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Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. sect

by T. A. Jones, J. -y. Zou, S. W. Cowan, M. Kjeldgaard - A , 1991
"... Map interpretation remains a critical step in solving the structure of a macromolecule. Errors introduced at this early stage may persist throughout crystallo-graphic refinement and result in an incorrect struc-ture. The normally quoted crystallographic residual is often a poor description for the q ..."
Abstract - Cited by 1051 (9 self) - Add to MetaCart
Map interpretation remains a critical step in solving the structure of a macromolecule. Errors introduced at this early stage may persist throughout crystallo-graphic refinement and result in an incorrect struc-ture. The normally quoted crystallographic residual is often a poor description for the quality of the model. Strategies and tools are described that help to alleviate this problem. These simplify the model-building process, quantify the goodness of fit of the model on a per-residue basis and locate possible errors in pep-tide and side-chain conformations.

Improved methods for tests of long-run abnormal stock returns

by John D. Lyon, Brad M. Barber, Chih-ling Tsai, Raghu Rau, Jay Ritter, René Stulz, Brett Trueman, Ralph Walkling - Journal of Finance , 1999
"... We analyze tests for long-run abnormal returns and document that two approaches yield well-specified test statistics in random samples. The first uses a traditional event study framework and buy-and-hold abnormal returns calculated using carefully constructed reference portfolios. Inference is based ..."
Abstract - Cited by 375 (12 self) - Add to MetaCart
samples, misspecification in nonrandom samples is pervasive. Thus, analysis of long-run abnormal returns is treacherous. COMMONLY USED METHODS TO TEST for long-run abnormal stock returns yield misspecified test statistics, as documented by Barber and Lyon ~1997a! and Kothari and Warner ~1997!. 1

Improving retrieval performance by relevance feedback

by Gerard Salton, Chris Buckley - Journal of the American Society for Information Science , 1990
"... Relevance feedback is an automatic process, introduced over 20 years ago, designed to produce improved query formulations following an initial retrieval operation. The principal relevance feedback methods described over the years are examined briefly, and evaluation data are included to demonstrate ..."
Abstract - Cited by 756 (6 self) - Add to MetaCart
Relevance feedback is an automatic process, introduced over 20 years ago, designed to produce improved query formulations following an initial retrieval operation. The principal relevance feedback methods described over the years are examined briefly, and evaluation data are included to demonstrate

Improved Boosting Algorithms Using Confidence-rated Predictions

by Robert E. Schapire , Yoram Singer - MACHINE LEARNING , 1999
"... We describe several improvements to Freund and Schapire’s AdaBoost boosting algorithm, particularly in a setting in which hypotheses may assign confidences to each of their predictions. We give a simplified analysis of AdaBoost in this setting, and we show how this analysis can be used to find impr ..."
Abstract - Cited by 940 (26 self) - Add to MetaCart
improved parameter settings as well as a refined criterion for training weak hypotheses. We give a specific method for assigning confidences to the predictions of decision trees, a method closely related to one used by Quinlan. This method also suggests a technique for growing decision trees which turns

SPEA2: Improving the Strength Pareto Evolutionary Algorithm

by Eckart Zitzler, Marco Laumanns, Lothar Thiele , 2001
"... The Strength Pareto Evolutionary Algorithm (SPEA) (Zitzler and Thiele 1999) is a relatively recent technique for finding or approximating the Pareto-optimal set for multiobjective optimization problems. In different studies (Zitzler and Thiele 1999; Zitzler, Deb, and Thiele 2000) SPEA has shown very ..."
Abstract - Cited by 708 (19 self) - Add to MetaCart
, and Zamboglou 2001). In this paper, an improved version, namely SPEA2, is proposed, which incorporates in contrast to its predecessor a fine-grained fitness assignment strategy, a density estimation technique, and an enhanced archive truncation method. The comparison of SPEA2 with SPEA and two other modern

Making the most of statistical analyses: Improving interpretation and presentation

by Gary King, Michael Tomz, Jason Wittenberg - American Journal of Political Science , 2000
"... Social scientists rarely take full advantage of the information available in their statistical results. As a consequence, they miss opportunities to present quantities that are of greatest substantive interest for their research and express the appropriate degree of certainty about these quantities. ..."
Abstract - Cited by 600 (26 self) - Add to MetaCart
. In this article, we offer an approach, built on the technique of statistical simulation, to extract the currently overlooked information from any statistical method and to interpret and present it in a reader-friendly manner. Using this technique requires some expertise,

Novel methods improve prediction of species’ distributions from occurrence data

by Jane Elith, Catherine H. Graham, Robert P. Anderson, Miroslav Dudík, Simon Ferrier, Antoine Guisan, Robert J. Hijmans, Falk Huettmann, John R. Leathwick, Anthony Lehmann, Jin Li, Lucia G. Lohmann, Bette A. Loiselle, Glenn Manion, Craig Moritz, Miguel Nakamura, Yoshinori Nakazawa, Jacob Mcc Overton, A. Townsend Peterson, Steven J. Phillips, Karen Richardson, Ricardo Scachetti-pereira, Robert E. Schapire, Jorge Soberón, Stephen Williams, Mary S. Wisz, Niklaus E. Zimmermann - Ecography , 2006
"... occurrence data ..."
Abstract - Cited by 482 (8 self) - Add to MetaCart
occurrence data

Ontologies: Principles, methods and applications

by Mike Uschold, Michael Gruninger - KNOWLEDGE ENGINEERING REVIEW , 1996
"... This paper is intended to serve as a comprehensive introduction to the emerging field concerned with the design and use of ontologies. We observe that disparate backgrounds, languages, tools, and techniques are a major barrier to effective communication among people, organisations, and/or software s ..."
Abstract - Cited by 582 (3 self) - Add to MetaCart
systems. We show how the development and implementation of an explicit account of a shared understanding (i.e. an `ontology') in a given subject area, can improve such communication, which in turn, can give rise to greater reuse and sharing, inter-operability, and more reliable software. After

Theoretical improvements in algorithmic efficiency for network flow problems

by Jack Edmonds, Richard M. Karp - , 1972
"... This paper presents new algorithms for the maximum flow problem, the Hitchcock transportation problem, and the general minimum-cost flow problem. Upper bounds on ... the numbers of steps in these algorithms are derived, and are shown to compale favorably with upper bounds on the numbers of steps req ..."
Abstract - Cited by 560 (0 self) - Add to MetaCart
required by earlier algorithms. First, the paper states the maximum flow problem, gives the Ford-Fulkerson labeling method for its solution, and points out that an improper choice of flow augmenting paths can lead to severe computational difficulties. Then rules of choice that avoid these difficulties

Improved prediction of signal peptides -- SignalP 3.0

by Jannick Dyrløv Bendtsen, Henrik Nielsen, Gunnar von Heijne, Søren Brunak - J. MOL. BIOL. , 2004
"... We describe improvements of the currently most popular method for prediction of classically secreted proteins, SignalP. SignalP consists of two different predictors based on neural network and hidden Markov model algorithms, where both components have been updated. Motivated by the idea that the cle ..."
Abstract - Cited by 654 (7 self) - Add to MetaCart
We describe improvements of the currently most popular method for prediction of classically secreted proteins, SignalP. SignalP consists of two different predictors based on neural network and hidden Markov model algorithms, where both components have been updated. Motivated by the idea
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