Theory of computation

In response to the massive amounts of data that make up a large number of bioinformatics datasets, it has become increasingly necessary for researchers to use computers to aid them in their endeavors. With difficulties such as high dimensionality, class imbalance, noisy data, and difficult to learn class boundaries, being present within the data, bioinformatics datasets are a challenge to work with. One potential source of assistance is the domain of data mining and machine learning, a field which focuses on working with these large amounts of data and develops techniques to discover new trends and patterns that are hidden within the data and to increases the capability of researchers and practitioners to work with this data. Within this domain there are techniques designed to eliminate irrelevant or redundant features, balance the membership of the classes, handle errors found in the data, and build predictive models for future data.

One of the main applications of machine learning in bioinformatics is the construction of classification models which can accurately classify new instances using information gained from previous instances. With the help of machine learning algorithms (such as supervised classification and gene selection) new meaningful knowledge can be extracted from bioinformatics datasets that can help in disease diagnosis and prognosis as well as in prescribing the right treatment for a disease. One particular challenge encountered when analyzing bioinformatics datasets is data noise, which refers to incorrect or missing values in datasets. Noise can be introduced as a result of experimental errors (e.g. faulty microarray chips, insufficient resolution, image corruption, and incorrect laboratory procedures), as well as other errors (errors
during data processing, transfer, and/or mining). A special type of data noise
called class noise, which occurs when an instance/example is mislabeled. Previous
research showed that class noise has a detrimental impact on machine learning algorithms (e.g. worsened classification performance and unstable feature selection). In
addition to data noise, gene expression datasets can suffer from the problems of high
dimensionality (a very large feature space) and class imbalance (unequal distribution
of instances between classes). As a result of these inherent problems, constructing accurate classification models becomes more challenging.