scholarly journals An Ensembled Deep Learning Model Outperforms Human Experts in Diagnosing Biliary Atresia from Sonographic Gallbladder Images

2020 ◽  
Author(s):  
Wenying Zhou ◽  
Yang Yang ◽  
Cheng Yu ◽  
Juxian Liu ◽  
Xingxing Duan ◽  
...  
Keyword(s):  
Deep Learning ◽  
Biliary Atresia ◽  
External Validation ◽  
Learning Model ◽  
Video Sequences ◽  
Validation Dataset ◽  
Patient Level ◽  
Small Set ◽  
Level Performance ◽  
Deep Learning Model

AbstractIt is still difficult to make accurate diagnosis of biliary atresia (BA) by sonographic gallbladder images particularly in rural area lacking relevant expertise. To provide an artificial intelligence solution to help diagnose BA based on sonographic gallbladder images, an ensembled deep learning model was developed based on a small set of sonographic images. The model yielded a patient-level sensitivity 93.1% and specificity 93.9% (with AUROC 0.956) on the multi-center external validation dataset, superior to that of human experts. With the help of the model, the performance of human experts with various levels would be improved further. Moreover, the diagnosis based on smartphone photos of sonographic gallbladder images through a smartphone app and based on video sequences by the model still yielded expert-level performance. Our study provides a deep learning solution to help radiologists improve BA diagnosis in various clinical application scenarios, particularly in rural and undeveloped regions with limited expertise.

scholarly journals Ensembled deep learning model outperforms human experts in diagnosing biliary atresia from sonographic gallbladder images

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Wenying Zhou ◽  
Yang Yang ◽  
Cheng Yu ◽  
Juxian Liu ◽  
Xingxing Duan ◽  
...  
Keyword(s):  
Deep Learning ◽  
Biliary Atresia ◽  
Operating Characteristic ◽  
Characteristic Curve ◽  
External Validation ◽  
Learning Model ◽  
Video Sequences ◽  
Validation Dataset ◽  
Patient Level ◽  
Deep Learning Model

AbstractIt is still challenging to make accurate diagnosis of biliary atresia (BA) with sonographic gallbladder images particularly in rural area without relevant expertise. To help diagnose BA based on sonographic gallbladder images, an ensembled deep learning model is developed. The model yields a patient-level sensitivity 93.1% and specificity 93.9% [with areas under the receiver operating characteristic curve of 0.956 (95% confidence interval: 0.928-0.977)] on the multi-center external validation dataset, superior to that of human experts. With the help of the model, the performances of human experts with various levels are improved. Moreover, the diagnosis based on smartphone photos of sonographic gallbladder images through a smartphone app and based on video sequences by the model still yields expert-level performances. The ensembled deep learning model in this study provides a solution to help radiologists improve the diagnosis of BA in various clinical application scenarios, particularly in rural and undeveloped regions with limited expertise.

scholarly journals DeepHBV: A deep learning model to predict hepatitis B virus (HBV) integration sites.

2021 ◽  
Author(s):  
Canbiao Wu ◽  
Xiaofang Guo ◽  
Mengyuan Li ◽  
Xiayu Fu ◽  
Zeliang Hou ◽  
...  
Keyword(s):  
Deep Learning ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Binding Sites ◽  
Learning Model ◽  
Validation Dataset ◽  
B Virus ◽  
Integration Sites ◽  
Deep Learning Model ◽  
Pan Cancer

Hepatitis B virus (HBV) is one of the main causes for viral hepatitis and liver cancer. Previous studies showed HBV can integrate into host genome and further promote malignant transformation. In this study, we developed an attention-based deep learning model DeepHBV to predict HBV integration sites by learning local genomic features automatically. We trained and tested DeepHBV using the HBV integration sites data from dsVIS database. Initially, DeepHBV showed AUROC of 0.6363 and AUPR of 0.5471 on the dataset. Adding repeat peaks and TCGA Pan Cancer peaks can significantly improve the model performance, with an AUROC of 0.8378 and 0.9430 and an AUPR of 0.7535 and 0.9310, respectively. On independent validation dataset of HBV integration sites from VISDB, DeepHBV with HBV integration sequences plus TCGA Pan Cancer (AUROC of 0.7603 and AUPR of 0.6189) performed better than HBV integration sequences plus repeat peaks (AUROC of 0.6657 and AUPR of 0.5737). Next, we found the transcriptional factor binding sites (TFBS) were significantly enriched near genomic positions that were paid attention to by convolution neural network. The binding sites of AR-halfsite, Arnt, Atf1, bHLHE40, bHLHE41, BMAL1, CLOCK, c-Myc, COUP-TFII, E2A, EBF1, Erra and Foxo3 were highlighted by DeepHBV attention mechanism in both dsVIS dataset and VISDB dataset, revealing the HBV integration preference. In summary, DeepHBV is a robust and explainable deep learning model not only for the prediction of HBV integration sites but also for further mechanism study of HBV induced cancer.

