605.624.81 - Logic: Systems, Semantics, and Models

Course Structure

The course materials are divided into modules which can be accessed by clicking Modules on the course menu. A module will have several sections including the overview, content, readings, discussions, and assignments. You are encouraged to preview all sections of the module before starting. Most modules run for a period of seven (7) days, exceptions are noted in the Course Outline. You should regularly check the Calendar and Announcements for assignment due dates.

Course Topics

Course Topics

• Categorical and Propositional Logic
• Predicate Logic
• Modal Logics
• Ontological Realism
• Social Ontology
• Basic Formal Ontology
• Ontological Engineering
• Semantic Web Standards: OWL2, RDFS, RDF, and SPARQL

Course Goals

Specific Outcomes for this course include:

• Students will gain experience formulating statements and generating proofs in various logical systems, including categorical, propositional, predicate logic.
• Students will gain experience in modal logics, including both standard modal logics (K-S5) and other extensions of K, including deontic logic.
• Students will learn how to general tree proofs for System K and M, how these rules might be extended to other systems, and as well as how trees may be used to identify counter examples.
• Students will gain experience developing ontologies in the web ontology language.
• Students will gain experience with executing SPARQL queries on knowledge graphs.

Textbooks

Required

• Garson, James W. Modal Logic for Philosophers. Cambridge University Press, 2006. Cambridge University Press, https://doi.org/10.1017/CBO9780511617737.
• Arp, Robert, et al. Building Ontologies with Basic Formal Ontology. MIT Press, 2015. https://mitpress.mit.edu/books/building-ontologies-basic-formal-ontology

Required Software

Protege Ontology Editor
https://protege.stanford.edu/ 

GraphDB
https://www.ontotext.com/products/graphdb/

Student Coursework Requirements

Course Expectations & Grading

Every class will generally consist of a set of video lectures, wiki discussions, and assignments. These assignments will vary in form, from translating English sentences into logical expressions, creating truth tables, executing deductive proofs, and truth trees, to writing short response papers and implementing ontologies.

Inference Rules

In the course, we introduce a system of natural deduction and a set of inference rules. Students are encouraged to finish all assignments using only these rules. However, students who wish to introduce their own rules in order to shorten proofs may do so, provided they first prove the validity of such rules in a separate proof using no rules other than those we have introduced in the course. No exceptions allowed.

Final Project

Students must choose at the end of the course whether to write a paper targeted for an academic journal on a topic relevant to the course, or to create an ontology using the ontology editor Protégé, along with a set of slides describing it.

Final Paper Option

The paper should be 8-12 pages in Times New Roman, double spaced, with a references section following MLA, and must not have a cover page. Topics for final papers should be approved with the instructor in advance (the purpose of which is to ensure the topic is germane to the class, and brainstorm research tips). Sample paper topics may include:

• A presentation of an axiomatization of a set of rules in some domain (e.g. axioms for consumer transactions, cyber security, video gaming, international policy) in one of the systems studied in the class.
• Describing a use case for a software system representing some state of affairs in one of the logical systems we discuss (e.g. a set of deontic logic axioms describing a library loan system).
• Critiquing a logical system for its inability to capture an important inference and suggestions on improving or revising it to address this issue.
• A research paper that criticizes, or defends from criticism, Quine’s approach to ontology.
• A research paper that criticizes or improves on Basic Formal Ontology.

Final Ontology Option

Students who choose to create an ontology are advised to start early, as these topics are only covered in the latter half of the course. The ontology should be implemented in the format Turtle, should be able to be opened in Protégé, and should seek to represent some domain of interest. Every class and relation must be well-defined and import at least one ontology (e.g. Basic Formal Ontology) that it uses and extends. The classes must be relevant to the domain, or be required for returning a particular query of interest. In addition, the ontology must be accompanied by a slide deck of PowerPoint slides that present the ontology. The ‘notes’ section of each slide should be filled out, discussing the content of each slide as though you these were a transcript of a presentation on the ontology. This presentation should include describing the domain of the ontology, describing how the ontology represents that domain, and describing how the ontology might be used to solve a problem within that domain.

Examples include:

• An ontology of potentially cancer-causing lifestyle habits that could be used to annotate cancer studies to identify mentions of particular lifestyle habits linked to cancer.
• An ontology of sensor data that could be used to serve as a common vocabulary for different sensor types.
• An ontology of features of movies that could be used to better train a recommendation algorithm for a streaming service.  

This course will consist of the following basic student requirements:

Preparation and Participation (30% of Final Grade Calculation)

You are responsible for carefully reading all assigned material and being prepared for discussion.

Post your initial response to the discussion questions by the evening of day 3 for that module week. Posting a response to the discussion question is part one of your grade for module discussions (i.e., Timeliness).

