COURSE SYLLABUS AND OUTLINE
CSE 5095
COMPUTATIONAL MEDICAL INFORMATICS
| LECTURE:
KNS 301, Mon/Wed 11am — 12:15pm
|
LAB:
ITEB 138, Mon 9/20, 10/18, 11/15, 11am-12:15pm
|
| INSTRUCTOR:
Jinbo Bi Phone: 486-1458 Email: jinbo@engr.uconn.edu Office hours: Mon/Wed 3 pm — 4pm Office: ITEB 233 |
TEACHING ASSISTANT:
Jiangwen (Javon) Sun Phone: 486-0510 Email: jiangwen.sun@uconn.edu Office hours: to be determined Office: ITEB 213 |
PURPOSE AND APPROACH:
The purpose of this course is to introduce to the students the general topics and techniques of data mining and machine learning with specific application focus on medical informatics. This course introduces multiple real-world medical problems with real patient data, and how multiple analytic algorithms have been used in an integrated fashion to cope with these problems. It covers some cutting-edge data mining technology which can successfully tackle problems that are complex, highly dimensional, and/or ambiguous in labeling. General topics of data mining, such as clustering, classification, regression, dimension reduction, will be described. However, efforts will also be given to more advanced and recent topics, including multiple instance learning, multi-task learning, collaborative filtering, clustering with dimension reduction etc. Throughout the entire course, practical medical/healthcare problems will be used as examples to demonstrate the adoption and effectiveness of data mining methods.
The course will consist of lectures, labs, paper reviews and projects. Lectures will serve as the vehicle to introduce new information to the students. Labs will be used to enforce the material given in lectures and students paper reviews will be used to study the state-of-the-art work from researchers in the field. Participation is encouraged during the class.
As part of the course, the students will work on a term project with the goal of applying any of the studied techniques to a problem selected from a list of projects. Students are also encouraged to propose and design their own problems which need to be approved by the instructor for class suitability. Teams of two-three students will be created for each project. Each team is required to present in the classroom and submit a project report, of 15-20 pages, which includes the definition of the problem, techniques used to solve the problem and experimental results obtained. This exercise will help the team gain a hands-on understanding of the material studied in this course and promotes collaborations among team members.
COURSE OBJECTIVES:
- Get to know some general topics in medical informatics
- Focus on some high-demanding medical informatics problems with hands-on experience of applying data mining techniques
- Equip students with knowledge about the basic concepts of machine learning and the state-of-the-art literature in data mining/machine learning
TEXTBOOKS:
- Introduction to Data Mining by Pang-Ning Tan, Michael Steinbach, and Vipin Kumar, ISBN-10: 0321321367
- Pattern Classification (2nd Edition) by Richard O. Duda, Peter E. Hart and David G. Stork, ISBN-10: 0471056693
- Pattern Recognition and Machine Learning (Information Science and Statistics) by Christopher M. Bishop, ISBN-10: 0387310738
GRADING:
- In-Class Lab Assignments (3): 30%
- Paper review (2): 30%
- Term Project (1): 30%
- Participation: 10%
CURVE:
- 90.0 – 100.0 — A
- 85.0 – 89.99 — A-
- 80.0 – 84.99 — B+
- 75.0 – 79.99 — B
- 70.0 – 74.99 — B-
- 65.0 – 69.99 — C+
- 60.0 – 64.99 — C
TENTATIVE SCHEDULE:
| Week | Lecture dates | Topics | Notes |
| 1 | 8/30 | Introduction | |
| 9/1 | Review of basic algebra and probability | Hand-outs will be given at most of the class meetings | |
| 2 | 9/6 | Labor Day | Due: survey |
| 9/8 | General clustering topics, k-means | Topics of papers for review (1) | |
| 3 | 9/13 | Hierarchical clustering: traditional techniques | |
| 9/15 | Spectral clustering: modern techniques | Due: list of papers selected by students for review session (1) | |
| 4 | 9/20 | Medical problem 1: Cardiac Ultrasound Image Categorization (deal with medical images) | |
| 9/22 | Lab (1): matlab introduction and conduct clustering assignments on cardiac image data | ||
| 5 | 9/27 | Students paper review presentation (1) | 5-10min discussion for lab (1) Discussion of term projects, form teams |
| 9/29 | Student paper review presentation (1) cont. | ||
| 6 | 10/4 | General classification and regression | Due: lab (1) assignment |
| 10/6 | Linear models for regression | ||
| 7 | 10/11 | Back-propagation neural nets | |
| 10/13 | Support vector machines | Due: list of papers selected by students for review session (2) | |
| 8 | 10/18 | Medical problem 2: Computerized Decision Support for Trauma Patients (deal with physiological data) | |
| 10/20 | Lab (2): conduct classification assignments on physiological features | ||
| 9 | 10/25 | Students paper review presentation (2) | Due: lab (2) assignment |
| 10/27 | Student paper review presentation (2) cont. | ||
| 10 | 11/1 | General topics on dimension reduction | Round-table discussion about final project topics |
| 11/3 | Unsupervised dim reduction: PCA, CCA, ICA | ||
| 11 | 11/8 | Supervised dim reduction: LASSO, group LASSO, or 1-norm SVM | |
| 11/10 | Medical problem 3: Computerized Diagnostic Coding (deal with natural language text data) | ||
| 12 | 11/15 | Lab (3): conduct dimension reduction assignments on diagnostic coding data | |
| 11/17 | State of the art research: multiple instance learning | ||
| 13 | 11/29 | State of the art research: multi-task learning, collaborative filtering | Due: lab (3) assignment |
| 12/1 | State of the art research: uncertainty in expert labeling/annotation | ||
| 14 | 12/6 | Presentation of final term projects | |
| 12/8 | Presentation of final term projects (cont.) | ||
| 15 | 12/13 | Presentation of final term projects (cont.) | Due: term project report |
| 12/15 | Final exam (for make-up) |
Final project report will be due on Wednesday of the Final Exam week, 12/15/2010.
