Management and Treatment of Patients With Obstructive Sleep Apnea Using an Intelligent Monitoring System Based on Machine Learning Aiming to Improve Continuous Positive Airway Pressure Treatment Compliance: Randomized Controlled Trial.

BACKGROUND: Continuous positive airway pressure (CPAP) is an effective treatment for obstructive sleep apnea (OSA), but treatment compliance is often unsatisfactory. OBJECTIVE: The aim of this study was to assess the effectiveness and cost-effectiveness of an intelligent monitoring system for improving CPAP compliance. METHODS: This is a prospective, open label, parallel, randomized controlled trial including 60 newly diagnosed patients with OSA requiring CPAP (Apnea-Hypopnea Index [AHI] >15) from Lleida, Spain. Participants were randomized (1:1) to standard management or the MiSAOS intelligent monitoring system, involving (1) early compliance detection, thus providing measures of patient's CPAP compliance from the very first days of usage; (2) machine learning-based prediction of midterm future CPAP compliance; and (3) rule-based recommendations for the patient (app) and care team. Clinical and anthropometric variables, daytime sleepiness, and quality of life were recorded at baseline and after 6 months, together with patient's compliance, satisfaction, and health care costs. RESULTS: Randomized patients had a mean age of 57 (SD 11) years, mean AHI of 50 (SD 27), and 13% (8/60) were women. Patients in the intervention arm had a mean (95% CI) of 1.14 (0.04-2.23) hours/day higher adjusted CPAP compliance than controls (P=.047). Patients' satisfaction was excellent in both arms, and up to 88% (15/17) of intervention patients reported willingness to keep using the MiSAOS app in the future. No significant differences were found in costs (control: mean €90.2 (SD 53.14) (US $105.76 [SD 62.31]); intervention: mean €96.2 (SD 62.13) (US $112.70 [SD 72.85]); P=.70; €1=US $1.17 was considered throughout). Overall costs combined with results on compliance demonstrated cost-effectiveness in a bootstrap-based simulation analysis. CONCLUSIONS: A machine learning-based intelligent monitoring system increased daily compliance, reported excellent patient satisfaction similar to that reported in usual care, and did not incur in a substantial increase in costs, thus proving cost-effectiveness. This study supports the implementation of intelligent eHealth frameworks for the management of patients with CPAP-treated OSA and confirms the value of patients' empowerment in the management of chronic diseases. TRIAL REGISTRATION: ClinicalTrials.gov NCT03116958; https://clinicaltrials.gov/ct2/show/NCT03116958.

Comparative analysis of predictive methods for early assessment of compliance with continuous positive airway pressure therapy.

BACKGROUND: Patients suffering obstructive sleep apnea are mainly treated with continuous positive airway pressure (CPAP). Although it is a highly effective treatment, compliance with this therapy is problematic to achieve with serious consequences for the patients' health. Unfortunately, there is a clear lack of clinical analytical tools to support the early prediction of compliant patients. METHODS: This work intends to take a further step in this direction by building compliance classifiers with CPAP therapy at three different moments of the patient follow-up, before the therapy starts (baseline) and at months 1 and 3 after the baseline. RESULTS: Results of the clinical trial shows that month 3 was the time-point with the most accurate classifier reaching an f1-score of 87% and 84% in cross-validation and test. At month 1, performances were almost as high as in month 3 with 82% and 84% of f1-score. At baseline, where no information of patients' CPAP use was given yet, the best classifier achieved 73% and 76% of f1-score in cross-validation and test set respectively. Subsequent analyzes carried out with the best classifiers of each time point revealed baseline factors (i.e. headaches, psychological symptoms, arterial hypertension and EuroQol visual analog scale) closely related to the prediction of compliance independently of the time-point. In addition, among the variables taken only during the follow-up of the patients, Epworth and the average nighttime hours were the most important to predict compliance with CPAP. CONCLUSIONS: Best classifiers reported high performances after one month of treatment, being the third month when significant differences were achieved with respect to the baseline. Four baseline variables were reported relevant for the prediction of compliance with CPAP at each time-point. Two characteristics more were also highlighted for the prediction of compliance at months 1 and 3. TRIAL REGISTRATION: ClinicalTrials.gov Identifier, NCT03116958 . Retrospectively registered on 17 April 2017.

SVGMap: configurable image browser for experimental data.

