CMPE 185 Winter 2003 Syllabus (2003)
rld-Wide Web browsers, I'll also provide PDF files generated directly from the L A T E X originals. These will generally produce a better-looking printed copy that will take up less paper. There will...
Bioinformatics: A New Field In Engineering Education (2001)
Bioinformatics is a new engineering field poorly served by traditional engineering curricula. Bioinformatics can be defined in several ways, but the emphasis is always on the use of computer and...
Classifying G-protein coupled receptors with support vector machines (2001)
Rachel Karchin, Kevin Karplus, David Haussler
Motivation: The enormous amount of protein sequence data uncovered by genome research has increased the demand for computer software that can automate the recognition of new proteins. We discuss the...
Scoring Hidden Markov Models (2001)
Christian Barrett, Richard Hughey, Kevin Karplus
1.1 Motivation Statistical sequence comparison techniques, such as hidden Markov models and generalized profiles, calculate the probability that a sequence was generated by a given model. Log-odds...
Kimmen Sjolander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, ...
This paper presents the mathematical foundations of Dirichlet mixtures, which have been used to improve database search results for homologous sequences, when a variable number of sequences from a...
Kevin Karplus, Cowell Dining, Hall Mon
ally makes mistakes, so there may be some strange behavior. Although it is possible to print directly from many World-Wide Web browsers, I'll also provide PostScript les generated directly from the L...
Getting the most from your hidden Markov models (1999)
Kevin Karplus, Christian Barrett, Melissa Cline, Mark Diekhans, Leslie Grate, ...
den Markov model (HMM) for searching databases or aligning sequences. { Search results and alignments for searching PDB (or Swissprot or NR) with the HMM. SAM-T98 master web page...
Evaluating Regularizers for Estimating Distributions of Amino Acids (1999)
This paper makes a quantitative comparison of dierent methods, called regularizers, for estimating the distribution of amino acids in a specic context, given a very small sample of amino acids from...
Predicting Protein Structure using only Sequence Information (1999)
Kevin Karplus, Christian Barrett, Melissa Cline, Mark Diekhans, Leslie Grate, Richard Hughey
This paper presents results of blind predictions submitted to the CASP3 protein structure prediction experiment. We made predictions using the SAM-T98 method, an iterative hidden Markov model based...
Kimmen Sjolander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, ...
This paper presents the mathematical foundations of Dirichlet mixtures, which have been used to improve database search results for homologous sequences, when a variable number of sequences from a...
Kimmen Sjolander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, ...
This paper presents the mathematical foundations of Dirichlet mixtures, which have been used to improve database search results for homologous sequences, when a variable number of sequences from a...
Hidden Markov Models for Detecting Remote Protein Homologies (1998)
Kevin Karplus, Christian Barrett, Richard Hughey
Motivation A new hidden Markov model method (SAM-T98) for finding remote homologs of protein sequences is described and evaluated. The method begins with a single target sequence and iteratively...
Kimmen Sjolander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, ...
This paper presents the mathematical foundations of Dirichlet mixtures, which have been used to improve database search results for homologous sequences, when a variable number of sequences from a...
Predicting protein structure using hidden Markov models (1998)
Kevin Karplus, Christian Barrett, Melissa Cline, David Haussler, Richard Hughey, Liisa Holm, ...
We discuss how methods based on hidden Markov models performed in the fold-recognition section of the CASP2 experiment. Hidden Markov models were built for a representative set of just over one...
Scoring Hidden Markov Models (1997)
Christian Barrett, Richard Hughey, Kevin Karplus
1.1 Motivation Statistical sequence comparison techniques, such as hidden Markov models and generalized profiles, calculate the probability that a sequence was generated by a given model. Log-odds...
Scoring Hidden Markov Models (1997)
Christian Barrett, Richard Hughey, Kevin Karplus
1.1 Motivation Statistical sequence comparison techniques, such as hidden Markov models and generalized profiles, calculate the probability that a sequence was generated by a given model. Log-odds...
