scholarly journals Assessing PD-L1 Expression Level via Preoperative MRI in HCC Based on Integrating Deep Learning and Radiomics Features

Diagnostics ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1875
Author(s):  
Yuchi Tian ◽  
Temitope Emmanuel Komolafe ◽  
Jian Zheng ◽  
Guofeng Zhou ◽  
Tao Chen ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Deep Learning ◽  
Cross Validation ◽  
Predictive Ability ◽  
Feature Space ◽  
Integrated Model ◽  
Expression Level ◽  
Deep Learning Features ◽  
Expression Status ◽  
Fold Cross Validation

To assess if quantitative integrated deep learning and radiomics features can predict the PD-L1 expression level in preoperative MRI of hepatocellular carcinoma (HCC) patients. The data in this study consist of 103 hepatocellular carcinoma patients who received immunotherapy in a single center. These patients were divided into a high PD-L1 expression group (30 patients) and a low PD-L1 expression group (73 patients). Both radiomics and deep learning features were extracted from their MRI sequence of T2-WI, which were merged into an integrative feature space for machine learning for the prediction of PD-L1 expression. The five-fold cross-validation was adopted to validate the performance of the model, while the AUC was used to assess the predictive ability of the model. Based on the five-fold cross-validation, the integrated model achieved the best prediction performance, with an AUC score of 0.897 ± 0.084, followed by the deep learning-based model with an AUC of 0.852 ± 0.043 then the radiomics-based model with AUC of 0.794 ± 0.035. The feature set integrating radiomics and deep learning features is more effective in predicting PD-L1 expression level than only one feature type. The integrated model can achieve fast and accurate prediction of PD-L1 expression status in preoperative MRI of HCC patients.

scholarly journals Deep6mA: A deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species

2021 ◽  
Vol 17 (2) ◽  
pp. e1008767
Author(s):  
Zutan Li ◽  
Hangjin Jiang ◽  
Lingpeng Kong ◽  
Yuanyuan Chen ◽  
Kun Lang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Prediction Accuracy ◽  
Cross Validation ◽  
Biological Processes ◽  
Biological Functions ◽  
Learning Framework ◽  
Wide Range ◽  
Genomic Scale ◽  
Downstream Gene Expression ◽  
Fold Cross Validation

N6-methyladenine (6mA) is an important DNA modification form associated with a wide range of biological processes. Identifying accurately 6mA sites on a genomic scale is crucial for under-standing of 6mA’s biological functions. However, the existing experimental techniques for detecting 6mA sites are cost-ineffective, which implies the great need of developing new computational methods for this problem. In this paper, we developed, without requiring any prior knowledge of 6mA and manually crafted sequence features, a deep learning framework named Deep6mA to identify DNA 6mA sites, and its performance is superior to other DNA 6mA prediction tools. Specifically, the 5-fold cross-validation on a benchmark dataset of rice gives the sensitivity and specificity of Deep6mA as 92.96% and 95.06%, respectively, and the overall prediction accuracy is 94%. Importantly, we find that the sequences with 6mA sites share similar patterns across different species. The model trained with rice data predicts well the 6mA sites of other three species: Arabidopsis thaliana, Fragaria vesca and Rosa chinensis with a prediction accuracy over 90%. In addition, we find that (1) 6mA tends to occur at GAGG motifs, which means the sequence near the 6mA site may be conservative; (2) 6mA is enriched in the TATA box of the promoter, which may be the main source of its regulating downstream gene expression.

scholarly journals Urine biomarker: novel approach to hepatocellular carcinoma screening

2020 ◽  
Author(s):  
Amy K Kim ◽  
James P. Hamilton ◽  
Selena Y. Lin ◽  
Ting-Tsung Chang ◽  
Hie-Won Hann ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cross Validation ◽  
Learning Algorithm ◽  
Early Stage ◽  
High Risk Patient ◽  
Circulating Tumor Dna ◽  
Urine Samples ◽  
Detection Rates ◽  
Non Invasive ◽  
Fold Cross Validation

