Investigating data mining techniques for extracting information from Alzheimer\u27s disease data

Data mining techniques have been used widely in many areas such as business, science, engineering and more recently in clinical medicine. These techniques allow an enormous amount of high dimensional data to be analysed for extraction of interesting information as well as the construction of models for prediction. One of the foci in health related research is Alzheimer\u27s disease which is currently a non-curable disease where diagnosis can only be confirmed after death via an autopsy. Using multi-dimensional data and the applications of data mining techniques, researchers hope to find biomarkers that will diagnose Alzheimer\u27s disease as early as possible. The primary purpose of this research project is to investigate the application of data mining techniques for finding interesting biomarkers from a set of Alzheimer\u27s disease related data. The findings from this project will help to analyse the data more effectively and contribute to methods of providing earlier diagnosis of the disease

Novel biomarkers of renal transplant failure/dysfunction via spectroscopic phenotyping

Successful renal transplantation not only improves patients’ quality and duration of life, but also confers a substantial economic healthcare cost saving. With the growing burden of end-stage renal disease and the requirement for renal replacement therapy, strategies to augment transplant success and subsequent graft survival become more vital than ever. Herein, an objective means of characterising renal function across the transplant journey, and appropriately stratifying in accordance to individual contingencies/factors (including the early detection of renal dysfunction), based on metabolism is explored. Patient pairs, recipients and donors, were metabolically phenotyped prior to (24 h) and post (days 1–5) transplantation using a multi-platform analytical approach (i.e., Nuclear Magnetic Resonance Spectroscopy (NMR) and Mass Spectrometry (MS)) of urine and plasma (n = 50). Using advanced statistics, the resulting metabolic profiles were subsequently modelled, and related to multiple clinical phenotypes (and outcomes), to increase the understanding of molecular changes/signatures across transplantation, capturing valuable information pertinent to transplant type, cause, co-morbidity, modality, immunology and complication (p-value < 0.05) – over donors as well as recipients. An attempt to then develop predictive algorithms for the early detection of renal dysfunction was preliminary defined within the confines of the study design, where integrated NMR and MS metabolic data improved patient stratification for complications over clinical measures (receiver operator characteristic area under curve over 0.900) and potentially replace current measures. While prospective/multicentre studies are imperative for subsequent real-world adoption (qualification/validation), the work conducted herein encompassed much of the first stage of marker development – discovery – where metabolic phenotyping renal transplantation has provided a deeper characterisation of patient journeys with new insights into multiple contingencies/factors (including complication). Such findings infer the value of metabolic phenotyping to augment and potentially replace current measures and methods to better inform decision making in the clinic on the individual/precision level.Open Acces

Robust identification of Parkinson\u27s disease subtypes using radiomics and hybrid machine learning

OBJECTIVES: It is important to subdivide Parkinson\u27s disease (PD) into subtypes, enabling potentially earlier disease recognition and tailored treatment strategies. We aimed to identify reproducible PD subtypes robust to variations in the number of patients and features. METHODS: We applied multiple feature-reduction and cluster-analysis methods to cross-sectional and timeless data, extracted from longitudinal datasets (years 0, 1, 2 & 4; Parkinson\u27s Progressive Marker Initiative; 885 PD/163 healthy-control visits; 35 datasets with combinations of non-imaging, conventional-imaging, and radiomics features from DAT-SPECT images). Hybrid machine-learning systems were constructed invoking 16 feature-reduction algorithms, 8 clustering algorithms, and 16 classifiers (C-index clustering evaluation used on each trajectory). We subsequently performed: i) identification of optimal subtypes, ii) multiple independent tests to assess reproducibility, iii) further confirmation by a statistical approach, iv) test of reproducibility to the size of the samples. RESULTS: When using no radiomics features, the clusters were not robust to variations in features, whereas, utilizing radiomics information enabled consistent generation of clusters through ensemble analysis of trajectories. We arrived at 3 distinct subtypes, confirmed using the training and testing process of k-means, as well as Hotelling\u27s T2 test. The 3 identified PD subtypes were 1) mild; 2) intermediate; and 3) severe, especially in terms of dopaminergic deficit (imaging), with some escalating motor and non-motor manifestations. CONCLUSION: Appropriate hybrid systems and independent statistical tests enable robust identification of 3 distinct PD subtypes. This was assisted by utilizing radiomics features from SPECT images (segmented using MRI). The PD subtypes provided were robust to the number of the subjects, and features

Image Quality Improvement of Medical Images using Deep Learning for Computer-aided Diagnosis

