Human activity recognition from inertial sensor time-series using batch normalized deep LSTM recurrent networks

In recent years machine learning methods for human activity recognition have been found very effective. These classify discriminative features generated from raw input sequences acquired from body-worn inertial sensors. However, it involves an explicit feature extraction stage from the raw data, and although human movements are encoded in a sequence of successive samples in time most state-of-the-art machine learning methods do not exploit the temporal correlations between input data samples. In this paper we present a Long-Short Term Memory (LSTM) deep recurrent neural network for the classification of six daily life activities from accelerometer and gyroscope data. Results show that our LSTM can processes featureless raw input signals, and achieves 92 % average accuracy in a multi-class-scenario. Further, we show that this accuracy can be achieved with almost four times fewer training epochs by using a batch normalization approach

MaLT - combined motor and language therapy tool for brain injury patients using Kinect

Background: The functional connectivity and structural proximity of elements of the language and motor systems result in frequent co-morbidity post brain injury. Although rehabilitation services are becoming increasingly multidisciplinary and "integrated", treatment for language and motor functions often occurs in isolation. Thus, behavioural therapies which promote neural reorganisation do not reflect the high intersystem connectivity of the neurologically intact brain. As such, there is a pressing need for rehabilitation tools which better reflect and target the impaired cognitive networks. Objectives: The objective of this research is to develop a combined high dosage therapy tool for language and motor rehabilitation. The rehabilitation therapy tool developed, MaLT (Motor and Language Therapy), comprises a suite of computer games targeting both language and motor therapy that use the Kinect sensor as an interaction device. The games developed are intended for use in the home environment over prolonged periods of time. In order to track patients' engagement with the games and their rehabilitation progress, the game records patient performance data for the therapist to interrogate. Methods: MaLT incorporates Kinect-based games, a database of objects and language parameters, and a reporting tool for therapists. Games have been developed that target four major language therapy tasks involving single word comprehension, initial phoneme identification, rhyme identification and a naming task. These tasks have 8 levels each increasing in difficulty. A database of 750 objects is used to programmatically generate appropriate questions for the game, providing both targeted therapy and unique gameplay every time. The design of the games has been informed by therapists and by discussions with a Public Patient Involvement (PPI) group. Results: Pilot MaLT trials have been conducted with three stroke survivors for the duration of 6 to 8 weeks. Patients' performance is monitored through MaLT's reporting facility presented as graphs plotted from patient game data. Performance indicators include reaction time, accuracy, number of incorrect responses and hand use. The resultant games have also been tested by the PPI with a positive response and further suggestions for future modifications made. Conclusion: MaLT provides a tool that innovatively combines motor and language therapy for high dosage rehabilitation in the home. It has demonstrated that motion sensor technology can be successfully combined with a language therapy task to target both upper limb and linguistic impairment in patients following brain injury. The initial studies on stroke survivors have demonstrated that the combined therapy approach is viable and the outputs of this study will inform planned larger scale future trials

Impact of co-morbid burden on mortality in patients with coronary heart disease, heart failure, and cerebrovascular accident: a systematic review and meta-analysis.

Aims: We sought to investigate the prognostic impact of co-morbid burden as defined by the Charlson Co-morbidity Index (CCI) in patients with a range of prevalent cardiovascular diseases. Methods and results: We searched MEDLINE and EMBASE to identify studies that evaluated the impact of CCI on mortality in patients with cardiovascular disease. A random-effects meta-analysis was undertaken to evaluate the impact of CCI on mortality in patients with coronary heart disease (CHD), heart failure (HF), and cerebrovascular accident (CVA). A total of 11 studies of acute coronary syndrome (ACS), 2 stable coronary disease, 5 percutaneous coronary intervention (PCI), 13 HF, and 4 CVA met the inclusion criteria. An increase in CCI score per point was significantly associated with a greater risk of mortality in patients with ACS [pooled relative risk ratio (RR) 1.33; 95% CI 1.15-1.54], PCI (RR 1.21; 95% CI 1.12-1.31), stable coronary artery disease (RR 1.38; 95% CI 1.29-1.48), and HF (RR 1.21; 95% CI 1.13-1.29), but not CVA. A CCI score of >2 significantly increased the risk of mortality in ACS (RR 2.52; 95% CI 1.58-4.04), PCI (RR 3.36; 95% CI 2.14-5.29), HF (RR 1.76; 95% CI 1.65-1.87), and CVA (RR 3.80; 95% CI 1.20-12.01). Conclusion: Increasing co-morbid burden as defined by CCI is associated with a significant increase in risk of mortality in patients with underlying CHD, HF, and CVA. CCI provides a simple way of predicting adverse outcomes in patients with cardiovascular disease and should be incorporated into decision-making processes when counselling patients

