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Table 1 Evaluation of protein clustering tools. The F-measure (between 0 and 1) measures the agreement between a clustering resulting from a given algorithm and a reference clustering provided with the dataset. An F-measure of 1 indicates perfect agreement. ASTRAL95_1_161 and ASTRAL95_2_161 refer to the two datasets of SCOP v1.61 used by Paccanaro et al. for spectral clustering [7]. All reported values, except for our algorithm FORCE and for Affinity Propagation, are from the same reference.

From: Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing

Dataset Method F-measure
ASTRAL95_1_161 FORCE 0.85
ASTRAL95_1_161 Spectral clustering 0.81
ASTRAL95_1_161 Affinity Propagation 0.65
ASTRAL95_1_161 GeneRAGE 0.47
ASTRAL95_1_161 TribeMCL 0.32
ASTRAL95_1_161 Hierarchical clustering 0.26
ASTRAL95_2_161 FORCE 0.89
ASTRAL95_2_161 Spectral clustering 0.82
ASTRAL95_2_161 Affinity Propagation 0.69
ASTRAL95_2_161 GeneRAGE 0.54
ASTRAL95_2_161 TribeMCL 0.52
ASTRAL95_2_161 Hierarchical clustering 0.42
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