ABSTRACTBackground & AimsContinued limitations in hepatocellular carcinoma (HCC) screening have led to late diagnosis with poor survival, despite well-defined high-risk patient populations. Our aim is to develop a non-invasive urine circulating tumor DNA (ctDNA) biomarker panel for HCC screening to aid in early detection.MethodsCandidate ctDNA biomarkers was prescreened in urine samples obtained from HCC, cirrhosis, and hepatitis patients. Then, 609 patient urine samples with HCC, cirrhosis, or chronic hepatitis B were collected from five academic medical centers and evaluated by serum alpha feto-protein (AFP) and urine ctDNA panel using logistic regression, a Two-Step machine learning algorithm, and iterated 10-fold cross-validation.ResultsMutated TP53, and methylated RASSF1a and GSTP1, were selected for the urine ctDNA panel. The sensitivity of AFP-alone (9.8 ng/mL cut-off) to detect HCC was 71% by Two-Step. The combination of ctDNA and AFP increased the sensitivity to 81% at a specificity of 90%. The AUROC for the combination of ctDNA and AFP vs. AFP-alone were 0.925 (95% CI, 0.924-0.925) and 0.877 (95% CI, 0.876-0.877), respectively. Notably, among the patients with AFP <20 ng/mL, the combination panel correctly identified 64% of HCC cases. The panel performed superiorly to AFP-alone in early-stage HCC (BCLC A) with 80% sensitivity and 90% specificity. In an iterated 10-fold cross-validation analysis, the AUROC for the combination panel was 0.898 (95% CI, 0.895-0.901).ConclusionsThe combination of urine ctDNA and serum AFP can increase HCC detection rates including in those patients with low-AFP. Given the ease of collection, a urine ctDNA panel could be a potential non-invasive HCC screening test.

scholarly journals CV-α: designing validations sets to increase the precision and enable multiple comparison tests in genomic prediction

2020 ◽  
Author(s):  
Rafael Massahiro Yassue ◽  
José Felipe Gonzaga Sabadin ◽  
Giovanni Galli ◽  
Filipe Couto Alves ◽  
Roberto Fritsche-Neto
Keyword(s):  
Genomic Prediction ◽  
Cross Validation ◽  
Prediction Models ◽  
Mean Squared Error ◽  
Predictive Ability ◽  
Proof Of Concept ◽  
Squared Error ◽  
High Effect ◽  
The Mean ◽  
Fold Cross Validation

AbstractUsually, the comparison among genomic prediction models is based on validation schemes as Repeated Random Subsampling (RRS) or K-fold cross-validation. Nevertheless, the design of training and validation sets has a high effect on the way and subjectiveness that we compare models. Those procedures cited above have an overlap across replicates that might cause an overestimated estimate and lack of residuals independence due to resampling issues and might cause less accurate results. Furthermore, posthoc tests, such as ANOVA, are not recommended due to assumption unfulfilled regarding residuals independence. Thus, we propose a new way to sample observations to build training and validation sets based on cross-validation alpha-based design (CV-α). The CV-α was meant to create several scenarios of validation (replicates x folds), regardless of the number of treatments. Using CV-α, the number of genotypes in the same fold across replicates was much lower than K-fold, indicating higher residual independence. Therefore, based on the CV-α results, as proof of concept, via ANOVA, we could compare the proposed methodology to RRS and K-fold, applying four genomic prediction models with a simulated and real dataset. Concerning the predictive ability and bias, all validation methods showed similar performance. However, regarding the mean squared error and coefficient of variation, the CV-α method presented the best performance under the evaluated scenarios. Moreover, as it has no additional cost nor complexity, it is more reliable and allows the use of non-subjective methods to compare models and factors. Therefore, CV-α can be considered a more precise validation methodology for model selection.

scholarly journals 0616 Validation of a Sleep Headband for Detecting Obstructive Sleep Apnea

SLEEP ◽  
2020 ◽  
Vol 43 (Supplement_1) ◽  
pp. A236-A236
Author(s):  
A Guillot ◽  
T Moutakanni ◽  
M Harris ◽  
P J Arnal ◽  
V Thorey
Keyword(s):  
Obstructive Sleep Apnea ◽  
Deep Learning ◽  
Sleep Apnea ◽  
Cross Validation ◽  
Apnea Hypopnea Index ◽  
Learning Approach ◽  
Specificity And Sensitivity ◽  
Obstructive Sleep ◽  
Fold Cross Validation ◽  
At Home