Asthma Phenotypes in Childhood

INTRODUCTION: Asthma is no longer thought of as a single disease, but rather a collection of varying symptoms expressing different disease patterns. One of the ongoing challenges is understanding the underlying pathophysiological mechanisms that may be responsible for the varying responses to treatment. Areas Covered: This review provides an overview of our current understanding of the asthma phenotype concept in childhood and describes key findings from both conventional and data-driven methods. Expert Commentary: With the vast amounts of data generated from cohorts, there is hope that we can elucidate distinct pathophysiological mechanisms, or endotypes. In return, this would lead to better patient stratification and disease management, thereby providing true personalised medicine

The Extended Dawid-Skene Model:Fusing Information from Multiple Data Schemas

While label fusion from multiple noisy annotations is a well understood concept in data wrangling (tackled for example by the Dawid-Skene (DS) model), we consider the extended problem of carrying out learning when the labels themselves are not consistently annotated with the same schema. We show that even if annotators use disparate, albeit related, label-sets, we can still draw inferences for the underlying full label-set. We propose the Inter-Schema AdapteR (ISAR) to translate the fully-specified label-set to the one used by each annotator, enabling learning under such heterogeneous schemas, without the need to re-annotate the data. We apply our method to a mouse behavioural dataset, achieving significant gains (compared with DS) in out-of-sample log-likelihood (-3.40 to -2.39) and F1-score (0.785 to 0.864).Comment: Updated with Author-Preprint version following Publication in P. Cellier and K. Driessens (Eds.): ECML PKDD 2019 Workshops, CCIS 1167, pp. 121 - 136, 202

Analysis of ChIP-seq data via Bayesian finite mixture models with a non-parametric component

In large discrete data sets which requires classification into signal and noise components, the distribution of the signal is often very bumpy and does not follow a standard distribution. Therefore the signal distribution is further modelled as a mixture of component distributions. However, when the signal component is modelled as a mixture of distributions, we are faced with the challenges of justifying the number of components and the label switching problem (caused by multimodality of the likelihood function). To circumvent these challenges, we propose a non-parametric structure for the signal component. This new method is more efficient in terms of precise estimates and better classifications. We demonstrated the efficacy of the methodology using a ChIP-sequencing data set

Evaluation of clinical prediction models (part 1):from development to external validation

Evaluating the performance of a clinical prediction model is crucial to establish its predictive accuracy in the populations and settings intended for use. In this article, the first in a three part series, Collins and colleagues describe the importance of a meaningful evaluation using internal, internal-external, and external validation, as well as exploring heterogeneity, fairness, and generalisability in model performance

Three-dimensional (3D) magnetic resonance volume assessment and loco-regional failure in anal cancer: early evaluation case-control study

Background The primary aim was to test the hypothesis that deriving pre-treatment 3D magnetic resonance tumour volume (mrTV) quantification improves performance characteristics for the prediction of loco-regional failure compared with standard maximal tumour diameter (1D) assessment in patients with squamous cell carcinoma of the anus undergoing chemoradiotherapy. Methods We performed an early evaluation case-control study at two UK centres (2007–2014) in 39 patients with loco-regional failure (cases), and 41 patients disease-free at 3 years (controls). mrTV was determined using the summation of areas method (Volsum). Reproducibility was assessed using intraclass concordance correlation (ICC) and Bland-Altman limits of agreements. We derived receiver operating curves using logistic regression models and expressed accuracy as area under the curve (ROCAUC). Results The median time per patient for Volsum quantification was 7.00 (inter-quartile range, IQR: 0.57–12.48) minutes. Intra and inter-observer reproducibilities were generally good (ICCs from 0.79 to 0.89) but with wide limits of agreement (intra-observer: − 28 to 31%; inter-observer: − 28 to 46%). Median mrTVs were greater for cases (32.6 IQR: 21.5–53.1 cm3) than controls (9.9 IQR: 5.7–18.1 cm3, p < 0.0001). The ROCAUC for mrT-size predicting loco-regional failure was 0.74 (95% CI: 0.63–0.85) improving to 0.82 (95% CI: 0.72–0.92) when replaced with mrTV (test for ROC differences, p = 0.024). Conclusion Preliminary results suggest that the replacement of mrTV for mrT-size improves prediction of loco-regional failure after chemoradiotherapy for squamous cell carcinoma of the anus. However, mrTV calculation is time consuming and variation in its reproducibility are drawbacks with the current technology