ix

Contents

vii

uction

1

e responsive gene discovery problem

2

e peptide function discovery problem

3

e molecular interaction discovery problem

4

e spectral molecular discovery problem

5

e whole-genome pattern discovery problem

6

e global optimisation pattern discovery problem

7

e chapters

8

nsive Gene Discovery

12

biological question — essential gene discovery

13

nsity estimation

15

.1 The histogram approach

16

.2 The parametric approach

22

.3 The non-parametric approach

26

2.2.3.1 The kernel method

26

2.2.3.2 The K-nearest neighbour approach

28

.4 The semi-parametric approach

30

2.2.4.1 The Gaussian mixture

30

2.2.4.2 The Gamma mixture

34

.5 The multivariate density estimation

36

uster analysis

37

.1 The hierarchical cluster analysis algorithm

39

.2 The K-means cluster analysis algorithm

47

.3 The fuzzy C-means cluster analysis algorithm

58

.4 The mixture model cluster analysis algorithm

60

.5 The other clustering algorithms

64

e gene essentiality pattern discovery problem

65

.1 The data

65

.2 The properties of the transposon statistics

67