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Clustering (Xu, R. and Wunsch, D.C.; 2008) [Book review]

Article  in  IEEE Pulse · July 2010

DOI: 10.1109/MPUL.2010.937237

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 BOOK REVIEWS
Four Books for the Scientist’s Library
Paul King
Clustering
R
ui Xu and Donald C. Wunsch, II,
Wiley-IEEE Press, 2008. ISBN-
13: 978-0470276808, 358 pages,
US$122.50.
The modern world is teeming with
data. Computers enable us to collect,
store, and transmit huge amounts of in-
formation almost effortlessly. The fields
of biomedical engineering and bioinfor-
matics are no exception. Advances in im-
aging, signal processing, and gene map-
ping techniques have created a plethora
of data much of which awaits analysis to
uncover hidden information. Quite often,
very little or no prior information about
internal dependencies in the data is avail-
able, highlighting the need for unsuper-
vised methods of information processing,
such as clustering.
Clustering is a comprehensive book
dedicated exclusively to the area of clus-
ter analysis and finding similarities in
data. The book focuses on theory and
practice of clustering and can be appeal-
ing to a broad variety of readers. Applied
mathematicians and computer scientists
will find it useful as a reference material,
summarizing most of the current day al-
gorithms. Biomedical engineers and bio-
informatics researchers will appreciate
the large number of practical examples in
gene data analysis, image segmentation,
computer vision, and other applications.
A substantial number of the end-of-chap-
ter problems make this book suitable as a
textbook in graduate-level courses in sci-
ence or engineering.
The book contains 11 chapters start-
ing from the introduction to the field of
Digital Object Identifier 10.1109/MPUL.2010.937237
74 IEEE PULSE ▼ JULY/AUGUST 2010
NEURO ENGINEERING
of partitional clustering. The chapter
starts with formulations of traditional
k-means and expectation maximization
algorithms, which are followed by more
recent algorithms, such as fuzzy c-means
and fuzzy c-shells. Another point of inter-
est is description of search-based cluster-
ing methods based on genetic algorithms,
simulated annealing, and particle swarm
cluster analysis and proximity measures optimization. Four different application
and progressing on to descriptions of ad- examples highlight the use of partition
vanced clustering techniques. The writ- clustering in bioinformatics, computer
ing style is easy to understand and clear. vision, and medical diagnostics. Chapter
Multiple illustrations and tables also posi- 5 deals with the use of artificial neural
tively contribute to the ease of reading. networks in cluster analysis. A larger por-
An extensive bibliography is a valuable tion of this chapter is dedicated to vari-
resource to anyone seeking to find addi- ous flavors of adaptive resonance theory,
tional information of the subject. followed by discussion of learning vec-
A typical chapter starts with an intro- tor quantization, self-organizing maps,
duction to a specific issue and neural gas. Applica-
covered in that chapter. tion examples demonstrate
The introduction is fol- An extensive the use of neural-network
lowed by an extensive de- bibliography is a clus tering in magnetic
scription of a wide variety resonance image (MRI)
of clustering algorithms.
valuable resource segmentation, gene dat a
Clustering methodologies to anyone seeking analysis, and other appli-
are described in their to find additional cations. Chapter 6 pro-
mathematical and algo- information of the gresses to a description
rithmic formulations and subject. of recent advances in ker-
illustrated by flowcharts. nel-based clustering and
Each chapter concludes introduces such concepts
with examples of applying the discussed as kernel principal component analysis,
techniques to solution of real-world clustering with kernel functions and sup-
problems. These examples can make the port vector clustering. Chapter 7 introduc-
book an invaluable resource to a beginner es clustering of sequential data in which
or a practitioner and allow for easy bridg- the sequence in which observations are
ing between the theory and practice. presented is as important as other fea-
The following is a brief overview of tures. Discussion of sequence similarity is
each chapter: followed by introduction of use of Hidden
Chapter 1 introduces the reader to the Markov Models and other model-based
basic concepts of cluster analysis, such as methods. Application examples here fo-
definition of clusters and applications of cus on genomic and biological sequence
clustering. Chapter 2 provides a review clustering. Chapter 8 discusses issues
of different proximity measures for con- associated with clustering of very large
tinuous, discrete, and mixed variables. data sets and describes random sampling,
Chapter 3 focuses on agglomerative and condensation-based, density-based, grid-
divisive hierarchical clustering. Illus- based, and other methods followed by
trated application examples include gene several application examples. Chapter 9
expression data analysis and clustering of illustrates application of clustering for vi-
extensible markup language (XML) doc- sualization of high-dimensional data and
uments. Chapter 4 discusses techniques discusses several linear (such as principal
 component analysis and independent
component analysis) and nonlinear
(such as nonlinear principal component
analysis, multidimensional scaling, and
isometric feature mapping) projection
techniques. Application examples dem-
onstrate practical use of these techniques
in visualization. Chapter 10 focuses on
description of various methods for testing
validity of the clustering results. Among
described methods are external, internal
and relative validity criteria and other ap-
proaches of establishing cluster validity.