Part two of your grade for module discussions is your interaction (i.e., responding to classmate postings with thoughtful responses) with at least two classmates (i.e., Critical Thinking). Just posting your response to a discussion question is not sufficient; I want you to interact with your classmates: debate, engage, brainstorm, and share. Be detailed in your postings and in your responses to your classmates' postings. Feel free to agree or disagree with your classmates, but (of course) always ensure that your postings are civil and constructive.

I will monitor module discussions and will respond to some of the discussions as they are posted.

Evaluation of preparation and participation is based on contribution to discussions.

Preparation and participation is evaluated by the following grading elements:

• Timeliness (50%)
• Critical Thinking (50%)

Preparation and participation is graded as follows:

• 100–90 = A—Timeliness [regularly participates; all required postings; early in discussion; throughout the discussion]; Critical Thinking [rich in content; demonstrates clarity, insight, and analysis].
• 89–80 = B—Timeliness [frequently participates; all required postings; some not in time for others to read and respond]; Critical Thinking [substantial information; thought, insight, and analysis has taken place].
• 79–70 = C—Timeliness [infrequently participates; all required postings; most at the last minute without allowing for response time]; Critical Thinking [generally competent; information is thin and commonplace].
• <70 = F—Timeliness [rarely participates; some, or all required postings missing]; Critical Thinking [rudimentary and superficial; no analysis or insight is displayed].

Assignments (40% of Final Grade Calculation) and Final Project (30% of Final Grade Calculation)

Written assignments should be turned in as .docx files. These will be graded using Word’s trach change feature. Tree proofs, Venn diagrams, and formal proofs may be graphically drawn or hand drawn, scanned, and then submitted. They must be submitted as PDF files. Any scanned assignment should be examined carefully to ensure that it is clearly legible (illegible scans will result in a deduction of points).

All assignments are due according to the dates in the Calendar.

Late submissions will be reduced by one letter grade for each week late (no exceptions without prior coordination with the instructors).

If, after submitting a written assignment you are not satisfied with the grade received, you are encouraged to redo the assignment and resubmit it. If the resubmission results in a better grade, that grade will be substituted for the previous grade.

Important: Formal proofs will receive partial credit even if they are not finished, or where they contain mistakes. This should provide ample reason for showing your work and getting as far as you can, even if you find yourself unable to finish.

Written assignments and final projects are graded as follows:

• 100–90 = A—The writing is of very high quality. It is precise, exacting, and insightful. A problem is described clearly and addressed. Examples are relevant and related back to the core arguments and positions raised in the paper. The organization of the work has a clear thesis with clear supporting premises. Counterexamples and contrary positions are addressed. All arguments are clear and focused. The writing demonstrates clear engagement with outside research. All work is on time. One feels the author went through multiple drafts.
• 89–80 = B— The writing is mostly free of grammatical errors, with some exceptions. A problem is described clearly. Examples are largely relevant. The organization of the work has a clear thesis with clear support. All arguments are mostly clear and focused. Demonstrated some engagement with outside research. The work may be turned in somewhat late. One feels the author didn’t spend enough time revising, but may have started early enough.
• 79–70=C— The writing is unclear in a few key areas and contains basic grammatical errors that should have been caught in editing. A problem is described but may not be clearly addressed. Examples are mentioned but not related to the paper by the author. The organization of the work sags, with a few meandering passages or a conclusion that never materializes. There are few arguments and ideas are only described but really not supported, criticized, improved upon, or in some other way acted upon. The author is passively describing research rather than engaging with it, like a passenger in a bus listing the names of road signs seen from out a window. The work may be turned in somewhat late.
• <70=F— The writing is generally unclear and the quality of the writing poor. There is no or little research or engagement with the research performed. The central topic of the paper may be a moving target. Examples are not articulated, or are mentioned but not tied to the paper. The work lacks organization and there are few to no clear arguments. The work may be turned in somewhat late. One has the sense that the writer needed to have spent more time on the work, to have started earlier, or to have worked with another person to help them address issues in the quality of their writing.

For those who choose creating an ontology as the final option, the ontology and the PowerPoint slides shall be graded as follows:

• 100–90 = A—The ontology (and any of its required imports) is provided in turtle and opens without issue in Protege. The classes, relations, and any individuals in the ontology are clearly defined and labeled within the ontology according to the standards provided in the Building Ontologies with Basic Formal Ontology text. The number of classes appears sufficiently for covering the most important areas in the domain of interest, or are sufficient for facilitating the creation of a key query described in the slides. If the domain is very large and the classes are inadequate, the scope of future work is discussed in the slides. The slides clearly describe what the ontology is intended to represent, and any application that may later use the ontology. The presentation notes are clear and well-written. References in MLA format are included at the end for all the research that informed the presentation.
• 89–80 = B— The ontology (and any of its required imports) is provided in turtle and opens without issue in Protege.
• 79–70=C— The ontology (and any of its required imports) is provided in turtle and opens without issue in Protege.
• <70=F— The ontology is provided in a syntax of OWL, but may not open properly in Protégé. It’s necessary imports may be missing.

