The Transition Matrix Method for Comparing Sequences; Its use in Describing and Classifying Proteins by their Amino Acid Sequences

Gibbs, Adrian; Dale, M. B.; Kinns, H.R.; MacKenzie, H. G.

doi:10.1093/sysbio/20.4.417

Cited by 7 publications

(1 citation statement)

References 16 publications

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“…Person B, in contrast, performs frame assuming and frame stating on far fewer occasions and focuses on implementation and implementation evaluation earlier and more often. We used the transitions between phases to create a transition matrix from each sequence that reduces the variance between problem-solving processes and provides a data structure that permits comparison between participants (Gibbs et al 1971, Abbott 1995, Pentland 2003b. Following Lipshitz and Bar-Ilan (1996), each cell in the matrix represents a transition between two phases.…”

Section: Discussionmentioning

confidence: 99%

Microfoundations of Problem Solving: Attentional Engagement Predicts Problem-Solving Strategies

Laureiro-Martinez,

Arrieta,

Brusoni

2023

Organization Science

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Organizations use a plethora of methods and tools to help their members solve problems effectively. Yet the specifics of how individuals solve problems remain largely unexplored. We propose and test a cognitive model of problem solving that integrates dual process theories into the attention-based view. The model suggests that diverse problem-solving strategies emerge in response to how individuals deliberate. Three studies provide observational and causal evidence in support of our model. The first study explores the strategies managers use to solve problems. We use think-aloud protocols combined with content, sequence, and cluster analyses to extract the key differences in how experienced managers solve problems. Two problem-solving strategies emerge from the data: one emphasizes mental activities related to framing, and the other emphasizes mental activities related to implementation. In the second study, we use a mixed factorial experimental design and mouse-tracking analysis to uncover the causal mechanism that explains the emergence of these two strategies. We then retest our hypotheses in a third, preregistered, study. We find that manipulating attention toward mental activities related to framing increases deliberation aimed at restructuring the problem elements. In contrast, directing attention toward mental activities related to implementation increases deliberation on the potential contingencies and consequences of the solution. Our findings provide empirical evidence about how problems are actually solved and support the idea that attentional processes are malleable enough to affect the choice of problem-solving strategies. History: This paper has been accepted for the Organization Science Special Issue on Experiments in Organizational Theory. Funding: For Study 1, funding from EC NEST-2006-PATH-Cul, CID-Cultural and Innovation Dynamics: FP6-043345 is gratefully acknowledged. Supplemental Material: The supplemental material is available at https://doi.org/10.1287/orsc.2019.13213 .

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Section: Discussionmentioning

confidence: 99%

Microfoundations of Problem Solving: Attentional Engagement Predicts Problem-Solving Strategies

Laureiro-Martinez,

Arrieta,

Brusoni

2023

Organization Science

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Statistical distance between texts and filtration methods in sequence comparison

Pevzner

1992

Bioinformatics

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Upon searching local similarities in long sequences, the necessity of a 'rapid' similarity search becomes acute. Quadratic complexity of dynamic programming algorithms forces the employment of filtration methods that allow elimination of the sequences with a low similarity level. The paper is devoted to the theoretical substantiations of the filtration method based on the statistical distance between texts. The notion of the filtration efficiency is introduced and the efficiency of several filters is estimated. It is shown that the efficiency of the statistical ltuple filtration upon DNA database search is associated with a potential extension of the original four-letter alphabet and grows exponentially with increasing I. The formula that allows one to estimate the filtration parameters is presented. 1991) are impractical for searching large databases, filtration methods (/-tuple analysis) for similarity search in the genetic databases were proposed in the pioneering papers of Wilbur and Lipman (1983) and Lipman and Pearson (1985) (for other filtration methods see Gusev et al.The filtration methods for fast similarity search are based on the simple observation that similar sequences share the same

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Alignment-free sequence comparison—a review

Vinga¹,

Almeida²

2003

Bioinformatics

712

514

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The Transition Matrix Method for Comparing Sequences; Its use in Describing and Classifying Proteins by their Amino Acid Sequences

Cited by 7 publications

References 16 publications

Microfoundations of Problem Solving: Attentional Engagement Predicts Problem-Solving Strategies

Microfoundations of Problem Solving: Attentional Engagement Predicts Problem-Solving Strategies

Statistical distance between texts and filtration methods in sequence comparison

Alignment-free sequence comparison—a review

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