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Modeling and simulation of genetic regulatory systems: A literature review

by Hidde De Jong - JOURNAL OF COMPUTATIONAL BIOLOGY , 2002
"... In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between ..."
Abstract - Cited by 738 (14 self) - Add to MetaCart
DNA, RNA, proteins, and small molecules. As most genetic regulatory networks of interest involve many components connected through interlocking positive and negative feedback loops, an intuitive understanding of their dynamics is hard to obtain. As a consequence, formal methods and computer tools

Bandera: Extracting Finite-state Models from Java Source Code

by James C. Corbett, Matthew B. Dwyer, John Hatcliff, Shawn Laubach, Corina S. Pasareanu, Hongjun Zheng - IN PROCEEDINGS OF THE 22ND INTERNATIONAL CONFERENCE ON SOFTWARE ENGINEERING , 2000
"... Finite-state verification techniques, such as model checking, have shown promise as a cost-effective means for finding defects in hardware designs. To date, the application of these techniques to software has been hindered by several obstacles. Chief among these is the problem of constructing a fini ..."
Abstract - Cited by 654 (33 self) - Add to MetaCart
finite-state model that approximates the executable behavior of the software system of interest. Current best-practice involves handconstruction of models which is expensive (prohibitive for all but the smallest systems), prone to errors (which can result in misleading verification results

The strength of weak learnability

by Robert E. Schapire - MACHINE LEARNING , 1990
"... This paper addresses the problem of improving the accuracy of an hypothesis output by a learning algorithm in the distribution-free (PAC) learning model. A concept class is learnable (or strongly learnable) if, given access to a Source of examples of the unknown concept, the learner with high prob ..."
Abstract - Cited by 871 (26 self) - Add to MetaCart
of learnability are equivalent. A method is described for converting a weak learning algorithm into one that achieves arbitrarily high accuracy. This construction may have practical applications as a tool for efficiently converting a mediocre learning algorithm into one that performs extremely well. In addition

Fab: Content-based, collaborative recommendation

by Marko Balabanovic, Yoav Shoham - Communications of the ACM , 1997
"... Fab is a recommendation system designed to help users sift through the enormous amount of information available in the World Wide Web. Operational since Dec. 1994, this system combines the content-based and collaborative methods of recommendation in a way that exploits the advantages of the two appr ..."
Abstract - Cited by 682 (0 self) - Add to MetaCart
for Computing Machinery Inc. By combining both collaborative and content-based filtering systems, Fab may eliminate many of the weaknesses found in each approach. Online readers are in need of tools to help them cope with the mass of content available on the World-Wide Web. In traditional media, readers

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

by Stephen F Altschul , Thomas L Madden , Alejandro A Schäffer , Jinghui Zhang , Zheng Zhang , Webb Miller , David J Lipman - Nucleic Acids Res. , 1997
"... ABSTRACT The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantia ..."
Abstract - Cited by 8572 (88 self) - Add to MetaCart
ABSTRACT The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased

Featherweight Java: A Minimal Core Calculus for Java and GJ

by Atsushi Igarashi, Benjamin C. Pierce, Philip Wadler - ACM Transactions on Programming Languages and Systems , 1999
"... Several recent studies have introduced lightweight versions of Java: reduced languages in which complex features like threads and reflection are dropped to enable rigorous arguments about key properties such as type safety. We carry this process a step further, omitting almost all features of the fu ..."
Abstract - Cited by 659 (23 self) - Add to MetaCart
computational “feel, ” providing classes, methods, fields, inheritance, and dynamic typecasts with a semantics closely following Java’s. A proof of type safety for Featherweight Java thus illustrates many of the interesting features of a safety proof for the full language, while remaining pleasingly compact

From Data Mining to Knowledge Discovery in Databases.

by Usama Fayyad , Gregory Piatetsky-Shapiro , Padhraic Smyth - AI Magazine, , 1996
"... ■ Data mining and knowledge discovery in databases have been attracting a significant amount of research, industry, and media attention of late. What is all the excitement about? This article provides an overview of this emerging field, clarifying how data mining and knowledge discovery in database ..."
Abstract - Cited by 538 (0 self) - Add to MetaCart
research directions in the field. A cross a wide variety of fields, data are being collected and accumulated at a dramatic pace. There is an urgent need for a new generation of computational theories and tools to assist humans in extracting useful information (knowledge) from the rapidly growing volumes

Automatic predicate abstraction of C programs

by Thomas Ball , Rupak Majumdar, Todd Millstein, Sriram K. Rajamani - IN PROC. ACM PLDI , 2001
"... Model checking has been widely successful in validating and debugging designs in the hardware and protocol domains. However, state-space explosion limits the applicability of model checking tools, so model checkers typically operate on abstractions of systems. Recently, there has been significant in ..."
Abstract - Cited by 488 (33 self) - Add to MetaCart
Model checking has been widely successful in validating and debugging designs in the hardware and protocol domains. However, state-space explosion limits the applicability of model checking tools, so model checkers typically operate on abstractions of systems. Recently, there has been significant

Pyramid-Based Texture Analysis/Synthesis

by David J. Heeger, James R. Bergen , 1995
"... This paper describes a method for synthesizing images that match the texture appearanceof a given digitized sample. This synthesis is completely automatic and requires only the "target" texture as input. It allows generation of as much texture as desired so that any object can be covered. ..."
Abstract - Cited by 480 (0 self) - Add to MetaCart
, and has potential to be a practically useful tool for graphics applications. 1 Introduction Computer renderings of objects with surface texture are more interesting and realistic than those without texture. Texture mapping [15] is a technique for adding the appearance of surface detail by wrapping

Methodologies in spectral analysis of large dimensional random matrices, a review

by Z. D. Bai - STATIST. SINICA , 1999
"... In this paper, we give a brief review of the theory of spectral analysis of large dimensional random matrices. Most of the existing work in the literature has been stated for real matrices but the corresponding results for the complex case are also of interest, especially for researchers in Electri ..."
Abstract - Cited by 454 (39 self) - Add to MetaCart
In this paper, we give a brief review of the theory of spectral analysis of large dimensional random matrices. Most of the existing work in the literature has been stated for real matrices but the corresponding results for the complex case are also of interest, especially for researchers
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