How Much Does it Cost? Optimization of Costs in Sequence Analysis of Social Science Data

Sociological Methods and Research, Forthcoming

Posted: 23 Oct 2008 Last revised: 10 Sep 2009

See all articles by Jacques-Antoine Gauthier

Jacques-Antoine Gauthier

University of Lausanne

Eric D. Widmer

University of Geneva

Philipp Bucher

École Polytechnique Fédérale de Lausanne

Cédric Notredame

Centre de Regulacio Genomica (CRG)

Date Written: October 12, 2007

Abstract

One major methodological problem in analysis of sequence data is the determination of costs from which distances between sequences are derived. If this problem is currently not optimally dealt with in the social sciences, it has some similarity with problems solved in bioinformatics for three decades. In this article, we propose an optimization of substitution and deletion/insertion costs based on computational methods. We provide an empirical way of determining costs for cases, frequent in the social sciences, in which theory does not clearly promote one cost scheme over another. Using three distinct datasets we tested the distances and cluster solutions produced by the new cost scheme in comparison with solutions based on cost schemes associated with other research strategies. We found that the proposed method performs well compared with other cost setting strategies, while it alleviates the justification problem of cost schemes.

Keywords: sequence analysis, optimal matching, trajectories, empirical cost optimization

Suggested Citation

Gauthier, Jacques-Antoine and Widmer, Eric D. and Bucher, Philipp and Notredame, Cédric, How Much Does it Cost? Optimization of Costs in Sequence Analysis of Social Science Data (October 12, 2007). Sociological Methods and Research, Forthcoming, Available at SSRN: https://ssrn.com/abstract=1288012

Jacques-Antoine Gauthier (Contact Author)

University of Lausanne ( email )

Quartier Chambronne
Lausanne, Vaud CH-1015
Switzerland

Eric D. Widmer

University of Geneva ( email )

102 Bd Carl-Vogt
Genève, CH - 1205
Switzerland

Philipp Bucher

École Polytechnique Fédérale de Lausanne ( email )

Station 5
Odyssea 1.04
1015 Lausanne, CH-1015
Switzerland

Cédric Notredame

Centre de Regulacio Genomica (CRG) ( email )

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