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(Created page with "Intelligence Analysis: A Philosophical Introduction '''Registration''': :Class#: [http://www.buffalo.edu/class-schedule?switch=showclass&semester=spring&division=GRAD&dept=P...")
 
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Intelligence Analysis: A Philosophical Introduction
 
Intelligence Analysis: A Philosophical Introduction
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Special Topic PHI 589
  
 
'''Registration''':  
 
'''Registration''':  
 
:Class#: [http://www.buffalo.edu/class-schedule?switch=showclass&semester=spring&division=GRAD&dept=PHI&regnum=XXXXX XXXXX] (PHI)
 
:Class#: [http://www.buffalo.edu/class-schedule?switch=showclass&semester=spring&division=GRAD&dept=PHI&regnum=XXXXX XXXXX] (PHI)
  
'''Instructors'': [http://ontology.buffalo.edu/smith/shortcv.htm Barry Smith], [http://davidglimbaugh.com/ David Limbaugh]
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'''Instructors''': [http://ontology.buffalo.edu/smith/shortcv.htm Barry Smith], [http://davidglimbaugh.com/ David Limbaugh]
  
 
'''Prerequisites''': Open to all persons with an undergraduate degree.
 
'''Prerequisites''': Open to all persons with an undergraduate degree.
  
'''Office hours''': By appointment via email at [mailto:phismith@buffalo.edu phismith@buffalo.edu]  
+
'''Office hours''': By appointment via email at [mailto:phismith@buffalo.edu phismith@buffalo.edu] or [mailto:dglimbau@buffalo.edu dglimbau@buffalo.edu]
  
 
== '''The Course''' ==
 
== '''The Course''' ==
'''Course Description:''' The aim of the course is to provide an introduction to philosophy by focusing on a series of topics of interest to intelligence analysts. This will include topics and motivating examples in areas such as: the cognitive processes involved in intelligence analyst, the different types of evidence, the definition of 'classification' and 'clearance', the goals of intelligence analysis, statistical aspects of analytic reasoning, analytic reasong and deep learning. Philosophical ideas introduced and used will include those of epistemology, social ontology, cognitive ontology, and the philosophy of computing and information.  
+
'''Course Description:''' The aim of the course is to provide a philosophical introduction to intelligence analysis. This will involve applying the methods of philosophy to a range of topics including: the cognitive processes involved in intelligence analyst, the different types of evidence, the goals of intelligence analysis, statistical aspects of analytic reasoning, analytic reasong and deep learning. Philosophical methods employed will include those of epistemology, social ontology, cognitive ontology, and the philosophy of computing and information.  
  
'''Course Structure:''' This will be a three credit hour graduate seminar. The final session will be structured around youtube videos created by the students in the class. In addition, components of each three-hour seminar will be incorporated into a series of on-line videos.
+
'''Course Structure:''' This will be a three credit hour graduate seminar. Components of each three-hour seminar will be incorporated into a series of on-line videos. The final session will be structured around youtube videos created by the students in the class.
 +
  
'''Schedule:'''  
+
'''Background Reading:''' Robert Arp, Barry Smith and Andrew Spear, [https://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology], Cambridge, MA: MIT Press, August 2015.
==August 27: Introduction to Ontology==
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:What is an ontology?
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:Key elements of an ontology
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:What are ontologies useful for?
+
  
[https://buffalo.box.com/s/wmdex6j6xulekx31yc3tju5r9pdzjmk0 Slides]
+
Jobst Landgrebe and Barry Smith, "[https://arxiv.org/pdf/1901.02918.pdf Making AI Meaningful Again]", ''arXiv'', 2019.
[https://www.youtube.com/watch?v=9AsRE437e7I Video]
+
  
First class assignment: write a 2-page essay summarizing the key elements of an ontology as identified in the lecture and comparing them to the view of an ontology offered in [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4652617/ Hoehndorf, Schofield & Gkoutos, 2015]). Deadline: noon, September 6.
+
'''Intelligence Analysis in Buffalo''': UB scientists are involved in a variety of projects in which intelligence analysis plays a role.
 
