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.Peer ReviewedPostprint (published version

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.This work is part of the myOSA project (RTC-2014-3138-1), funded by the Spanish Ministry of Economy and Competitiveness (Ministerio de Economía y Competitividad) under the framework “Retos-Colaboración”, State Scientific and Technical Research and Innovation Plan 2013-2016. The study was also partially funded by the European Community under “H2020-EU.3.1. – Societal Challenges – Health, demographic change and well-being” programme, project grant agreement number 689802 (CONNECARE)

Ansiedad competitiva y clima motivacional en jóvenes futbolistas de competición, en relación con las habilidades y el rendimiento percibido por sus entrenadores

En este estudio se analizan las relaciones existentes entre la ansiedad competitiva (en sus facetas cognitiva y somática) y el clima motivacional percibido (de ego y de maestría) en una población de 54 jóvenes futbolistas decompetición de edad media de 9,45 años, respecto de la percepción de sus habilidades y rendimiento deportivos por parte de sus 4 entrenadores, que también participaron en el estudio. Para ello se les administró las versiones españolas del SAS-2 (Sport Anxiety Scale-2, Smith, Smoll, Cumming y Grossbard, 2006) y el MCSYS (Motivational Climate Scale for Youth Sports,Smith, Cumming y Smoll, 2008), así como dos escalas ad hoc para evaluar la percepción de su habilidad y rendimiento. Los resultados muestran, por una parte, que los jóvenes futbolistas perciben y discriminan claramente los climas motivacionales, que se distribuyen casi al 50% entre ego y maestría; por otra, que aparece ansiedad competitiva, aunque más cognitiva que somática, y que no existe relación significativa con las percepciones de habilidad y rendimiento por parte de los entrenadores. Finalmente, estos resultados se discuten y se comparan con otros similares en poblaciones preadolescentesThis study analysed the relationships between competitive anxiety (both cognitive and somatic) and perceived motivational climate (ego and mastery) in 54 young competitive soccer players (mean age: 9.45 years), related to their four coaches' perceptions of the soccer players' skills and performance. We administered the Spanish versions of the SAS-2 (Sport Anxiety Scale-2, Smith, Smoll, Cumming and Grossbard, 2006) and the MCSYS (Motivational Climate Scale for Youth Sports, Smith, Cumming and Smoll, 2008), along with two ad hoc scales to evaluate perceived skills and performance.The results show that 1) young players perceived and discriminated clearly between motivational climates (which were more or less equally distributed between ego and mastery orientations), 2) some performance-related anxiety (mostly cognitive rather than somatic) appeared and 3) no significant relationships were found between their coaches' perceptions of their skills and their performance. Lastly, the results are discussed and compared with similar results from preadolescent player

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.This work is part of the myOSA project (RTC-2014-3138-1), funded by the Spanish Ministry of Economy, Industry and Competitiveness (Ministerio de Economía, Industria y Competitividad) and Agencia Estatal de Investigación, under the framework “Retos-Colaboración”, State Scientific and Technical Research and Innovation Plan 2013-2016. The work was cofunded by the European Regional Development Fund (ERDF), “A way to make Europe”. JdB acknowledges receiving financial support from the Catalan Health Department (Pla Estratègic de Recerca i Innovació en Salut [PERIS] 2016: SLT002/16/00364) and Instituto de Salud Carlos III (ISCIII; Miguel Servet 2019: CP19/00108), co-funded by the European Social Fund (ESF), “Investing in your future”. Funding organizations had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication

Detection, quantification, malignancy prediction and growth forecasting of pulmonary nodules using deep learning in follow-up CT scans

