111 - 120 of 217 results for: CS

Techniques for design and analysis of efficient geometric algorithms for objects in 2-, 3-, and higher dimensions. Topics: convexity, triangulations and simplicial complexes, sweeping, partitioning, and point location. Voronoi/Delaunay diagrams and their properties. Arrangements of curves and surfaces. Intersection and visibility problems. Geometric searching and optimization. Random sampling methods. Impact of numerical issues in geometric computation. Example applications to robotic motion planning, visibility preprocessing and rendering in graphics, model-based recognition in computer vision, and structural molecular biology. Prerequisite: discrete algorithms at the level of 161. Recommended: 164.

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.

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. Because the team projects start in the first week of class, attendance that week is strongly recommended. Prerequisites: BIOMEDIN 210 or 211 or 214 or 217 or consent of instructor.

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/.

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.

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.

Focus on symbolic data for music applications including advanced notation systems, optical music recognition, musical data conversion, and internal structure of MIDI files.

Leveraging off three synchronized sets of symbolic data resources for notation and analysis, the lab portion introduces students to the open-source Humdrum Toolkit for music representation and analysis. Issues of data content and quality as well as methods of information retrieval, visualization, and summarization are considered in class. Grading based primarily on student projects. Prerequisite: 253 or consent of instructor.

Text information retrieval systems; efficient text indexing; Boolean, vector space, and probabilistic retrieval models; ranking and rank aggregation; evaluating IR systems. Text clustering and classification: classification algorithms, latent semantic indexing, taxonomy induction; Web search engines including crawling and indexing, link-based algorithms, and web metadata. Prerequisites: CS 107, CS 109, CS 161.