Deep-Learning Approach to Predict Survival Outcomes Using Wearable Actigraphy Device Among End-Stage Cancer Patients.
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ABSTRACT:
SUBMITTER: Yang TY
PROVIDER: S-EPMC8695752 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Unobtrusive home sleep monitoring using wrist-worn wearable photoplethysmography (PPG) could open the way for better sleep disorder screening and health monitoring. However, PPG is rarely included in large sleep studies with gold-standard sleep annotation from polysomnography. Therefore, training data-intensive state-of-the-art deep neural networks is challenging. In this work a deep recurrent neural network is first trained using a large sleep data set with electrocardiogram (ECG) data (292 participants, 584 recordings) to perform 4-class sleep stage classification (wake, rapid-eye-movement, N1/N2, and N3). A small part of its weights is adapted to a smaller, newer PPG data set (60 healthy participants, 101 recordings) through three variations of transfer learning. Best results (Cohen's kappa of 0.65 ± 0.11, accuracy of 76.36 ± 7.57%) were achieved with the domain and decision combined transfer learning strategy, significantly outperforming the PPG-trained and ECG-trained baselines. This performance for PPG-based 4-class sleep stage classification is unprecedented in literature, bringing home sleep stage monitoring closer to clinical use. The work demonstrates the merit of transfer learning in developing reliable methods for new sensor technologies by reusing similar, older non-wearable data sets. Further study should evaluate our approach in patients with sleep disorders such as insomnia and sleep apnoea.
| S-EPMC8443610 | biostudies-literature
Project description:BackgroundData collected by an actigraphy device worn on the wrist or waist can provide objective measurements for studies related to physical activity; however, some data may contain intervals where values are missing. In previous studies, statistical methods have been applied to impute missing values on the basis of statistical assumptions. Deep learning algorithms, however, can learn features from the data without any such assumptions and may outperform previous approaches in imputation tasks.ObjectiveThe aim of this study was to impute missing values in data using a deep learning approach.MethodsTo develop an imputation model for missing values in accelerometer-based actigraphy data, a denoising convolutional autoencoder was adopted. We trained and tested our deep learning-based imputation model with the National Health and Nutrition Examination Survey data set and validated it with the external Korea National Health and Nutrition Examination Survey and the Korean Chronic Cerebrovascular Disease Oriented Biobank data sets which consist of daily records measuring activity counts. The partial root mean square error and partial mean absolute error of the imputed intervals (partial RMSE and partial MAE, respectively) were calculated using our deep learning-based imputation model (zero-inflated denoising convolutional autoencoder) as well as using other approaches (mean imputation, zero-inflated Poisson regression, and Bayesian regression).ResultsThe zero-inflated denoising convolutional autoencoder exhibited a partial RMSE of 839.3 counts and partial MAE of 431.1 counts, whereas mean imputation achieved a partial RMSE of 1053.2 counts and partial MAE of 545.4 counts, the zero-inflated Poisson regression model achieved a partial RMSE of 1255.6 counts and partial MAE of 508.6 counts, and Bayesian regression achieved a partial RMSE of 924.5 counts and partial MAE of 605.8 counts.ConclusionsOur deep learning-based imputation model performed better than the other methods when imputing missing values in actigraphy data.
| S-EPMC7413283 | biostudies-literature
Project description:Recent advances of wearable computing technology have allowed continuous health monitoring in large observational studies and clinical trials. Examples of data collected by wearable devices include minute-by-minute physical activity proxies measured by accelerometers or heart rate. The analysis of data generated by wearable devices has so far been quite limited to crude summaries, for example, the mean activity count over the day. To better utilize the full data and account for the dynamics of activity level in the time domain, we introduce a two-stage regression model for the minute-by-minute physical activity proxy data. The model allows for both time-varying parameters and time-invariant parameters, which helps capture both the transition dynamics between active/inactive periods (Stage 1) and the activity intensity dynamics during active periods (Stage 2). The approach extends methods developed for zero-inflated Poisson data to account for the high-dimensionality and time-dependence of the high density data generated by wearable devices. Methods are motivated by and applied to the Baltimore Longitudinal Study of Aging.
| S-EPMC5893449 | biostudies-literature
Project description:BackgroundProfound heterogeneity in prognosis has been observed in colorectal cancer (CRC) patients with intermediate levels of disease (stage II-III), advocating the identification of valuable biomarkers that could improve the prognostic stratification. This study aims to develop a deep learning-based pipeline for fully automatic quantification of immune infiltration within the stroma region on immunohistochemical (IHC) whole-slide images (WSIs) and further analyze its prognostic value in CRC.MethodsPatients from two independent cohorts were divided into three groups: the development group (N = 200), the internal (N = 134), and the external validation group (N = 90). We trained a convolutional neural network for tissue classification of CD3 and CD8 stained WSIs. A scoring system, named stroma-immune score, was established by quantifying the density of CD3+ and CD8+ T-cells infiltration in the stroma region.ResultsPatients with higher stroma-immune scores had much longer survival. In the development group, 5-year survival rates of the low and high scores were 55.7% and 80.8% (hazard ratio [HR] for high vs. low 0.39, 95% confidence interval [CI] 0.24-0.63, P < 0.001). These results were confirmed in the internal and external validation groups with 5-year survival rates of low and high scores were 57.1% and 78.8%, 63.9% and 88.9%, respectively (internal: HR for high vs. low 0.49, 95% CI 0.28-0.88, P = 0.017; external: HR for high vs. low 0.35, 95% CI 0.15-0.83, P = 0.018). The combination of stroma-immune score and tumor-node-metastasis (TNM) stage showed better discrimination ability for survival prediction than using the TNM stage alone.ConclusionsWe proposed a stroma-immune score via a deep learning-based pipeline to quantify CD3+ and CD8+ T-cells densities within the stroma region on WSIs of CRC and further predict survival.
