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BIODS 237: Deep Learning in Genomics and Biomedicine (BIOMEDIN 273B, CS 273B, GENE 236)

Recent breakthroughs in high-throughput 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 high-throughput 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 CS 109, and basic machine learning such as CS 229. No prior knowledge of genomics is necessary.
Terms: Aut | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOMEDIN 273B: Deep Learning in Genomics and Biomedicine (BIODS 237, CS 273B, GENE 236)

Recent breakthroughs in high-throughput 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 high-throughput 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 CS 109, and basic machine learning such as CS 229. No prior knowledge of genomics is necessary.
Terms: Aut | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)

CS 229: Machine Learning (STATS 229)

Topics: statistical pattern recognition, linear and non-linear regression, non-parametric methods, exponential family, GLMs, support vector machines, kernel methods, model/feature selection, learning theory, VC dimension, clustering, density estimation, EM, dimensionality reduction, ICA, PCA, reinforcement learning and adaptive control, Markov decision processes, approximate dynamic programming, and policy search. Prerequisites: linear algebra, and basic probability and statistics.
Terms: Aut | Units: 3-4 | Grading: Letter or Credit/No Credit

CS 229A: Applied Machine Learning

You will learn to implement and apply machine learning algorithms. This course emphasizes practical skills, and focuses on giving you skills to make these algorithms work. You will learn about commonly used learning techniques including supervised learning algorithms (logistic regression, linear regression, SVM, neural networks/deep learning), unsupervised learning algorithms (k-means), as well as learn about specific applications such as anomaly detection and building recommender systems. This class is taught in the flipped-classroom format. You will watch videos and complete in-depth programming assignments and online quizzes at home, then come to class for discussion sections. This class will culminate in an open-ended final project, which the teaching team will help you on. Prerequisites: Programming at the level of CS106B or 106X, and basic linear algebra such as Math 51.
Terms: Spr | Units: 3-4 | Grading: Letter or Credit/No Credit

CS 229T: Statistical Learning Theory (STATS 231)

How do we formalize what it means for an algorithm to learn from data? This course focuses on developing mathematical tools for answering this question. We will present various common learning algorithms and prove theoretical guarantees about them. Topics include classical asymptotics, method of moments, generalization bounds via uniform convergence, kernel methods, online learning, and multi-armed bandits. Prerequisites: A solid background in linear algebra and probability theory, statistics and machine learning (STATS 315A or CS 229). Convex optimization (EE 364A) is helpful but not required.
Terms: not given this year | Units: 3 | Grading: Letter or Credit/No Credit

CS 230: Deep Learning

Deep Learning is one of the most highly sought after skills in AI. We will help you become good at Deep Learning. In this course, you will learn the foundations of Deep Learning, understand how to build neural networks, and learn how to lead successful machine learning projects. You will learn about Convolutional networks, RNNs, LSTM, Adam, Dropout, BatchNorm, Xavier/He initialization, and more. You will work on case studies from healthcare, autonomous driving, sign language reading, music generation, and natural language processing. You will master not only the theory, but also see how it is applied in industry. You will practice all these ideas in Python and in TensorFlow, which we will teach. AI is transforming multiple industries. After this course, you will likely find creative ways to apply it to your work. This class is taught in the flipped-classroom format. You will watch videos and complete in-depth programming assignments and online quizzes at home, then come in to class for advanced discussions and work on projects. This class will culminate in an open-ended final project, which the teaching team will help you on. Prerequisites: Familiarity with programming in Python and Linear Algebra (matrix / vector multiplications). CS 229 may be taken concurrently.
Terms: Aut, Win, Spr | Units: 3-4 | Grading: Letter or Credit/No Credit

CS 273B: Deep Learning in Genomics and Biomedicine (BIODS 237, BIOMEDIN 273B, GENE 236)

Recent breakthroughs in high-throughput 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 high-throughput 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 CS 109, and basic machine learning such as CS 229. No prior knowledge of genomics is necessary.
Terms: Aut | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)

CS 325B: Data for Sustainable Development (EARTHSYS 162, EARTHSYS 262)

The sustainable development goals (SDGs) encompass many important aspects of human and ecosystem well-being that are traditionally difficult to measure. This project-based course will focus on ways to use inexpensive, unconventional data streams to measure outcomes relevant to SDGs, including poverty, hunger, health, governance, and economic activity. Students will apply machine learning techniques to various projects outlined at the beginning of the quarter. The main learning goals are to gain experience conducting and communicating original research. Prior knowledge of machine learning techniques, such as from CS 221, CS 229, CS 231N, STATS 202, or STATS 216 is required. Open to both undergraduate and graduate students. Enrollment limited to 24. Students must apply for the class by filling out the form at https://goo.gl/forms/9LSZF7lPkHadix5D3. A permission code will be given to admitted students to register for the class.
Terms: Aut, Win | Units: 3-5 | Repeatable for credit | Grading: Letter or Credit/No Credit

CS 326: Topics in Advanced Robotic Manipulation

This course provides a survey of the most important and influential concepts in autonomous robotic manipulation. It includes classical concepts that are still widely used and recent approaches that have changed the way we look autonomous manipulation. We cover approaches towards motion planning and control using visual and tactile perception as well as machine learning. This course is especially concerned with new approaches for overcoming challenges in generalization from experience, exploration of the environment, and learning representation so that these methods can scale to real problems. Students are expected to present one paper in a tutorial, debate a paper once from the Pro and once from the Con side. They are also expected to propose an original research project and work on it towards a research paper. Recommended: CS 131, 223A, 229 or equivalents.
Terms: Aut | Units: 3-4 | Grading: Letter or Credit/No Credit
Instructors: ; Bohg, J. (PI); Lee, M. (TA)

