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Table 2 Cluster accuracy and stability on the completely synthetic data with four repeated measurements at low noise level

From: Clustering gene-expression data with repeated measurements

(a) Cluster accuracy*

Algorithm

Similarity measure/model

Average

SD-weighted

CV-weighted

FITSS

IMM

Average linkage

Elliptical

NA

NA

NA

NA

0.957 (0.089)

Complete linkage

Elliptical

NA

NA

NA

NA

0.957 (0.090)

MCLUST-HC

NA

0.930 (0.100)

NA

NA

0.902 (0.123)

NA

Average linkage

Distance

0.877 (0.191)

0.927 (0.100)

0.876 (0.192)

0.804 (0.155)

NA

Centroid linkage

Distance

0.840 (0.178)

0.927 (0.100)

0.927 (0.100)

0.840 (0.178)

NA

k-means

Distance

0.877 (0.191)

0.927 (0.100)

0.876 (0.192)

NA

NA

Average linkage

Spherical

NA

NA

NA

NA

0.926 (0.102)

Complete linkage

Distance

0.925 (0.102)

0.876 (0.192)

0.925 (0.103)

0.840 (0.179)

NA

Complete linkage

Spherical

NA

NA

NA

NA

0.897 (0.088)

Centroid linkage

Correlation

0.765 (0.115)

0.575 (0.179)

0.527 (0.141)

0.765 (0.115)

NA

Average linkage

Correlation

0.764 (0.114)

0.576 (0.201)

0.597 (0.210)

0.718 (0.222)

NA

k-means

Correlation

0.764 (0.114)

0.707 (0.140)

0.652 (0.116)

NA

NA

Complete linkage

Correlation

0.755 (0.116)

0.584 (0.189)

0.599 (0.194)

0.609 (0.201)

NA

(b) Cluster stability

Algorithm

Similarity measure/model

Average

SD-weighted

CV-weighted

FITSS

IMM

Average linkage

Distance

0.970 (0.055)

0.998 (0.003)

0.998 (0.002)

0.979 (0.018)

NA

Centroid linkage

Distance

0.984 (0.025)

0.998 (0.002)

0.986 (0.027)

0.984 (0.025)

NA

k-means

Distance

0.954 (0.062)

0.998 (0.003)

0.967 (0.070)

NA

NA

Average linkage

Correlation

0.958 (0.054)

0.832 (0.095)

0.854 (0.060)

0.984 (0.025)

NA

Complete linkage

Distance

0.968 (0.041)

0.923 (0.131)

0.981 (0.037)

0.918 (0.055)

NA

Average linkage

Elliptical

NA

NA

NA

NA

0.961 (0.081)

Complete linkage

Elliptical

NA

NA

NA

NA

0.960 (0.083)

Centroid linkage

Correlation

0.959 (0.054)

0.861 (0.119)

0.866 (0.026)

0.959 (0.054)

NA

k-means

Correlation

0.958 (0.054)

0.693 (0.144)

0.634 (0.098)

NA

NA

Complete linkage

Correlation

0.947 (0.067)

0.580 (0.140)

0.671 (0.100)

0.915 (0.049)

NA

MCLUST-HC

NA

0.935 (0.089)

NA

NA

0.916 (0.066)

NA

Average linkage

Spherical

NA

NA

NA

NA

0.852 (0.089)

Complete linkage

Spherical

NA

NA

NA

NA

0.779 (0.091)

  1. *Each entry shows the average adjusted Rand index of the corresponding clustering approach with the six classes. We ran our experiments on five randomly generated synthetic datasets, and show the average results with the SD of the adjusted Rand index in brackets. A high average adjusted Rand index represents close agreement with the classes on average. Each entry shows the average adjusted Rand index of the original clustering result with clusters from remeasured data. The SD of the average adjusted Rand indices over five sets of randomly generated synthetic remeasured data is shown in brackets. A high average adjusted Rand index means that clusters from remeasured data are in close agreement with clusters from the original data. The external knowledge is not used in evaluating cluster stability. For both parts of the table, the maximum average adjusted Rand index of each row is shown in bold. The algorithms (rows) are sorted in descending order of the maximum average adjusted Rand index in each row.