Computational Intelligence Based Classifier Fusion Models for Biomedical Classification Applications

The generalization abilities of machine learning algorithms often depend on the algorithms’ initialization, parameter settings, training sets, or feature selections. For instance, SVM classifier performance largely relies on whether the selected kernel functions are suitable for real application data. To enhance the performance of individual classifiers, this dissertation proposes classifier fusion models using computational intelligence knowledge to combine different classifiers. The first fusion model called T1FFSVM combines multiple SVM classifiers through constructing a fuzzy logic system. T1FFSVM can be improved by tuning the fuzzy membership functions of linguistic variables using genetic algorithms. The improved model is called GFFSVM. To better handle uncertainties existing in fuzzy MFs and in classification data, T1FFSVM can also be improved by applying type-2 fuzzy logic to construct a type-2 fuzzy classifier fusion model (T2FFSVM). T1FFSVM, GFFSVM, and T2FFSVM use accuracy as a classifier performance measure. AUC (the area under an ROC curve) is proved to be a better classifier performance metric. As a comparison study, AUC-based classifier fusion models are also proposed in the dissertation. The experiments on biomedical datasets demonstrate promising performance of the proposed classifier fusion models comparing with the individual composing classifiers. The proposed classifier fusion models also demonstrate better performance than many existing classifier fusion methods. The dissertation also studies one interesting phenomena in biology domain using machine learning and classifier fusion methods. That is, how protein structures and sequences are related each other. The experiments show that protein segments with similar structures also share similar sequences, which add new insights into the existing knowledge on the relation between protein sequences and structures: similar sequences share high structure similarity, but similar structures may not share high sequence similarity

Thrombophilia screening: An artificial neural network approach

Thrombotic disorders have severe consequences for the patients and for the society in general, being one of the main causes of death. These facts reveal that it is extremely important to be preventive; being aware of how probable is to have that kind of syndrome. Indeed, this work will focus on the development of a decision support system that will cater for an individual risk evaluation with respect to the surge of thrombotic complaints. The Knowledge Representation and Reasoning procedures used will be based on an extension to the Logic Programming language, allowing the handling of incomplete and/or default data. The computational framework in place will be centered on Artificial Neural Networks.This work is funded by National Funds through the FCT – Fundação para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) within projects PEst-OE/EEI/UI0752/2014 and PEst-OE/QUI/UI0619/2012

Support Vector Machine-based Fuzzy Systems for Quantitative Prediction of Peptide Binding Affinity

Reliable prediction of binding affinity of peptides is one of the most challenging but important complex modelling problems in the post-genome era due to the diversity and functionality of the peptides discovered. Generally, peptide binding prediction models are commonly used to find out whether a binding exists between a certain peptide(s) and a major histocompatibility complex (MHC) molecule(s). Recent research efforts have been focused on quantifying the binding predictions. The objective of this thesis is to develop reliable real-value predictive models through the use of fuzzy systems. A non-linear system is proposed with the aid of support vector-based regression to improve the fuzzy system and applied to the real value prediction of degree of peptide binding. This research study introduced two novel methods to improve structure and parameter identification of fuzzy systems. First, the support-vector based regression is used to identify initial parameter values of the consequent part of type-1 and interval type-2 fuzzy systems. Second, an overlapping clustering concept is used to derive interval valued parameters of the premise part of the type-2 fuzzy system. Publicly available peptide binding affinity data sets obtained from the literature are used in the experimental studies of this thesis. First, the proposed models are blind validated using the peptide binding affinity data sets obtained from a modelling competition. In that competition, almost an equal number of peptide sequences in the training and testing data sets (89, 76, 133 and 133 peptides for the training and 88, 76, 133 and 47 peptides for the testing) are provided to the participants. Each peptide in the data sets was represented by 643 bio-chemical descriptors assigned to each amino acid. Second, the proposed models are cross validated using mouse class I MHC alleles (H2-Db, H2-Kb and H2-Kk). H2-Db, H2-Kb, and H2-Kk consist of 65 nona-peptides, 62 octa-peptides, and 154 octa-peptides, respectively. Compared to the previously published results in the literature, the support vector-based type-1 and support vector-based interval type-2 fuzzy models yield an improvement in the prediction accuracy. The quantitative predictive performances have been improved as much as 33.6\% for the first group of data sets and 1.32\% for the second group of data sets. The proposed models not only improved the performance of the fuzzy system (which used support vector-based regression), but the support vector-based regression benefited from the fuzzy concept also. The results obtained here sets the platform for the presented models to be considered for other application domains in computational and/or systems biology. Apart from improving the prediction accuracy, this research study has also identified specific features which play a key role(s) in making reliable peptide binding affinity predictions. The amino acid features "Polarity", "Positive charge", "Hydrophobicity coefficient", and "Zimm-Bragg parameter" are considered as highly discriminating features in the peptide binding affinity data sets. This information can be valuable in the design of peptides with strong binding affinity to a MHC I molecule(s). This information may also be useful when designing drugs and vaccines

