doi:10.1016/j.csda.2006.09.035
Copyright © 2006 Elsevier B.V. All rights reserved.
Algorithms for compact letter displays: Comparison and evaluation
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Jens Gramma, Jiong Guob, Falk Hüffnerb,
,
, Rolf Niedermeierb, Hans-Peter Piephoc,
and Ramona Schmida
aWilhelm-Schickard-Institut für Informatik, Universität Tübingen, Sand 13, D-72076 Tübingen, Germany
bInstitut für Informatik, Friedrich-Schiller-Universität Jena, Ernst-Abbe-Platz 2, D-07743 Jena, Germany
cFachgruppe Bioinformatik, Universität Hohenheim, D-70593 Stuttgart, Germany
Available online 19 October 2006.
Abstract
Multiple pairwise comparisons are one of the most frequent tasks in applied statistics. In this context, letter displays may be used for a compact presentation of results of multiple comparisons. A heuristic previously proposed for this task is compared with two new algorithmic approaches. The latter rely on the equivalence of computing compact letter displays to computing clique covers in graphs, a problem that is well-studied in theoretical computer science. A thorough discussion of the three approaches aims to give a comparison of the algorithms’ advantages and disadvantages. The three algorithms are compared in a series of experiments on simulated and real data, e.g., using data from wheat and triticale yield trials.
Keywords: Multiple pairwise comparison; Line display; NP-hard problem; Graph problem; Clique cover; Efficient algorithm
Fig. 1. (a) Line display for Example 1. (b) Letter display for Example 2. (c) Letter display for Example 1. Treatments connected by a common line (a) or having a common letter (b, c) are not significantly different.
Fig. 2. Equivalence of CLD-C and CLIQUE COVER: consider the CLD-C instance with n=5 and H={{1,5},{2,3},{2,5},{3,5}}. This instance can be translated into the graph G=(V,E) with V={1,2,3,4,5} and E={{1,2},{1,3},{1,4},{2,4},{3,4},{4,5}}, shown in (a): treatments correspond to vertices in the graph, and two vertices i and j are connected iff {i,j} is not in H. In (b) we give a letter display for H and in (c) the corresponding clique cover: columns in the letter display correspond to cliques in the graph where the “1”-entries of the column determine the set of vertices in the corresponding clique.
Fig. 3. Comparison of the output quality of the three algorithms. Averaged over 10 random instances.
Fig. 4. Comparison of the runtime of the three algorithms. Averaged over 10 random instances.
Table 1.
Overview on the theoretical characteristics of the three algorithms solving COMPACT LETTER DISPLAY, with respect to their runtime and their guarantees of producing a solution with a minimum number of columns or a minimum number of 1s

Table 2.
Comparison of the performance of the Search-Tree algorithm, the Clique-Growing heuristic, and the Insert–Absorb heuristic on five datasets from real-world statistical analyses. For each dataset and each heuristic we report the number of columns of the computed letter display (cols), the number of 1s (1s), and the runtime in seconds (time)

Table 3.
Overview on the empirical analysis of the three algorithms solving COMPACT LETTER DISPLAY, with respect to their runtime and their performance in producing a solution with a small number of columns or a small number of 1s. We indicate the ranking (first, second, third) of the algorithms with respect to each criterion


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