Predicting protein structure using hidden Markov models (1997)
Kevin Karplus, Kimmen Sjolander, Christian Barrett, Melissa Cline, David Haussler, Richard Hughey, ...
We discuss how methods based on hidden Markov models performed in the fold-recognition section of the CASP2 experiment. Hidden Markov models were built for a representative set of just over one...
Kestrel: Design of an 8-bit SIMD parallel processor (1997)
David M. Dahle, Jeffrey D. Hirschberg, Kevin Karplus, Hansjorg Keller, Eric Rice, Don Speck, ...
Kestrel is a high-performance programmable parallel co-processor. Its design is the result of examination and reexamination of algorithmic, architectural, packaging, and silicon design issues, and...
Predicting protein structure using hidden Markov models (1997)
Kevin Karplus, Kimmen Sjolander, Christian Barrett, Melissa Cline, David Haussler, Richard Hughey, ...
We discuss how methods based on hidden Markov models performed in the fold-recognition section of the CASP2 experiment. Hidden Markov models were built for a representative set of just over one...
Kimmen Sjolander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, ...
We present a method for condensing the information in multiple alignments of proteins into a mixture of Dirichlet densities over amino acid distributions. Dirichlet mixture densities are designed to...
Kimmen Sjolander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, ...
We present a method for condensing the information in multiple alignments of proteins into a mixture of Dirichlet densities over amino acid distributions. Dirichlet mixture densities are designed to...
Kestrel: A Programmable Array for Sequence Analysis (1996)
Jeffrey D. Hirschberg, Richard Hughey, Kevin Karplus, Don Speck
Kestrel is a programmable linear systolic array processor designed for sequence analysis. Among other features, Kestrel includes an 8-bit word, a single-cycle add-and-minimize instruction, and...
A Flexible Motif Search Technique Based on Generalized Profiles (1996)
Kevin Karplus, Nicolas Moeri, Kay Hofmann
this paper is to define the search method for generalized profiles by an exact formulation of the mathematical problem, leaving no ambiguities to its implementation by a specific algorithm....
A Flexible Motif Search Technique Based on Generalized Profiles (1996)
Kevin Karplus, Nicolas Moeri, Kay Hofmann
this paper is to define the search method for generalized profiles by an exact formulation of the mathematical problem, leaving no ambiguities to its implementation by a specific algorithm....
Leslie Grate, Richard Hughey, Kevin Karplus
Contents 1 Introduction 3 2 Mathematical Foundations of Stochastic Models 4 2.1 What is a model? : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 4 2.2 Bayesian...
Leslie Grate, Richard Hughey, Kevin Karplus, Kimmen Sjolander
Contents 1 Introduction 3 2 Mathematical Foundations of Stochastic Models 4 2.1 What is a model? : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 4 2.2 Bayesian...
Kimmen Sjolander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, ...
We present a method for condensing the information in multiple alignments of proteins into a mixture of Dirichlet densities over amino acid distributions. Dirichlet mixture densities are designed to...
Automatic Synthesis of Self-Test using ASyST (1996)
Joel Ferguson, Kevin Karplus, Tracy Larrabee, Peter Johnson
vi Acknowledgments vii 1. Introduction 1 1.1 Problems with Conventional Methods : : : : : : : : : : : : : : : : : : : : : 1 1.2 Built-In Self-Test : : : : : : : : : : : : : : : : : : : : : : : : : :...
Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, David Haussler
This paper presents the mathematical foundations of Dirichlet mixtures, which have been used to improve database search results for homologous sequences, when a variable number of sequences from a...
Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, David Haussler
This paper presents the mathematical foundations of Dirichlet mixtures, which have been used to improve database search results for homologous sequences, when a variable number of sequences from a...
Regularizers for Estimating Distributions of Amino Acids from Small Samples (1995)
This paper examines several different methods for estimating the distribution of amino acids in a specific context, given a very small sample of amino acids from that distribution. These distribution...
This paper presents a technique for using simple Markov models and hidden Markov models (hmms) to search for interesting sequences in a database of DNA sequences. The models are used to create a cost...