Abstract Introduction Polysomnography (PSG) is the gold-standard to diagnose obstructive sleep apnea (OSA). OSA severity diagnosis is defined by the apnea-hypopnea index (AHI) defined as the number of apnea and hypopnea events measured per hour of sleep. The Dreem2 headband (DH) is a self-administered, easy to use device that measure EEG, breathing frequency, heart rate and sound at-home. In our study, we assessed the performance of the DH to automatically detects OSA compared to 3 sleep’s experts scoring on PSG. Methods 41 subjects (8 females, 42.6 ± 13.7 y.o.) having a suspicion of OSA performed a night at-home wearing both a PSG and the DH. Each PSG record was scored for apnea and hypopnea events by 3 independent trained sleep experts following AASM guidelines. The deep learning approach DOSED, was trained on the DH signals using the manual apnea scoring. 10-fold cross-validation was used to provide predictions for each of the 41 subjects with the DH. Results We observed an average AHI expert’s scoring of 13.6 ± 10.1 CI[10.5, 16.5] compared to 12.9 ± 10.3 CI[9.6, 15.8] for the DH. Both, the correlation between the 3 scorers (r= 0.88, p &lt; 0.001) and the DH and the scorers (r=0.79, p&lt; 0.001) were significant. The specificity and sensitivity to detect mild OSA (AHI ≤ 5) was 84.4 % and 96.4 % for the DH and 86.5 % and 86.0% for the scorers. Conclusion The results show that the DH using deep learning can detect OSA with an accuracy similar to the sleep experts. The use of DH paves the way for longitudinal monitoring of patients with a suspicion of OSA and its accessibility could lead to better screening of the general population. Support This Study has been supported by Dreem sas.

scholarly journals Improving Prediction Accuracy Using Multi-allelic Haplotype Prediction and Training Population Optimization in Wheat

2020 ◽  
Vol 10 (7) ◽  
pp. 2265-2273 ◽  
Author(s):  
Ahmad H. Sallam ◽  
Emily Conley ◽  
Dzianis Prakapenka ◽  
Yang Da ◽  
James A. Anderson
Keyword(s):  
Population Structure ◽  
Protein Content ◽  
Prediction Accuracy ◽  
Cross Validation ◽  
Predictive Ability ◽  
Training Population ◽  
Percentage Points ◽  
And Training ◽  
Fold Cross Validation ◽  
Single Snps

The use of haplotypes may improve the accuracy of genomic prediction over single SNPs because haplotypes can better capture linkage disequilibrium and genomic similarity in different lines and may capture local high-order allelic interactions. Additionally, prediction accuracy could be improved by portraying population structure in the calibration set. A set of 383 advanced lines and cultivars that represent the diversity of the University of Minnesota wheat breeding program was phenotyped for yield, test weight, and protein content and genotyped using the Illumina 90K SNP Assay. Population structure was confirmed using single SNPs. Haplotype blocks of 5, 10, 15, and 20 adjacent markers were constructed for all chromosomes. A multi-allelic haplotype prediction algorithm was implemented and compared with single SNPs using both k-fold cross validation and stratified sampling optimization. After confirming population structure, the stratified sampling improved the predictive ability compared with k-fold cross validation for yield and protein content, but reduced the predictive ability for test weight. In all cases, haplotype predictions outperformed single SNPs. Haplotypes of 15 adjacent markers showed the best improvement in accuracy for all traits; however, this was more pronounced in yield and protein content. The combined use of haplotypes of 15 adjacent markers and training population optimization significantly improved the predictive ability for yield and protein content by 14.3 (four percentage points) and 16.8% (seven percentage points), respectively, compared with using single SNPs and k-fold cross validation. These results emphasize the effectiveness of using haplotypes in genomic selection to increase genetic gain in self-fertilized crops.

