Bioinformatics and Computational Biology
In addition to the use of online tools for analysis, it
is common practice for research groups to access these
databases and utilities locally. Different communities
of bioinformatics programmers have set up free and
open source projects such as EMBOSS (http://emboss.
sourceforge.net/, Rice et al., 2000), Bioconductor (http://
www.bioconductor.org), BioPerl, (http://www.bioperl.
org, Stajich et al., 2002), BioPython (http://www.
biopython.org), and BioJava (http://www.biojava.org),
which develop and distribute shared programming tools
and objects. Several integrated software tools are also
available, such as Taverna for bioinformatics workflow
and distributed systems (http://taverna.sourceforge.
net/), or Quantum 3.1 for drug discovery (http://www.
q-pharm.com/home/contents/drug_d/soft).
FUTURE TRENDS
We have identified a broad set of problems and tools
used within bioinformatics. In this section we focus
specifically on the future of machine learning within
bioinformatics. While a large set of data mining or
machine learning tools have captured attention in the
field of bioinformatics, it is worth noting that in ap-
plication fields where a similarity measure has to be
built, either to classify, cluster, predict or estimate,
the use of support vector machines (SVM) and ker-
nel methods (KM) are increasingly popular. This has
been especially significant in computational biology,
due to performance in real-world applications, strong
modularity, mathematical elegance and convenience.
Applications are encountered in a wide range of prob-
lems, from the classification of tumors to the automatic
annotation of proteins. Their ability to work with high
dimensional data, to process and efficiently integrate
non-vectorial data (strings and images), along with a
natural and consistent mathematical framework, make
them very suitable to solve various problems arising
in computational biology.
Since the early papers using SVM in bioinformatics
(Mukherjee et. al., 1998; Jaakkola et. al., 1999), the
application of these methods has grown exponentially.
More than a mere application of well-established
methods to new datasets, the use of kernel methods
in computational biology has been accompanied by
new developments to match the specificities and the
needs of bioinformatics, such as methods for feature
selection in combination with the classification of high-
dimensional data, the introduction of string kernels to
process biological sequences, or the development of B
methods to learn from several kernels simultaneously
(‘composite kernels’). The reader can find references
in the book by Schölkopf et al. (2004), and a compre-
hensive introduction in (Vert, 2006). Several kernels
for structured data, such as sequences, trees or graphs,
widely developed and used in computational biology,
are also presented in detail by Shawe-Taylor and Cris-
tianini (2004).
In the near future, developments in transductive
learning (improving learning through exploiting un-
labeled samples), refinements in feature selection and
string-based algorithms, and design of biological-based
kernels will take place. Certainly, many computational
biology tasks are transductive and/or can be specified
through optimizing similarity criteria on strings. In
addition, exploiting the nature of these learning tasks
through engineered and problem-dependent kernels
may lead to improved performance in many biologi-
cal domains. In conclusion, the development of new
methods for specific problems under the paradigm of
kernel methods is gaining popularity and how far these
methods can be extended is an unanswered question.
CONCLUSION
In this chapter, we have given an overview of the field
of bioinformatics and computational biology, with its
needs and demands. We have exposed the main research
topics and pointed out common tools and software to
tackle existing problems. We noted that the paradigm
of kernel methods can be useful to develop a consis-
tent formalism for a number of these problems. The
application of advanced machine learning techniques
to solve problems based on biological data will surely
bring greater insight into the functionality of the human
body. What the future will bring is unknown, but the
challenging questions answered so far and the set of
new and powerful methods developed ensure exciting
results in the near future.
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