Machine Learning Approaches for the Prediction of Obesity using Publicly Available Genetic Profiles

This paper presents a novel approach based on the analysis of genetic variants from publicly available genetic profiles and the manually curated database, the National Human Genome Research Institute Catalog. Using data science techniques, genetic variants are identified in the collected participant profiles then indexed as risk variants in the National Human Genome Research Institute Catalog. Indexed genetic variants or Single Nucleotide Polymorphisms are used as inputs in various machine learning algorithms for the prediction of obesity. Body mass index status of participants is divided into two classes, Normal Class and Risk Class. Dimensionality reduction tasks are performed to generate a set of principal variables - 13 SNPs - for the application of various machine learning methods. The models are evaluated using receiver operator characteristic curves and the area under the curve. Machine learning techniques including gradient boosting, generalized linear model, classification and regression trees, K-nearest neighbours, support vector machines, random forest and multilayer neural network are comparatively assessed in terms of their ability to identify the most important factors among the initial 6622 variables describing genetic variants, age and gender, to classify a subject into one of the body mass index related classes defined in this study. Our simulation results indicated that support vector machine generated high accuracy value of 90.5%

Intelligent Systems Approach for Classification and Management of Patients with Headache

Primary headache disorders are the most common complaints worldwide. The socioeconomic and personal impact of headache disorders is enormous, as it is the leading cause of workplace absence. Headache patients’ consultations are increasing as the population has increased in size, live longer and many people have multiple conditions, however, access to specialist services across the UK is currently inequitable because the numbers of trained consultant neurologists in the UK are 10 times lower than other European countries. Additionally, more than two third of headache cases presented to primary care were labelled with unspecified headache. Therefore, an alternative pathway to diagnose and manage patients with primary headache could be crucial to reducing the need for specialist assessment and increase capacity within the current service model. Several recent studies have targeted this issue through the development of clinical decision support systems, which can help non-specialist doctors and general practitioners to diagnose patients with primary headache disorders in primary clinics. However, the majority of these studies were following a rule-based system style, in which the rules were summarised and expressed by a computer engineer. This style carries many downsides, and we will discuss them later on in this dissertation. In this study, we are adopting a completely different approach. The use of machine learning is recruited for the classification of primary headache disorders, for which a dataset of 832 records of patients with primary headaches was considered, originating from three medical centres located in Turkey. Three main types of primary headaches were derived from the data set including Tension Type Headache in both episodic and chronic forms, Migraine with and without Aura, followed by Trigeminal Autonomic Cephalalgia that further subdivided into Cluster headache, paroxysmal hemicrania and short-lasting unilateral neuralgiform headache attacks with conjunctival injection and tearing. Six popular machine-learning based classifiers, including linear and non-linear ensemble learning, in addition to one regression based procedure, have been evaluated for the classification of primary headaches within a supervised learning setting, achieving highest aggregate performance outcomes of AUC 0.923, sensitivity 0.897, and overall classification accuracy of 0.843. This study also introduces the proposed HydroApp system, which is an M-health based personalised application for the follow-up of patients with long-term conditions such as chronic headache and hydrocephalus. We managed to develop this system with the supervision of headache specialists at Ashford hospital, London, and neurology experts at Walton Centre and Alder Hey hospital Liverpool. We have successfully investigated the acceptance of using such an M-health based system via an online questionnaire, where 86% of paediatric patients and 60% of adult patients were interested in using HydroApp system to manage their conditions. Features and functions offered by HydroApp system such as recording headache score, recording of general health and well-being as well as alerting the treating team, have been perceived as very or extremely important aspects from patients’ point of view. The study concludes that the advances in intelligent systems and M-health applications represent a promising atmosphere through which to identify alternative solutions, which in turn increases the capacity in the current service model and improves diagnostic capability in the primary headache domain and beyond

Development of medical image/video segmentation via deep learning models

Image segmentation has a critical role in medical diagnosis systems as it is mostly the initial stage, and any error would be propagated in the subsequent analysis. Certain challenges, including Irregular border, low quality of images, small Region of Interest (RoI) and complex structures such as overlapping cells in images impede the improvement of medical image analysis. Deep learning-based algorithms have recently brought superior achievements in computer vision. However, there are limitations to their application in the medical domain including data scarcity, and lack of pretrained models on medical data. This research addresses the issues that hinder the progress of deep learning methods on medical data. Firstly, the effectiveness of transfer learning from a pretrained model with dissimilar data is investigated. The model is improved by integrating feature maps from the frequency domain into the spatial feature maps of Convolutional Neural Network (CNN). Training from scratch and the challenges ahead were explored as well. The proposed model shows higher performance compared to state-of-the-art methods by %2:2 and %17 in Jaccard index for tasks of lesion segmentation and dermoscopic feature segmentation respectively. Furthermore, the proposed model benefits from significant improvement for noisy images without preprocessing stage. Early stopping and drop out layers were considered to tackle the overfitting and network hyper-parameters such as different learning rate, weight initialization, kernel size, stride and normalization techniques were investigated to enhance learning performance. In order to expand the research into video segmentation, specifically left ventricular segmentation, U-net deep architecture was modified. The small RoI and confusion between overlapped organs are big challenges in MRI segmentation. The consistent motion of LV and the continuity of neighbor frames are important features that were used in the proposed architecture. High level features including optical flow and contourlet were used to add temporal information and the RoI module to the Unet model. The proposed model surpassed the results of original Unet model for LV segmentation by a %7 increment in Jaccard index

ESSE 2017. Proceedings of the International Conference on Environmental Science and Sustainable Energy

Environmental science is an interdisciplinary academic field that integrates physical-, biological-, and information sciences to study and solve environmental problems. ESSE - The International Conference on Environmental Science and Sustainable Energy provides a platform for experts, professionals, and researchers to share updated information and stimulate the communication with each other. In 2017 it was held in Suzhou, China June 23-25, 2017

Smart Flow Control Processes in Micro Scale

In recent years, microfluidic devices with a large surface-to-volume ratio have witnessed rapid development, allowing them to be successfully utilized in many engineering applications. A smart control process has been proposed for many years, while many new innovations and enabling technologies have been developed for smart flow control, especially concerning “smart flow control” at the microscale. This Special Issue aims to highlight the current research trends related to this topic, presenting a collection of 33 papers from leading scholars in this field. Among these include studies and demonstrations of flow characteristics in pumps or valves as well as dynamic performance in roiling mill systems or jet systems to the optimal design of special components in smart control systems