Deep Neural Networks for Survival Analysis Using Pseudo Values.
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ABSTRACT:
SUBMITTER: Zhao L
PROVIDER: S-EPMC8056290 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundThe use of alternative modeling techniques for predicting patient survival is complicated by the fact that some alternative techniques cannot readily deal with censoring, which is essential for analyzing survival data. In the current study, we aimed to demonstrate that pseudo values enable statistically appropriate analyses of survival outcomes when used in seven alternative modeling techniques.MethodsIn this case study, we analyzed survival of 1282 Dutch patients with newly diagnosed Head and Neck Squamous Cell Carcinoma (HNSCC) with conventional Kaplan-Meier and Cox regression analysis. We subsequently calculated pseudo values to reflect the individual survival patterns. We used these pseudo values to compare recursive partitioning (RPART), neural nets (NNET), logistic regression (LR) general linear models (GLM) and three variants of support vector machines (SVM) with respect to dichotomous 60-month survival, and continuous pseudo values at 60 months or estimated survival time. We used the area under the ROC curve (AUC) and the root of the mean squared error (RMSE) to compare the performance of these models using bootstrap validation.ResultsOf a total of 1282 patients, 986 patients died during a median follow-up of 66 months (60-month survival: 52% [95% CI: 50%-55%]). The LR model had the highest optimism corrected AUC (0.791) to predict 60-month survival, followed by the SVM model with a linear kernel (AUC 0.787). The GLM model had the smallest optimism corrected RMSE when continuous pseudo values were considered for 60-month survival or the estimated survival time followed by SVM models with a linear kernel. The estimated importance of predictors varied substantially by the specific aspect of survival studied and modeling technique used.ConclusionsThe use of pseudo values makes it readily possible to apply alternative modeling techniques to survival problems, to compare their performance and to search further for promising alternative modeling techniques to analyze survival time.
| S-EPMC4065009 | biostudies-literature
Project description:Introduction:Chronic kidney damage is routinely assessed semiquantitatively by scoring the amount of fibrosis and tubular atrophy in a renal biopsy sample. Although image digitization and morphometric techniques can better quantify the extent of histologic damage, we need more widely applicable ways to stratify kidney disease severity. Methods:We leveraged a deep learning architecture to better associate patient-specific histologic images with clinical phenotypes (training classes) including chronic kidney disease (CKD) stage, serum creatinine, and nephrotic-range proteinuria at the time of biopsy, and 1-, 3-, and 5-year renal survival. Trichrome-stained images processed from renal biopsy samples were collected on 171 patients treated at the Boston Medical Center from 2009 to 2012. Six convolutional neural network (CNN) models were trained using these images as inputs and the training classes as outputs, respectively. For comparison, we also trained separate classifiers using the pathologist-estimated fibrosis score (PEFS) as input and the training classes as outputs, respectively. Results:CNN models outperformed PEFS across the classification tasks. Specifically, the CNN model predicted the CKD stage more accurately than the PEFS model (? = 0.519 vs. 0.051). For creatinine models, the area under curve (AUC) was 0.912 (CNN) versus 0.840 (PEFS). For proteinuria models, AUC was 0.867 (CNN) versus 0.702 (PEFS). AUC values for the CNN models for 1-, 3-, and 5-year renal survival were 0.878, 0.875, and 0.904, respectively, whereas the AUC values for PEFS model were 0.811, 0.800, and 0.786, respectively. Conclusion:The study demonstrates a proof of principle that deep learning can be applied to routine renal biopsy images.
| S-EPMC5932308 | biostudies-literature
Project description:Hazard ratios are ubiquitously used in time to event analysis to quantify treatment effects. Although hazard ratios are invaluable for hypothesis testing, other measures of association, both relative and absolute, may be used to fully elucidate study results. Restricted mean survival time (RMST) differences between groups have been advocated as useful measures of association. Recent work focused on model-free estimates of the difference in restricted mean survival through follow-up times, instead of focusing on a single time horizon. The resulting curve can be used to quantify the association in time units with a simultaneous confidence band. In this work a model-based estimate of the curve is proposed using pseudo-values allowing for possible covariate adjustment. The method is easily implementable with available software and makes possible to compute a simultaneous confidence region for the curve. The pseudo-values regression using multiple restriction times is in good agreement with the estimates obtained by standard direct regression models fixing a single restriction time. Moreover, the proposed method is flexible enough to reproduce the results of the non-parametric approach when no covariates are considered. Examples where it is important to adjust for baseline covariates will be used to illustrate the different methods together with some simulations.