SUMMARY: Spatial data visualization is very useful to represent biological data and quickly interpret the results. For instance, to show the expression pattern of a gene in different tissues of a fly, an intuitive approach is to draw the fly with the corresponding tissues and color the expression of the gene in each of them. However, the creation of these visual representations may be a burdensome task. Here we present SVGMap, a java application that automatizes the generation of high-quality graphics for singular data items (e.g. genes) and biological conditions. SVGMap contains a browser that allows the user to navigate the different images created and can be used as a web-based results publishing tool. AVAILABILITY: SVGMap is freely available as precompiled java package as well as source code at http://bg.upf.edu/svgmap. It requires Java 6 and any recent web browser with JavaScript enabled. The software can be run on Linux, Mac OS X and Windows systems. CONTACT: nuria.lopez@upf.edu

Computer-assisted diagnosis for an early identification of lung cancer in chest X rays.

Computer-assisted diagnosis (CAD) algorithms have shown its usefulness for the identification of pulmonary nodules in chest x-rays, but its capability to diagnose lung cancer (LC) is unknown. A CAD algorithm for the identification of pulmonary nodules was created and used on a retrospective cohort of patients with x-rays performed in 2008 and not examined by a radiologist when obtained. X-rays were sorted according to the probability of pulmonary nodule, read by a radiologist and the evolution for the following three years was assessed. The CAD algorithm sorted 20,303 x-rays and defined four subgroups with 250 images each (percentiles ≥ 98, 66, 33 and 0). Fifty-eight pulmonary nodules were identified in the ≥ 98 percentile (23,2%), while only 64 were found in lower percentiles (8,5%) (p < 0.001). A pulmonary nodule was confirmed by the radiologist in 39 out of 173 patients in the high-probability group who had follow-up information (22.5%), and in 5 of them a LC was diagnosed with a delay of 11 months (12.8%). In one quarter of the chest x-rays considered as high-probability for pulmonary nodule by a CAD algorithm, the finding is confirmed and corresponds to an undiagnosed LC in one tenth of the cases.

Prediction of Lung Nodule Progression with an Uncertainty-Aware Hierarchical Probabilistic Network.

Predicting whether a lung nodule will grow, remain stable or regress over time, especially early in its follow-up, would help doctors prescribe personalized treatments and better surgical planning. However, the multifactorial nature of lung tumour progression hampers the identification of growth patterns. In this work, we propose a deep hierarchical generative and probabilistic network that, given an initial image of the nodule, predicts whether it will grow, quantifies its future size and provides its expected semantic appearance at a future time. Unlike previous solutions, our approach also estimates the uncertainty in the predictions from the intrinsic noise in medical images and the inter-observer variability in the annotations. The evaluation of this method on an independent test set reported a future tumour growth size mean absolute error of 1.74 mm, a nodule segmentation Dice's coefficient of 78% and a tumour growth accuracy of 84% on predictions made up to 24 months ahead. Due to the lack of similar methods for providing future lung tumour growth predictions, along with their associated uncertainty, we adapted equivalent deterministic and alternative generative networks (i.e., probabilistic U-Net, Bayesian test dropout and Pix2Pix). Our method outperformed all these methods, corroborating the adequacy of our approach.

Re-Identification and growth detection of pulmonary nodules without image registration using 3D siamese neural networks.

Lung cancer follow-up is a complex, error prone, and time consuming task for clinical radiologists. Several lung CT scan images taken at different time points of a given patient need to be individually inspected, looking for possible cancerogenous nodules. Radiologists mainly focus their attention in nodule size, density, and growth to assess the existence of malignancy. In this study, we present a novel method based on a 3D siamese neural network, for the re-identification of nodules in a pair of CT scans of the same patient without the need for image registration. The network was integrated into a two-stage automatic pipeline to detect, match, and predict nodule growth given pairs of CT scans. Results on an independent test set reported a nodule detection sensitivity of 94.7%, an accuracy for temporal nodule matching of 88.8%, and a sensitivity of 92.0% with a precision of 88.4% for nodule growth detection.

Integration of convolutional neural networks for pulmonary nodule malignancy assessment in a lung cancer classification pipeline.

