Multiple Imputation based Clustering Validation (MIV) for Big Longitudinal Trial Data with Missing Values in eHealth

Web-delivered trials are an important component in eHealth services. These trials, mostly behavior-based, generate big heterogeneous data that are longitudinal, high dimensional with missing values. Unsupervised learning methods have been widely applied in this area, however, validating the optimal number of clusters has been challenging. Built upon our multiple imputation (MI) based fuzzy clustering, MIfuzzy, we proposed a new multiple imputation based validation (MIV) framework and corresponding MIV algorithms for clustering big longitudinal eHealth data with missing values, more generally for fuzzy-logic based clustering methods. Specifically, we detect the optimal number of clusters by auto-searching and -synthesizing a suite of MI-based validation methods and indices, including conventional (bootstrap or cross-validation based) and emerging (modularity-based) validation indices for general clustering methods as well as the specific one (Xie and Beni) for fuzzy clustering. The MIV performance was demonstrated on a big longitudinal dataset from a real web-delivered trial and using simulation. The results indicate MI-based Xie and Beni index for fuzzy-clustering are more appropriate for detecting the optimal number of clusters for such complex data. The MIV concept and algorithms could be easily adapted to different types of clustering that could process big incomplete longitudinal trial data in eHealth services

Attribute Equilibrium Dominance Reduction Accelerator (DCCAEDR) Based on Distributed Coevolutionary Cloud and Its Application in Medical Records

© 2013 IEEE. Aimed at the tremendous challenge of attribute reduction for big data mining and knowledge discovery, we propose a new attribute equilibrium dominance reduction accelerator (DCCAEDR) based on the distributed coevolutionary cloud model. First, the framework of N-populations distributed coevolutionary MapReduce model is designed to divide the entire population into N subpopulations, sharing the reward of different subpopulations' solutions under a MapReduce cloud mechanism. Because the adaptive balancing between exploration and exploitation can be achieved in a better way, the reduction performance is guaranteed to be the same as those using the whole independent data set. Second, a novel Nash equilibrium dominance strategy of elitists under the N bounded rationality regions is adopted to assist the subpopulations necessary to attain the stable status of Nash equilibrium dominance. This further enhances the accelerator's robustness against complex noise on big data. Third, the approximation parallelism mechanism based on MapReduce is constructed to implement rule reduction by accelerating the computation of attribute equivalence classes. Consequently, the entire attribute reduction set with the equilibrium dominance solution can be achieved. Extensive simulation results have been used to illustrate the effectiveness and robustness of the proposed DCCAEDR accelerator for attribute reduction on big data. Furthermore, the DCCAEDR is applied to solve attribute reduction for traditional Chinese medical records and to segment cortical surfaces of the neonatal brain 3-D-MRI records, and the DCCAEDR shows the superior competitive results, when compared with the representative algorithms

An overview of clustering methods with guidelines for application in mental health research

Cluster analyzes have been widely used in mental health research to decompose inter-individual heterogeneity by identifying more homogeneous subgroups of individuals. However, despite advances in new algorithms and increasing popularity, there is little guidance on model choice, analytical framework and reporting requirements. In this paper, we aimed to address this gap by introducing the philosophy, design, advantages/disadvantages and implementation of major algorithms that are particularly relevant in mental health research. Extensions of basic models, such as kernel methods, deep learning, semi-supervised clustering, and clustering ensembles are subsequently introduced. How to choose algorithms to address common issues as well as methods for pre-clustering data processing, clustering evaluation and validation are then discussed. Importantly, we also provide general guidance on clustering workflow and reporting requirements. To facilitate the implementation of different algorithms, we provide information on R functions and librarie

Systematic Review on Missing Data Imputation Techniques with Machine Learning Algorithms for Healthcare

Missing data is one of the most common issues encountered in data cleaning process especially when dealing with medical dataset. A real collected dataset is prone to be incomplete, inconsistent, noisy and redundant due to potential reasons such as human errors, instrumental failures, and adverse death. Therefore, to accurately deal with incomplete data, a sophisticated algorithm is proposed to impute those missing values. Many machine learning algorithms have been applied to impute missing data with plausible values. However, among all machine learning imputation algorithms, KNN algorithm has been widely adopted as an imputation for missing data due to its robustness and simplicity and it is also a promising method to outperform other machine learning methods. This paper provides a comprehensive review of different imputation techniques used to replace the missing data. The goal of the review paper is to bring specific attention to potential improvements to existing methods and provide readers with a better grasps of imputation technique trends