Grading Policy

Assignments are due according to the dates posted in your Canvas course site. You may check these due dates in the Course Calendar or the Assignments in the corresponding modules. I will post grades one week after assignment due dates.

A grade of A indicates achievement of consistent excellence and distinction throughout the course—that is, conspicuous excellence in all aspects of assignments and discussion in every week.

A grade of B indicates work that meets all course requirements on a level appropriate for graduate academic work. These criteria apply to both undergraduates and graduate students taking the course.

EP uses a +/- grading system (see “Grading System”, Graduate Programs catalog, p. 10).

100-98 = A+ 97-94 = A 93-90 = A− 89-87 = B+ 86-83 = B 82-80 = B− 79-77 = C+ 76-73 = C 72-70 = C− 69-67 = D+ 66-63 = D <63 = F

Course Policies

Academic Integrity

Academic Misconduct Policy

All students are required to read, know, and comply with the Johns Hopkins University Krieger School of Arts and Sciences (KSAS) / Whiting School of Engineering (WSE) Procedures for Handling Allegations of Misconduct by Full-Time and Part-Time Graduate Students.

This policy prohibits academic misconduct, including but not limited to the following: cheating or facilitating cheating; plagiarism; reuse of assignments; unauthorized collaboration; alteration of graded assignments; and unfair competition. You may request a paper copy of this policy at this by contacting jhep@jhu.edu.

Ethics

The strength of the university depends on academic and personal integrity. In this course, you must be honest and truthful, abiding by the Computer Science Academic Integrity Policy:

Cheating is wrong. Cheating hurts our community by undermining academic integrity, creating mistrust, and fostering unfair competition. The university will punish cheaters with failure on an assignment, failure in a course, permanent transcript notation, suspension, and/or expulsion. Offenses may be reported to medical, law or other professional or graduate schools when a cheater applies.

Violations can include cheating on exams, plagiarism, reuse of assignments without permission, improper use of the Internet and electronic devices, unauthorized collaboration, alteration of graded assignments, forgery and falsification, lying, facilitating academic dishonesty, and unfair competition. Ignorance of these rules is not an excuse.

Academic honesty is required in all work you submit to be graded. Except where the instructor specifies group work, you must solve all homework and programming assignments without the help of others. For example, you must not look at anyone else’s solutions (including program code) to your homework problems. However, you may discuss assignment specifications (not solutions) with others to be sure you understand what is required by the assignment.

If your instructor permits using fragments of source code from outside sources, such as your textbook or on-line resources, you must properly cite the source. Not citing it constitutes plagiarism. Similarly, your group projects must list everyone who participated.

Falsifying program output or results is prohibited.

Your instructor is free to override parts of this policy for particular assignments. To protect yourself: (1) Ask the instructor if you are not sure what is permissible. (2) Seek help from the instructor, TA or CAs, as you are always encouraged to do, rather than from other students. (3) Cite any questionable sources of help you may have received.

On every exam, you will sign the following pledge: "I agree to complete this exam without unauthorized assistance from any person, materials or device. [Signed and dated]". Your course instructors will let you know where to find copies of old exams, if they are available.

You can find more information about university misconduct policies on the web at these sites:

• For undergraduates: http://e-catalog.jhu.edu/undergrad-students/student-life-policies/
• For graduate students: http://e-catalog.jhu.edu/grad-students/graduate-specific-policies/

Policy on Disability Services

Johns Hopkins University (JHU) is committed to creating a welcoming and inclusive environment for students, faculty, staff and visitors with disabilities. The University does not discriminate on the basis of race, color, sex, religion, sexual orientation, national or ethnic origin, age, disability or veteran status in any student program or activity, or with regard to admission or employment. JHU works to ensure that students, employees and visitors with disabilities have equal access to university programs, facilities, technology and websites.

Under Section 504 of the Rehabilitation Act of 1973, the Americans with Disabilities Act (ADA) of 1990 and the ADA Amendments Act of 2008, a person is considered to have a disability if c (1) he or she has a physical or mental impairment that substantially limits one or more major life activities (such as hearing, seeing, speaking, breathing, performing manual tasks, walking, caring for oneself, learning, or concentrating); (2) has a record of having such an impairment; or (3) is regarded as having such an impairment class. The University provides reasonable and appropriate accommodations to students and employees with disabilities. In most cases, JHU will require documentation of the disability and the need for the specific requested accommodation.