COURSE POLICY:
- Computers are allowed in classroom for taking notes or any activity related to the current class meeting.
- Assignments must be submitted electronically via HuskyCT. If the assignment is handed in late, 10 credits will be reduced for each additional day.
- Participation in paper review itself will earn 80 credits for each review assignment. Paper review presentation slides need to be turned in via HuskyCT before the class that the presentation is scheduled. The quality of your paper review presentation will be judged by the instructor (10 credits) and scoring of peer students in the class (10 credits).
- Assignments and paper reviews will be graded by the teaching assistant assigned to this course under guidance and consulting of the instructor.
- Final term projects will be graded by the instructor based on the clarity and creativity of the project report and the comparison of final presentation of all teams.
MAKEUP PLAN:
- If a lab assignment or a paper review presentation is missed, there will be a take-home final exam to make up the credits.
- If two of the lab assignments or paper reviews are missed, there will be an additional assignment and a take-home exam to make up each of the two items.
HUSKYCT:
A HuskyCT site has been set up for the class. You can access it by logging in with your NetID and password. You must use HuskyCT for submitting assignments and check it regularly for class materials, grades, problem clarifications, changes in class schedule, and other class announcements.
PROJECT MATERIALS:
Possible projects (below are some websites for benchmark data):
- UCI Machine learning repository
- SIGKDD CUP 2006
- SIGKDD CUP 2007
- SIGKDD CUP 2008
- Challenges in Machine Learning
- CMC NLP Challenge on ICD-9-CM automatic coding
- PhysioNet: Physiologic signal archives for biomedical research
TOOLS:
Tools that may help with course projects (to be complete)
- Matlab Optimization Toolbox
- SVM_Light (support vector machines)
- LIBSVM (support vector machines)
- Bayesian Knowledge Discoverer (BKD): computer program able to learn Bayesian Belief Networks from databases
- Bayes net toolbox for Matlab
- TSP Demo
- LeNet (neural networks)
- Neural networks demo
- Neural networks flash demo
- GAUL (genetic algorithm)
- Java genetic algorithm demo
- A complete notebook GA
- A system for distributing statistical software, datasets, and information by electronic mail, FTP and WWW
- Tools for mining large databases C5.0 and See5
- Description of the SLIPPER rule learner, that is a system that learns sets of rules from data based on original RIPPER rule learner
- Information about Data Mining and knowledge discovery in Databases
- Clustering Algorithms
ACADEMIC INTEGRITY:
You are expected to adhere to the highest standards of academic honesty. Unless otherwise specified, collaboration on assignments is not allowed. Use of published materials is allowed, but the sources should be explicitly stated in your solutions. Violations will be reviewed and sanctioned according to the University Policy on Academic Integrity. Collaborations among team members are only allowed for the final term projects that are selected.
Academic integrity is the pursuit of scholarly activity free from fraud and deception and is an educational objective of this institution. Academic dishonesty includes, but is not limited to, cheating, plagiarizing, fabricating of information or citations, facilitating acts of academic dishonesty by others, having unauthorized possession of examinations, submitting work for another person or work previously used without informing the instructor, or tampering with the academic work of other students.
DISABILITY STATEMENT:
If you have a documented disability for which you are or may be requesting an accommodation, you are encouraged to contact the instructor and the Center for Students with Disabilities or the University Program for College Students with Learning Disabilities as soon as possible to better ensure that such accommodations are implemented in a timely fashion.
Jinbo Bi 2010/8-2010/12
Last revised: 8/27/2010