| S-EPMC8931966 | biostudies-literature
Project description:Amyotrophic lateral sclerosis (ALS) is a prototypical neurodegenerative disease characterized by progressive degeneration of motor neurons to severely effect the functionality to control voluntary muscle movement. Most of the non-additive genetic aberrations responsible for ALS make its molecular classification very challenging along with limited sample size, curse of dimensionality, class imbalance and noise in the data. Deep learning methods have been successful in many other related areas but have low minority class accuracy and suffer from the lack of explainability when used directly with RNA expression features for ALS molecular classification. In this paper, we propose a deep-learning-based molecular ALS classification and interpretation framework. Our framework is based on training a convolution neural network (CNN) on images obtained from converting RNA expression values into pixels based on DeepInsight similarity technique. Then, we employed Shapley additive explanations (SHAP) to extract pixels with higher relevance to ALS classifications. These pixels were mapped back to the genes which made them up. This enabled us to classify ALS samples with high accuracy for a minority class along with identifying genes that might be playing an important role in ALS molecular classifications. Taken together with RNA expression images classified with CNN, our preliminary analysis of the genes identified by SHAP interpretation demonstrate the value of utilizing Machine Learning to perform molecular classification of ALS and uncover disease-associated genes.
| S-EPMC8626003 | biostudies-literature
Project description:BackgroundWe used the Surveillance, Epidemiology, and End Results (SEER) database to develop and validate deep survival neural network machine learning (ML) algorithms to predict survival following a spino-pelvic chondrosarcoma diagnosis.MethodsThe SEER 18 registries were used to apply the Risk Estimate Distance Survival Neural Network (RED_SNN) in the model. Our model was evaluated at each time window with receiver operating characteristic curves and areas under the curves (AUCs), as was the concordance index (c-index).ResultsThe subjects (n?=?1088) were separated into training (80%, n?=?870) and test sets (20%, n?=?218). The training data were randomly sorted into training and validation sets using 5-fold cross validation. The median c-index of the five validation sets was 0.84 (95% confidence interval 0.79-0.87). The median AUC of the five validation subsets was 0.84. This model was evaluated with the previously separated test set. The c-index was 0.82 and the mean AUC of the 30 different time windows was 0.85 (standard deviation 0.02). According to the estimated survival probability (by 62?months), we divided the test group into five subgroups. The survival curves of the subgroups showed statistically significant separation (p?<?0.001).ConclusionsThis study is the first to analyze population-level data using artificial neural network ML algorithms for the role and outcomes of surgical resection and radiation therapy in spino-pelvic chondrosarcoma.
| S-EPMC6945432 | biostudies-literature
Project description:PurposeVenoarterial extracorporeal membrane oxygenation (VA-ECMO) is a complex and high-risk life support modality used in severe cardiorespiratory failure. ECMO survival scores are used clinically for patient prognostication and outcomes risk adjustment. This study aims to create the first artificial intelligence (AI)-driven ECMO survival score to predict in-hospital mortality based on a large international patient cohort.MethodsA deep neural network, ECMO Predictive Algorithm (ECMO PAL) was trained on a retrospective cohort of 18,167 patients from the international Extracorporeal Life Support Organisation (ELSO) registry (2017-2020), and performance was measured using fivefold cross-validation. External validation was performed on all adult registry patients from 2021 (N = 5015) and compared against existing prognostication scores: SAVE, Modified SAVE, and ECMO ACCEPTS for predicting in-hospital mortality.ResultsMean age was 56.8 ± 15.1 years, with 66.7% of patients being male and 50.2% having a pre-ECMO cardiac arrest. Cross-validation demonstrated an inhospital mortality sensitivity and precision of 82.1 ± 0.2% and 77.6 ± 0.2%, respectively. Validation accuracy was only 2.8% lower than training accuracy, reducing from 75.5% to 72.7% [99% confidence interval (CI) 71.1-74.3%]. ECMO PAL accuracy outperformed the ECMO ACCEPTS (54.7%), SAVE (61.1%), and Modified SAVE (62%) scores.ConclusionsECMO PAL is the first AI-powered ECMO survival score trained and validated on large international patient cohorts. ECMO PAL demonstrated high generalisability across ECMO regions and outperformed existing, widely used scores. Beyond ECMO, this study highlights how large international registry data can be leveraged for AI prognostication for complex critical care therapies.
