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CS 275: Translational Bioinformatics (BIOMEDIN 217)

Analytic, storage, 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; analysis of microarray data; analysis of polymorphisms, proteomics, and protein interactions; 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: Win | Units: 4

CS 275A: Symbolic Musical Information (MUSIC 253)

Focus on symbolic data for music applications including advanced notation systems, optical music recognition, musical data conversion, and internal structure of MIDI files.
Terms: Win | Units: 2-4
Instructors: Sapp, C. (PI) ; Selfridge-Field, E. (PI)

CS 334A: Convex Optimization I (CME 364A, EE 364A)

Convex sets, functions, and optimization problems. The basics of convex analysis and theory of convex programming: optimality conditions, duality theory, theorems of alternative, and applications. Least-squares, linear and quadratic programs, semidefinite programming, and geometric programming. Numerical algorithms for smooth and equality constrained problems; interior-point methods for inequality constrained problems. Applications to signal processing, communications, control, analog and digital circuit design, computational geometry, statistics, machine learning, and mechanical engineering. Prerequisite: linear algebra such as EE263, basic probability.
Terms: Win, Sum | Units: 3

CS 344G: Network Application Studio

Graduate project class on computer networking, emphasizing end-to-end applications and protocols. Students will propose and execute an original project in teams of 2-3, culminating in a final writeup and presentation/demonstration. Each week, students will read, present, and lead a discussion about a seminal paper or system. Prerequisites: programming experience.
Terms: Win | Units: 3
Instructors: Winstein, K. (PI)

CS 369A: Topics in Analysis of Algorithms: Advanced Approximation Algorithms

Optimization problems are ubiquitous, yet most are NP-hard to solve exactly. One popular approach to circumvent this intractability is to design approximation algorithms, i.e. efficient algorithms that produce solutions with value close to the optimum. This course will cover major advances in the field of approximation algorithms in the past decade or so. Prerequisites: Students will be expected to have a strong background in algorithms and probability. Familiarity with basic approximation algorithms (or permission of instructor).
Terms: Win | Units: 3
Instructors: Charikar, M. (PI) ; Yu, N. (TA)

CS 371: Computational Biology in Four Dimensions (BIOMEDIN 371, BIOPHYS 371, CME 371)

Computational approaches to understanding the three-dimensional spatial organization of biological systems and how that organization evolves over time. The course will cover cutting-edge research in both physics-based simulation and computational analysis of experimental data, at scales ranging from individual molecules to entire cells. 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).
Terms: Win | Units: 3
Instructors: Dror, R. (PI)

CS 390A: Curricular Practical Training

Educational opportunities in high technology research and development labs in the computing industry. Qualified computer science students engage in internship work and integrate that work into their academic program. Students register during the quarter they are employed and complete a research report outlining their work activity, problems investigated, results, and follow-on projects they expect to perform. 390 A, B, and C may each be taken once.
Terms: Aut, Win, Spr, Sum | Units: 1
Instructors: Agrawala, M. (PI) ; Aiken, A. (PI) ; Akeley, K. (PI) ; Altman, R. (PI) ; Baker, M. (PI) ; Barbagli, F. (PI) ; Batzoglou, S. (PI) ; Bejerano, G. (PI) ; Bernstein, M. (PI) ; Blikstein, P. (PI) ; Boneh, D. (PI) ; Bradski, G. (PI) ; Brafman, R. (PI) ; Cain, J. (PI) ; Cao, P. (PI) ; Casado, M. (PI) ; Charikar, M. (PI) ; Cheriton, D. (PI) ; Cooper, S. (PI) ; Dally, B. (PI) ; De-Micheli, G. (PI) ; Dill, D. (PI) ; Dwork, C. (PI) ; Engler, D. (PI) ; Fedkiw, R. (PI) ; Feigenbaum, E. (PI) ; Fikes, R. (PI) ; Fischer, M. (PI) ; Fisher, K. (PI) ; Fogg, B. (PI) ; Fox, A. (PI) ; Garcia-Molina, H. (PI) ; Genesereth, M. (PI) ; Gill, J. (PI) ; Girod, B. (PI) ; Goel, A. (PI) ; Goodman, N. (PI) ; Guibas, L. (PI) ; Hanrahan, P. (PI) ; Heer, J. (PI) ; Hennessy, J. (PI) ; Horowitz, M. (PI) ; James, D. (PI) ; Johari, R. (PI) ; Johnson, M. (PI) ; Jurafsky, D. (PI) ; Katti, S. (PI) ; Kay, M. (PI) ; Khatib, O. (PI) ; Klemmer, S. (PI) ; Koller, D. (PI) ; Koltun, V. (PI) ; Konolige, K. (PI) ; Kozyrakis, C. (PI) ; Lam, M. (PI) ; Landay, J. (PI) ; Latombe, J. (PI) ; Lee, C. (PI) ; Leskovec, J. (PI) ; Levis, P. (PI) ; Levitt, M. (PI) ; Levoy, M. (PI) ; Li, F. (PI) ; Liang, P. (PI) ; Manna, Z. (PI) ; Manning, C. (PI) ; Mazieres, D. (PI) ; McCarthy, J. (PI) ; McCluskey, E. (PI) ; McKeown, N. (PI) ; Meng, T. (PI) ; Mitchell, J. (PI) ; Mitra, S. (PI) ; Motwani, R. (PI) ; Musen, M. (PI) ; Nass, C. (PI) ; Nayak, P. (PI) ; Ng, A. (PI) ; Nilsson, N. (PI) ; Olukotun, O. (PI) ; Ousterhout, J. (PI) ; Paepcke, A. (PI) ; Pande, V. (PI) ; Parlante, N. (PI) ; Pea, R. (PI) ; Piech, C. (PI) ; Plotkin, S. (PI) ; Plummer, R. (PI) ; Prabhakar, B. (PI) ; Pratt, V. (PI) ; Raghavan, P. (PI) ; Rajaraman, A. (PI) ; Re, C. (PI) ; Roberts, E. (PI) ; Rosenblum, M. (PI) ; Roughgarden, T. (PI) ; Sahami, M. (PI) ; Salisbury, J. (PI) ; Savarese, S. (PI) ; Schwarz, K. (PI) ; Shoham, Y. (PI) ; Sosic, R. (PI) ; Stepp, M. (PI) ; Thrun, S. (PI) ; Tobagi, F. (PI) ; Trevisan, L. (PI) ; Ullman, J. (PI) ; Valiant, G. (PI) ; Van Roy, B. (PI) ; Widom, J. (PI) ; Wiederhold, G. (PI) ; Williams, R. (PI) ; Williams, V. (PI) ; Winograd, T. (PI) ; Winstein, K. (PI) ; Young, P. (PI) ; Zelenski, J. (PI)