Fuzzy ART

Adaptive Resonance Theory (ART) models are real-time neural networks for category learning, pattern recognition, and prediction. Unsupervised fuzzy ART and supervised fuzzy ARTMAP synthesize fuzzy logic and ART networks by exploiting the formal similarity between the computations of fuzzy subsethood and the dynamics of ART category choice, search, and learning. Fuzzy ART self-organizes stable recognition categories in response to arbitrary sequences of analog or binary input patterns. It generalizes the binary ART 1 model, replacing the set-theoretic: intersection (∩) with the fuzzy intersection (∧), or component-wise minimum. A normalization procedure called complement coding leads to a symmetric: theory in which the fuzzy inter:>ec:tion and the fuzzy union (∨), or component-wise maximum, play complementary roles. Complement coding preserves individual feature amplitudes while normalizing the input vector, and prevents a potential category proliferation problem. Adaptive weights :otart equal to one and can only decrease in time. A geometric interpretation of fuzzy AHT represents each category as a box that increases in size as weights decrease. A matching criterion controls search, determining how close an input and a learned representation must be for a category to accept the input as a new exemplar. A vigilance parameter (p) sets the matching criterion and determines how finely or coarsely an ART system will partition inputs. High vigilance creates fine categories, represented by small boxes. Learning stops when boxes cover the input space. With fast learning, fixed vigilance, and an arbitrary input set, learning stabilizes after just one presentation of each input. A fast-commit slow-recode option allows rapid learning of rare events yet buffers memories against recoding by noisy inputs. Fuzzy ARTMAP unites two fuzzy ART networks to solve supervised learning and prediction problems. A Minimax Learning Rule controls ARTMAP category structure, conjointly minimizing predictive error and maximizing code compression. Low vigilance maximizes compression but may therefore cause very different inputs to make the same prediction. When this coarse grouping strategy causes a predictive error, an internal match tracking control process increases vigilance just enough to correct the error. ARTMAP automatically constructs a minimal number of recognition categories, or "hidden units," to meet accuracy criteria. An ARTMAP voting strategy improves prediction by training the system several times using different orderings of the input set. Voting assigns confidence estimates to competing predictions given small, noisy, or incomplete training sets. ARPA benchmark simulations illustrate fuzzy ARTMAP dynamics. The chapter also compares fuzzy ARTMAP to Salzberg's Nested Generalized Exemplar (NGE) and to Simpson's Fuzzy Min-Max Classifier (FMMC); and concludes with a summary of ART and ARTMAP applications.Advanced Research Projects Agency (ONR N00014-92-J-4015); National Science Foundation (IRI-90-00530); Office of Naval Research (N00014-91-J-4100

ART-EMAP: A Neural Network Architecture for Object Recognition by Evidence Accumulation

A new neural network architecture is introduced for the recognition of pattern classes after supervised and unsupervised learning. Applications include spatio-temporal image understanding and prediction and 3-D object recognition from a series of ambiguous 2-D views. The architecture, called ART-EMAP, achieves a synthesis of adaptive resonance theory (ART) and spatial and temporal evidence integration for dynamic predictive mapping (EMAP). ART-EMAP extends the capabilities of fuzzy ARTMAP in four incremental stages. Stage 1 introduces distributed pattern representation at a view category field. Stage 2 adds a decision criterion to the mapping between view and object categories, delaying identification of ambiguous objects when faced with a low confidence prediction. Stage 3 augments the system with a field where evidence accumulates in medium-term memory (MTM). Stage 4 adds an unsupervised learning process to fine-tune performance after the limited initial period of supervised network training. Each ART-EMAP stage is illustrated with a benchmark simulation example, using both noisy and noise-free data. A concluding set of simulations demonstrate ART-EMAP performance on a difficult 3-D object recognition problem.Advanced Research Projects Agency (ONR N00014-92-J-4015); National Science Foundation (IRI-90-00530); Office of Naval Research (N00014-91-J-4100); Air Force Office of Scientific Research (90-0083