+
Advance reading (prior to September 10 lecture): 1. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/ Scheuermann, Ceusters and Smith, 2009]. 2. [https://www.annualreviews.org/doi/pdf/10.1146/annurev-biodatasci-080917-013459 Haendel ''et. al.'', 2018]
+
'''Schedule:'''  
 
+
==August 26: Introduction to Intelligence Analysis==
==September 3: Labor Day – No class==
+
 
+
==September 10 Basic Formal Ontology==
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+
:Top-level ontologies
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:Introduction to BFO
+
 
+
BFO can be reviewed [http://www.ontobee.org/ontology/bfo here]
+
  
[https://buffalo.box.com/s/4nkf3nykjqgb7dbuquc7qiaagsixmxx7 Slides] [https://www.youtube.com/watch?v=9LVfIgBpuaY Video]
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==September 2: Labor Day – No class==
  
Advance reading (prior to September 24 lecture): [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3912703/ SW Smith and Koppel, 2014]
+
==September 9 Basic Formal Ontology==
  
==September 17: Ontology and Information Engineering in the Healthcare Domain==
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==September 16: Ontology and Information Engineering in the Healthcare Domain==
  
 
:Ontology look-alikes
 
:Ontology look-alikes
Line 53: Line 42:
 
Advance reading (prior to October 1 lecture): [https://www.hindawi.com/journals/bmri/2014/134023/ Merelli, ''et al'', 2014]
 
Advance reading (prior to October 1 lecture): [https://www.hindawi.com/journals/bmri/2014/134023/ Merelli, ''et al'', 2014]
  
==September 24: Ontology of Disease==
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==September 23: Ontology of Disease==
  
 
:Disease from the clinician’s perspective,
 
:Disease from the clinician’s perspective,
Line 65: Line 54:
 
Advance reading (prior to September 17 lecture): Chapters 5 and 6 of Arp, Smith and Spear, 2016
 
Advance reading (prior to September 17 lecture): Chapters 5 and 6 of Arp, Smith and Spear, 2016
  
==October 1: Disease / Aging / Ontology Building ==
+
==September 30: Disease / Aging / Ontology Building ==
  
 
Ontology of Disease (Continued)
 
Ontology of Disease (Continued)
Line 85: Line 74:
 
:[https://philpapers.org/rec/SCHTAO-29 Toward an Ontological Treatment of Disease and Diagnosis]
 
:[https://philpapers.org/rec/SCHTAO-29 Toward an Ontological Treatment of Disease and Diagnosis]
  
==October 8: Introduction to Protégé ==
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==October 7: Introduction to Protégé ==
  
 
[https://protege.stanford.edu/ Protégé] is the leading open-source ontology editor
 
[https://protege.stanford.edu/ Protégé] is the leading open-source ontology editor
Line 96: Line 85:
 
Fourth class assignment: Create a simple ontology using Protégé. Deadline: noon, 25 October.
 
Fourth class assignment: Create a simple ontology using Protégé. Deadline: noon, 25 October.
  
==October 15: Pain / Bruxism / Embryontology ==
+
==October 14: Pain / Bruxism / Embryontology ==
  
 
Ontology of Pain
 
Ontology of Pain
Line 118: Line 107:
 
Fifth class assignment: Create a plan for your presentation on December 3
 
Fifth class assignment: Create a plan for your presentation on December 3
  
==October 22: Joint Doctrine Ontology / Building an Ethical Warfighter / Terrorism==
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==October 21: Joint Doctrine Ontology / Building an Ethical Warfighter / Terrorism==
  
 
Joint Doctrine Ontology (JDO)
 
Joint Doctrine Ontology (JDO)
Line 137: Line 126:
 