Big data analytics for preventive medicine

© 2019, Springer-Verlag London Ltd., part of Springer Nature. Medical data is one of the most rewarding and yet most complicated data to analyze. How can healthcare providers use modern data analytics tools and technologies to analyze and create value from complex data? Data analytics, with its promise to efficiently discover valuable pattern by analyzing large amount of unstructured, heterogeneous, non-standard and incomplete healthcare data. It does not only forecast but also helps in decision making and is increasingly noticed as breakthrough in ongoing advancement with the goal is to improve the quality of patient care and reduces the healthcare cost. The aim of this study is to provide a comprehensive and structured overview of extensive research on the advancement of data analytics methods for disease prevention. This review first introduces disease prevention and its challenges followed by traditional prevention methodologies. We summarize state-of-the-art data analytics algorithms used for classification of disease, clustering (unusually high incidence of a particular disease), anomalies detection (detection of disease) and association as well as their respective advantages, drawbacks and guidelines for selection of specific model followed by discussion on recent development and successful application of disease prevention methods. The article concludes with open research challenges and recommendations

Clustering of longitudinal viral loads in the Western Cape

Introduction: Routine viral load (VL) monitoring is important for assessing the effectiveness of ART in South Africa. There is little information however, on how the longitudinal VL patterns change for subgroups of persons living with HIV (PLHIV) who have experienced at least one elevated VL. We investigated the possible longitudinal VL patterns that may exist among this unique population. Methods: This mini-dissertation offers three components; a research protocol (Section A), a literature review (Section B) and a journal ready manuscript (Section C). We examined HIV VL data for the Western Cape from 2008 to 2018, taken from the National Health Laboratory Services (NHLS). Using< 1000 copies/mL as a threshold for viral suppression, we identified 109092 individuals who had at least one instance of an elevated VL. A nonparametric (KML-Shape) and a model-based (LCMM) clustering technique were used to identify latent subgroups of longitudinal VL trajectories among these individuals. Results: Both the KML-Shape and LCMM clustering techniques identified five latent viral load trajectory subgroups. KML-Shape found majority of individuals' trajectories belonged to clusters that had a decreasing longitudinal VL trend (76.6% of individuals), while LCMM found a smaller proportion of individuals' trajectories belonged to clusters that had a decreasing longitudinal trend (52.5% of individuals). Most of the trajectory subgroups identified had long periods of low-level viremia. Conclusion: Although majority of individuals belonged to clusters that had downward trends, further research is needed to better understand factors contributing to membership of clusters that did not have a downward longitudinal trend. Understanding these factors may help in the development of targeted HIV prevention programs for these individuals

Intelligent data mining using artificial neural networks and genetic algorithms : techniques and applications