| S-EPMC10499722 | biostudies-literature
Project description:Many neurological and musculoskeletal diseases impair movement, which limits people's function and social participation. Quantitative assessment of motion is critical to medical decision-making but is currently possible only with expensive motion capture systems and highly trained personnel. Here, we present a method for predicting clinically relevant motion parameters from an ordinary video of a patient. Our machine learning models predict parameters include walking speed (r?=?0.73), cadence (r?=?0.79), knee flexion angle at maximum extension (r?=?0.83), and Gait Deviation Index (GDI), a comprehensive metric of gait impairment (r?=?0.75). These correlation values approach the theoretical limits for accuracy imposed by natural variability in these metrics within our patient population. Our methods for quantifying gait pathology with commodity cameras increase access to quantitative motion analysis in clinics and at home and enable researchers to conduct large-scale studies of neurological and musculoskeletal disorders.
| S-EPMC7426855 | biostudies-literature
Project description:Accurate quantification of uptake on PET images depends on accurate attenuation correction in reconstruction. Current MR-based attenuation correction methods for body PET use a fat and water map derived from a 2-echo Dixon MRI sequence in which bone is neglected. Ultrashort-echo-time or zero-echo-time (ZTE) pulse sequences can capture bone information. We propose the use of patient-specific multiparametric MRI consisting of Dixon MRI and proton-density-weighted ZTE MRI to directly synthesize pseudo-CT images with a deep learning model: we call this method ZTE and Dixon deep pseudo-CT (ZeDD CT). Methods: Twenty-six patients were scanned using an integrated 3-T time-of-flight PET/MRI system. Helical CT images of the patients were acquired separately. A deep convolutional neural network was trained to transform ZTE and Dixon MR images into pseudo-CT images. Ten patients were used for model training, and 16 patients were used for evaluation. Bone and soft-tissue lesions were identified, and the SUVmax was measured. The root-mean-squared error (RMSE) was used to compare the MR-based attenuation correction with the ground-truth CT attenuation correction. Results: In total, 30 bone lesions and 60 soft-tissue lesions were evaluated. The RMSE in PET quantification was reduced by a factor of 4 for bone lesions (10.24% for Dixon PET and 2.68% for ZeDD PET) and by a factor of 1.5 for soft-tissue lesions (6.24% for Dixon PET and 4.07% for ZeDD PET). Conclusion: ZeDD CT produces natural-looking and quantitatively accurate pseudo-CT images and reduces error in pelvic PET/MRI attenuation correction compared with standard methods.
| S-EPMC5932530 | biostudies-literature
Project description:The Machine Recognition of Crystallization Outcomes (MARCO) initiative has assembled roughly half a million annotated images of macromolecular crystallization experiments from various sources and setups. Here, state-of-the-art machine learning algorithms are trained and tested on different parts of this data set. We find that more than 94% of the test images can be correctly labeled, irrespective of their experimental origin. Because crystal recognition is key to high-density screening and the systematic analysis of crystallization experiments, this approach opens the door to both industrial and fundamental research applications.
| S-EPMC6010233 | biostudies-other
Project description:This paper describes a method based on a deep neural network (DNN) for estimating the number of tillers on a plant. A tiller is a branch on a grass plant, and the number of tillers is one of the most important determinants of yield. Traditionally, the tiller number is usually counted by hand, and so an automated approach is necessary for high-throughput phenotyping. Conventional methods use heuristic features to estimate the tiller number. Based on the successful application of DNNs in the field of computer vision, the use of DNN-based features instead of heuristic features is expected to improve the estimation accuracy. However, as DNNs generally require large volumes of data for training, it is difficult to apply them to estimation problems for which large training datasets are unavailable. In this paper, we use two strategies to overcome the problem of insufficient training data: the use of a pretrained DNN model and the use of pretext tasks for learning the feature representation. We extract features using the resulting DNNs and estimate the tiller numbers through a regression technique. We conducted experiments using side-view whole plant images taken with plan backgroud. The experimental results show that the proposed methods using a pretrained model and specific pretext tasks achieve better performance than the conventional method.
| S-EPMC9880423 | biostudies-literature