:[https://www.researchgate.net/publication/328145335_From_Affective_Science_to_Psychiatric_Disorder_Ontology_as_a_Semantic_Bridge R. R. Larsen and J. Hastings, "From Affective Science to Psychiatric Disorder: Ontology as a Semantic Bridge" (2018)]
 
:[https://www.researchgate.net/publication/328145335_From_Affective_Science_to_Psychiatric_Disorder_Ontology_as_a_Semantic_Bridge R. R. Larsen and J. Hastings, "From Affective Science to Psychiatric Disorder: Ontology as a Semantic Bridge" (2018)]
  
==October 29: Top-Level Ontologies / The Six-Category Ontology / Truth and Maps==
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==October 28: Top-Level Ontologies / The Six-Category Ontology / Truth and Maps==
  
 
Top-Level Ontologies
 
Top-Level Ontologies
Line 156: Line 145:
 
:http://ncorwiki.buffalo.edu/index.php/Basic_Formal_Ontology_2.0 Basic Formal Ontology]
 
:http://ncorwiki.buffalo.edu/index.php/Basic_Formal_Ontology_2.0 Basic Formal Ontology]
  
==November 5: From Speech Acts to Document Acts / Social Agency / Deontics ==
+
==November 4: From Speech Acts to Document Acts / Social Agency / Deontics ==
  
 
From speech acts to document acts
 
From speech acts to document acts
Line 170: Line 159:
 
[https://buffalo.box.com/s/xrpf0b84619qcxuvcdi08ri3ufhh9zp1 Slides] [https://www.youtube.com/watch?v=g7vplac5JP0 Video]
 
[https://buffalo.box.com/s/xrpf0b84619qcxuvcdi08ri3ufhh9zp1 Slides] [https://www.youtube.com/watch?v=g7vplac5JP0 Video]
  
==November 12: Artificial Intelligence, Deep Learning, Machine Learning / Money  ==
+
==November 11: Artificial Intelligence, Deep Learning, Machine Learning / Money  ==
  
 
:Overview of machine learning and other approaches to the exploitation of Big Data (presented by [https://krkeane.github.io/about/ Kevin Keane])
 
:Overview of machine learning and other approaches to the exploitation of Big Data (presented by [https://krkeane.github.io/about/ Kevin Keane])
Line 186: Line 175:
 
:[http://arxiv.org/abs/1801.00631 G. Marcus (2018), "Deep Learning: A Critical Appraisal"]
 
:[http://arxiv.org/abs/1801.00631 G. Marcus (2018), "Deep Learning: A Critical Appraisal"]
  
==November 19: The Ontology of the Eruv ==
+
==November 18: The Ontology of the Eruv ==
  
 
The Ontology of the Eruv
 
The Ontology of the Eruv
Line 198: Line 187:
 
:[https://philpapers.org/archive/SMIOPA-3.pdf The Ontology of the Eruv]
 
:[https://philpapers.org/archive/SMIOPA-3.pdf The Ontology of the Eruv]
  
==November 26: Why computer science needs philosophy / Why I am not a Philosopher ==
+
==November 25: Why computer science needs philosophy / Why I am not a Philosopher ==
  
 
Why computer science needs philosophy
 
Why computer science needs philosophy
Line 208: Line 197:
 
[https://buffalo.box.com/s/y74umhxrfod6jr5zhh9g659pgea2weld Slides] [https://youtu.be/e5zjZnbi-ZA Video]
 
[https://buffalo.box.com/s/y74umhxrfod6jr5zhh9g659pgea2weld Slides] [https://youtu.be/e5zjZnbi-ZA Video]
  
==December 3: Student Projects ==
+
==December 2: Student Projects ==
  
1:05pm Botan Dolun: The Metaphysics of States
 
 
[https://buffalo.box.com/s/rl2mo4l5uq43g6b2ypj9ka5gq3vyijuo Slides]
 
