Roberto Teixeira Alves

An artificial immune system for fuzzy-rule induction in data mining

This work proposes a classification-rule discovery algorithm integrating artificial immune systems and fuzzy systems. The algorithm consists of two parts: a sequential covering procedure and a rule evolution procedure. Each antibody (candidate solution) corresponds to a classification rule. The classification of new examples (antigens) considers not only the fitness of a fuzzy rule based on the entire training set, but also the affinity between the rule and the new example. This affinity must be greater than a threshold in order for the fuzzy rule to be activated, and it is proposed an adaptive procedure for computing this threshold for each rule. This paper reports results for the proposed algorithm in several data sets. Results are analyzed with respect to both predictive accuracy and rule set simplicity, and are compared with C4.5rules, a very popular data mining algorithm.

Multi-label Hierarchical Classification of Protein Functions with Artificial Immune Systems

This work proposes two versions of an Artificial Immune System (AIS) - a relatively recent computational intelligence paradigm --- for predicting protein functions described in the Gene Ontology (GO). The GO has functional classes (GO terms) specified in the form of a directed acyclic graph, which leads to a very challenging multi-label hierarchical classification problem where a protein can be assigned multiple classes (functions, GO terms) across several levels of the GOs term hierarchy. Hence, the proposed approach, called MHC-AIS (Multi-label Hierarchical Classification with an Artificial Immune System), is a sophisticated classification algorithm tailored to both multi-label and hierarchical classification. The first version of the MHC-AIS builds a global classifier to predict all classes in the application domain, whilst the second version builds a local classifier to predict each class. In both versions of the MHC-AIS the classifier is expressed as a set of IF-THEN classification rules, which have the advantage of representing comprehensible knowledge to biologist users. The two MHC-AIS versions are evaluated on a dataset of DNA-binding and ATPase proteins.

Knowledge discovery with Artificial Immune Systems for hierarchical multi-label classification of protein functions

This work presents a system for knowledge discovery from protein databases, based on an Artificial Immune System. The discovered rules have the advantage of representing comprehensible knowledge to biologist users. This task leads to a very challenging problem since a protein can be assigned multiple classes (functions or Gene Ontology (GO) terms) across several levels of the GOs term hierarchy. To solve this problem we present two versions of an algorithm called MHC-AIS (Multi-label Hierarchical Classification with an Artificial Immune System), which is a sophisticated classification algorithm tailored to both multi-label and hierarchical classification. The first version of MHC-AIS builds a global classifier to predict all classes in the dataset, whilst the second version builds a local classifier to predict each class. The proposed versions and an algorithm chosen for comparison are evaluated on a protein dataset, and the results show that MHC-AIS outperformed the compared algorithm in general.

Induction of fuzzy rules with artificial immune systems in acgh based er status breast cancer characterization

Genomic DNA copy number aberrations are frequent in solid tumours although their underlying causes remain obscure. In this paper we show how Artificial Immune System (AIS) paradigm can be successfully employed in the elucidation of biological dynamics of cancerous processes using a novel fuzzy rule induction system for data mining (IFRAIS). Competitive results have been obtained using IFRAIS. A biological interpretation of the results, carried out using Gene Ontology, followed the statistical assessment and put in evidence interesting patterns that are currently under investigation.

Artificial Immune Systems in Bioinformatics

Artificial Immune Systems (AIS) represent one of the most recent and promising approaches in the branch of bio-inspired techniques. Although this open field of research is still in its infancy, several relevant results have been achieved by using the AIS paradigm in demanding tasks such as the ones coming from computational biology and biochemistry. The chapter will show how AIS have been successfully used in computational biology problems and will give readers further hints about possible implementations in unexplored fields. The main goal of the contribution lays in providing both theoretical foundations and hands-on experience that allow researchers to figure out novel applications of AIS in bioinformatics and, at the same time, providing researchers with necessary insights for implementation in daily research. The contribution will be organised in 5 sections.

Fuzzy rule induction and artificial immune systems in female breast cancer familiarity profiling

Genomic DNA copy number aberrations are frequent in solid tumours although their underlying causes of chromosomal instability in tumours remain obscure. In this paper we show how Artificial Immune System (AIS) paradigm can be successfully employed in the elucidation of biological dynamics of cancerous processes using a novel fuzzy rule induction system for data mining (IFRAIS) [1] of aCGH data. Competitive results have been obtained using IFRAIS. A biological interpretation of the results carried out using Gene Ontology is currently under investigation.