- author = "Richard Llewellyn Smith",
- title = "Genetic Programming and Domain Knowledge in Hierarchical Multi-Classification",
- school = "University of Wales, Aberystwyth",
- year = "2006",
- address = "UK",
- month = mar,
- email = "rlsNO@SPAMhwyl.org",
- keywords = "genetic algorithms, genetic programming, backpropagation, feedback, hierarchical, multiclass, multilabel, classification",
-
URL = "
http://www.hwyl.org/research/papers/thesis.ps",
-
URL = "http://www.cs.ucl.ac.uk/staff/W.Langdon/ftp/papers/RichSmith_2006_thesis.ps.gz",
- size = "294 pages",
-
abstract = "This thesis describes an exploration of the
application of Genetic Programming to classification
problems in the domain of functional genomics. In the
course of the investigation a GP system was developed
which includes several novel features designed to
specifically target the features of the problem domain.
These features, which are described and investigated,
include: a graph-based program representation scheme; a
packaging system allowing for the construction of
programs in an arbitrary number of layers, designed to
facilitate multiple outputs; a gene pool communal to
the GP population, which, in conjunction with the
layering feature, increases the amount of of effective
code present in the population; a generic ``genetic
engineering'' process for imposing constraints on the
programs of the system; and a backpropagation-inspired
feedback mechanism which increases the speed at which
the system learns.
These features were then tested on data sets exhibiting the properties of genomic data sets -- in particular, multiple non-disjoint classes, and hierarchical classification schemes. These features are then developed, along with fitness measures and the evolutionary process to best model data sets of this type. An exploratory attempt to produce classifications in conjunction with a graph-based classification scheme is also performed.
The developed system is then applied to classifying hard genomic data sets, and the thesis ultimately makes some predictions concerning previously unclassified genes.",