The Disability Services program within the Office of Institutional Equity oversees the coordination of reasonable accommodations for students and employees with disabilities, and serves as the central point of contact for information on physical and programmatic access at the University. More information on this policy may be found at the Disabilities Services website or by contacting (410) 516-8075.

Disability Services

Johns Hopkins Engineering for Professionals is committed to providing reasonable and appropriate accommodations to students with disabilities.

Students requiring accommodations are encouraged to contact Disability Services at least four weeks before the start of the academic term or as soon as possible. Although requests can be made at any time, students should understand that there may be a delay of up to two weeks for implementation depending on the nature of the accommodations requested.

Requesting Accommodation

New students must submit a Disability Services Graduate Registration Form  along with supporting documentation from a qualified diagnostician that:

• Identifies the type of disability
• Describes the current level of functioning in an academic setting
• Lists recommended accommodations

Questions about disability resources and requests for accommodation at Johns Hopkins Engineering for Professionals should be directed to:

EP Disability Services Phone: 410-516-2306 Fax: 410-579-8049 E-mail: ep-disability-svcs@jhu.edu

Academic Policies

Deadlines for Adding, Dropping and Withdrawing from Courses

Students may add a course up to one week after the start of the term for that particular course. Students may drop courses according to the drop deadlines outlined in the EP academic calendar (https://ep.jhu.edu/student-services/academic-calendar/). Between the 6th week of the class and prior to the final withdrawal deadline, a student may withdraw from a course with a W on their academic record. A record of the course will remain on the academic record with a W appearing in the grade column to indicate that the student registered and withdrew from the course.

Academic Misconduct Policy

All students are required to read, know, and comply with the Johns Hopkins University Krieger School of Arts and Sciences (KSAS) / Whiting School of Engineering (WSE) Procedures for Handling Allegations of Misconduct by Full-Time and Part-Time Graduate Students.

This policy prohibits academic misconduct, including but not limited to the following: cheating or facilitating cheating; plagiarism; reuse of assignments; unauthorized collaboration; alteration of graded assignments; and unfair competition. Course materials (old assignments, texts, or examinations, etc.) should not be shared unless authorized by the course instructor. Any questions related to this policy should be directed to EP’s academic integrity officer at ep-academic-integrity@jhu.edu.

Students with Disabilities - Accommodations and Accessibility

Johns Hopkins University values diversity and inclusion. We are committed to providing welcoming, equitable, and accessible educational experiences for all students. Students with disabilities (including those with psychological conditions, medical conditions and temporary disabilities) can request accommodations for this course by providing an Accommodation Letter issued by Student Disability Services (SDS). Please request accommodations for this course as early as possible to provide time for effective communication and arrangements.

For further information or to start the process of requesting accommodations, please contact Student Disability Services at Engineering for Professionals, ep-disability-svcs@jhu.edu.

Student Conduct Code

The fundamental purpose of the JHU regulation of student conduct is to promote and to protect the health, safety, welfare, property, and rights of all members of the University community as well as to promote the orderly operation of the University and to safeguard its property and facilities. As members of the University community, students accept certain responsibilities which support the educational mission and create an environment in which all students are afforded the same opportunity to succeed academically. 

For a full description of the code please visit the following website: https://studentaffairs.jhu.edu/policies-guidelines/student-code/

Classroom Climate

JHU is committed to creating a classroom environment that values the diversity of experiences and perspectives that all students bring. Everyone has the right to be treated with dignity and respect. Fostering an inclusive climate is important. Research and experience show that students who interact with peers who are different from themselves learn new things and experience tangible educational outcomes. At no time in this learning process should someone be singled out or treated unequally on the basis of any seen or unseen part of their identity. 
 
If you have concerns in this course about harassment, discrimination, or any unequal treatment, or if you seek accommodations or resources, please reach out to the course instructor directly. Reporting will never impact your course grade. You may also share concerns with your program chair, the Assistant Dean for Diversity and Inclusion, or the Office of Institutional Equity. In handling reports, people will protect your privacy as much as possible, but faculty and staff are required to officially report information for some cases (e.g. sexual harassment).

Course Auditing

When a student enrolls in an EP course with “audit” status, the student must reach an understanding with the instructor as to what is required to earn the “audit.” If the student does not meet those expectations, the instructor must notify the EP Registration Team [EP-Registration@exchange.johnshopkins.edu] in order for the student to be retroactively dropped or withdrawn from the course (depending on when the "audit" was requested and in accordance with EP registration deadlines). All lecture content will remain accessible to auditing students, but access to all other course material is left to the discretion of the instructor.