CS 390B: Curricular Practical Training

Educational opportunities in high technology research and development labs in the computing industry. Qualified computer science students engage in internship work and integrate that work into their academic program. Students register during the quarter they are employed and complete a research report outlining their work activity, problems investigated, results, and follow-on projects they expect to perform. 390A,B,C may each be taken once.
Terms: Aut, Win, Spr, Sum | Units: 1
Instructors: Agrawala, M. (PI) ; Aiken, A. (PI) ; Akeley, K. (PI) ; Altman, R. (PI) ; Baker, M. (PI) ; Barbagli, F. (PI) ; Batzoglou, S. (PI) ; Bejerano, G. (PI) ; Bernstein, M. (PI) ; Blikstein, P. (PI) ; Boneh, D. (PI) ; Bradski, G. (PI) ; Brafman, R. (PI) ; Cain, J. (PI) ; Cao, P. (PI) ; Casado, M. (PI) ; Charikar, M. (PI) ; Cheriton, D. (PI) ; Cooper, S. (PI) ; Dally, B. (PI) ; De-Micheli, G. (PI) ; Dill, D. (PI) ; Dwork, C. (PI) ; Engler, D. (PI) ; Ermon, S. (PI) ; Fedkiw, R. (PI) ; Feigenbaum, E. (PI) ; Fikes, R. (PI) ; Fisher, K. (PI) ; Fogg, B. (PI) ; Fox, A. (PI) ; Garcia-Molina, H. (PI) ; Genesereth, M. (PI) ; Gill, J. (PI) ; Girod, B. (PI) ; Goel, A. (PI) ; Guibas, L. (PI) ; Hanrahan, P. (PI) ; Heer, J. (PI) ; Hennessy, J. (PI) ; Horowitz, M. (PI) ; James, D. (PI) ; Johari, R. (PI) ; Johnson, M. (PI) ; Jurafsky, D. (PI) ; Katti, S. (PI) ; Kay, M. (PI) ; Khatib, O. (PI) ; Klemmer, S. (PI) ; Koller, D. (PI) ; Koltun, V. (PI) ; Konolige, K. (PI) ; Kozyrakis, C. (PI) ; Lam, M. (PI) ; Latombe, J. (PI) ; Lee, C. (PI) ; Leskovec, J. (PI) ; Levis, P. (PI) ; Levitt, M. (PI) ; Levoy, M. (PI) ; Li, F. (PI) ; Liang, P. (PI) ; Manna, Z. (PI) ; Manning, C. (PI) ; Mazieres, D. (PI) ; McCarthy, J. (PI) ; McCluskey, E. (PI) ; McKeown, N. (PI) ; Meng, T. (PI) ; Mitchell, J. (PI) ; Mitra, S. (PI) ; Motwani, R. (PI) ; Musen, M. (PI) ; Nass, C. (PI) ; Nayak, P. (PI) ; Ng, A. (PI) ; Nilsson, N. (PI) ; Olukotun, O. (PI) ; Ousterhout, J. (PI) ; Paepcke, A. (PI) ; Parlante, N. (PI) ; Pea, R. (PI) ; Plotkin, S. (PI) ; Plummer, R. (PI) ; Prabhakar, B. (PI) ; Pratt, V. (PI) ; Raghavan, P. (PI) ; Rajaraman, A. (PI) ; Re, C. (PI) ; Roberts, E. (PI) ; Rosenblum, M. (PI) ; Roughgarden, T. (PI) ; Sahami, M. (PI) ; Salisbury, J. (PI) ; Savarese, S. (PI) ; Schwarz, K. (PI) ; Shoham, Y. (PI) ; Sosic, R. (PI) ; Stepp, M. (PI) ; Thrun, S. (PI) ; Tobagi, F. (PI) ; Trevisan, L. (PI) ; Ullman, J. (PI) ; Valiant, G. (PI) ; Van Roy, B. (PI) ; Widom, J. (PI) ; Wiederhold, G. (PI) ; Williams, R. (PI) ; Winograd, T. (PI) ; Young, P. (PI) ; Zelenski, J. (PI)

