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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 217: Hardware Accelerators for Machine Learning

This course provides in-depth coverage of the architectural techniques used to design accelerators for training and inference in machine learning systems. This course will cover classical ML algorithms such as linear regression and support vector machines as well as DNN models such as convolutional neural nets, and recurrent neural nets. We will consider both training and inference for these models and discuss the impact of parameters such as batch size, precision, sparsity and compression on the accuracy of these models. We will cover the design of accelerators for ML model inference and training. Students will become familiar with hardware implementation techniques for using parallelism, locality, and low precision to implement the core computational kernels used in ML. To design energy-efficient accelerators, students will develop the intuition to make trade-offs between ML model parameters and hardware implementation techniques. Students will read recent research papers and complete a design project. Prerequisites: CS 149 or EE 180. CS 229 is ideal, but not required.
Terms: Win | Units: 3-4 | Grading: Letter or Credit/No Credit

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, deep learning, model/feature selection, learning theory, ML advice, clustering, density estimation, EM, dimensionality reduction, ICA, PCA, reinforcement learning and adaptive control, Markov decision processes, approximate dynamic programming, and policy search. Prerequisites: knowledge of basic computer science principles and skills at a level sufficient to write a reasonably non-trivial computer program in Python/numpy, familiarity with probability theory to the equivalency of CS109 or STATS116, and familiarity with multivariable calculus and linear algebra to the equivalency of MATH51.
Terms: Aut, Spr, Sum | Units: 3-4 | 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 | UG Reqs: WAY-AQR, WAY-FR | Grading: Letter or Credit/No Credit

CS 236: Deep Generative Models

Generative models are widely used in many subfields of AI and Machine Learning. Recent advances in parameterizing these models using neural networks, combined with progress in stochastic optimization methods, have enabled scalable modeling of complex, high-dimensional data including images, text, and speech. In this course, we will study the probabilistic foundations and learning algorithms for deep generative models, including Variational Autoencoders (VAE), Generative Adversarial Networks (GAN), and flow models. The course will also discuss application areas that have benefitted from deep generative models, including computer vision, speech and natural language processing, and reinforcement learning. Prerequisites: Basic knowledge about machine learning from at least one of CS 221, 228, 229 or 230. Students will work with computational and mathematical models and should have a basic knowledge of probabilities and calculus. Proficiency in some programming language, preferably Python, required.
Terms: Aut | Units: 3 | 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 | 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); Heravi, N. (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 330: Deep Multi-task and Meta Learning

While deep learning has achieved remarkable success in supervised and reinforcement learning problems, such as image classification, speech recognition, and game playing, these models are, to a large degree, specialized for the single task they are trained for. This course will cover the setting where there are multiple tasks to be solved, and study how the structure arising from multiple tasks can benleveraged to learn more efficiently or effectively. This includes: goal-conditioned reinforcement learning techniques that leverage the structure of the provided goal space to learn many tasks significantly faster; meta-learning methods that aim to learn efficient learning algorithms that can learn new tasks quickly; curriculum and lifelong learning, where the problem requires learning a sequence of tasks, leveraging their shared structure to enable knowledge transfer. This is a graduate-level course. By the end of the course, students should be able to understand andnimplement the state-of-the-art multi-task learning algorithms and be ready to conduct research on these topics. Prerequisites: CS 229 or equivalent. Familiarity with deep learning, reinforcement learning, and machine learning is assumed.
Terms: Aut | 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 | 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 | Units: 3-5 | Repeatable for credit | Grading: Letter or Credit/No Credit

EE 292D: Machine Learning on Embedded Systems

This is a project-based class where students will learn how to develop machine learning models for execution in resource constrained environments such as embedded systems. In this class students will learn about techniques to optimize machine learning models and deploy them on a device such as a Arduino, Raspberry PI, Jetson, or Edge TPUs. The class has a significant project component. Prerequisites: CS 107(required), CS 229 (recommended), CS 230 (recommended).
Terms: Spr | Units: 3 | Grading: Letter (ABCD/NP)
Instructors: ; Asgar, Z. (PI); Zhang, K. (TA)

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)

MATH 51: Linear Algebra, Multivariable Calculus, and Modern Applications

This course provides unified coverage of linear algebra and multivariable differential calculus, and the free course e-text connects the material to many fields. Linear algebra in large dimensions underlies the scientific, data-driven, and computational tasks of the 21st century. The linear algebra portion includes orthogonality, linear independence, matrix algebra, and eigenvalues with applications such as least squares, linear regression, and Markov chains (relevant to population dynamics, molecular chemistry, and PageRank); the singular value decomposition (essential in image compression, topic modeling, and data-intensive work in many fields) is introduced in the final chapter of the e-text. The multivariable calculus portion includes unconstrained optimization via gradients and Hessians (used for energy minimization), constrained optimization (via Lagrange multipliers, crucial in economics), gradient descent and the multivariable Chain Rule (which underlie many machine learning algorithms, such as backpropagation), and Newton's method (an ingredient in GPS and robotics). The course emphasizes computations alongside an intuitive understanding of key ideas. The widespread use of computers makes it important for users of math to understand concepts: novel users of quantitative tools in the future will be those who understand ideas and how they fit with examples and applications. This is the only course at Stanford whose syllabus includes nearly all the math background for CS 229, which is why CS 229 and CS 230 specifically recommend it (or other courses resting on it). For frequently asked questions about the differences between Math 51 and CME 100, see the FAQ on the placement page on the Math Department website. Prerequisite: Math 21, Math 42, or the math placement diagnostic (offered through the Math Department website) in order to register for this course.
Terms: Aut, Win, Spr, Sum | Units: 5 | UG Reqs: GER:DB-Math, WAY-FR | Grading: Letter or Credit/No Credit
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