CS 329M: Topics in Artificial Intelligence: Algorithms of Advanced Machine Learning

This advanced graduate course explores in depth several important classes of algorithms in modern machine learning. We will focus on understanding the mathematical properties of these algorithms in order to gain deeper insights on when and why they perform well. We will also study applications of each algorithm on interesting, real-world settings. Topics include: spectral clustering, tensor decomposition, Hamiltonian Monte Carlo, adversarial training, and variational approximation. Students will learn mathematical techniques for analyzing these algorithms and hands-on experience in using them. We will supplement the lectures with latest papers and there will be a significant research project component to the class. Prerequisites: Probability (CS 109), linear algebra (Math 113), machine learning (CS 229), and some coding experience.
Terms: not given this year | Units: 3 | Grading: Letter or Credit/No Credit

CS 345S: Data-intensive Systems for the Next 1000x

The last decade saw enormous shifts in the design of large-scale data-intensive systems due to the rise of Internet services, cloud computing, and Big Data processing. Where will we see the next 1000x increases in scale and data volume, and how should data-intensive systems accordingly evolve? This course will critically examine a range of trends, including the Internet of Things, drones, smart cities, and emerging hardware capabilities, through the lens of software systems research and design. Students will perform a comparative analysis by reading and discussing cutting-edge research while performing their own original research. Prerequisites: Strong background in software systems, especially databases (CS 245) and distributed systems (CS 244B), and/or machine learning (CS 229). Undergraduates who have completed CS 245 are strongly encouraged to attend.
Terms: not given this year | Units: 3-4 | Grading: Letter or Credit/No Credit

EARTHSYS 162: Data for Sustainable Development (CS 325B, EARTHSYS 262)

The sustainable development goals (SDGs) encompass many important aspects of human and ecosystem well-being that are traditionally difficult to measure. This project-based course will focus on ways to use inexpensive, unconventional data streams to measure outcomes relevant to SDGs, including poverty, hunger, health, governance, and economic activity. Students will apply machine learning techniques to various projects outlined at the beginning of the quarter. The main learning goals are to gain experience conducting and communicating original research. Prior knowledge of machine learning techniques, such as from CS 221, CS 229, CS 231N, STATS 202, or STATS 216 is required. Open to both undergraduate and graduate students. Enrollment limited to 24. Students must apply for the class by filling out the form at https://goo.gl/forms/9LSZF7lPkHadix5D3. A permission code will be given to admitted students to register for the class.
Terms: Aut, Win | Units: 3-5 | Repeatable for credit | Grading: Letter or Credit/No Credit

EARTHSYS 262: Data for Sustainable Development (CS 325B, EARTHSYS 162)

The sustainable development goals (SDGs) encompass many important aspects of human and ecosystem well-being that are traditionally difficult to measure. This project-based course will focus on ways to use inexpensive, unconventional data streams to measure outcomes relevant to SDGs, including poverty, hunger, health, governance, and economic activity. Students will apply machine learning techniques to various projects outlined at the beginning of the quarter. The main learning goals are to gain experience conducting and communicating original research. Prior knowledge of machine learning techniques, such as from CS 221, CS 229, CS 231N, STATS 202, or STATS 216 is required. Open to both undergraduate and graduate students. Enrollment limited to 24. Students must apply for the class by filling out the form at https://goo.gl/forms/9LSZF7lPkHadix5D3. A permission code will be given to admitted students to register for the class.
Terms: Aut, Win | Units: 3-5 | Repeatable for credit | Grading: Letter or Credit/No Credit

GENE 236: Deep Learning in Genomics and Biomedicine (BIODS 237, BIOMEDIN 273B, CS 273B)

Recent breakthroughs in high-throughput 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 high-throughput 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 CS 109, and basic machine learning such as CS 229. No prior knowledge of genomics is necessary.
Terms: Aut | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)

MS&E 234: Data Privacy and Ethics

This course engages with difficult ethical challenges in the modern practice of data science. The three main focuses are data privacy, personalization and targeting algorithms, and online experimentation. The focus on privacy will raise both practical and theoretical considerations. As part of the module on experimentation, students will be required to complete the Stanford IRB training for social and behavioral research. The course will assume a strong familiarity with the practice of machine learning and and data science. Recommended: MS&E 226, MS&E 231, CS 229, or equivalents.
Terms: Spr | Units: 3 | Grading: Letter or Credit/No Credit

STATS 231: Statistical Learning Theory (CS 229T)

How do we formalize what it means for an algorithm to learn from data? This course focuses on developing mathematical tools for answering this question. We will present various common learning algorithms and prove theoretical guarantees about them. Topics include classical asymptotics, method of moments, generalization bounds via uniform convergence, kernel methods, online learning, and multi-armed bandits. Prerequisites: A solid background in linear algebra and probability theory, statistics and machine learning (STATS 315A or CS 229). Convex optimization (EE 364A) is helpful but not required.
Terms: not given this year | Units: 3 | Grading: Letter or Credit/No Credit
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