DPVis: Visual Analytics with Hidden Markov Models for Disease Progression Pathways

Clinical researchers use disease progression models to understand patient status and characterize progression patterns from longitudinal health records. One approach for disease progression modeling is to describe patient status using a small number of states that represent distinctive distributions over a set of observed measures. Hidden Markov models (HMMs) and its variants are a class of models that both discover these states and make inferences of health states for patients. Despite the advantages of using the algorithms for discovering interesting patterns, it still remains challenging for medical experts to interpret model outputs, understand complex modeling parameters, and clinically make sense of the patterns. To tackle these problems, we conducted a design study with clinical scientists, statisticians, and visualization experts, with the goal to investigate disease progression pathways of chronic diseases, namely type 1 diabetes (T1D), Huntington's disease, Parkinson's disease, and chronic obstructive pulmonary disease (COPD). As a result, we introduce DPVis which seamlessly integrates model parameters and outcomes of HMMs into interpretable and interactive visualizations. In this study, we demonstrate that DPVis is successful in evaluating disease progression models, visually summarizing disease states, interactively exploring disease progression patterns, and building, analyzing, and comparing clinically relevant patient subgroups.Comment: to appear at IEEE Transactions on Visualization and Computer Graphic

Temporal Clustering for Behavior Variation and Anomaly Detection from Data Acquired Through IoT in Smart Cities

In this chapter, we propose a methodology for behavior variation and anomaly detection from acquired sensory data, based on temporal clustering models. Data are collected from five prominent European smart cities, and Singapore, that aim to become fully “elderly-friendly,” with the development and deployment of ubiquitous systems for assessment and prediction of early risks of elderly Mild Cognitive Impairments (MCI) and frailty, and for supporting generation and delivery of optimal personalized preventive interventions that mitigate those risks, utilizing smart city datasets and IoT infrastructure. Low level data collected from IoT devices are preprocessed as sequences of activities, with temporal and causal variations in sequences classified as normal or anomalous behavior. The goals of proposed methodology are to (1) recognize significant behavioral variation patterns and (2) support early identification of pattern changes. Temporal clustering models are applied in detection and prediction of the following variation types: intra-activity (single activity, single citizen) and inter-activity (multiple-activities, single citizen). Identified behavioral variations and anomalies are further mapped to MCI/frailty onset behavior and risk factors, following the developed geriatric expert model

Towards A Robust Arabic Speech Recognition System Based On Reservoir Computing

In this thesis we investigate the potential of developing a speech recognition system based on a recently introduced artificial neural network (ANN) technique, namely Reservoir Computing (RC). This technique has, in theory, a higher capability for modelling dynamic behaviour compared to feed-forward ANNs due to the recurrent connections between the nodes in the reservoir layer, which serves as a memory. We conduct this study on the Arabic language, (one of the most spoken languages in the world and the official language in 26 countries), because there is a serious gap in the literature on speech recognition systems for Arabic, making the potential impact high. The investigation covers a variety of tasks, including the implementation of the first reservoir-based Arabic speech recognition system. In addition, a thorough evaluation of the developed system is conducted including several comparisons to other state- of-the-art models found in the literature, and baseline models. The impact of feature extraction methods are studied in this work, and a new biologically inspired feature extraction technique, namely the Auditory Nerve feature, is applied to the speech recognition domain. Comparing different feature extraction methods requires access to the original recorded sound, which is not possible in the only publicly accessible Arabic corpus. We have developed the largest public Arabic corpus for isolated words, which contains roughly 10,000 samples. Our investigation has led us to develop two novel approaches based on reservoir computing, ESNSVMs (Echo State Networks with Support Vector Machines) and ESNEKMs (Echo State Networks with Extreme Kernel Machines). These aim to improve the performance of the conventional RC approach by proposing different readout architectures. These two approaches have been compared to the conventional RC approach and other state-of-the- art systems. Finally, these developed approaches have been evaluated on the presence of different types and levels of noise to examine their resilience to noise, which is crucial for real world applications

Amharic spoken digits recognition using convolutional neural network

Authors would like to acknowledge and thanks to the participants in the collection of voice samples.Peer reviewe

Mobile Sensing, Simulation and Machine-learning Techniques: Improving Observations in Public Health

Entering an era where mobile phones equipped with numerous sensors have become an integral part of our lives and wearable devices such as activity trackers are very popular, studying and analyzing the data collected by these devices can give insights to the researchers and policy makers about the ongoing illnesses, outbreaks and public health in general. In this regard, new machine learning techniques can be utilized for population screening, informing centers of disease control and prevention of potential threats and outbreaks. Big data streams if not present, will limit investigating the feasibility of such new techniques in this domain. To overcome this shortcoming, simulation models even if grounded by small-size data can represent a simple platform of the more complicated systems and then be utilized as safe and still precise environments for generating synthetic ground truth big data. The objective of this thesis is to use an agent-based model (ABM) which depicts a city consisting of restaurants, consumers, and an inspector, to investigate the practicability of using smartphones data in the machine-learning component of Hidden Markov Model trained by synthetic ground-truth data generated by the ABM model to detect food-borne related outbreaks and inform the inspector about them. To this end, we also compared the results of such arrangement with traditional outbreak detection methods. We examine this method in different formations and scenarios. As another contribution, we analyzed smart phone data collected through a real world experiment where the participants were using an application Ethica Data on their phones named. This application as the first platform turning smartphones into micro research labs allows passive sensor monitoring and sending over context-dependent surveys. The collected data was later analyzed to get insights into the participants' food consumption patterns. Our results indicate that Hidden Markov Models supplied with smart phone data provide accurate systems for foodborne outbreak detection. The results also support the applicability of smart phone data to obtain information about foodborne diseases. The results also suggest that there are some limitations in using Hidden Markov Models to detect the exact source of outbreaks

Understanding and Improving Recurrent Networks for Human Activity Recognition by Continuous Attention

Deep neural networks, including recurrent networks, have been successfully applied to human activity recognition. Unfortunately, the final representation learned by recurrent networks might encode some noise (irrelevant signal components, unimportant sensor modalities, etc.). Besides, it is difficult to interpret the recurrent networks to gain insight into the models' behavior. To address these issues, we propose two attention models for human activity recognition: temporal attention and sensor attention. These two mechanisms adaptively focus on important signals and sensor modalities. To further improve the understandability and mean F1 score, we add continuity constraints, considering that continuous sensor signals are more robust than discrete ones. We evaluate the approaches on three datasets and obtain state-of-the-art results. Furthermore, qualitative analysis shows that the attention learned by the models agree well with human intuition.Comment: 8 pages. published in The International Symposium on Wearable Computers (ISWC) 201

Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads

Background Recent technology advances have enabled sequencing of individual genomes, promising to revolutionize biomedical research. However, deep sequencing remains more expensive than microarrays for performing whole-genome SNP genotyping. Results In this paper we introduce a new multi-locus statistical model and computationally efficient genotype calling algorithms that integrate shotgun sequencing data with linkage disequilibrium (LD) information extracted from reference population panels such as Hapmap or the 1000 genomes project. Experiments on publicly available 454, Illumina, and ABI SOLiD sequencing datasets suggest that integration of LD information results in genotype calling accuracy comparable to that of microarray platforms from sequencing data of low-coverage. A software package implementing our algorithm, released under the GNU General Public License, is available at http://dna.engr.uconn.edu/software/GeneSeq/. Conclusions Integration of LD information leads to significant improvements in genotype calling accuracy compared to prior LD-oblivious methods, rendering low-coverage sequencing as a viable alternative to microarrays for conducting large-scale genome-wide association studies