BACKGROUND AND OBJECTIVE: The early identification of malignant pulmonary nodules is critical for a better lung cancer prognosis and less invasive chemo or radio therapies. Nodule malignancy assessment done by radiologists is extremely useful for planning a preventive intervention but is, unfortunately, a complex, time-consuming and error-prone task. This explains the lack of large datasets containing radiologists malignancy characterization of nodules; METHODS: In this article, we propose to assess nodule malignancy through 3D convolutional neural networks and to integrate it in an automated end-to-end existing pipeline of lung cancer detection. For training and testing purposes we used independent subsets of the LIDC dataset; RESULTS: Adding the probabilities of nodules malignity in a baseline lung cancer pipeline improved its F1-weighted score by 14.7%, whereas integrating the malignancy model itself using transfer learning outperformed the baseline prediction by 11.8% of F1-weighted score; CONCLUSIONS: Despite the limited size of the lung cancer datasets, integrating predictive models of nodule malignancy improves prediction of lung cancer.

Pipeline design to identify key features and classify the chemotherapy response on lung cancer patients using large-scale genetic data.

BACKGROUND: During the last decade, the interest to apply machine learning algorithms to genomic data has increased in many bioinformatics applications. Analyzing this type of data entails difficulties for managing high-dimensional data, class imbalance for knowledge extraction, identifying important features and classifying individuals. In this study, we propose a general framework to tackle these challenges with different machine learning algorithms and techniques. We apply the configuration of this framework on lung cancer patients, identifying genetic signatures for classifying response to drug treatment response. We intersect these relevant SNPs with the GWAS Catalog of the National Human Genome Research Institute and explore the Regulomedb, GTEx databases for functional analysis purposes. RESULTS: The machine learning based solution proposed in this study is a scalable and flexible alternative to the classical uni-variate regression approach to analyze large-scale data. From 36 experiments executed using the machine learning framework design, we obtain good classification performance from the top 5 models with the highest cross-validation score and the smallest standard deviation. One thousand two hundred twenty four SNPs corresponding to the key features from the top 20 models (cross validation F1 mean >= 0.65) were compared with the GWAS Catalog finding no intersection with genome-wide significant reported hits. From these, new genetic signatures in MAE, CEP104, PRKCZ and ADRB2 show relevant biological regulatory functionality related to lung physiology. CONCLUSIONS: We have defined a machine learning framework using data with an unbalanced large data-set of SNP-arrays and imputed genotyping data from a pharmacogenomics study in lung cancer patients subjected to first-line platinum-based treatment. This approach found genome signals with no genome-wide significance in the uni-variate regression approach (GWAS Catalog) that are valuable for classifying patients, only few of them with related biological function. The effect results of these variants can be explained by the recently proposed omnigenic model hypothesis, which states that complex traits can be influenced mostly by genes outside not only by the "core genes", mainly found by the genome-wide significant SNPs, but also by the rest of genes outside of the "core pathways" with apparent unrelated biological functionality.

A Multifunctional Brain-Computer Interface Intended for Home Use: An Evaluation with Healthy Participants and Potential End Users with Dry and Gel-Based Electrodes.

Current brain-computer interface (BCIs) software is often tailored to the needs of scientists and technicians and therefore complex to allow for versatile use. To facilitate home use of BCIs a multifunctional P300 BCI with a graphical user interface intended for non-expert set-up and control was designed and implemented. The system includes applications for spelling, web access, entertainment, artistic expression and environmental control. In addition to new software, it also includes new hardware for the recording of electroencephalogram (EEG) signals. The EEG system consists of a small and wireless amplifier attached to a cap that can be equipped with gel-based or dry contact electrodes. The system was systematically evaluated with a healthy sample, and targeted end users of BCI technology, i.e., people with a varying degree of motor impairment tested the BCI in a series of individual case studies. Usability was assessed in terms of effectiveness, efficiency and satisfaction. Feedback of users was gathered with structured questionnaires. Two groups of healthy participants completed an experimental protocol with the gel-based and the dry contact electrodes (N = 10 each). The results demonstrated that all healthy participants gained control over the system and achieved satisfactory to high accuracies with both gel-based and dry electrodes (average error rates of 6 and 13%). Average satisfaction ratings were high, but certain aspects of the system such as the wearing comfort of the dry electrodes and design of the cap, and speed (in both groups) were criticized by some participants. Six potential end users tested the system during supervised sessions. The achieved accuracies varied greatly from no control to high control with accuracies comparable to that of healthy volunteers. Satisfaction ratings of the two end-users that gained control of the system were lower as compared to healthy participants. The advantages and disadvantages of the BCI and its applications are discussed and suggestions are presented for improvements to pave the way for user friendly BCIs intended to be used as assistive technology by persons with severe paralysis.