MEBI 550: Knowledge Representation and Applications

Course learning objectives for MEBI 550

At the completion of the course, students will have a working knowledge of ideas, methods and open questions in formal knowledge representation and their application to biology, medicine and public health. They will be able to:

• Distinguish among various kinds of data representations and encodings used in biomedicine and give examples of the use of each,
• Translate biological, medical or public health factual assertions or statements of knowledge into formal logic using traditional logic notation and in a form that can be used directly by a computer program or system,
• Perform simple logic proofs,
• Describe basic properties of frame systems and write frame representations for examples of biomedical knowledge,
• Perform subsumption and classification of statements written in a description logic,
• Apply basic Bayesian probability formulas to answer questions about probabilistic biomedical problems,
• Analyze biomedical knowledge representation and reasoning problems and give reasons for using or not using particular programming languages, software environments or methodologies.

In addition, students will have gained basic skills with programming in Common Lisp. At the end of the course, students will be able to perform the following representative tasks, illustrating a solid basic knowledge of core programming concepts:

• Write small Common Lisp programs (100--200 lines of code).
• Write functions in the Common Lisp programming language, that illustrate the following techniques:
  • conditional expressions,
  • recursion, with lists and trees,
  • iteration,
  • the use of auxiliary or helper functions,
  • the use of user defined structured types.
• Given a list of expressions or function definitions in Common Lisp, identify which ones cause side effects and which do not.
• Given a small function definition (10 to 20 lines of code), determine if it is syntactically correct.
• Given a statement of an algorithm for a simple computation, or an implementation in code, determine whether it will terminate on all valid inputs.
• Utilize in their programs elements of the Common Lisp Object System.