This paper presents a technique for using simple Markov models and hidden Markov models (hmms) to search for interesting sequences in a database of DNA sequences. The models are used to create a cost...
Xtmap: Generate-and-Test Mapper for Table-Lookup Gate Arrays (1993)
Technology mapping is the process of taking a finegrain network describing a multiple-output logic function, and covering it with cells to get a network that is legal in a given technology. The goals...
Carafe: An Inductive Fault Analysis Tool For CMOS VLSI Circuits (1992)
F. Joel Ferguson, Kevin Karplus, Tracy Larrabee
Traditional fault models for testing CMOS VLSI circuits do not take into account the actual mechanisms that precipitate faults. As a result, the failure modes of a circuit as predicted by these fault...
style file Kevin Karplus (1992)
This technical report describes how to use L a T E X to produce technical reports in the proper format for the UCSC Baskin Center for Computer Engineering and Information Sciences series. The style...
Representing Boolean Functions with If-Then-Else DAGs (1992)
This article describes the use of binary decision diagrams (BDDs) and if-then-else dags
Using if-then-else DAGs for Multi-Level Logic Minimization (1992)
This article describes the use of if-then-else dags for multi-level logic minimization. A new canonical form for if-then-else dags, analogous to Bryant's canonical form for binary decision diagrams...
Representing Boolean Functions with If-Then-Else DAGs (1991)
This article describes the use of binary decision diagrams (BDDs) and if-then-else dags for representing and manipulating Boolean functions.
Using if-then-else DAGs for Multi-Level Logic Minimization (1991)
This article describes the use of if-then-else dags for multi-level logic minimization.
ROPE: A New Twist in Computer Architectures (1987)
Karplus, Kevin, Nicolau, Alexandru
Supercomputer architectures are not as fast as logic technology allows because memories are slow than the CPU, conditional jumps limit the usefulness of pipelining and prefetching mechanisms, and...
ROPE: A New Twist in Computer Architectures (1987)
Karplus, Kevin, Nicolau, Alexandru
Supercomputer architectures are not as fast as logic technology allows because memories are slow than the CPU, conditional jumps limit the usefulness of pipelining and prefetching mechanisms, and...
Finding Minimal Perfect Hash Functions (1984)
A heuristic is given for finding minimal perfect hash functions without extensive searching. The procedure is to construct a set of graph (or hypergraph) models for the dictionary, then choose one of...
Finding Minimal Perfect Hash Functions (1984)
A heuristic is given for finding minimal perfect hash functions without extensive searching. The procedure is to construct a set of graph (or hypergraph) models for the dictionary, then choose one of...
Formal Model of MOS Clocking Disciples (1984)
This paper presents a formalization of clocking disciplines used to prevent race conditions in VLSI circuits. A signal-labeling scheme for the two-phase clocking discipline informally described in...
Formal Model of MOS Clocking Disciples (1984)
This paper presents a formalization of clocking disciplines used to prevent race conditions in VLSI circuits. A signal-labeling scheme for the two-phase clocking discipline informally described in...
CHISEL : an extension to the programming language C for VLSI layout / (1983)
Thesis (Ph. D.)--Stanford University, 1983.
CHISEL :--an extension to the programming language C for VLSI layout /--Kevin Karplus. (1983)
Thesis (Ph. D.)--Stanford University, 1983.
Chisel, an extension to the programming language C for VLSI layout / (1983)
Thesis (Ph. D.)--Stanford University, 1983.
Fong, Jiunn C. N., Karplus, Kevin, Schoolnik, Gary K., Yildiz, Fitnat H.
Phase variation between smooth and rugose colony variants of Vibrio cholerae is predicted to be important for the pathogen's survival in its natural aquatic ecosystems. The rugose variant forms...
Fong, Jiunn C. N., Karplus, Kevin, Schoolnik, Gary K., Yildiz, Fitnat H.
Phase variation between smooth and rugose colony variants of Vibrio cholerae is predicted to be important for the pathogen's survival in its natural aquatic ecosystems. The rugose variant forms...