 
1:20pm Angie Li: Ontology Representing Human Artificial Reproductive Technologies
 
 
[https://buffalo.box.com/s/s42d2e2ped7omg9u9964rx14v742plqy Slides]
 
 
1:35pm Zihe Luo: The Music Ontology
 
 
[https://buffalo.box.com/s/1n5o83lwwep7k7p8t29584lci08gsgua Slides]
 
 
1:50pm Jinwei Hu: Patient Conditions: Referent Tracking and Prognostic Terms
 
 
[https://buffalo.box.com/s/036e757j35vmyv6lnrd9duei47v6w4qr Slides]
 
 
2:05pm Alexander Anderson:  Quantum Realism
 
 
[https://buffalo.box.com/s/q7l143q7pp0vrww3cm6e7u6ikgusd7qj Slides]
 
 
2:20pm Shyamashree Srinha: Opioid Use Disorder in the
 
Light of Ontology
 
 
[https://buffalo.box.com/s/392qu8r1zksf5ezww8zr1aejxa56log9 Slides]
 
 
2:40pm William Mangione: The Drug Repurposing Ontology
 
 
[https://buffalo.box.com/s/xt1ho7gqfnshm2vg2txxgbs4ogxrx7lc Slides]
 
 
3:00pm Jonathan Vajda: On the Relation Between a Biospecimen and its Source
 
 
[https://buffalo.box.com/s/5f9854k2zdu1qv8yq7vyg6a933d4ihrq Slides]
 
 
3:20pm Eric Merrell: Ontology of Fictional Entities
 
 
[https://buffalo.box.com/s/g9hl0xcp934pe52mzy1m63b2tp7paei1 Slides]
 
 
3:35pm Arlen Brickman: Defining Cancer
 
 
'''Background Reading:''' Robert Arp, Barry Smith and Andrew Spear, [https://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology], Cambridge, MA: MIT Press, August 2015.
 
 
Jobst Landgrebe and Barry Smith, "[https://arxiv.org/pdf/1901.02918.pdf Making AI Meaningful Again]", ''arXiv'', 2019.
 
 
'''Intelligence Analysis in Buffalo''': UB scientists are involved in a variety of projects in which intelligence analysis plays a role.
 
 
== '''Schedule''' ==
 
  
  

Revision as of 13:12, 24 February 2019

Intelligence Analysis: A Philosophical Introduction Special Topic PHI 589

Registration:

Class#: XXXXX (PHI)

Instructors: Barry Smith, David Limbaugh

Prerequisites: Open to all persons with an undergraduate degree.

Office hours: By appointment via email at phismith@buffalo.edu or dglimbau@buffalo.edu

The Course

Course Description: The aim of the course is to provide a philosophical introduction to intelligence analysis. This will involve applying the methods of philosophy to a range of topics including: the cognitive processes involved in intelligence analyst, the different types of evidence, the goals of intelligence analysis, statistical aspects of analytic reasoning, analytic reasong and deep learning. Philosophical methods employed will include those of epistemology, social ontology, cognitive ontology, and the philosophy of computing and information.

Course Structure: This will be a three credit hour graduate seminar. Components of each three-hour seminar will be incorporated into a series of on-line videos. The final session will be structured around youtube videos created by the students in the class.


Background Reading: Robert Arp, Barry Smith and Andrew Spear, Building Ontologies with Basic Formal Ontology, Cambridge, MA: MIT Press, August 2015.

Jobst Landgrebe and Barry Smith, "Making AI Meaningful Again", arXiv, 2019.

Intelligence Analysis in Buffalo: UB scientists are involved in a variety of projects in which intelligence analysis plays a role.