Chapter 11 concludes the book with au-
thors’ remarks.
Overall, the book clearly achieves
its aim as a comprehensive reference on
advanced cluster analysis. A plethora of
practical examples makes it a good choice
for anyone interested in applications of
clustering techniques in processing of
biomedical data.
Edward Sazonov
Clarkson University
Potsdam, New York
Information Retrieval in
Biomedicine: Natural Language
Processing for Knowledge
Integration
Violaine Prince and Mathieu Roche, IGI
Global, 2009. ISBN: 978-1-60566-274-9.
432 pages, hardcover. US$225.00.
Natural language processing (NLP) is
a subfield of computational sciences, ad-
dressing the operation and management
of texts as inputs or outputs of compu-
tational devices. As such, this domain
includes a large amount of distinct top-
ics depending on the particular service
considered. In today‘s Internet-based
knowledge-sharing world, NLP is highly
solicited by various scientific communi-
ties as a tremendous help for the follow-
ing endeavors: information retrieval and
knowledge extraction, knowledge inte-
gration to existing devices, and using and
applying existing knowledge structures
for services in information retrieval.
This book is written by subject mat-
ter experts, comprises six sections, and
provides relevant theoretical frameworks
and the latest empirical research findings
in the area of BioNLP according to a lin-
guistic granularity. As a critical mass of
Digital Object Identifier 10.1109/MPUL.2010.937238
76 IEEE PULSE ▼ JULY/AUGUST 2010
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advanced knowledge, this book presents words in context and investigates broader
original applications, going beyond ex- linguistic granularity to overcome ambi-
isting publications while opening up the guity of terms. Chapters VII and VIII have
road for a broader use of NLP in biomedi- shown the effects of ambiguity: Intrinsic
cine. The chapter titled “Text Mining in ambiguity (localized in ontologies them-
Biomedicine” is an introduction written selves) and induced ambiguity detected in
by Sophia Ananiadou, one of the most texts. The sentence context might erase
renowned leaders in BioNLP, who pres- lexical ambiguities effects in some cases.
ents the grounding principles of NLP and Chapter IX, named “Information Extrac-
emphasizes the needs, the requirements, tion of Protein Phosphorylation from Bio-
the nature of the issues and their stakes, medical Literature,” presents a rule-based
and the achievements of system to capture the lexi-
the state of the art. There cal, syntactical, and se-
are four core sections of mantic constraints found
the book: Three that fol- In today‘s Internet- in sentences expressing
low the NLP granularity based knowledge- phosphorylation infor-
scope, ranging from the sharing world, NLP mation from MEDLINE
lexical level in Section I is highly solicited abstracts since isolated
to the sentence level in words or phrases could
by various scientific
Section II, and to the dis- potentially be thematic
course level in Section III, communities. clues but can by no means
and one devoted to select- account for the different
ed existing software tools stages of a process. Chapter
(Section IV). Chapters belonging to these X, “CorTag: A Language for a Contextual
sections are numbered from II to XIX. Tagging of the Words Within Their Sen-
Section I, titled “Works at a Lexi- tence,” complements the preceding one,
cal Level: Crossroads Between NLP and presents a design to extract contextual
Ontological Knowledge Management,” knowledge from sentences, deals with
includes nine chapters and is by far the knowledge discovery, and how to induce
largest since the research on words, con- relations between concepts recognized in
cepts, and word-to-word relations is well texts. Chapter XI, titled “Analyzing the
established and has reached a recognized Text of Clinical Literature for Question
maturity. The order in which chapters Answering,” introduces a method, a de-
have been organized is by the following sign, and a system to not only deal with
pattern: 1) Using existing resources to complex information at the sentence level
perform document processing tasks, in- but also present argumentative articula-
cluding indexation (Chapter II), catego- tion between fragments of sentences and
rization (Chapter III), and information intersection between the sentence-level
retrieval (Chapter IV); indexation and and the discourse-level investigations.
categorization could be seen as prerequi- This chapter is also highly recommended
sites to an intelligent information retriev- to readers who need an accurate survey of
al since they prestructure textual data current question answering systems.
according to topics, domain, keywords, Section III, titled “Pragmatics, Dis-
or interest areas; 2) Dealing with the course Structures and Segment Level as
cross-linguistic terminological problem: the Last Stage in the NLP Offer to Bio-
From a specialists language to general medicine,” groups three chapters and
language within one tongue (Chapter V) presents works on mining techniques that
or across different tongues (Chapter VI); focus more on structures than on words,
3) Enriching terminology: The begin- on the use of neural-network architec-
ning of a strong lexical NLP involvement ture to improve retrieval, and the need in
(Chapter VII); 4) Increasing lexical NLP clinical domains, taking the reader from
involvement in biomedical application the theoretical to the practical applica-
(Chapter VIII). tions of mining techniques. Chapter XII,
Section II, titled “Going Beyond “Discourse Processing for Text Mining,”
Words: NLP Approaches Involving the presents discourse processing, the nature
Sentence Level” includes three chapters and effects of text structures, as well as
and concentrates on research that looks at the broad panel of intersentence relations