Nowadays, lung cancer assessment is a complex and tedious task mainly per- formed by radiological visual inspection of suspicious pulmonary nodules, using computed tomography (CT) scan images taken to patients over time. Several computational tools relying on conventional artificial intelligence and computer vision algorithms have been proposed for supporting lung cancer de- tection and classification. These solutions mostly rely on the analysis of indi- vidual lung CT images of patients and on the use of hand-crafted image de- scriptors. Unfortunately, this makes them unable to cope with the complexity and variability of the problem. Recently, the advent of deep learning has led to a major breakthrough in the medical image domain, outperforming conven- tional approaches. Despite recent promising achievements in nodule detection, segmentation, and lung cancer classification, radiologists are still reluctant to use these solutions in their day-to-day clinical practice. One of the main rea- sons is that current solutions do not provide support to automatic analysis of the temporal evolution of lung tumours. The difficulty to collect and annotate longitudinal lung CT cases to train models may partially explain the lack of deep learning studies that address this issue. In this dissertation, we investigate how to automatically provide lung can- cer assessment through deep learning algorithms and computer vision pipelines, especially taking into consideration the temporal evolution of the pulmonary nodules. To this end, our first goal consisted on obtaining accurate methods for lung cancer assessment (diagnostic ground truth) based on individual lung CT images. Since these types of labels are expensive and difficult to collect (e.g. usually after biopsy), we proposed to train different deep learning models, based on 3D convolutional neural networks (CNN), to predict nodule malig- nancy based on radiologist visual inspection annotations (which are reasonable to obtain). These classifiers were built based on ground truth consisting of the nodule malignancy, the position and the size of the nodules to classify. Next, we evaluated different ways of synthesizing the knowledge embedded by the nodule malignancy neural network, into an end-to-end pipeline aimed to detect pul- monary nodules and predict lung cancer at the patient level, given a lung CT image. The positive results confirmed the convenience of using CNNs for mod- elling nodule malignancy, according to radiologists, for the automatic prediction of lung cancer. Next, we focused on the analysis of lung CT image series. Thus, we first faced the problem of automatically re-identifying pulmonary nodules from dif- ferent lung CT scans of the same patient. To do this, we present a novel method based on a Siamese neural network (SNN) to rank similarity between nodules, overpassing the need for image registration. This change of paradigm avoided introducing potentially erroneous image deformations and provided computa- tionally faster results. Different configurations of the SNN were examined, in- cluding the application of transfer learning, using different loss functions, and the combination of several feature maps of different network levels. This method obtained state-of-the-art performances for nodule matching both in an isolated manner and embedded in an end-to-end nodule growth detection pipeline. Afterwards, we moved to the core problem of supporting radiologists in the longitudinal management of lung cancer. For this purpose, we created a novel end-to-end deep learning pipeline, composed of four stages that completely au- tomatize from the detection of nodules to the classification of cancer, through the detection of growth in the nodules. In addition, the pipeline integrated a novel approach for nodule growth detection, which relies on a recent hierarchi- cal probabilistic segmentation network adapted to report uncertainty estimates. Also, a second novel method was introduced for lung cancer nodule classification, integrating into a two stream 3D-CNN the estimated nodule malignancy prob- abilities derived from a pre-trained nodule malignancy network. The pipeline was evaluated in a longitudinal cohort and the reported outcomes (i.e. nodule detection, re-identification, growth quantification, and malignancy prediction) were comparable with state-of-the-art work, focused on solving one or a few of the functionalities of our pipeline. Thereafter, we also investigated how to help clinicians to prescribe more accurate tumour treatments and surgical planning. Thus, we created a novel method to forecast nodule growth given a single image of the nodule. Partic- ularly, the method relied on a hierarchical, probabilistic and generative deep neural network able to produce multiple consistent future segmentations of the nodule at a given time. To do this, the network learned to model the mul- timodal posterior distribution of future lung tumour segmentations by using variational inference and injecting the posterior latent features. Eventually, by applying Monte-Carlo sampling on the outputs of the trained network, we esti- mated the expected tumour growth mean and the uncertainty associated with the prediction. Although further evaluation in a larger cohort would be highly recommended, the proposed methods reported accurate results to adequately support the ra- diological workflow of pulmonary nodule follow-up. Beyond this specific appli- cation, the outlined innovations, such as the methods for integrating CNNs into computer vision pipelines, the re-identification of suspicious regions over time based on SNNs, without the need to warp the inherent image structure, or the proposed deep generative and probabilistic network to model tumour growth considering ambiguous images and label uncertainty, they could be easily appli- cable to other types of cancer (e.g. pancreas), clinical diseases (e.g. Covid-19) or medical applications (e.g. therapy follow-up).Avui en dia, l’avaluació del càncer de pulmó ´es una tasca complexa i tediosa, principalment realitzada per inspecció