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    ABSTRACT: Microarray data allows an unprecedented view of the biochemical mechanisms contained within a cell although deriving useful information from the data is still proving to be a difficult task. In this paper, a novel method based on a multi-objective genetic algorithm is investigated that evolves a near-optimal trade-off between Artificial Neural Network (ANN) classifier accuracy (sensitivity and specificity) and size (number of genes). This hybrid method is shown to work on four well-established gene expression data sets taken from the literature. The results provide evidence for the rule discovery ability of the hybrid method and indicate that the approach can return biologically intelligible as well as plausible results and requires no pre-filtering or pre-selection of genes.
    No preview · Article · Jun 2013 · International Journal of Data Mining and Bioinformatics
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    ABSTRACT: The Relevance Vector Machine (RVM) is a sparse classifier in which complexity is controlled with the Automatic Relevance Determination prior. However, sparsity is dependent on kernel choice and severe over-fitting can occur.We describe multi-objective evolutionary algorithms (MOEAs) which optimise RVMs allowing selection of the best operating true and false positive rates and complexity from the Pareto set of optimal trade-offs. We introduce several cross-validation methods for use during evolutionary optimisation. Comparisons on benchmark datasets using multi-resolution kernels show that the MOEAs can locate markedly sparser RVMs than the standard, with comparable accuracies.
    No preview · Article · Sep 2012 · Pattern Recognition
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    ABSTRACT: Multi-modal multiphoton microscopy was used to investigate tissue microstructure in the zone of calcified cartilage, focussing on the collagen fibre organisation at the tidemark and cement line. Thick, unstained and unfixed sagittal sections were prepared from the equine metacarpophalangeal joint. Second harmonic generation (SHG) provided contrast for collagen, two-photon fluorescence (TPF) for endogenous fluorophores, and coherent anti-Stokes Raman scattering (CARS) allowed the cells to be visualised. The structure of radial and calcified cartilage was found to vary with location across the joint, with the palma regions showing a more ordered parallel arrangement of collagen fibres than the cortical ridge and dorsal regions. These patterns may be associated with regional variations in joint loading. In addition, the cell lacunae had a greater diameter in the dorsal region than in the palmar region. At the cement line some collagen fibres were observed crossing between the calcified cartilage and the subchondral bone. At the tidemark the fibres were parallel and continuous between the radial and calcified cartilage. Beneath early superficial lesions the structure of the tidemark and calcified cartilage was disrupted with discontinuities and gaps in the fibrillar organisation. Cartilage microstructure varies in the deep zones between regions of different loading. The variations in collagen structure observed may be significant to the local mechanical properties of the cartilage and therefore may be important to its mechanical interactions with the subchondral bone. The calcified cartilage is altered even below early superficial lesions and therefore is important in the understanding of the aetiology of osteoarthritis.
    No preview · Article · Feb 2012 · Journal of Anatomy
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