Portland Campus · School of Medicine
BCB II: Statistical Methods
- Winter 2022
- 4 Credits
- 01/03/2022 to 03/18/2022
- Modified 12/30/2021
This course will be a problem-driven examination of the quantitative issues in computational biology. The course will provide students with the statistical fundamentals underlying the techniques covered. Topics will include applications involving MCMC Models, Maximum Likelihood, Random Walks, Hidden Markov Models, Estimating Genealogical Relationships and Networks. Students will be evaluated on written assignments and a programming project.
Note: 4 credits includes 1 credit Lab
Offering: On Campus: Winter
This syllabus is for BMI 551 PDX W22, BMI 651 PDX W22
James E. Jacobs, MD, MPH, Instructor, Division of Pediatric Hematology/Oncology, Department of Pediatrics and Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology.
E-mail: [email protected]
Office hours: TBD
Shannon K. McWeeney, Ph.D., Professor, Division of Biostatistics, Department of Public Health & Preventive Medicine AND Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology Location: 14D72 Hatfield Mail code: CR-145 Phone: (503) 494-8347
E-mail: [email protected]
COURSE TIME AND LOCATION:
Tuesday & Thursday 9:00-10:20
Classes will be in person: BICC Room 124
Required: Hastie, Tibshirani and Friedman. The Elements of Statistical Learning: Data Mining, Inference, and Prediction (2009) Second Edition
James G, et al. An Introduction to Statistical Learning with Applications in R (2015)
Hahne F, Huber W, Gentleman R Bioconductor Case Studies (Use R) (2008). 1st Edition.
Ewens WJ and GR Grant. Statistical Methods in Bioinformatics (2005) 2nd Edition
Notes: We will be supplementing the textbook with lecture handouts and articles throughout the quarter.
Course Competencies, Outcomes, and Objectives
- Understand the basic structure of supervised and unsupervised statistical learning methods
- Know the importance of testing error vs. training error when determining the parameters for a given learning model
- Learn how statistical learning methods vary in terms of the bias-variance trade-offs
- Understand the process of model assessment and model selection when presented with real-world data analyses
- Develop a basic knowledge of stochastic vs. deterministic processes and their applications in various learning methods
- Be able to identify and account for issues surrounding multiple hypothesis testing
HOMEWORK: There will be weekly homework assignments, generally assigned during class and due the following week.
METHODS OF EVALUATION: The course grade will be based on 20% class participation; 30% homework; 20% midterm examination; 30% final – analytics project submission via Kaggle.
Course & Instructor Evaluations
Course Policies and Resources
School Policies and Resources
Graduate Studies Guidelines:
Students are responsible for following all OHSU School of Medicine, Graduate Studies, and program/department guidelines & policies. For more information, please visit here. For program/department guidelines & policies, please inquiry with the program/department director and/or coordinator.
School of Medicine Conduct Policy (housed under the graduate studies guidelines section)
Students are responsible for their own academic work. Students are expected to have read and practice principles of academic honesty, as presented in the Graduate Studies Student Handbook.
The School of Medicine reserves the privilege of retaining only those students who, in the judgement of the faculty, satisfy the requirements of scholarship and clinical performance necessary to maintain the highest standards. The Student Handbook has information about academic standards and probation and dismissal policies.
Grading Criteria, Academic Standards, & Release of Final Grades:
Graduate Studies in the OHSU School of Medicine is committed to providing grades to students in a timely manner. Course instructors will provide students with information in writing at the beginning of each course that describes the grading policies and procedures including but not limited to evaluation criteria, expected time needed to grade individual student examinations and type of feedback they will provide.
All coursework applied towards degree requirements must meet the minimum cumulative grade point average of at least 3.0.
Refer to the School of Medicine Graduate Studies Forms & Policies for withdraw, incomplete, and in-progress grading standards. Final course grades will be posted with the OHSU Registrar the Monday following the last day of the term. On those occasions when a grade has not been submitted by the deadline, the following procedure shall be followed:
- The Department*/Program** Coordinator will immediately contact the Instructor requesting the missing grade, with a copy to the Program Director and Registrar.
- If the grade is still overdue by the end of next week, the Department*/Program** Coordinator will email the Department Chair directly, with a copy to the Instructor and Program Director requesting resolution of the missing grade.
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*For courses that are run by a specific department.
**For the conjoined courses (course number is preceded by CON) that are run by Graduate Studies.
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Graduate Studies Copyright Information
Every reasonable effort has been made to protect the copyright requirements of materials used in this course. Class participants are warned not to copy, audio, or videotape in violation of copyright laws. Journal articles will be kept on reserve at the library or online for student access. Copyright law does allow for making one personal copy of each article from the original article. This limit also applies to electronic sources.
DMICE Communication Policy
- If the syllabus directs the student to contact the TA before contacting the instructor, the student should do so. Otherwise, the student should contact the instructor and allow 2 business days (not including weekends) for a response.
- If the student does not receive a response from the instructor within 2 business days, s/he should contact the TA (if there is one). When contacting the TA s/he should cc the instructor and Vanessa Reeves at [email protected].
- If a student does not receive a response from the TA within 1 business day (not including weekends), s/he should contact Vanessa Reeves at [email protected] and cc the instructor and the TA.
- If Vanessa does not reply within 1 business day (not including weekends), the student should contact Andrea Ilg at [email protected].
- Students having difficulties with Sakai should contact the Sakai Help Desk at [email protected] or at (877) 972-5249. Sakai help is available M-F from 8am to 10-pm and weekends from Noon to 5pm. Do not contact the instructor.
