printer friendly pageCS 235: Computational Methods for Biomedical Image Analysis and Interpretation (BIOMEDIN 260, BMP 260, RAD 260)
The latest biological and medical imaging modalities and their applications in research and medicine. Focus is on computational analytic and interpretive approaches to optimize extraction and use of biological and clinical imaging data for diagnostic and therapeutic translational medical applications. Topics include major image databases, fundamental methods in image processing and quantitative extraction of image features, structured recording of image information including semantic features and ontologies, indexing, search and content-based image retrieval. Case studies include linking image data to genomic, phenotypic and clinical data, developing representations of image phenotypes for use in medical decision support and research applications and the role that biomedical imaging informatics plays in new questions in biomedical science. Includes a project. Enrollment for 3 units requires instructor consent. Prerequisites: programming ability at the level of
CS 106A, familiarity with statistics, basic biology. Knowledge of Matlab or Python highly recommended.
Terms: Spr
| Units: 3-4
Instructors:
Rusu, M. (PI)
;
Rubin, D. (SI)
;
Bravo Sanchez, L. (TA)
...
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Instructors:
Rusu, M. (PI)
;
Rubin, D. (SI)
;
Bravo Sanchez, L. (TA)
;
Franke, C. (TA)
;
Lozano Garcia, E. (TA)
CS 236G: Generative Adversarial Networks
Generative Adversarial Networks (GANs) have rapidly emerged as the state-of-the-art technique in realistic image generation. This course presents theoretical intuition and practical knowledge on GANs, from their simplest to their state-of-the-art forms. Their benefits and applications span realistic image editing that is omnipresent in popular app filters, enabling tumor classification under low data schemes in medicine, and visualizing realistic scenarios of climate change destruction. This course also examines key challenges of GANs today, including reliable evaluation, inherent biases, and training stability. After this course, students should be familiar with GANs and the broader generative models and machine learning contexts in which these models are situated. Prerequisites: linear algebra, statistics,
CS106B, plus a graduate-level AI course such as:
CS230,
CS229 (or
CS129), or
CS221.
Last offered: Winter 2022
CS 275: Translational Bioinformatics (BIOE 217, BIOMEDIN 217, GENE 217)
Analytic and interpretive methods to optimize the transformation of genetic, genomic, and biological data into diagnostics and therapeutics for medicine. Topics: access and utility of publicly available data sources; types of genome-scale measurements in molecular biology and genomic medicine; linking genome-scale data to clinical data and phenotypes; and new questions in biomedicine using bioinformatics. Case studies. Prerequisites: programming ability at the level of
CS 106A and familiarity with statistics and biology.
Terms: Spr
| Units: 3-4
CS 279: Computational Biology: Structure and Organization of Biomolecules and Cells (BIOE 279, BIOMEDIN 279, BIOPHYS 279, CME 279)
Computational techniques for investigating and designing the three-dimensional structure and dynamics of biomolecules and cells. These computational methods play an increasingly important role in drug discovery, medicine, bioengineering, and molecular biology. Course topics include protein structure prediction, protein design, drug screening, molecular simulation, cellular-level simulation, image analysis for microscopy, and methods for solving structures from crystallography and electron microscopy data. Prerequisites: elementary programming background (
CS 106A or equivalent) and an introductory course in biology or biochemistry.
Terms: Aut
| Units: 3
Instructors:
Dror, R. (PI)
;
Bresette, L. (TA)
;
Li, D. (TA)
;
McAvity, J. (TA)
;
Sayana, R. (TA)
;
Suriana, P. (TA)
;
Xu, J. (TA)
CS 309A: Cloud Computing Seminar
For science, engineering, computer science, business, education, medicine, and law students. Cloud computing is bringing information systems out of the back office and making it core to the entire economy. Furthermore with the advent of smarter machines cloud computing will be integral to building a more precision planet. This class is intended for all students who want to begin to understand the implications of this technology. Guest industry experts are public company CEOs who are either delivering cloud services or using cloud services to transform their businesses.
Terms: Aut
| Units: 1
| Repeatable
for credit
Instructors:
Chou, T. (PI)
CS 337: AI-Assisted Care (MED 277)
AI has been advancing quickly, with its impact everywhere. In healthcare, innovation in AI could help transforming of our healthcare system. This course offers a diverse set of research projects focusing on cutting edge computer vision and machine learning technologies to solve some of healthcare's most important problems. The teaching team and teaching assistants will work closely with students on research projects in this area. Research projects include Care for Senior at Senior Home, Surgical Quality Analysis, AI Assisted Parenting, Burn Analysis & Assessment and more. AI areas include Video Understanding, Image Classification, Object Detection, Segmentation, Action Recognition, Deep Learning, Reinforcement Learning, HCI and more. The course is open to students in both school of medicine and school of engineering.
