and murder he didn’t commit, although all evidence was against him.
This class has been offered in:
- UB Discovery Seminar Program – Spring 2009: Course Introduction, The time of a 'killing', Introduction to 'meaning', Introduction to Realism-based Ontology, Identifying types of entities, Entities and their relationships, Entities and their relationships - How the homework should have been done , Entities and their relationships- Correction of the March 26 assignment.
- UB Discovery Seminar Program – Fall 2008: Course introduction, The deadly (?) injection, The time of a killing, On 'definitions', Definitions of 'killing', Using Aristotelian definitions to build an ontology -Introduction- Relations in realism-based ontology - Introduction, Relations and the killing problem, Relations and the killing problem - the students’ views, Relations and the killing problem - towards an adequate ontology.
- UB Discovery Seminar Program – Spring 2008: The implanted chip, Crime Terminology, Building a Realism-based Crime Ontology - Introduction, Building a Realism-based Crime Ontology - Realism-based Relationships, Final Assignment, Privacy and the Implanted Chip problem
Difficult Problems, Easy Solutions: Referent Tracking in Biomedicine. UB Discovery Seminar Program – Fall 2007.
In laboratories throughout the world, researchers are making strides towards improving the way we live through amazing advances in biomedical science. From discovering cures for diseases to developing innovative new drugs, to testing safety and efficacy, biomedical research depends on computer technology to progress. But for this, all of the data produced, at all of the stages of discovery – including patient data collected in patient records - needs to be capable of being integrated and computer applications need to be able to understand each other. This seminar will uncover the role of Referent Tracking in Biomedicine, an innovative technique combining the distinct disciplines of biomedicine, philosophy, and informatics. It will be shown how common sense and logical thinking can lead to solutions that give software agents the capacity to know what natural language terms refer to. By allowing many different types of information resources to be exchanged, life-saving scientific research can be shared across disciplines.
Class materials
- Understanding the problem
- Realism-based ontologies
- A detailed account of realism-based ontologies
- Assignment (Comments and corrections are in the notes)