When Problems Arise
It is critical to contact the appropriate person when problems arise:
- For basic Sakai problems and course issues (e.g., cannot log in, after-hours technical assistance, Course Materials or Forum not available/accessible during regular business hours/days), contact the Sakai Help Desk: Toll-Free - (877) 972-5249; email - [email protected]. Sakai help is available M-F from 8 am to 9 pm and weekends from Noon to 5pm.
- For questions about course content (e.g., do not understand a topic or disagree with homework quiz answer), contact the Teaching Assistant, who will be announced at the beginning of the course: go to the Email Tab after logging into the course and choose “Associate” role to send message to the TA or post a question in the Forums.
It is OHSU policy that any exam offered online and worth more than 10% of the final course grade must be virtually proctored. In this course, we will be using the services of Examity, a remote proctoring services company. You will be required to schedule your exam three (3) weeks ahead of time. There is no cost to the student. More information will be provided to you regarding setup, scheduling, and requirements in the Course Materials.
Turn It In
In an effort to uphold the principles and practice of academic honesty, faculty members at OHSU may use originality checking systems such as Turnitin to compare a student’s submitted work against multiple sources. To protect student privacy in this process, it will be necessary to remove all personal information, i.e. student name, email address, student u-number, or any other personal information, from documents BEFORE submission.
Sakai and TLC Help Desk
You will learn through the Sakai learning management software at http://sakai.ohsu.edu. The online component includes reading material, lectures (including streaming presentations and handouts), project material, learning assignments, and online discussions. If you have any technical questions or if you need help logging in, please contact the Sakai Help Desk, which is open Mon – Fri, 8 am – 9 pm and weekends 12 pm – 5 pm, Pacific Time.
(Email) [email protected]
Please use professional etiquette when communicating with peers and the instructor. This means avoiding aggressive or offensive language, showing respect for others’ opinions and positions, and conducting yourself as if you were face to face with them. Please pay special attention to etiquette in class forums and when using email. If you notice someone violating this policy, please make the instructor and TA aware of the problem.
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List of OHSU Graduation Core Competencies
- Professional Knowledge and Skills
- Information Literacy
- Community Engagement, Social Justice and Equity
- Patient Centered Care
To access a descriptive list of OHSU Graducation Core Competencies: OHSU Graduation Core Competencies
Institutional Policies and Resources
Statement Regarding Students with Disabilities:
OHSU is committed to inclusive and accessible learning environments in compliance with federal and state law. If you have a disability or think you may have a disability (mental health, attention-related, learning, vision, hearing, physical or health impacts) contact the Office for Student Access at (503) 494-0082 or OHSU Student Access to have a confidential conversation about academic accommodations. Information is also available at Student Access Website. Because accommodations may take time to implement and cannot be applied retroactively, it is important to have this discussion as soon as possible.
Student Evaluation of Courses:
Course evaluation results are extremely important and used to help improve courses and the learning experience of future students. Responses will always remain anonymous and will only be available to instructors after grades have been posted. The results of scaled questions and comments go to both the instructor and their unit head/supervisor. Refer to Student Evaluation of Courses and Instructional Effectiveness, *Policy No. 02-50-035.
*To access the OHSU Student Evaluation of Courses and Instructional Effectiveness Policy, you must log into the OHSU O2 website.
Copyright laws and fair use policies protect the rights of those who have produced the material. The copy in this course has been provided for private study, scholarship, or research. Other uses may require permission from the copyright holder. The user of this work is responsible for adhering to copyright law of the U.S. (Title 17, U.S. Code). To help you familiarize yourself with copyright and fair use policies, the University encourages you to visit its Copyright Web Page
Sakai course web sites contain material protected by copyrights held by the instructor, other individuals or institutions. Such material is used for educational purposes in accord with copyright law and/or with permission given by the owners of the original material. You may download one copy of the materials on any single computer for non-commercial, personal, or educational purposes only, provided that you (1) do not modify it, (2) use it only for the duration of this course, and (3) include both this notice and any copyright notice originally included with the material. Beyond this use, no material from the course web site may be copied, reproduced, re-published, uploaded, posted, transmitted, or distributed in any way without the permission of the original copyright holder. The instructor assumes no responsibility for individuals who improperly use copyrighted material placed on the web site.
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Syllabi are considered to be a learning agreement between students and the faculty of record. Information contained in syllabi, other than the minimum requirements, may be subject to change as deemed appropriate by the faculty of record in concurrence with the academic program and the Office of the Provost. Refer to the *Course Syllabi Policy, 02-50-050.
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Modified Operations, Policy 01-40-010:
Portland Campus: Marquam Hill and South Waterfront
Students should review O2 or call OHSU’s weather alert line at 503-494-9021 for the most up-to-date information on OHSU-wide modified operations which include but are not limited to delays or closures for inclement weather.
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Remote Learning Resources
The Remote Learning webpage on O2 contains concise, practical resources, and strategies for students that need to quickly transition to a fully remote instructional format.
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Concourse Syllabus Management
For help with accessing your Concourse Syllabus: Please contact the Sakai help Desk for all other Concourse inquiries please visit the Concourse Support - Sakai or please contact the Mark Rivera at [email protected] or call 503-494-0934
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Wellness Center Information
Wellness Center Website
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Library: Biomedical Information Communication Center
BICC Library Hours of Operation
Privacy While Learning Remotely
Students may be asked to take classes remotely through videoconferencing software like WebEx. Some of these remote classes will be recorded. Any recording will capture the presenter’s audio, video, and computer screen. Student video and audio will be recorded if and when you unmute your audio and share your video during the recorded sessions. These recordings will not be shared with or accessible to the public without prior written consent.