Prediction models establishment and comparison for guiding force of high-temperature superconducting maglev based on deep learning algorithms

2021 ◽  
Author(s):  
Zhihao Ke ◽  
Xiaoning Liu ◽  
Yining Chen ◽  
Hongfu Shi ◽  
Zigang Deng
Keyword(s):  
Deep Learning ◽  
High Temperature ◽  
Prediction Accuracy ◽  
Cross Validation ◽  
Learning Algorithms ◽  
Learning Rate ◽  
Force Prediction ◽  
Validation Method ◽  
Hts Maglev ◽  
Fold Cross Validation

Abstract By the merits of self-stability and low energy consumption, high temperature superconducting (HTS) maglev has the potential to become a novel type of transportation mode. As a key index to guarantee the lateral self-stability of HTS maglev, guiding force has strong non-linearity and is determined by multitudinous factors, and these complexities impede its further researches. Compared to traditional finite element and polynomial fitting method, the prosperity of deep learning algorithms could provide another guiding force prediction approach, but the verification of this approach is still blank. Therefore, this paper establishes 5 different neural network models (RBF, DNN, CNN, RNN, LSTM) to predict HTS maglev guiding force, and compares their prediction efficiency based on 3720 pieces of collected data. Meanwhile, two adaptively iterative algorithms for parameters matrix and learning rate adjustment are proposed, which could effectively reduce computing time and unnecessary iterations. And according to the results, it is revealed that, the DNN model shows the best fitting goodness, while the LSTM model displays the smoothest fitting curve on guiding force prediction. Based on this discovery, the effects of learning rate and iterations on prediction accuracy of the constructed DNN model are studied. And the learning rate and iterations at the highest guiding force prediction accuracy are 0.00025 and 90000, respectively. Moreover, the K-fold cross validation method is also applied to this DNN model, whose result manifests the generalization and robustness of this DNN model. The imperative of K-fold cross validation method to ensure universality of guiding force prediction model is likewise assessed. This paper firstly combines HTS maglev guiding force prediction with deep learning algorithms considering different field cooling height, real-time magnetic flux density, liquid nitrogen temperature and motion direction of bulk. Additionally, this paper gives a convenient and efficient method for HTS guiding force prediction and parameter optimization.

Multiclass Kernel Function Evaluation

2012 ◽  
Vol 542-543 ◽  
pp. 1438-1442
Author(s):  
Ting Hua Wang ◽  
Cai Yun Cai ◽  
Yan Liao
Keyword(s):  
Cross Validation ◽  
Selection Criterion ◽  
Feature Space ◽  
Function Evaluation ◽  
Support Vector ◽  
Computationally Efficient ◽  
Computational Overhead ◽  
Vector Machines ◽  
Validation Technique ◽  
Fold Cross Validation

Kernel is a key component of the support vector machines (SVMs) and other kernel methods. Based on the data distributions of classes in the feature space, this paper proposed a model selection criterion to evaluate the goodness of a kernel in multiclass classification scenario. This criterion is computationally efficient and is differentiable with respect to the kernel parameters. Compared with the k-fold cross validation technique which is often regarded as a benchmark, this criterion is found to yield about the same performance with much less computational overhead.

scholarly journals Classification of Traffic Vehicle Density Using Deep Learning

2020 ◽  
Vol 14 (1) ◽  
pp. 69
Author(s):  
Abdul Kholik ◽  
Agus Harjoko ◽  
Wahyono Wahyono
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Cross Validation ◽  
Classification Model ◽  
Density Level ◽  
Vehicle Density ◽  
The Impact ◽  
Fold Cross Validation

The volume density of vehicles is a problem that often occurs in every city, as for the impact of vehicle density is congestion. Classification of vehicle density levels on certain roads is required because there are at least 7 vehicle density level conditions. Monitoring conducted by the police, the Department of Transportation and the organizers of the road currently using video-based surveillance such as CCTV that is still monitored by people manually. Deep Learning is an approach of synthetic neural network-based learning machines that are actively developed and researched lately because it has succeeded in delivering good results in solving various soft-computing problems, This research uses the convolutional neural network architecture. This research tries to change the supporting parameters on the convolutional neural network to further calibrate the maximum accuracy. After the experiment changed the parameters, the classification model was tested using K-fold cross-validation, confusion matrix and model exam with data testing. On the K-fold cross-validation test with an average yield of 92.83% with a value of K (fold) = 5, model testing is done by entering data testing amounting to 100 data, the model can predict or classify correctly i.e. 81 data.