Retina image analysis is an important screening tool for early detection of multiple dis eases such as diabetic retinopathy which greatly impairs visual function. Image analy sis and pathology detection can be accomplished both by ophthalmologists and by the use of computer-aided diagnosis systems. Advancements in hardware technology led to more portable and less expensive imaging devices for medical image acquisition. This promotes large scale remote diagnosis by clinicians as well as the implementation of computer-aided diagnosis systems for local routine disease screening. However, lower cost equipment generally results in inferior quality images. This may jeopardize the reliability of the acquired images and thus hinder the overall performance of the diagnos tic tool. To solve this open challenge, we carried out an in-depth study on using different deep learning-based frameworks for improving retina image quality while maintaining the underlying morphological information for the diagnosis. Our results demonstrate that using a Cycle Generative Adversarial Network for unpaired image-to-image trans lation leads to successful transformations of retina images from a low- to a high-quality domain. The visual evidence of this improvement was quantitatively affirmed by the two proposed validation methods. The first used a retina image quality classifier to confirm a significant prediction label shift towards a quality enhance. On average, a 50% increase of images being classified as high-quality was verified. The second analysed the perfor mance modifications of a diabetic retinopathy detection algorithm upon being trained with the quality-improved images. The latter led to strong evidence that the proposed solution satisfies the requirement of maintaining the images’ original information for diagnosis, and that it assures a pathology-assessment more sensitive to the presence of pathological signs. These experimental results confirm the potential effectiveness of our solution in improving retina image quality for diagnosis. Along with the addressed con tributions, we analysed how the construction of the data sets representing the low-quality domain impacts the quality translation efficiency. Our findings suggest that by tackling the problem more selectively, that is, constructing data sets more homogeneous in terms of their image defects, we can obtain more accentuated quality transformations

EEG-Based Emotion Recognition Using Regularized Graph Neural Networks

Electroencephalography (EEG) measures the neuronal activities in different brain regions via electrodes. Many existing studies on EEG-based emotion recognition do not fully exploit the topology of EEG channels. In this paper, we propose a regularized graph neural network (RGNN) for EEG-based emotion recognition. RGNN considers the biological topology among different brain regions to capture both local and global relations among different EEG channels. Specifically, we model the inter-channel relations in EEG signals via an adjacency matrix in a graph neural network where the connection and sparseness of the adjacency matrix are inspired by neuroscience theories of human brain organization. In addition, we propose two regularizers, namely node-wise domain adversarial training (NodeDAT) and emotion-aware distribution learning (EmotionDL), to better handle cross-subject EEG variations and noisy labels, respectively. Extensive experiments on two public datasets, SEED and SEED-IV, demonstrate the superior performance of our model than state-of-the-art models in most experimental settings. Moreover, ablation studies show that the proposed adjacency matrix and two regularizers contribute consistent and significant gain to the performance of our RGNN model. Finally, investigations on the neuronal activities reveal important brain regions and inter-channel relations for EEG-based emotion recognition

Generative Embedding for Model-Based Classification of fMRI Data

Decoding models, such as those underlying multivariate classification algorithms, have been increasingly used to infer cognitive or clinical brain states from measures of brain activity obtained by functional magnetic resonance imaging (fMRI). The practicality of current classifiers, however, is restricted by two major challenges. First, due to the high data dimensionality and low sample size, algorithms struggle to separate informative from uninformative features, resulting in poor generalization performance. Second, popular discriminative methods such as support vector machines (SVMs) rarely afford mechanistic interpretability. In this paper, we address these issues by proposing a novel generative-embedding approach that incorporates neurobiologically interpretable generative models into discriminative classifiers. Our approach extends previous work on trial-by-trial classification for electrophysiological recordings to subject-by-subject classification for fMRI and offers two key advantages over conventional methods: it may provide more accurate predictions by exploiting discriminative information encoded in ‘hidden’ physiological quantities such as synaptic connection strengths; and it affords mechanistic interpretability of clinical classifications. Here, we introduce generative embedding for fMRI using a combination of dynamic causal models (DCMs) and SVMs. We propose a general procedure of DCM-based generative embedding for subject-wise classification, provide a concrete implementation, and suggest good-practice guidelines for unbiased application of generative embedding in the context of fMRI. We illustrate the utility of our approach by a clinical example in which we classify moderately aphasic patients and healthy controls using a DCM of thalamo-temporal regions during speech processing. Generative embedding achieves a near-perfect balanced classification accuracy of 98% and significantly outperforms conventional activation-based and correlation-based methods. This example demonstrates how disease states can be detected with very high accuracy and, at the same time, be interpreted mechanistically in terms of abnormalities in connectivity. We envisage that future applications of generative embedding may provide crucial advances in dissecting spectrum disorders into physiologically more well-defined subgroups

Recent developments and application of metabolomics in cancer diseases

      Metabolomics studies provide useful information about health and disease status. Metabolite based investigations on various cancers is a powerful approach to diagnosis, prognosis and therapy of cancer diseases. Recently by using advanced analytical techniques such as NMR and MS and its hyphenation methods, global metabolic profiling of diseases has been possible. It is predictable that international contributions and software developments in the future will lead to accurate instrumental analysis based on  a large number of  human samples that finally will improve validation methods and reach this field from the research phase to the clinical phase. In this review, we also discussed the latest developments in analytical methods, application of data analysis, investigation of useful databases and the curent application of metabolomics in cancer diseases that have led to the identification of related biomarkers. In continuation, we listed biomarkers involved in cancer diseases that have been published during recent years.