BIODS 232: Consulting Workshop on Biomedical Data Science
The Data Studio is a collaboration between Spectrum (The Stanford Center for Clinical and Translational research and Education) and the Department of Biomedical Data Science (DBDS). The educational goal of this workshop is to provide data science consultation training for students. Data Studio is open to the Stanford community, and we expect it to have educational value for students and postdocs interested in biomedical data science. Most sessions are workshops that provide an extensive and indepth consultation for a Medical School researcher based on research questions, data, statistical models, and other material prepared by the researcher with the aid of our facilitator. At the workshop, the researcher explains the project, goals, and needs. Experts in the area across campus will be invited and contribute to the brainstorming. After the workshop, the facilitator will follow up,helping with immediate action items and summary of the discussion. The last session of each month is devot
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The Data Studio is a collaboration between Spectrum (The Stanford Center for Clinical and Translational research and Education) and the Department of Biomedical Data Science (DBDS). The educational goal of this workshop is to provide data science consultation training for students. Data Studio is open to the Stanford community, and we expect it to have educational value for students and postdocs interested in biomedical data science. Most sessions are workshops that provide an extensive and indepth consultation for a Medical School researcher based on research questions, data, statistical models, and other material prepared by the researcher with the aid of our facilitator. At the workshop, the researcher explains the project, goals, and needs. Experts in the area across campus will be invited and contribute to the brainstorming. After the workshop, the facilitator will follow up,helping with immediate action items and summary of the discussion. The last session of each month is devoted to dropin consulting. DBDS faculty are available to provide assistance with your research questions. Skills required of practicing biomedical consultants, including exposed to biomedical and health science applications, identification of data science related questions, selection or development of appropriate statistical and analytic approaches to answer research needs. Students are required to attend the regular workshops and participate one to two consulting projects as team members under the supervision of faculty members or senior staff. Depending on the nature of the consulting service, the students may need to conduct numerical simulation, plan sample size, design study, and analyze client data. the formal written report needs to be completed at the end of consulting projects. May be repeated for credit. Prerequisites: course work in applied statistics, data analysis, and consent of instructor.
Terms: Aut, Win, Spr

Units: 2

Repeatable for credit

Grading: Medical Satisfactory/No Credit
Instructors:
Lu, Y. (PI)
;
Sabatti, C. (PI)
;
Tian, L. (PI)
;
Desai, M. (SI)
;
Efron, B. (SI)
;
Lavori, P. (SI)
;
Narasimhan, B. (SI)
;
Stell, L. (TA)
BIODS 237: Deep Learning in Genomics and Biomedicine (BIOMEDIN 273B, CS 273B, GENE 236)
Recent breakthroughs in highthroughput genomic and biomedical data are transforming biological sciences into "big data" disciplines. In parallel, progress in deep neural networks are revolutionizing fields such as image recognition, natural language processing and, more broadly, AI. This course explores the exciting intersection between these two advances. The course will start with an introduction to deep learning and overview the relevant background in genomics and highthroughput biotechnology, focusing on the available data and their relevance. It will then cover the ongoing developments in deep learning (supervised, unsupervised and generative models) with the focus on the applications of these methods to biomedical data, which are beginning to produced dramatic results. In addition to predictive modeling, the course emphasizes how to visualize and extract interpretable, biological insights from such models. Recent papers from the literature will be presented and discussed. Stude
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Recent breakthroughs in highthroughput genomic and biomedical data are transforming biological sciences into "big data" disciplines. In parallel, progress in deep neural networks are revolutionizing fields such as image recognition, natural language processing and, more broadly, AI. This course explores the exciting intersection between these two advances. The course will start with an introduction to deep learning and overview the relevant background in genomics and highthroughput biotechnology, focusing on the available data and their relevance. It will then cover the ongoing developments in deep learning (supervised, unsupervised and generative models) with the focus on the applications of these methods to biomedical data, which are beginning to produced dramatic results. In addition to predictive modeling, the course emphasizes how to visualize and extract interpretable, biological insights from such models. Recent papers from the literature will be presented and discussed. Students will be introduced to and work with popular deep learning software frameworks. Students will work in groups on a final class project using real world datasets. Prerequisites: College calculus, linear algebra, basic probability and statistics such as
CS109, and basic machine learning such as
CS229. No prior knowledge of genomics is necessary.
Terms: Aut

Units: 3

Grading: Medical Option (MedLtrCR/NC)
Instructors:
Kundaje, A. (PI)
;
Zou, J. (PI)
BIODS 248: Clinical Trial Design in the Age of Precision Medicine and Health (STATS 248)
Advances in panomic technologies and system biology have led to novel therapies in the era of precision medicine. This course introduces innovative study designs to meet the challenges in designing confirmatory (pivotal) randomized controlled trials to evaluate these new treatments, including enrichment designs and master protocols, and examples of their recent successes in gaining regulatory approval of novel stroke and cancer therapies. Prerequisite:
Stats 245/P or equivalent.
Terms: Aut

Units: 24

Grading: Letter or Credit/No Credit
Instructors:
Lai, T. (PI)
;
Lavori, P. (PI)
BIODS 260A: Workshop in Biostatistics (STATS 260A)
Applications of statistical techniques to current problems in medical science. To receive credit for one or two units, a student must attend every workshop. To receive two units, in addition to attending every workshop, the student is required to write an acceptable one page summary of two of the workshops, with choices made by the student.
Terms: Aut

Units: 12

Repeatable for credit

Grading: Medical Satisfactory/No Credit
Instructors:
Palacios, J. (PI)
;
Sabatti, C. (PI)
BIODS 299: Directed Reading and Research
For students wishing to receive credit for directed reading or research time. Prerequisite: consent of instructor.
Terms: Aut, Win, Spr, Sum

Units: 118

Repeatable for credit

Grading: Medical Option (MedLtrCR/NC)
Instructors:
Bustamante, C. (PI)
;
Hastie, T. (PI)
;
Olshen, R. (PI)
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Instructors:
Bustamante, C. (PI)
;
Hastie, T. (PI)
;
Olshen, R. (PI)
;
Rivas, M. (PI)
;
Sabatti, C. (PI)
;
Salzman, J. (PI)
;
Tibshirani, R. (PI)
;
Zou, J. (PI)