scholarly journals Deep Learning Based Pectoral Muscle Segmentation on MIAS Mammograms

2020 ◽  
Author(s):  
Young Jae Kim ◽  
Eun Young Yoo ◽  
Kwang Gi Kim
Keyword(s):  
Breast Cancer ◽  
Image Processing ◽  
Deep Learning ◽  
Cross Validation ◽  
Pectoral Muscle ◽  
Training Data ◽  
Dice Similarity Coefficient ◽  
Detection Accuracy ◽  
Pectoral Muscle Detection ◽  
Fold Cross Validation

Abstract Background: The purpose of this study was to propose a deep learning-based method for automated detection of the pectoral muscle, in order to reduce misdetection in a computer-aided diagnosis (CAD) system for diagnosing breast cancer in mammography. This study also aimed to assess the performance of the deep learning method for pectoral muscle detection by comparing it to an image processing-based method using the random sample consensus (RANSAC) algorithm. Methods: Using the 322 images in the Mammographic Image Analysis Society (MIAS) database, the pectoral muscle detection model was trained with the U-Net architecture. Of the total data, 80% was allocated as training data and 20% was allocated as test data, and the performance of the deep learning model was tested by 5-fold cross validation. Results: The image processing-based method for pectoral muscle detection using RANSAC showed 92% detection accuracy. Using the 5-fold cross validation, the deep learning-based method showed a mean sensitivity of 95.55%, mean specificity of 99.88%, mean accuracy of 99.67%, and mean Dice similarity coefficient (DSC) of 95.88%. Conclusions: The proposed deep learning-based method of pectoral muscle detection performed better than an existing image processing-based method. In the future, by collecting data from various medical institutions and devices to further train the model and improve its reliability, we expect that this model could greatly reduce misdetection rates by CAD systems for breast cancer diagnosis.

scholarly journals Deep Learning to Predict EGFR Mutation and PD-L1 Expression Status in Non-Small-Cell Lung Cancer on Computed Tomography Images

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Chengdi Wang ◽  
Xiuyuan Xu ◽  
Jun Shao ◽  
Kai Zhou ◽  
Kefu Zhao ◽  
...  
Keyword(s):  
Neural Network ◽  
Lung Cancer ◽  
Deep Learning ◽  
Prognostic Model ◽  
Egfr Mutation ◽  
Small Cell ◽  
Small Cell Lung ◽  
Lung Cancer Patients ◽  
Deep Learning Features ◽  
Expression Status

Objective. The detection of epidermal growth factor receptor (EGFR) mutation and programmed death ligand-1 (PD-L1) expression status is crucial to determine the treatment strategies for patients with non-small-cell lung cancer (NSCLC). Recently, the rapid development of radiomics including but not limited to deep learning techniques has indicated the potential role of medical images in the diagnosis and treatment of diseases. Methods. Eligible patients diagnosed/treated at the West China Hospital of Sichuan University from January 2013 to April 2019 were identified retrospectively. The preoperative CT images were obtained, as well as the gene status regarding EGFR mutation and PD-L1 expression. Tumor region of interest (ROI) was delineated manually by experienced respiratory specialists. We used 3D convolutional neural network (CNN) with ROI information as input to construct a classification model and established a prognostic model combining deep learning features and clinical features to stratify survival risk of lung cancer patients. Results. The whole cohort (N = 1262) was divided into a training set (N = 882, 70%), validation set (N = 125, 10%), and test set (N = 255, 20%). We used a 3D convolutional neural network (CNN) to construct a prediction model, with AUCs of 0.96 (95% CI: 0.94–0.98), 0.80 (95% CI: 0.72–0.88), and 0.73 (95% CI: 0.63–0.83) in the training, validation, and test cohorts, respectively. The combined prognostic model showed a good performance on survival prediction in NSCLC patients (C-index: 0.71). Conclusion. In this study, a noninvasive and effective model was proposed to predict EGFR mutation and PD-L1 expression status as a clinical decision support tool. Additionally, the combination of deep learning features with clinical features demonstrated great stratification capabilities in the prognostic model. Our team would continue to explore the application of imaging markers for treatment selection of lung cancer patients.

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