CS 390C: Curricular Practical Training

Educational opportunities in high technology research and development labs in the computing industry. Qualified computer science students engage in internship work and integrate that work into their academic program. Students register during the quarter they are employed and complete a research report outlining their work activity, problems investigated, results, and follow-on projects they expect to perform. 390A,B,C may each be taken once.
Terms: Aut, Win, Spr, Sum | Units: 1
Instructors: Aiken, A. (PI) ; Akeley, K. (PI) ; Altman, R. (PI) ; Baker, M. (PI) ; Barbagli, F. (PI) ; Batzoglou, S. (PI) ; Bejerano, G. (PI) ; Bernstein, M. (PI) ; Blikstein, P. (PI) ; Boneh, D. (PI) ; Bradski, G. (PI) ; Brafman, R. (PI) ; Cain, J. (PI) ; Cao, P. (PI) ; Casado, M. (PI) ; Charikar, M. (PI) ; Cheriton, D. (PI) ; Cooper, S. (PI) ; Dally, B. (PI) ; De-Micheli, G. (PI) ; Dill, D. (PI) ; Dwork, C. (PI) ; Engler, D. (PI) ; Fedkiw, R. (PI) ; Feigenbaum, E. (PI) ; Fikes, R. (PI) ; Fisher, K. (PI) ; Fogg, B. (PI) ; Fox, A. (PI) ; Garcia-Molina, H. (PI) ; Genesereth, M. (PI) ; Gill, J. (PI) ; Girod, B. (PI) ; Goel, A. (PI) ; Goodman, N. (PI) ; Guibas, L. (PI) ; Hanrahan, P. (PI) ; Heer, J. (PI) ; Hennessy, J. (PI) ; Horowitz, M. (PI) ; James, D. (PI) ; Johari, R. (PI) ; Johnson, M. (PI) ; Jurafsky, D. (PI) ; Katti, S. (PI) ; Kay, M. (PI) ; Khatib, O. (PI) ; Klemmer, S. (PI) ; Koller, D. (PI) ; Koltun, V. (PI) ; Konolige, K. (PI) ; Kozyrakis, C. (PI) ; Lam, M. (PI) ; Latombe, J. (PI) ; Leskovec, J. (PI) ; Levis, P. (PI) ; Levitt, M. (PI) ; Levoy, M. (PI) ; Li, F. (PI) ; Liang, P. (PI) ; Manna, Z. (PI) ; Manning, C. (PI) ; Mazieres, D. (PI) ; McCarthy, J. (PI) ; McCluskey, E. (PI) ; McKeown, N. (PI) ; Meng, T. (PI) ; Mitchell, J. (PI) ; Mitra, S. (PI) ; Motwani, R. (PI) ; Musen, M. (PI) ; Nass, C. (PI) ; Nayak, P. (PI) ; Ng, A. (PI) ; Nilsson, N. (PI) ; Olukotun, O. (PI) ; Ousterhout, J. (PI) ; Paepcke, A. (PI) ; Parlante, N. (PI) ; Pea, R. (PI) ; Plotkin, S. (PI) ; Plummer, R. (PI) ; Prabhakar, B. (PI) ; Pratt, V. (PI) ; Raghavan, P. (PI) ; Rajaraman, A. (PI) ; Re, C. (PI) ; Roberts, E. (PI) ; Rosenblum, M. (PI) ; Roughgarden, T. (PI) ; Sahami, M. (PI) ; Salisbury, J. (PI) ; Savarese, S. (PI) ; Schwarz, K. (PI) ; Shoham, Y. (PI) ; Thrun, S. (PI) ; Tobagi, F. (PI) ; Trevisan, L. (PI) ; Ullman, J. (PI) ; Valiant, G. (PI) ; Van Roy, B. (PI) ; Widom, J. (PI) ; Wiederhold, G. (PI) ; Williams, R. (PI) ; Winograd, T. (PI) ; Young, P. (PI) ; Zelenski, J. (PI)