Terms: Aut
| Units: 1-4
Instructors:
Adeli, E. (PI)
;
Milstein, A. (PI)
;
Schulman, K. (PI)
...
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Instructors:
Adeli, E. (PI)
;
Milstein, A. (PI)
;
Schulman, K. (PI)
;
Kaushal, A. (SI)
;
Li, F. (SI)
CS 342: Building for Digital Health (MED 253)
This project-based course will provide a comprehensive overview of key requirements in the design and full-stack implementation of a digital health research application. Several pre-vetted and approved projects from the Stanford School of Medicine will be available for students to select from and build. Student teams learn about all necessary approval processes to deploy a digital health solution (data privacy clearance/I RB approval, etc.) and be guided in the development of front-end and back-end infrastructure using best practices. The final project will be the presentation and deployment of a fully approved digital health research application.
CS106A,
CS106B, Recommended:
CS193P/A,
CS142,
CS47,
CS110. Limited enrollment for this course. Apply for enrollment permission here:
https://stanforduniversity.qualtrics.com/jfe/form/SV_9ThVhqf4zyhzheS
Terms: Win
| Units: 3-4
Instructors:
Aalami, O. (PI)
;
Guestrin, C. (SI)
CS 371: Computational Biology in Four Dimensions (BIOMEDIN 371, BIOPHYS 371, CME 371)
Cutting-edge research on computational techniques for investigating and designing the three-dimensional structure and dynamics of biomolecules, cells, and everything in between. These techniques, which draw on approaches ranging from physics-based simulation to machine learning, play an increasingly important role in drug discovery, medicine, bioengineering, and molecular biology. Course is devoted primarily to reading, presentation, discussion, and critique of papers describing important recent research developments. Prerequisite:
CS 106A or equivalent, and an introductory course in biology or biochemistry. Recommended: some experience in mathematical modeling (does not need to be a formal course).
Last offered: Winter 2023
CS 372: Artificial Intelligence for Precision Medicine and Psychiatric Disorders
Artificial intelligence, specifically deep learning, stands out as one of the most transformative technologies of the past decade. AI can already outperform humans in several computer vision and natural language processing tasks. However, we still face some of the same limitations and obstacles that led to the demise of the first AI boom phase five decades ago. This research-oriented course will first review and reveal the limitations (e.g., iid assumption on training and testing data, voluminous training data requirement, and lacking interpretability) of some widely used AI algorithms, including convolutional neural networks (CNNs), transformers, reinforcement learning, and generative adversarial networks (GANs). To address these limitations, we will then explore topics including transfer learning for remedying data scarcity, knowledge-guided multimodal learning for improving data diversity, out of distribution generalization, attention mechanisms for enabling Interpretability, meta l
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Artificial intelligence, specifically deep learning, stands out as one of the most transformative technologies of the past decade. AI can already outperform humans in several computer vision and natural language processing tasks. However, we still face some of the same limitations and obstacles that led to the demise of the first AI boom phase five decades ago. This research-oriented course will first review and reveal the limitations (e.g., iid assumption on training and testing data, voluminous training data requirement, and lacking interpretability) of some widely used AI algorithms, including convolutional neural networks (CNNs), transformers, reinforcement learning, and generative adversarial networks (GANs). To address these limitations, we will then explore topics including transfer learning for remedying data scarcity, knowledge-guided multimodal learning for improving data diversity, out of distribution generalization, attention mechanisms for enabling Interpretability, meta learning, and privacy-preserving training data management. The course will be taught through a combination of lecture and project sessions. Lectures on specialized AI applications (e.g., cancer/depression diagnosis and treatment, AI/VR for surgery, and health education) will feature guest speakers from academia and industry. Students will be assigned to work on an extensive project that is relevant to their fields of study (e.g., CS, Medicine, and Data Science). Projects may involve conducting literature surveys, formulating ideas, and implementing these ideas. Example project topics are but not limited to 1) knowledge guided GANs for improving training data diversity, 2) disease diagnosis via multimodal symptom checking, and 3) fake and biased news/information detection.
Terms: Spr
| Units: 3
Instructors:
Chang, E. (PI)
;
Jin, M. (TA)
CS 571: Surgical Robotics Seminar (ME 571)
Surgical robots developed and implemented clinically on varying scales. Seminar goal is to expose students from engineering, medicine, and business to guest lecturers from academia and industry. Engineering and clinical aspects connected to design and use of surgical robots, varying in degree of complexity and procedural role. May be repeated for credit.
Last offered: Winter 2019
| Repeatable
for credit
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