Data Mining (DM) refers to the analysis of observational datasets to find relationships and to summarize the data in ways that are both understandable and useful. Many DM techniques exist. Compared with other DM techniques, Intelligent Systems (ISs) based approaches, which include Artificial Neural Networks (ANNs), fuzzy set theory, approximate reasoning, and derivative-free optimization methods such as Genetic Algorithms (GAs), are tolerant of imprecision, uncertainty, partial truth, and approximation. They provide flexible information processing capability for handling real-life situations. This thesis is concerned with the ideas behind design, implementation, testing and application of a novel ISs based DM technique. The unique contribution of this thesis is in the implementation of a hybrid IS DM technique (Genetic Neural Mathematical Method, GNMM) for solving novel practical problems, the detailed description of this technique, and the illustrations of several applications solved by this novel technique. GNMM consists of three steps: (1) GA-based input variable selection, (2) Multi- Layer Perceptron (MLP) modelling, and (3) mathematical programming based rule extraction. In the first step, GAs are used to evolve an optimal set of MLP inputs. An adaptive method based on the average fitness of successive generations is used to adjust the mutation rate, and hence the exploration/exploitation balance. In addition, GNMM uses the elite group and appearance percentage to minimize the randomness associated with GAs. In the second step, MLP modelling serves as the core DM engine in performing classification/prediction tasks. An Independent Component Analysis (ICA) based weight initialization algorithm is used to determine optimal weights before the commencement of training algorithms. The Levenberg-Marquardt (LM) algorithm is used to achieve a second-order speedup compared to conventional Back-Propagation (BP) training. In the third step, mathematical programming based rule extraction is not only used to identify the premises of multivariate polynomial rules, but also to explore features from the extracted rules based on data samples associated with each rule. Therefore, the methodology can provide regression rules and features not only in the polyhedrons with data instances, but also in the polyhedrons without data instances. A total of six datasets from environmental and medical disciplines were used as case study applications. These datasets involve the prediction of longitudinal dispersion coefficient, classification of electrocorticography (ECoG)/Electroencephalogram (EEG) data, eye bacteria Multisensor Data Fusion (MDF), and diabetes classification (denoted by Data I through to Data VI). GNMM was applied to all these six datasets to explore its effectiveness, but the emphasis is different for different datasets. For example, the emphasis of Data I and II was to give a detailed illustration of how GNMM works; Data III and IV aimed to show how to deal with difficult classification problems; the aim of Data V was to illustrate the averaging effect of GNMM; and finally Data VI was concerned with the GA parameter selection and benchmarking GNMM with other IS DM techniques such as Adaptive Neuro-Fuzzy Inference System (ANFIS), Evolving Fuzzy Neural Network (EFuNN), Fuzzy ARTMAP, and Cartesian Genetic Programming (CGP). In addition, datasets obtained from published works (i.e. Data II & III) or public domains (i.e. Data VI) where previous results were present in the literature were also used to benchmark GNMM’s effectiveness. As a closely integrated system GNMM has the merit that it needs little human interaction. With some predefined parameters, such as GA’s crossover probability and the shape of ANNs’ activation functions, GNMM is able to process raw data until some human-interpretable rules being extracted. This is an important feature in terms of practice as quite often users of a DM system have little or no need to fully understand the internal components of such a system. Through case study applications, it has been shown that the GA-based variable selection stage is capable of: filtering out irrelevant and noisy variables, improving the accuracy of the model; making the ANN structure less complex and easier to understand; and reducing the computational complexity and memory requirements. Furthermore, rule extraction ensures that the MLP training results are easily understandable and transferrable

New Approach for Market Intelligence Using Artificial and Computational Intelligence

