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101 - 110 of 206 results for: CS

CS 262: Computational Genomics (BIOMEDIN 262)

Applications of computer science to genomics, and concepts in genomics from a computer science point of view. Topics: dynamic programming, sequence alignments, hidden Markov models, Gibbs sampling, and probabilistic context-free grammars. Applications of these tools to sequence analysis: comparative genomics, DNA sequencing and assembly, genomic annotation of repeats, genes, and regulatory sequences, microarrays and gene expression, phylogeny and molecular evolution, and RNA structure. Prerequisites: 161 or familiarity with basic algorithmic concepts. Recommended: basic knowledge of genetics.
Terms: Win | Units: 3

CS 263: Algorithms for Modern Data Models (MS&E 317)

We traditionally think of algorithms as running on data available in a single location, typically main memory. In many modern applications including web analytics, search and data mining, computational biology, finance, and scientific computing, the data is often too large to reside in a single location, is arriving incrementally over time, is noisy/uncertain, or all of the above. Paradigms such as map-reduce, streaming, sketching, Distributed Hash Tables, Bulk Synchronous Processing, and random walks have proved useful for these applications. This course will provide an introduction to the design and analysis of algorithms for these modern data models. Prerequisite: Algorithms at the level of CS 261.
Terms: Spr | Units: 3

CS 265: Randomized Algorithms and Probabilistic Analysis (CME 309)

Randomness pervades the natural processes around us, from the formation of networks, to genetic recombination, to quantum physics. Randomness is also a powerful tool that can be leveraged to create algorithms and data structures which, in many cases, are more efficient and simpler than their deterministic counterparts. The key tools of probabilistic analysis, and application of these tools to understand the behaviors of random processes and algorithms. Emphasis is on theoretical foundations, though we will apply this theory broadly, discussing applications in machine learning and data analysis, networking, and systems. Topics include tail bounds, the probabilistic method, Markov chains, and martingales, with applications to analyzing random graphs, metric embeddings, random walks, and a host of powerful and elegant randomized algorithms. Prerequisites: CS 161 and STAT 116, or equivalents and instructor consent.
Terms: Aut | Units: 3
Instructors: Valiant, G. (PI)

CS 267: Graph Algorithms

An introduction to advanced topics in graph algorithms. Focusing on a variety of graph problems, the course will explore topics such as small space graph data structures, approximation algorithms, dynamic algorithms, and algorithms for special graph classes. Topics include: approximation algorithms for shortest paths and graph matching, distance oracles, graph spanners, cliques and graph patterns, dynamic algorithms, graph coloring, algorithms for planar graphs. Prerequisites: 161 or the equivalent mathematical maturity.
Instructors: Williams, V. (PI)

CS 270: Modeling Biomedical Systems: Ontology, Terminology, Problem Solving (BIOMEDIN 210)

Methods for modeling biomedical systems and for making those models explicit in the context of building software systems. Emphasis is on intelligent systems for decision support and Semantic Web applications. Topics: knowledge representation, controlled terminologies, ontologies, reusable problem solvers, and knowledge acquisition. Recommended: exposure to object-oriented systems, basic biology.
Terms: Win | Units: 3

CS 272: Introduction to Biomedical Informatics Research Methodology (BIOE 212, BIOMEDIN 212, GENE 212)

Hands-on software building. Student teams conceive, design, specify, implement, evaluate, and report on a software project in the domain of biomedicine. Creating written proposals, peer review, providing status reports, and preparing final reports. Guest lectures from professional biomedical informatics systems builders on issues related to the process of project management. Software engineering basics. Prerequisites: BIOMEDIN 210, 211, 214, 217 or consent of instructor.
Terms: Spr | Units: 3
Instructors: Altman, R. (PI)

CS 273A: A Computational Tour of the Human Genome (BIOMEDIN 273A, DBIO 273A)

Introduction to computational biology through an informatic exploration of the human genome. Topics include: genome sequencing (technologies, assembly, personalized sequencing); functional landscape (genes, gene regulation, repeats, RNA genes, epigenetics); genome evolution (comparative genomics, ultraconservation, co-option). Additional topics may include population genetics, personalized genomics, and ancient DNA. Course includes primers on molecular biology, the UCSC Genome Browser, and text processing languages. Guest lectures from genomic researchers. No prerequisites. See http://cs273a.stanford.edu/.
Terms: Aut | Units: 3

CS 274: Representations and Algorithms for Computational Molecular Biology (BIOE 214, BIOMEDIN 214, GENE 214)

Topics: introduction to bioinformatics and computational biology, algorithms for alignment of biological sequences and structures, computing with strings, phylogenetic tree construction, hidden Markov models, Gibbs Sampling, basic structural computations on proteins, protein structure prediction, protein threading techniques, homology modeling, molecular dynamics and energy minimization, statistical analysis of 3D biological data, integration of data sources, knowledge representation and controlled terminologies for molecular biology, microarray analysis, machine learning (clustering and classification), and natural language text processing. Prerequisites: programming skills; consent of instructor for 3 units.
Terms: Aut | Units: 3-4
Instructors: Altman, R. (PI)

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
Instructors: Butte, A. (PI)

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
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