visual radiològica de nòduls pulmonars sospitosos, mitjançant imatges de tomografia computada (TC) preses als pacients al llarg del temps. Actualment, existeixen diverses eines computacionals basades en intel·ligència artificial i algorismes de visió per computador per donar suport a la detecció i classificació del càncer de pulmó. Aquestes solucions es basen majoritàriament en l’anàlisi d’imatges individuals de TC pulmonar dels pacients i en l’ús de descriptors d’imatges fets a mà. Malauradament, això les fa incapaces d’afrontar completament la complexitat i la variabilitat del problema. Recentment, l’aparició de l’aprenentatge profund ha permès un gran avenc¸ en el camp de la imatge mèdica. Malgrat els prometedors assoliments en detecció de nòduls, segmentació i classificació del càncer de pulmó, els radiòlegs encara són reticents a utilitzar aquestes solucions en el seu dia a dia. Un dels principals motius ´es que les solucions actuals no proporcionen suport automàtic per analitzar l’evolució temporal dels tumors pulmonars. La dificultat de recopilar i anotar cohorts longitudinals de TC pulmonar poden explicar la manca de treballs d’aprenentatge profund que aborden aquest problema. En aquesta tesi investiguem com abordar el suport automàtic a l’avaluació del càncer de pulmó, construint algoritmes d’aprenentatge profund i pipelines de visió per ordinador que, especialment, tenen en compte l’evolució temporal dels nòduls pulmonars. Així doncs, el nostre primer objectiu va consistir a obtenir mètodes precisos per a l’avaluació del càncer de pulmó basats en imatges de CT pulmonar individuals. Atès que aquests tipus d’etiquetes són costoses i difícils d’obtenir (per exemple, després d’una biòpsia), vam dissenyar diferents xarxes neuronals profundes, basades en xarxes de convolució 3D (CNN), per predir la malignitat dels nòduls basada en la inspecció visual dels radiòlegs (més senzilles de recol.lectar). A continuació, vàrem avaluar diferents maneres de sintetitzar aquest coneixement representat en la xarxa neuronal de malignitat, en una pipeline destinada a proporcionar predicció del càncer de pulmó a nivell de pacient, donada una imatge de TC pulmonar. Els resultats positius van confirmar la conveniència d’utilitzar CNN per modelar la malignitat dels nòduls, segons els radiòlegs, per a la predicció automàtica del càncer de pulmó. Seguidament, vam dirigir la nostra investigació cap a l’anàlisi de sèries d’imatges de TC pulmonar. Per tant, ens vam enfrontar primer a la reidentificació automàtica de nòduls pulmonars de diferents tomografies pulmonars. Per fer-ho, vam proposar utilitzar xarxes neuronals siameses (SNN) per classificar la similitud entre nòduls, superant la necessitat de registre d’imatges. Aquest canvi de paradigma va evitar possibles pertorbacions de la imatge i va proporcionar resultats computacionalment més ràpids. Es van examinar diferents configuracions del SNN convencional, que van des de l’aplicació de l’aprenentatge de transferència, utilitzant diferents funcions de pèrdua, fins a la combinació de diversos mapes de característiques de diferents nivells de xarxa. Aquest mètode va obtenir resultats d’estat de la tècnica per reidentificar nòduls de manera aïllada, i de forma integrada en una pipeline per a la quantificació de creixement de nòduls. A més, vam abordar el problema de donar suport als radiòlegs en la gestió longitudinal del càncer de pulmó. Amb aquesta finalitat, vam proposar una nova pipeline d’aprenentatge profund, composta de quatre etapes que s’automatitzen completament i que van des de la detecció de nòduls fins a la classificació del càncer, passant per la detecció del creixement dels nòduls. A més, la pipeline va integrar un nou enfocament per a la detecció del creixement dels nòduls, que es basava en una recent xarxa de segmentació probabilística jeràrquica adaptada per informar estimacions d’incertesa. A més, es va introduir un segon mètode per a la classificació dels nòduls del càncer de pulmó, que integrava en una xarxa 3D-CNN de dos fluxos les probabilitats estimades de malignitat dels nòduls derivades de la xarxa pre-entrenada de malignitat dels nòduls. La pipeline es va avaluar en una cohort longitudinal i va informar rendiments comparables a l’estat de la tècnica utilitzats individualment o en pipelines però amb menys components que la proposada. Finalment, també vam investigar com ajudar els metges a prescriure de forma més acurada tractaments tumorals i planificacions quirúrgiques més precises. Amb aquesta finalitat, hem realitzat un nou mètode per predir el creixement dels nòduls donada una única imatge del nòdul. Particularment, el mètode es basa en una xarxa neuronal profunda jeràrquica, probabilística i generativa capaç de produir múltiples segmentacions de nòduls futurs consistents del nòdul en un moment determinat. Per fer-ho, la xarxa aprèn a modelar la distribució posterior multimodal de futures segmentacions de tumors pulmonars mitjançant la utilització d’inferència variacional i la injecció de les característiques latents posteriors. Finalment, aplicant el mostreig de Monte-Carlo a les sortides de la xarxa, podem estimar la mitjana de creixement del tumor i la incertesa associada a la predicció. Tot i que es recomanable una avaluació posterior en una cohort més gran, els mètodes proposats en aquest treball han informat resultats prou precisos per donar suport adequadament al flux de treball radiològic del seguiment dels nòduls pulmonars. Més enllà d’aquesta aplicació especifica, les innovacions presentades com, per exemple, els mètodes per integrar les xarxes CNN a pipelines de visió per ordinador, la reidentificació de regions sospitoses al llarg del temps basades en SNN, sense la necessitat de deformar l’estructura de la imatge inherent o la xarxa probabilística per modelar el creixement del tumor tenint en compte imatges ambigües i la incertesa en les prediccions, podrien ser fàcilment aplicables a altres tipus de càncer (per exemple, pàncrees), malalties clíniques (per exemple, Covid-19) o aplicacions mèdiques (per exemple, seguiment de la teràpia)