Casimiro Curbelo Montañez

Casimiro Aday Curbelo Montañez, Paul Fergus, Carl Chalmers et al.

One of the most important challenges in the analysis of high-throughput genetic data is the development of efficient computational methods to identify statistically significant Single Nucleotide Polymorphisms (SNPs). Genome-wide association studies (GWAS) use single-locus analysis where each SNP is independently tested for association with phenotypes. The limitation with this approach, however, is its inability to explain genetic variation in complex diseases. Alternative approaches are required to model the intricate relationships between SNPs. Our proposed approach extends GWAS by combining deep learning stacked autoencoders (SAEs) and association rule mining (ARM) to identify epistatic interactions between SNPs. Following traditional GWAS quality control and association analysis, the most significant SNPs are selected and used in the subsequent analysis to investigate epistasis. SAERMA controls the classification results produced in the final fully connected multi-layer feedforward artificial neural network (MLP) by manipulating the interestingness measures, support and confidence, in the rule generation process. The best classification results were achieved with 204 SNPs compressed to 100 units (77% AUC, 77% SE, 68% SP, 53% Gini, logloss=0.58, and MSE=0.20), although it was possible to achieve 73% AUC (77% SE, 63% SP, 45% Gini, logloss=0.62, and MSE=0.21) with 50 hidden units - both supported by close model interpretation.

Paul Fergus, Carl Chalmers, Casimiro Curbelo Montanez et al.

Gynaecologists and obstetricians visually interpret cardiotocography (CTG) traces using the International Federation of Gynaecology and Obstetrics (FIGO) guidelines to assess the wellbeing of the foetus during antenatal care. This approach has raised concerns among professionals with regards to inter- and intra-variability where clinical diagnosis only has a 30\% positive predictive value when classifying pathological outcomes. Machine learning models, trained with FIGO and other user derived features extracted from CTG traces, have been shown to increase positive predictive capacity and minimise variability. This is only possible however when class distributions are equal which is rarely the case in clinical trials where case-control observations are heavily skewed in favour of normal outcomes. Classes can be balanced using either synthetic data derived from resampled case training data or by decreasing the number of control instances. However, this either introduces bias or removes valuable information. Concerns have also been raised regarding machine learning studies and their reliance on manually handcrafted features. While this has led to some interesting results, deriving an optimal set of features is considered to be an art as well as a science and is often an empirical and time consuming process. In this paper, we address both of these issues and propose a novel CTG analysis methodology that a) splits CTG time-series signals into n-size windows with equal class distributions, and b) automatically extracts features from time-series windows using a one dimensional convolutional neural network (1DCNN) and multilayer perceptron (MLP) ensemble. Collectively, the proposed approach normally distributes classes and removes the need to handcrafted features from CTG traces.

C. Chalmers, P. Fergus, C. Aday Curbelo Montanez et al.

The emergence of an ageing population is a significant public health concern. This has led to an increase in the number of people living with progressive neurodegenerative disorders like dementia. Consequently, the strain this is places on health and social care services means providing 24-hour monitoring is not sustainable. Technological intervention is being considered, however no solution exists to non-intrusively monitor the independent living needs of patients with dementia. As a result many patients hit crisis point before intervention and support is provided. In parallel, patient care relies on feedback from informal carers about significant behavioural changes. Yet, not all people have a social support network and early intervention in dementia care is often missed. The smart meter rollout has the potential to change this. Using machine learning and signal processing techniques, a home energy supply can be disaggregated to detect which home appliances are turned on and off. This will allow Activities of Daily Living (ADLs) to be assessed, such as eating and drinking, and observed changes in routine to be detected for early intervention. The primary aim is to help reduce deterioration and enable patients to stay in their homes for longer. A Support Vector Machine (SVM) and Random Decision Forest classifier are modelled using data from three test homes. The trained models are then used to monitor two patients with dementia during a six-month clinical trial undertaken in partnership with Mersey Care NHS Foundation Trust. In the case of load disaggregation for appliance detection, the SVM achieved (AUC=0.86074, Sen=0.756 and Spec=0.92838). While the Decision Forest achieved (AUC=0.9429, Sen=0.9634 and Spec=0.9634). ADLs are also analysed to identify the behavioural patterns of the occupant while detecting alterations in routine.