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  1. Fulltext How automated image analysis techniques help scientists in species identification and classification?
    Yousef Kalafi E, Town C, Kaur Dhillon S
    Folia Morphol (Warsz), 2018;77(2):179-193.
    PMID: 28868609 DOI: 10.5603/FM.a2017.0079
    Identification of taxonomy at a specific level is time consuming and reliant upon expert ecologists. Hence the demand for automated species identification incre-ased over the last two decades. Automation of data classification is primarily focussed on images while incorporating and analysing image data has recently become easier due to developments in computational technology. Research ef-forts on identification of species include specimens' image processing, extraction of identical features, followed by classifying them into correct categories. In this paper, we discuss recent automated species identification systems, mainly for categorising and evaluating their methods. We reviewed and compared different methods in step by step scheme of automated identification and classification systems of species images. The selection of methods is influenced by many variables such as level of classification, number of training data and complexity of images. The aim of writing this paper is to provide researchers and scientists an extensive background study on work related to automated species identification, focusing on pattern recognition techniques in building such systems for biodiversity studies. (Folia Morphol 2018; 77, 2: 179-193).
  2. Fulltext Automated identification of Monogeneans using digital image processing and K-nearest neighbour approaches
    Yousef Kalafi E, Tan WB, Town C, Dhillon SK
    BMC Bioinformatics, 2016 Dec 22;17(Suppl 19):511.
    PMID: 28155722 DOI: 10.1186/s12859-016-1376-z
    BACKGROUND: Monogeneans are flatworms (Platyhelminthes) that are primarily found on gills and skin of fishes. Monogenean parasites have attachment appendages at their haptoral regions that help them to move about the body surface and feed on skin and gill debris. Haptoral attachment organs consist of sclerotized hard parts such as hooks, anchors and marginal hooks. Monogenean species are differentiated based on their haptoral bars, anchors, marginal hooks, reproductive parts' (male and female copulatory organs) morphological characters and soft anatomical parts. The complex structure of these diagnostic organs and also their overlapping in microscopic digital images are impediments for developing fully automated identification system for monogeneans (LNCS 7666:256-263, 2012), (ISDA; 457-462, 2011), (J Zoolog Syst Evol Res 52(2): 95-99. 2013;). In this study images of hard parts of the haptoral organs such as bars and anchors are used to develop a fully automated identification technique for monogenean species identification by implementing image processing techniques and machine learning methods.

    RESULT: Images of four monogenean species namely Sinodiplectanotrema malayanus, Trianchoratus pahangensis, Metahaliotrema mizellei and Metahaliotrema sp. (undescribed) were used to develop an automated technique for identification. K-nearest neighbour (KNN) was applied to classify the monogenean specimens based on the extracted features. 50% of the dataset was used for training and the other 50% was used as testing for system evaluation. Our approach demonstrated overall classification accuracy of 90%. In this study Leave One Out (LOO) cross validation is used for validation of our system and the accuracy is 91.25%.

    CONCLUSIONS: The methods presented in this study facilitate fast and accurate fully automated classification of monogeneans at the species level. In future studies more classes will be included in the model, the time to capture the monogenean images will be reduced and improvements in extraction and selection of features will be implemented.

  3. Machine Learning and Deep Learning Approaches in Breast Cancer Survival Prediction Using Clinical Data
    Kalafi EY, Nor NAM, Taib NA, Ganggayah MD, Town C, Dhillon SK
    Folia Biol (Praha), 2019;65(5-6):212-220.
    PMID: 32362304
    Breast cancer survival prediction can have an extreme effect on selection of best treatment protocols. Many approaches such as statistical or machine learning models have been employed to predict the survival prospects of patients, but newer algorithms such as deep learning can be tested with the aim of improving the models and prediction accuracy. In this study, we used machine learning and deep learning approaches to predict breast cancer survival in 4,902 patient records from the University of Malaya Medical Centre Breast Cancer Registry. The results indicated that the multilayer perceptron (MLP), random forest (RF) and decision tree (DT) classifiers could predict survivorship, respectively, with 88.2 %, 83.3 % and 82.5 % accuracy in the tested samples. Support vector machine (SVM) came out to be lower with 80.5 %. In this study, tumour size turned out to be the most important feature for breast cancer survivability prediction. Both deep learning and machine learning methods produce desirable prediction accuracy, but other factors such as parameter configurations and data transformations affect the accuracy of the predictive model.
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