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Functional discovery via a compendium of expression profiles.

by Timothy R Hughes , Matthew J Marton , Allan R Jones , Christopher J Roberts , Roland Stoughton , Christopher D Armour , Holly A Bennett , Ernest Coffey , Hongyue Dai , Ross-Macdonald , Yudong D He , Matthew J Kidd , Amy M King , Michael R Meyer , David Slade , Pek Y Lum , Sergey B Stepaniants , Daniel D Shoemaker , Julian Simon , Martin Bard - Cell, , 2000
"... provided that the cellular transcriptional response to frames encode proteins required for sterol metabodisruption of different steps in the same pathway is lism, cell wall function, mitochondrial respiration, or similar, and that there are sufficiently unique transcripprotein synthesis. We also sh ..."
Abstract - Cited by 547 (9 self) - Add to MetaCart
show that the compendium tional responses to the perturbation of most cellular can be used to characterize pharmacological perturpathways, systematic characterization of novel mutants bations by identifying a novel target of the commonly could be carried out with a single genome-wide expresused drug

Heuristics for Internet Map Discovery

by Ramesh Govindan, Hongsuda Tangmunarunkit , 2000
"... Mercator is a program that uses hop-limited probes---the same primitive used in traceroute---to infer an Internet map. It uses informed random address probing to carefully exploring the IP address space when determining router adjacencies, uses source-route capable routers wherever possible to enhan ..."
Abstract - Cited by 385 (13 self) - Add to MetaCart
to enhance the fidelity of the resulting map, and employs novel mechanisms for resolving aliases (interfaces belonging to the same router). This paper describes the design of these heuristics and our experiences with Mercator, and presents some preliminary analysis of the resulting Internet map.

Empirical Bayes Analysis of a Microarray Experiment

by Bradley Efron, Robert Tibshirani, John D. Storey, Virginia Tusher - Journal of the American Statistical Association , 2001
"... Microarrays are a novel technology that facilitates the simultaneous measurement of thousands of gene expression levels. A typical microarray experiment can produce millions of data points, raising serious problems of data reduction, and simultaneous inference. We consider one such experiment in whi ..."
Abstract - Cited by 492 (20 self) - Add to MetaCart
Microarrays are a novel technology that facilitates the simultaneous measurement of thousands of gene expression levels. A typical microarray experiment can produce millions of data points, raising serious problems of data reduction, and simultaneous inference. We consider one such experiment

Clausal Discovery

by Luc De Raedt, Luc Dehaspe , 1997
"... The clausal discovery engine Claudien is presented. Claudien is an inductive logic programming engine that fits in the descriptive data mining paradigm. Claudien addresses characteristic induction from interpretations, a task which is related to existing formalisations of induction in logic. In ch ..."
Abstract - Cited by 199 (34 self) - Add to MetaCart
The clausal discovery engine Claudien is presented. Claudien is an inductive logic programming engine that fits in the descriptive data mining paradigm. Claudien addresses characteristic induction from interpretations, a task which is related to existing formalisations of induction in logic

Computational Discovery of Gene Modules, Regulatory Networks and Expression Programs

by Georg Kurt Gerber , 2007
"... High-throughput molecular data are revolutionizing biology by providing massive amounts of information about gene expression and regulation. Such information is applicable both to furthering our understanding of fundamental biology and to developing new diagnostic and treatment approaches for diseas ..."
Abstract - Cited by 236 (17 self) - Add to MetaCart
for diseases. However, novel mathematical methods are needed for extracting biological knowledge from highdimensional, complex and noisy data sources. In this thesis, I develop and apply three novel computational approaches for this task. The common theme of these approaches is that they seek to discover

A.: Learning syntactic patterns for automatic hypernym discovery.

by Rion Snow , Daniel Jurafsky , Andrew Y Ng - Advances in Neural Information Processing Systems , 2004
"... Abstract Semantic taxonomies such as WordNet provide a rich source of knowledge for natural language processing applications, but are expensive to build, maintain, and extend. Motivated by the problem of automatically constructing and extending such taxonomies, in this paper we present a new algori ..."
Abstract - Cited by 223 (6 self) - Add to MetaCart
general-purpose formalization and generalization of these patterns. Given a training set of text containing known hypernym pairs, our algorithm automatically extracts useful dependency paths and applies them to new corpora to identify novel pairs. On our evaluation task (determining whether two nouns in a

Finding motifs using random projections

by Jeremy Buhler, Martin Tompa , 2001
"... Pevzner and Sze [23] considered a precise version of the motif discovery problem and simultaneously issued an algorithmic challenge: find a motif Å of length 15, where each planted instance differs from Å in 4 positions. Whereas previous algorithms all failed to solve this (15,4)-motif problem, Pevz ..."
Abstract - Cited by 285 (6 self) - Add to MetaCart
, Pevzner and Sze introduced algorithms that succeeded. However, their algorithms failed to solve the considerably more difficult (14,4)-, (16,5)-, and (18,6)motif problems. We introduce a novel motif discovery algorithm based on the use of random projections of the input’s substrings. Experiments

Synthetic combinatorial libraries: novel discovery strategy for identification of antimicrobial agents. Antimicrob. Agents Chemother

by S E Blondelle, E Pérez-payá, R A Houghten, Sylvie E. Blondelle, Richard A. Houghten , 1996
"... antimicrobial agents. discovery strategy for identification of Synthetic combinatorial libraries: novel ..."
Abstract - Cited by 9 (2 self) - Add to MetaCart
antimicrobial agents. discovery strategy for identification of Synthetic combinatorial libraries: novel

Probabilistic discovery of time series motifs

by Bill Chiu, Eamonn Keogh, Stefano Lonardi , 2003
"... Several important time series data mining problems reduce to the core task of finding approximately repeated subsequences in a longer time series. In an earlier work, we formalized the idea of approximately repeated subsequences by introducing the notion of time series motifs. Two limitations of thi ..."
Abstract - Cited by 185 (26 self) - Add to MetaCart
of this work were the poor scalability of the motif discovery algorithm, and the inability to discover motifs in the presence of noise. Here we address these limitations by introducing a novel algorithm inspired by recent advances in the problem of pattern discovery in biosequences. Our algorithm

Learning words from sights and sounds: a computational model

by Deb K. Roy, Alex P. Pentland , 2002
"... This paper presents an implemented computational model of word acquisition which learns directly from raw multimodal sensory input. Set in an information theoretic framework, the model acquires a lexicon by finding and statistically modeling consistent cross-modal structure. The model has been imple ..."
Abstract - Cited by 270 (31 self) - Add to MetaCart
implemented in a system using novel speech processing, computer vision, and machine learning algorithms. In evaluations the model successfully performed speech segmentation, word discovery and visual categorization from spontaneous infant-directed speech paired with video images of single objects
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