Uncertainty and Interpretability Studies in Soft Computing with an Application to Complex Manufacturing Systems

In systems modelling and control theory, the benefits of applying neural networks have been extensively studied. Particularly in manufacturing processes, such as the prediction of mechanical properties of heat treated steels. However, modern industrial processes usually involve large amounts of data and a range of non-linear effects and interactions that might hinder their model interpretation. For example, in steel manufacturing the understanding of complex mechanisms that lead to the mechanical properties which are generated by the heat treatment process is vital. This knowledge is not available via numerical models, therefore an experienced metallurgist estimates the model parameters to obtain the required properties. This human knowledge and perception sometimes can be imprecise leading to a kind of cognitive uncertainty such as vagueness and ambiguity when making decisions. In system classification, this may be translated into a system deficiency - for example, small input changes in system attributes may result in a sudden and inappropriate change for class assignation. In order to address this issue, practitioners and researches have developed systems that are functional equivalent to fuzzy systems and neural networks. Such systems provide a morphology that mimics the human ability of reasoning via the qualitative aspects of fuzzy information rather by its quantitative analysis. Furthermore, these models are able to learn from data sets and to describe the associated interactions and non-linearities in the data. However, in a like-manner to neural networks, a neural fuzzy system may suffer from a lost of interpretability and transparency when making decisions. This is mainly due to the application of adaptive approaches for its parameter identification. Since the RBF-NN can be treated as a fuzzy inference engine, this thesis presents several methodologies that quantify different types of uncertainty and its influence on the model interpretability and transparency of the RBF-NN during its parameter identification. Particularly, three kind of uncertainty sources in relation to the RBF-NN are studied, namely: entropy, fuzziness and ambiguity. First, a methodology based on Granular Computing (GrC), neutrosophic sets and the RBF-NN is presented. The objective of this methodology is to quantify the hesitation produced during the granular compression at the low level of interpretability of the RBF-NN via the use of neutrosophic sets. This study also aims to enhance the disitnguishability and hence the transparency of the initial fuzzy partition. The effectiveness of the proposed methodology is tested against a real case study for the prediction of the properties of heat-treated steels. Secondly, a new Interval Type-2 Radial Basis Function Neural Network (IT2-RBF-NN) is introduced as a new modelling framework. The IT2-RBF-NN takes advantage of the functional equivalence between FLSs of type-1 and the RBF-NN so as to construct an Interval Type-2 Fuzzy Logic System (IT2-FLS) that is able to deal with linguistic uncertainty and perceptions in the RBF-NN rule base. This gave raise to different combinations when optimising the IT2-RBF-NN parameters. Finally, a twofold study for uncertainty assessment at the high-level of interpretability of the RBF-NN is provided. On the one hand, the first study proposes a new methodology to quantify the a) fuzziness and the b) ambiguity at each RU, and during the formation of the rule base via the use of neutrosophic sets theory. The aim of this methodology is to calculate the associated fuzziness of each rule and then the ambiguity related to each normalised consequence of the fuzzy rules that result from the overlapping and to the choice with one-to-many decisions respectively. On the other hand, a second study proposes a new methodology to quantify the entropy and the fuzziness that come out from the redundancy phenomenon during the parameter identification. To conclude this work, the experimental results obtained through the application of the proposed methodologies for modelling two well-known benchmark data sets and for the prediction of mechanical properties of heat-treated steels conducted to publication of three articles in two peer-reviewed journals and one international conference

Evolutionary Computation

This book presents several recent advances on Evolutionary Computation, specially evolution-based optimization methods and hybrid algorithms for several applications, from optimization and learning to pattern recognition and bioinformatics. This book also presents new algorithms based on several analogies and metafores, where one of them is based on philosophy, specifically on the philosophy of praxis and dialectics. In this book it is also presented interesting applications on bioinformatics, specially the use of particle swarms to discover gene expression patterns in DNA microarrays. Therefore, this book features representative work on the field of evolutionary computation and applied sciences. The intended audience is graduate, undergraduate, researchers, and anyone who wishes to become familiar with the latest research work on this field