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

Bayesian latent time joint mixed-effects model of progression in the Alzheimer's Disease Neuroimaging Initiative.

IntroductionWe characterize long-term disease dynamics from cognitively healthy to dementia using data from the Alzheimer's Disease Neuroimaging Initiative.MethodsWe apply a latent time joint mixed-effects model to 16 cognitive, functional, biomarker, and imaging outcomes in Alzheimer's Disease Neuroimaging Initiative. Markov chain Monte Carlo methods are used for estimation and inference.ResultsWe find good concordance between latent time and diagnosis. Change in amyloid positron emission tomography shows a moderate correlation with change in cerebrospinal fluid tau (ρ = 0.310) and phosphorylated tau (ρ = 0.294) and weaker correlation with amyloid-β 42 (ρ = 0.176). In comparison to amyloid positron emission tomography, change in volumetric magnetic resonance imaging summaries is more strongly correlated with cognitive measures (e.g., ρ = 0.731 for ventricles and Alzheimer's Disease Assessment Scale). The average disease trends are consistent with the amyloid cascade hypothesis.DiscussionThe latent time joint mixed-effects model can (1) uncover long-term disease trends; (2) estimate the sequence of pathological abnormalities; and (3) provide subject-specific prognostic estimates of the time until onset of symptoms

Developmental Stages of Perception and Language Acquisition in a Perceptually Grounded Robot

The objective of this research is to develop a system for language learning based on a minimum of pre-wired language-specific functionality, that is compatible with observations of perceptual and language capabilities in the human developmental trajectory. In the proposed system, meaning (in terms of descriptions of events and spatial relations) is extracted from video images based on detection of position, motion, physical contact and their parameters. Mapping of sentence form to meaning is performed by learning grammatical constructions that are retrieved from a construction inventory based on the constellation of closed class items uniquely identifying the target sentence structure. The resulting system displays robust acquisition behavior that reproduces certain observations from developmental studies, with very modest “innate” language specificity

AudExpCreator: A GUI-based Matlab tool for designing and creating auditory experiments with the Psychophysics Toolbox

We present AudExpCreator, a GUI-based Matlab tool for designing and creating auditory experiments. AudExpCreator allows users to generate auditory experiments that run on Matlab's Psychophysics Toolbox without having to write any code; rather, users simply follow instructions in GUIs to specify desired design parameters. The software comprises five auditory study types, including behavioral studies and integration with EEG and physiological response collection systems. Advanced features permit more complicated experimental designs as well as maintenance and update of previously created experiments. AudExpCreator alleviates programming barriers while providing a free, open-source alternative to commercial experimental design software.Comment: 15 pages, 6 figure