| S-EPMC8557607 | biostudies-literature
Project description:The purpose of this study was to assess the feasibility of machine learning (ML) in predicting the risk of end-stage kidney disease (ESKD) from patients with chronic kidney disease (CKD). Data were obtained from a longitudinal CKD cohort. Predictor variables included patients' baseline characteristics and routine blood test results. The outcome of interest was the presence or absence of ESKD by the end of 5 years. Missing data were imputed using multiple imputation. Five ML algorithms, including logistic regression, naïve Bayes, random forest, decision tree, and K-nearest neighbors were trained and tested using fivefold cross-validation. The performance of each model was compared to that of the Kidney Failure Risk Equation (KFRE). The dataset contained 748 CKD patients recruited between April 2006 and March 2008, with the follow-up time of 6.3 ± 2.3 years. ESKD was observed in 70 patients (9.4%). Three ML models, including the logistic regression, naïve Bayes and random forest, showed equivalent predictability and greater sensitivity compared to the KFRE. The KFRE had the highest accuracy, specificity, and precision. This study showed the feasibility of ML in evaluating the prognosis of CKD based on easily accessible features. Three ML models with adequate performance and sensitivity scores suggest a potential use for patient screenings. Future studies include external validation and improving the models with additional predictor variables.
| S-EPMC9120106 | biostudies-literature
Project description:The blood-brain barrier plays a crucial role in regulating the passage of 98% of the compounds that enter the central nervous system (CNS). Compounds with high permeability must be identified to enable the synthesis of brain medications for the treatment of various brain diseases, such as Parkinson's, Alzheimer's, and brain tumors. Throughout the years, several models have been developed to solve this problem and have achieved acceptable accuracy scores in predicting compounds that penetrate the blood-brain barrier. However, predicting compounds with "low" permeability has been a challenging task. In this study, we present a deep learning (DL) classification model to predict blood-brain barrier permeability. The proposed model addresses the fundamental issues presented in former models: high dimensionality, class imbalances, and low specificity scores. We address these issues to enhance the high-dimensional, imbalanced dataset before developing the classification model: the imbalanced dataset is addressed using oversampling techniques and the high dimensionality using a non-linear dimensionality reduction technique known as kernel principal component analysis (KPCA). This technique transforms the high-dimensional dataset into a low-dimensional Euclidean space while retaining invaluable information. For the classification task, we developed an enhanced feed-forward deep learning model and a convolutional neural network model. In terms of specificity scores (i.e., predicting compounds with low permeability), the results obtained by the enhanced feed-forward deep learning model outperformed those obtained by other models in the literature that were developed using the same technique. In addition, the proposed convolutional neural network model surpassed models used in other studies in multiple accuracy measures, including overall accuracy and specificity. The proposed approach solves the problem inevitably faced with obtaining low specificity resulting in high false positive rate.
| S-EPMC8205267 | biostudies-literature
Project description:ObjectiveTo develop and evaluate deep learning (DL) risk assessment models for predicting pain progression in subjects with or at risk of knee osteoarthritis (OA).Materials and methodsThe incidence and progression cohorts of the Osteoarthritis Initiative, a multi-center longitudinal study involving 9348 knees in 4674 subjects with or at risk of knee OA that began in 2004 and is ongoing, were used to conduct this retrospective analysis. A subset of knees without and with pain progression (defined as a 9-point or greater increase in pain score between baseline and two or more follow-up time points over the first 48 months) was randomly stratified into training (4200 knees with a mean age of 61.0 years and 60% female) and hold-out testing (500 knees with a mean age of 60.8 years and 60% female) datasets. A DL model was developed to predict pain progression using baseline knee radiographs. An artificial neural network was used to develop a traditional risk assessment model to predict pain progression using demographic, clinical, and radiographic risk factors. A combined model was developed to combine demographic, clinical, and radiographic risk factors with DL analysis of baseline knee radiographs. Area under the curve (AUC) analysis was performed using the hold-out testing dataset to evaluate model performance.ResultsThe traditional model had an AUC of 0.692 (66.9% sensitivity and 64.1% specificity). The DL model had an AUC of 0.770 (76.7% sensitivity and 70.5% specificity), which was significantly higher (p < 0.001) than the traditional model. The combined model had an AUC of 0.807 (72.3% sensitivity and 80.9% specificity), which was significantly higher (p < 0.05) than the traditional and DL models.ConclusionsDL models using baseline knee radiographs had higher diagnostic performance for predicting pain progression than traditional models using demographic, clinical, and radiographic risk factors.
