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529
Generic Properties of Combinatory Maps  Neutral Networks of RNA Secondary Structures
, 1995
"... Random graph theory is used to model relationships between sequences and secondary structures of RNA molecules. Sequences folding into identical structures form neutral networks which percolate sequence space if the fraction of neutral nearest neighbors exceeds a threshold value. The networks of any ..."
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Cited by 90 (38 self)
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Random graph theory is used to model relationships between sequences and secondary structures of RNA molecules. Sequences folding into identical structures form neutral networks which percolate sequence space if the fraction of neutral nearest neighbors exceeds a threshold value. The networks of any two different structures almost touch each other, and sequences folding into almost all "common" structures can be found in a small ball of an arbitrary location in sequence space. The results from random graph theory are compared with data obtained by folding large samples of RNA sequences. Differences are explained in terms of RNA molecular structures. 1.
Validation with Guided Search of the State Space
, 1998
"... In practice, model checkers are most useful when they find bugs, not when they prove a property. However, because large portions of the state space of the design actually satisfy the specification, model checkers devote much effort verifying correct portions of the design. In this paper, we enhance ..."
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Cited by 79 (0 self)
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In practice, model checkers are most useful when they find bugs, not when they prove a property. However, because large portions of the state space of the design actually satisfy the specification, model checkers devote much effort verifying correct portions of the design. In this paper, we enhance the bugfinding capability of a model checker by using heuristics to search the states that are most likely to lead to an error, first. Reductions of 1 to 3 orders of magnitude in the number of states needed to find bugs in industrial designs have been observed. Consequently, these heuristics can extend the capability of model checkers to find bugs in designs.
Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration
, 1996
"... Global relations between RNA sequences and secondary structues are understood as mappings from sequence space into shape space. These mappings are investigated by exhaustive folding of all GC and AU sequences with chain lengths up to 30. The technique od tries is used for economic data storage and f ..."
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Cited by 77 (35 self)
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Global relations between RNA sequences and secondary structues are understood as mappings from sequence space into shape space. These mappings are investigated by exhaustive folding of all GC and AU sequences with chain lengths up to 30. The technique od tries is used for economic data storage and fast retrieval of information. The computed structural data are evaluated through exhaustive enumeration and used as an exact reference for testing analytical results derived from mathematical models and sampling based of statistical methods. Several new concepts of RNA sequence to secondary structure mappings are investigated, among them the structure of neutral networks (being sets of sequences folding into the same structure), percolation of sequence space by neutral networks, and the principle of shape space covering . The data of exhaustive enumeration are compared to the analytical results of a random graph model that reveals the generic properties of sequence to structure mappings based on some base pairing logic. The differences between the numerical and the analytical results are interpreted in terms of specific biophysical properties of RNA molecules.
Errorfree coding
 IRE Trans. on Inf. Theory
, 1954
"... Some simple constructive procedures are given for coding sequences of symbols to be transmitted over noisy channels. A message encoded by such a process transmits a positive amount of information over the channel, with an error probability which the receiver may set to be as small as it pleases, wit ..."
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Cited by 65 (0 self)
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Some simple constructive procedures are given for coding sequences of symbols to be transmitted over noisy channels. A message encoded by such a process transmits a positive amount of information over the channel, with an error probability which the receiver may set to be as small as it pleases, without consulting the transmitter. The amount of information transmitted is less than the channel capacity, so the procedures are not ideal, but they are quite efficient for small error probabilities. It is shown that there exist codes of the same errorfree character which transmit information at rates arbitrarily near the channel capacity. I 'l
A stochastic programming approach for supply chain network design under uncertainty
, 2003
"... ..."
Some Applications of Coding Theory in Computational Complexity
, 2004
"... Errorcorrecting codes and related combinatorial constructs play an important role in several recent (and old) results in computational complexity theory. In this paper we survey results on locallytestable and locallydecodable errorcorrecting codes, and their applications to complexity theory ..."
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Cited by 59 (2 self)
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Errorcorrecting codes and related combinatorial constructs play an important role in several recent (and old) results in computational complexity theory. In this paper we survey results on locallytestable and locallydecodable errorcorrecting codes, and their applications to complexity theory and to cryptography.
Fitness Landscapes, Memetic Algorithms, and Greedy Operators for Graph Bipartitioning
 Evolutionary Computation
, 2000
"... The fitness landscape of the graph bipartitioning problem is investigated by performing a search space analysis for several types of graphs. The analysis shows that the structure of the search space is significantly different for the types of instances studied. Moreover, with increasing epistasis ..."
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Cited by 54 (13 self)
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The fitness landscape of the graph bipartitioning problem is investigated by performing a search space analysis for several types of graphs. The analysis shows that the structure of the search space is significantly different for the types of instances studied. Moreover, with increasing epistasis, the amount of gene interactions in the representation of a solution in an evolutionary algorithm, the number of local minima for one type of instance decreases and, thus, the search becomes easier. We suggest that other characteristics besides high epistasis might have greater influence on the hardness of a problem. To understand these characteristics, the notion of a dependency graph describing gene interactions is introduced.
Memetic Algorithms for Combinatorial Optimization Problems: Fitness Landscapes and Effective Search Strategies
, 2001
"... ..."
Extracting Team Mental Models Through Textual Analysis
 Journal of Organizational Behavior
, 1997
"... to Sara Kiesler and Doug Wholey for their involvement in the larger project and for their comments on an earlier version of this paper. I would also like to thank the reviewers for their extensive and very helpful comments. The comments of one reviewer in particular were incredibly valuable not just ..."
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Cited by 48 (12 self)
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to Sara Kiesler and Doug Wholey for their involvement in the larger project and for their comments on an earlier version of this paper. I would also like to thank the reviewers for their extensive and very helpful comments. The comments of one reviewer in particular were incredibly valuable not just for this paper, but for future work in this area. Extracting Team Mental Models Through Textual Analysis An approach, called map analysis, for extracting, analyzing and combining representations of individual’s mental models as cognitive maps is presented. This textual analysis technique allows the researcher to extract cognitive maps, locate similarities across maps, and combine maps to generate a team map. Using map analysis the researcher can address questions about the nature of team mental models and the extent to which sharing is necessary for effective teamwork. This technique is illustrated using data drawn from a study of software engineering teams. The impact of critical coding choices on the resultant findings is examined. It is shown that various coding choices have systematic effects on the