Schedule:

August 26: Introduction to Intelligence Analysis

September 2: Labor Day – No class

September 9 Basic Formal Ontology

September 16: Ontology and Information Engineering in the Healthcare Domain

Ontology look-alikes
Use of ontology and look-alikes in biomedical applications
BFO as benchmark for biomedical Information Engineering (IE)

Slides

Second class assignment: Summarize in a 2-page essay the problems discussed in (SW Smith and Koppel, 2014) and describe how Basic Formal Ontology can assist in dealing solving them

Advance reading (prior to October 1 lecture): Merelli, et al, 2014

September 23: Ontology of Disease

Disease from the clinician’s perspective,
Ontological approaches to disease,
The Ontology for General Medical Science

Slides

Third class assignment: Summarize in a 2-page essay the issues discussed in pages 16-21 of Haendel et. al., 2018 and describe how the framework offered by Scheuermann, Ceusters and Smith, 2009 might resolve them.

Advance reading (prior to September 17 lecture): Chapters 5 and 6 of Arp, Smith and Spear, 2016

September 30: Disease / Aging / Ontology Building

Ontology of Disease (Continued)

Slides Video

Ontology of Aging

Slides Video

Ontology Building

Slides Video

Reading:

Toward an Ontological Treatment of Disease and Diagnosis

October 7: Introduction to Protégé

Protégé is the leading open-source ontology editor

This class taught by Brian Donohue

Slides Video

Fourth class assignment: Create a simple ontology using Protégé. Deadline: noon, 25 October.

October 14: Pain / Bruxism / Embryontology

Ontology of Pain

Slides Video

Bruxism

Slides Video

Embryontology

Slides Video

Readings:

"Ontology of Pain"
"16 Days"

Fifth class assignment: Create a plan for your presentation on December 3

October 21: Joint Doctrine Ontology / Building an Ethical Warfighter / Terrorism

Joint Doctrine Ontology (JDO)

Slides Video

Building an Ethical Warfighter

Slides Video

Ontology of Terrorism

Slides Video

Readings:

Department of Defense Dictionary of Military and Associated Terms
P. Morossof et al., "Joint Doctrine Ontology: A Benchmark for Military Information Systems Interoperability" (2015)
R. R. Larsen and J. Hastings, "From Affective Science to Psychiatric Disorder: Ontology as a Semantic Bridge" (2018)

October 28: Top-Level Ontologies / The Six-Category Ontology / Truth and Maps

Top-Level Ontologies

Slides Video

The Six-Category Ontology

Slides Video

Truth and the Ontology of Maps

Slides Video

Readings:

DOLCE: An Upper-Level Ontology
SUMO Suggested Upper Merged Ontology
http://ncorwiki.buffalo.edu/index.php/Basic_Formal_Ontology_2.0 Basic Formal Ontology]

November 4: From Speech Acts to Document Acts / Social Agency / Deontics

From speech acts to document acts

Slides Video

Massively planned social agency

Slides Video

Deontic entities

Slides Video

November 11: Artificial Intelligence, Deep Learning, Machine Learning / Money

Overview of machine learning and other approaches to the exploitation of Big Data (presented by Kevin Keane)
Role of ontology in Data Science
Ontology of money

Slides Video

Readings:

Barry Smith and John Searle (2003) "The Construction of Social Reality: An Exchange"
Tom Mitchell, "Key Ideas in Machine Learning"
David Donoho, "50 years of Data Science"
G. Marcus (2018), "Deep Learning: A Critical Appraisal"

November 18: The Ontology of the Eruv

The Ontology of the Eruv

Slides Video

Reading:

The Ontology of Processes and Functions
The Ontology of the Eruv

November 25: Why computer science needs philosophy / Why I am not a Philosopher

Why computer science needs philosophy

Slides Video

Why I am not a philosopher

Slides Video

December 2: Student Projects

Provisional list of topics

Ontology, AI and Robotics
Services, Commodities, Infrastructure
Product Life Cycle Ontology
Ontology and Information Engineering in the Healthcare Domain
The Science of Document Informatics
Finance Ontology
The Ontology of Plans
Ontology of Military Logistics
Ontology and Intelligence Analysis
Ontology and Data Fusion
Ontology of Terrorism