| S-EPMC9232386 | biostudies-literature
Project description:Deep learning is a powerful tool for neural decoding, broadly applied to systems neuroscience and clinical studies. Interpretable and transparent models that can explain neural decoding for intended behaviors are crucial to identifying essential features of deep learning decoders in brain activity. In this study, we examine the performance of deep learning to classify mouse behavioral states from mesoscopic cortex-wide calcium imaging data. Our convolutional neural network (CNN)-based end-to-end decoder combined with recurrent neural network (RNN) classifies the behavioral states with high accuracy and robustness to individual differences on temporal scales of sub-seconds. Using the CNN-RNN decoder, we identify that the forelimb and hindlimb areas in the somatosensory cortex significantly contribute to behavioral classification. Our findings imply that the end-to-end approach has the potential to be an interpretable deep learning method with unbiased visualization of critical brain regions.
| S-EPMC10986998 | biostudies-literature
Project description:Collagen is the most abundant structural protein in humans, with dozens of sequence variants accounting for over 30% of the protein in an animal body. The fibrillar and hierarchical arrangements of collagen are critical in providing mechanical properties with high strength and toughness. Due to this ubiquitous role in human tissues, collagen-based biomaterials are commonly used for tissue repairs and regeneration, requiring chemical and thermal stability over a range of temperatures during materials preparation ex vivo and subsequent utility in vivo. Collagen unfolds from a triple helix to a random coil structure during a temperature interval in which the midpoint or Tm is used as a measure to evaluate the thermal stability of the molecules. However, finding a robust framework to facilitate the design of a specific collagen sequence to yield a specific Tm remains a challenge, including using conventional molecular dynamics modeling. Here we propose a de novo framework to provide a model that outputs the Tm values of input collagen sequences by incorporating deep learning trained on a large data set of collagen sequences and corresponding Tm values. By using this framework, we are able to quickly evaluate how mutations and order in the primary sequence affect the stability of collagen triple helices. Specifically, we confirm that mutations to glycines, mutations in the middle of a sequence, and short sequence lengths cause the greatest drop in Tm values.
| S-EPMC9514290 | biostudies-literature
Project description:Study objectivesTo compare the quality and consistency in sleep measurement of a consumer wearable device and a research-grade actigraph with polysomnography (PSG) in adolescents.MethodsFifty-eight healthy adolescents (aged 15-19 years; 30 males) underwent overnight PSG while wearing both a Fitbit Alta HR and a Philips Respironics Actiwatch 2 (AW2) for 5 nights, with either 5 hours or 6.5 hours time in bed (TIB) and for 4 nights with 9 hours TIB. AW2 data were evaluated using two different wake and immobility thresholds. Discrepancies in estimated total sleep time (TST) and wake after sleep onset (WASO) between devices and PSG, as well as epoch-by-epoch agreements in sleep/wake classification, were assessed. Fitbit-generated sleep staging was compared to PSG.ResultsFitbit and AW2 under default settings similarly underestimated TST and overestimated WASO (TST: medium setting (M10) ≤ 38 minutes, Fitbit ≤ 47 minutes; WASO: M10 ≤ 38 minutes; Fitbit ≤ 42 minutes). AW2 at the high motion threshold setting provided readings closest to PSG (TST: ≤ 12 minutes; WASO: ≤ 18 minutes). Sensitivity for detecting sleep was ≥ 90% for both wearable devices and further improved to 95% by using the high threshold (H5) setting for the AW2 (0.95). Wake detection specificity was highest in Fitbit (≥ 0.88), followed by the AW2 at M10 (≥ 0.80) and H5 thresholds (≤ 0.73). In addition, Fitbit inconsistently estimated stage N1 + N2 sleep depending on TIB, underestimated stage N3 sleep (21-46 min), but was comparable to PSG for rapid eye movement sleep. Fitbit sensitivity values for the detection of N1 + N2, N3 and rapid eye movement sleep were ≥ 0.68, ≥ 0.50, and ≥ 0.72, respectively.ConclusionsA consumer-grade wearable device can measure sleep duration as well as a research actigraph. However, sleep staging would benefit from further refinement before these methods can be reliably used for adolescents.Clinical trial registrationRegistry: ClinicalTrials.gov; Title: The Cognitive and Metabolic Effects of Sleep Restriction in Adolescents; Identifier: NCT03333512; URL: https://clinicaltrials.gov/ct2/show/NCT03333512.CitationLee XK, Chee NIYN, Ong JL, Teo TB, van Rijn E, Lo JC, Chee MWL. Validation of a consumer sleep wearable device with actigraphy and polysomnography in adolescents across sleep opportunity manipulations. J Clin Sleep Med. 2019;15(9):1337-1346.
| S-EPMC6760396 | biostudies-literature