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Dictionary of protein secondary structure: pattern recognition of hydrogenbonded and geometrical features
 Biopolymers
, 1983
"... structure ..."
2005 MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res
"... The accuracy of multiple sequence alignment program MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, HINSi, FINSi and GINSi, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed hig ..."
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Cited by 788 (5 self)
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The accuracy of multiple sequence alignment program MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, HINSi, FINSi and GINSi, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed
A calculus for cryptographic protocols: The spi calculus
 Information and Computation
, 1999
"... We introduce the spi calculus, an extension of the pi calculus designed for the description and analysis of cryptographic protocols. We show how to use the spi calculus, particularly for studying authentication protocols. The pi calculus (without extension) suffices for some abstract protocols; the ..."
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Cited by 919 (55 self)
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We introduce the spi calculus, an extension of the pi calculus designed for the description and analysis of cryptographic protocols. We show how to use the spi calculus, particularly for studying authentication protocols. The pi calculus (without extension) suffices for some abstract protocols; the spi calculus enables us to consider cryptographic issues in more detail. We represent protocols as processes in the spi calculus and state their security properties in terms of coarsegrained notions of protocol equivalence.
KodairaSpencer theory of gravity and exact results for quantum string amplitudes
 Commun. Math. Phys
, 1994
"... We develop techniques to compute higher loop string amplitudes for twisted N = 2 theories with ĉ = 3 (i.e. the critical case). An important ingredient is the discovery of an anomaly at every genus in decoupling of BRST trivial states, captured to all orders by a master anomaly equation. In a particu ..."
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Cited by 545 (60 self)
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We develop techniques to compute higher loop string amplitudes for twisted N = 2 theories with ĉ = 3 (i.e. the critical case). An important ingredient is the discovery of an anomaly at every genus in decoupling of BRST trivial states, captured to all orders by a master anomaly equation. In a
Concurrent Constraint Programming
, 1993
"... This paper presents a new and very rich class of (concurrent) programming languages, based on the notion of comput.ing with parhal information, and the concommitant notions of consistency and entailment. ’ In this framework, computation emerges from the interaction of concurrently executing agent ..."
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Cited by 502 (16 self)
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This paper presents a new and very rich class of (concurrent) programming languages, based on the notion of comput.ing with parhal information, and the concommitant notions of consistency and entailment. ’ In this framework, computation emerges from the interaction of concurrently executing agents that communicate by placing, checking and instantiating constraints on shared variables. Such a view of computation is interesting in the context of programming languages because of the ability to represent and manipulate partial information about the domain of discourse, in the context of concurrency because of the use of constraints for communication and control, and in the context of AI because of the availability of simple yet powerful mechanisms for controlling inference, and the promise that very rich representational/programming languages, sharing the same set of abstract properties, may be possible. To reflect this view of computation, [Sar89] develops the cc family of languages. We present here one member of the family, CC(.L,+) (pronounced “cc with Ask and Choose”) which provides the basic operations of blocking Ask and atomic Tell and an algebra of behaviors closed under prefixing, indeterministic choice, interleaving, and hiding, and provides a mutual recursion operator. cc(.L,t) is (intentionally!) very similar to Milner’s CCS, but for the radically different underlying concept of communication, which, in fact, pro’ The class is founded on the notion of “constraint logic programming ” [JL87,Mah87], fundamentally generalizes concurrent logic programming, and is the subject of the first author’s dissertation [Sar89], on which this paper is substantially based.
Monitoring the future: National survey results on drug use
 I: Secondary school students (NIH Publication No. 055726). Bethesda, MD: National Institute on Drug Abuse
, 2005
"... by ..."
Mining Sequential Patterns
, 1995
"... We are given a large database of customer transactions, where each transaction consists of customerid, transaction time, and the items bought in the transaction. We introduce the problem of mining sequential patterns over such databases. We present three algorithms to solve this problem, and empiri ..."
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Cited by 1534 (7 self)
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We are given a large database of customer transactions, where each transaction consists of customerid, transaction time, and the items bought in the transaction. We introduce the problem of mining sequential patterns over such databases. We present three algorithms to solve this problem, and empirically evaluate their performance using synthetic data. Two of the proposed algorithms, AprioriSome and AprioriAll, have comparable performance, albeit AprioriSome performs a little better when the minimum number of customers that must support a sequential pattern is low. Scaleup experiments show that both AprioriSome and AprioriAll scale linearly with the number of customer transactions. They also have excellent scaleup properties with respect to the number of transactions per customer and the number of items in a transaction.
A comparison of event models for Naive Bayes text classification
, 1998
"... Recent work in text classification has used two different firstorder probabilistic models for classification, both of which make the naive Bayes assumption. Some use a multivariate Bernoulli model, that is, a Bayesian Network with no dependencies between words and binary word features (e.g. Larkey ..."
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Cited by 1002 (27 self)
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Recent work in text classification has used two different firstorder probabilistic models for classification, both of which make the naive Bayes assumption. Some use a multivariate Bernoulli model, that is, a Bayesian Network with no dependencies between words and binary word features (e.g. Larkey and Croft 1996; Koller and Sahami 1997). Others use a multinomial model, that is, a unigram language model with integer word counts (e.g. Lewis and Gale 1994; Mitchell 1997). This paper aims to clarify the confusion by describing the differences and details of these two models, and by empirically comparing their classification performance on five text corpora. We find that the multivariate Bernoulli performs well with small vocabulary sizes, but that the multinomial performs usually performs even better at larger vocabulary sizesproviding on average a 27% reduction in error over the multivariate Bernoulli model at any vocabulary size.
Lag length selection and the construction of unit root tests with good size and power
 Econometrica
, 2001
"... It is widely known that when there are errors with a movingaverage root close to −1, a high order augmented autoregression is necessary for unit root tests to have good size, but that information criteria such as the AIC and the BIC tend to select a truncation lag (k) that is very small. We conside ..."
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Cited by 534 (14 self)
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It is widely known that when there are errors with a movingaverage root close to −1, a high order augmented autoregression is necessary for unit root tests to have good size, but that information criteria such as the AIC and the BIC tend to select a truncation lag (k) that is very small. We consider a class of Modified Information Criteria (MIC) with a penalty factor that is sample dependent. It takes into account the fact that the bias in the sum of the autoregressive coefficients is highly dependent on k and adapts to the type of deterministic components present. We use a local asymptotic framework in which the movingaverage root is local to −1 to document how the MIC performs better in selecting appropriate values of k. In montecarlo experiments, the MIC is found to yield huge size improvements to the DF GLS and the feasible point optimal PT test developed in Elliott, Rothenberg and Stock (1996). We also extend the M tests developed in Perron and Ng (1996) to allow for GLS detrending of the data. The MIC along with GLS detrended data yield a set of tests with desirable size and power properties.
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