CS 390P: Part-time Curricular Practical Training

For qualified computer science PhD students only. Permission number required for enrollment; see the CS PhD program administrator in Gates room 196. May be taken just once; not repeatable. Educational opportunities in high technology research and development labs in the computing industry. Qualified computer science students engage in research and integrate that work into their academic program. Students register during the quarter they are employed and complete a research report outlining their work activity, problems investigated, results, and follow-on projects they expect to perform. Students on F1 visas should be aware that completing 12 or more months of full-time CPT will make them ineligible for Optional Practical Training (OPT).
Terms: Aut, Win, Spr | Units: 1
Instructors: Aiken, A. (PI) ; Akeley, K. (PI) ; Altman, R. (PI) ; Baker, M. (PI) ; Barbagli, F. (PI) ; Batzoglou, S. (PI) ; Bejerano, G. (PI) ; Bernstein, M. (PI) ; Blikstein, P. (PI) ; Boneh, D. (PI) ; Boyd, S. (PI) ; Bradski, G. (PI) ; Brafman, R. (PI) ; Cain, J. (PI) ; Cao, P. (PI) ; Casado, M. (PI) ; Cheriton, D. (PI) ; Cooper, S. (PI) ; Dally, B. (PI) ; De-Micheli, G. (PI) ; Dill, D. (PI) ; Dror, R. (PI) ; Dwork, C. (PI) ; Engler, D. (PI) ; Fedkiw, R. (PI) ; Feigenbaum, E. (PI) ; Fikes, R. (PI) ; Fisher, K. (PI) ; Fogg, B. (PI) ; Fox, A. (PI) ; Garcia-Molina, H. (PI) ; Genesereth, M. (PI) ; Gill, J. (PI) ; Girod, B. (PI) ; Goel, A. (PI) ; Goodman, N. (PI) ; Guibas, L. (PI) ; Hanrahan, P. (PI) ; Heer, J. (PI) ; Hennessy, J. (PI) ; Horowitz, M. (PI) ; Johari, R. (PI) ; Johnson, M. (PI) ; Jurafsky, D. (PI) ; Katti, S. (PI) ; Kay, M. (PI) ; Khatib, O. (PI) ; Klemmer, S. (PI) ; Koller, D. (PI) ; Koltun, V. (PI) ; Konolige, K. (PI) ; Kozyrakis, C. (PI) ; Kundaje, A. (PI) ; Lam, M. (PI) ; Latombe, J. (PI) ; Leskovec, J. (PI) ; Levis, P. (PI) ; Levitt, M. (PI) ; Levoy, M. (PI) ; Li, F. (PI) ; Liang, P. (PI) ; Manna, Z. (PI) ; Manning, C. (PI) ; Mazieres, D. (PI) ; McCluskey, E. (PI) ; McKeown, N. (PI) ; Meng, T. (PI) ; Mitchell, J. (PI) ; Mitra, S. (PI) ; Montanari, A. (PI) ; Motwani, R. (PI) ; Musen, M. (PI) ; Nass, C. (PI) ; Nayak, P. (PI) ; Ng, A. (PI) ; Nilsson, N. (PI) ; Olukotun, O. (PI) ; Ousterhout, J. (PI) ; Paepcke, A. (PI) ; Pande, V. (PI) ; Parlante, N. (PI) ; Plotkin, S. (PI) ; Prabhakar, B. (PI) ; Pratt, V. (PI) ; Raghavan, P. (PI) ; Rajaraman, A. (PI) ; Re, C. (PI) ; Roberts, E. (PI) ; Rosenblum, M. (PI) ; Roughgarden, T. (PI) ; Sahami, M. (PI) ; Salisbury, J. (PI) ; Savarese, S. (PI) ; Schwarz, K. (PI) ; Shoham, Y. (PI) ; Thrun, S. (PI) ; Tobagi, F. (PI) ; Trevisan, L. (PI) ; Ullman, J. (PI) ; Valiant, G. (PI) ; Van Roy, B. (PI) ; Widom, J. (PI) ; Wiederhold, G. (PI) ; Williams, R. (PI) ; Williams, V. (PI) ; Winograd, T. (PI) ; Young, P. (PI) ; Zelenski, J. (PI)
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