Student Learning Outcomes

Program Outcomes/Competencies Instructional Method(s) Assessment Method(s)
The student will acquire a thorough knowledge of current ontology research in areas relating to engineering, data fusion, defense and intelligence Video lectures and online discussions Review of submitted online content and of participation in online discussion forum
The student will acquire experience in ontology development Video lectures and critique of successive drafts Review of results in the form of xsl spreadsheet or Protégé file
The student will acquire experience in communicating the results of work on ontology development Creation of youtube presentation and of associated documentation Review of results

Important dates

Jan 28 - first video released by Dr Smith at 9am
Feb 20 - about now start to discuss by email the content of your video and essay with Dr Smith
Feb 28 - submit a proposed title and abstract
Mar 16 - create a simple ontology using Protege
Mar 31 - submit a table of contents and 300 word summary plus draft of associated ppt slides
Apr 27 - submit penultimate draft of essay and powerpoint
May 4 - submit final version of essay and powerpoint and upload final version of video to youtube

Grading

Grading will be based on two factors:

I: understanding and criticism of the videos presented in classes 1-13

All students are required to ingest the content of all videos and to take an active part in on-line discussions throughout the semester.

II: preparation of a youtube video and associated documentation (including powerpoint slides and essay).

Content and structure of the essay should be discussed with Dr Smith. Where the essay takes the form of the documentation of a specific ontology developed by the student it should include:

Statement of scope of the ontology
Summary of existing ontologies in the relevant domain
Explanation of how your ontology differs from (or incorporates) these ontologies
Screenshots of parts of the ontology with some examples of important terms and definitions
Summaries of potential applications of the ontology

Grading Policy: Grading follows standard Graduate School policies. Grades will be weighted according to the following breakdown:

Weighting Assignment

26% - video summaries (2% per summary)
14% - forum participation
20% - youtube video
20% - powerpoint slides
20% - essay / ontology content

Final Grades

Grade Quality Percentage

A 4.0 93.0% -100.00%
A- 3.67 90.0% - 92.9%
B+ 3.33 87.0% - 89.9%
B 3.00 83.0% - 86.9%
B- 2.67 80.0% - 82.9%
C+ 2.33 77.0% - 79.9%
C 2.00 73.0% - 76.9%
C- 1.67 70.0% - 72.9%
D+ 1.33 67.0% - 69.9%
D 1.00 60.0% - 66.9%
F 0 59.9% or below

An interim grade of Incomplete (I) may be assigned if the student has not completed all requirements for the course. An interim grade of 'I' shall not be assigned to a student who did not attend the course. The default grade accompanying an interim grade of 'I' shall be 'U' and will be displayed on the UB record as 'IU.' The default Unsatisfactory (U) grade shall become the permanent course grade of record if the 'IU' is not changed through formal notice by the instructor upon the student's completion of the course.

Assignment of an interim 'IU' is at the discretion of the instructor. A grade of 'IU' can be assigned only if successful completion of unfulfilled course requirements can result in a final grade better than the default 'U' grade. The student should have a passing average in the requirements already completed. The instructor shall provide the student specification, in writing, of the requirements to be fulfilled.

The university’s Graduate Incomplete Policy can be found here.

Related Policies and Services

Academic integrity is a fundamental university value. Through the honest completion of academic work, students sustain the integrity of the university while facilitating the university's imperative for the transmission of knowledge and culture based upon the generation of new and innovative ideas. See http://grad.buffalo.edu/Academics/Policies-Procedures/Academic-Integrity.html.

Accessibility resources: If you have any disability which requires reasonable accommodations to enable you to participate in this course, please contact the Office of Accessibility Resources in 60 Capen Hall, 645-2608 and also the instructor of this course during the first week of class. The office will provide you with information and review appropriate arrangements for reasonable accommodations, which can be found on the web here.

Background Reading and Video Materials