Small and medium sized retailers are central to the private sector and a vital contributor to economic growth, but often they face enormous challenges in unleashing their full potential. Financial pitfalls, lack of adequate access to markets, and difficulties in exploiting technology have prevented them from achieving optimal productivity. Market Intelligence (MI) is the knowledge extracted from numerous internal and external data sources, aimed at providing a holistic view of the state of the market and influence marketing related decision-making processes in real-time. A related, burgeoning phenomenon and crucial topic in the field of marketing is Artificial Intelligence (AI) that entails fundamental changes to the skillssets marketers require. A vast amount of knowledge is stored in retailers’ point-of-sales databases. The format of this data often makes the knowledge they store hard to access and identify. As a powerful AI technique, Association Rules Mining helps to identify frequently associated patterns stored in large databases to predict customers’ shopping journeys. Consequently, the method has emerged as the key driver of cross-selling and upselling in the retail industry. At the core of this approach is the Market Basket Analysis that captures knowledge from heterogeneous customer shopping patterns and examines the effects of marketing initiatives. Apriori, that enumerates frequent itemsets purchased together (as market baskets), is the central algorithm in the analysis process. Problems occur, as Apriori lacks computational speed and has weaknesses in providing intelligent decision support. With the growth of simultaneous database scans, the computation cost increases and results in dramatically decreasing performance. Moreover, there are shortages in decision support, especially in the methods of finding rarely occurring events and identifying the brand trending popularity before it peaks. As the objective of this research is to find intelligent ways to assist small and medium sized retailers grow with MI strategy, we demonstrate the effects of AI, with algorithms in data preprocessing, market segmentation, and finding market trends. We show with a sales database of a small, local retailer how our Åbo algorithm increases mining performance and intelligence, as well as how it helps to extract valuable marketing insights to assess demand dynamics and product popularity trends. We also show how this results in commercial advantage and tangible return on investment. Additionally, an enhanced normal distribution method assists data pre-processing and helps to explore different types of potential anomalies.Små och medelstora detaljhandlare är centrala aktörer i den privata sektorn och bidrar starkt till den ekonomiska tillväxten, men de möter ofta enorma utmaningar i att uppnå sin fulla potential. Finansiella svårigheter, brist på marknadstillträde och svårigheter att utnyttja teknologi har ofta hindrat dem från att nå optimal produktivitet. Marknadsintelligens (MI) består av kunskap som samlats in från olika interna externa källor av data och som syftar till att erbjuda en helhetssyn av marknadsläget samt möjliggöra beslutsfattande i realtid. Ett relaterat och växande fenomen, samt ett viktigt tema inom marknadsföring är artificiell intelligens (AI) som ställer nya krav på marknadsförarnas färdigheter. Enorma mängder kunskap finns sparade i databaser av transaktioner samlade från detaljhandlarnas försäljningsplatser. Ändå är formatet på dessa data ofta sådant att det inte är lätt att tillgå och utnyttja kunskapen. Som AI-verktyg erbjuder affinitetsanalys en effektiv teknik för att identifiera upprepade mönster som statistiska associationer i data lagrade i stora försäljningsdatabaser. De hittade mönstren kan sedan utnyttjas som regler som förutser kundernas köpbeteende. I detaljhandel har affinitetsanalys blivit en nyckelfaktor bakom kors- och uppförsäljning. Som den centrala metoden i denna process fungerar marknadskorgsanalys som fångar upp kunskap från de heterogena köpbeteendena i data och hjälper till att utreda hur effektiva marknadsföringsplaner är. Apriori, som räknar upp de vanligt förekommande produktkombinationerna som köps tillsammans (marknadskorgen), är den centrala algoritmen i analysprocessen. Trots detta har Apriori brister som algoritm gällande låg beräkningshastighet och svag intelligens. När antalet parallella databassökningar stiger, ökar också beräkningskostnaden, vilket har negativa effekter på prestanda. Dessutom finns det brister i beslutstödet, speciellt gällande metoder att hitta sällan förekommande produktkombinationer, och i att identifiera ökande popularitet av varumärken från trenddata och utnyttja det innan det når sin höjdpunkt. Eftersom målet för denna forskning är att hjälpa små och medelstora detaljhandlare att växa med hjälp av MI-strategier, demonstreras effekter av AI med hjälp av algoritmer i förberedelsen av data, marknadssegmentering och trendanalys. Med hjälp av försäljningsdata från en liten, lokal detaljhandlare visar vi hur Åbo-algoritmen ökar prestanda och intelligens i datautvinningsprocessen och hjälper till att avslöja värdefulla insikter för marknadsföring, framför allt gällande dynamiken i efterfrågan och trender i populariteten av produkterna. Ytterligare visas hur detta resulterar i kommersiella fördelar och konkret avkastning på investering. Dessutom hjälper den utvidgade normalfördelningsmetoden i förberedelsen av data och med att hitta olika slags anomalier

Building trajectories through clinical data to model disease progression

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Clinical trials are typically conducted over a population within a defined time period in order to illuminate certain characteristics of a health issue or disease process. These cross-sectional studies provide a snapshot of these disease processes over a large number of people but do not allow us to model the temporal nature of disease, which is essential for modeling detailed prognostic predictions. Longitudinal studies, on the other hand, are used to explore how these processes develop over time in a number of people but can be expensive and time-consuming, and many studies only cover a relatively small window within the disease process. This thesis describes the application of intelligent data analysis techniques for extracting information from time series generated by different diseases. The aim of this thesis is to identify intermediate stages in a disease process and sub-categories of the disease exhibiting subtly different symptoms. It explores the use of a bootstrap technique that fits trajectories through the data generating “pseudo time-series”. It addresses issues including: how clinical variables interact as a disease progresses along the trajectories in the data; and how to automatically identify different disease states along these trajectories, as well as the transitions between them. The thesis documents how reliable time-series models can be created from large amounts of historical cross-sectional data and a novel relabling/latent variable approach has enabled the exploration of the temporal nature of disease progression. The proposed algorithms are tested extensively on simulated data and on three real clinical datasets. Finally, a study is carried out to explore whether we can “calibrate” pseudo time-series models with real longitudinal data in order to improve them. Plausible directions for future research are discussed at the end of the thesis