scholarly journals Preoperative CT-Based Deep Learning Model for Predicting Risk Stratification in Patients With Gastrointestinal Stromal Tumors

2021 ◽  
Vol 11 ◽  
Author(s):  
Bing Kang ◽  
Xianshun Yuan ◽  
Hexiang Wang ◽  
Songnan Qin ◽  
Xuelin Song ◽  
...  
Keyword(s):  
Deep Learning ◽  
Risk Stratification ◽  
Gastrointestinal Stromal Tumors ◽  
External Validation ◽  
Learning Model ◽  
Ct Images ◽  
Stromal Tumors ◽  
Contrast Enhanced Ct ◽  
Malignant Gists ◽  
Deep Learning Model

ObjectiveTo develop and evaluate a deep learning model (DLM) for predicting the risk stratification of gastrointestinal stromal tumors (GISTs).MethodsPreoperative contrast-enhanced CT images of 733 patients with GISTs were retrospectively obtained from two centers between January 2011 and June 2020. The datasets were split into training (n = 241), testing (n = 104), and external validation cohorts (n = 388). A DLM for predicting the risk stratification of GISTs was developed using a convolutional neural network and evaluated in the testing and external validation cohorts. The performance of the DLM was compared with that of radiomics model by using the area under the receiver operating characteristic curves (AUROCs) and the Obuchowski index. The attention area of the DLM was visualized as a heatmap by gradient-weighted class activation mapping.ResultsIn the testing cohort, the DLM had AUROCs of 0.90 (95% confidence interval [CI]: 0.84, 0.96), 0.80 (95% CI: 0.72, 0.88), and 0.89 (95% CI: 0.83, 0.95) for low-malignant, intermediate-malignant, and high-malignant GISTs, respectively. In the external validation cohort, the AUROCs of the DLM were 0.87 (95% CI: 0.83, 0.91), 0.64 (95% CI: 0.60, 0.68), and 0.85 (95% CI: 0.81, 0.89) for low-malignant, intermediate-malignant, and high-malignant GISTs, respectively. The DLM (Obuchowski index: training, 0.84; external validation, 0.79) outperformed the radiomics model (Obuchowski index: training, 0.77; external validation, 0.77) for predicting risk stratification of GISTs. The relevant subregions were successfully highlighted with attention heatmap on the CT images for further clinical review.ConclusionThe DLM showed good performance for predicting the risk stratification of GISTs using CT images and achieved better performance than that of radiomics model.

scholarly journals Predicting Tumor Cell Response to Synergistic Drug Combinations Using a Novel Simplified Deep Learning Model

2020 ◽  
Author(s):  
Heming Zhang ◽  
Jiarui Feng ◽  
Amanda Zeng ◽  
Philip Payne ◽  
Fuhai Li
Keyword(s):  
Deep Learning ◽  
Signaling Pathways ◽  
Drug Combination ◽  
Computational Models ◽  
Learning Model ◽  
Drug Combinations ◽  
Small Set ◽  
Novel Drug ◽  
Deep Learning Model ◽  
Synergistic Drug Combinations

AbstractDrug combinations targeting multiple targets/pathways are believed to be able to reduce drug resistance. Computational models are essential for novel drug combination discovery. In this study, we proposed a new simplified deep learning model, DeepSignalingSynergy, for drug combination prediction. Compared with existing models that use a large number of chemical-structure and genomics features in densely connected layers, we built the model on a small set of cancer signaling pathways, which can mimic the integration of multi-omics data and drug target/mechanism in a more biological meaningful and explainable manner. The evaluation results of the model using the NCI ALMANAC drug combination screening data indicated the feasibility of drug combination prediction using a small set of signaling pathways. Interestingly, the model analysis suggested the importance of heterogeneity of the 46 signaling pathways, which indicates that some new signaling pathways should be targeted to discover novel synergistic drug combinations.

scholarly journals Feasibility of Automated Deep Learning Design for Medical Image Classification by Healthcare Professionals with Limited Coding Experience

2019 ◽  
Author(s):  
Livia Faes ◽  
Siegfried K. Wagner ◽  
Dun Jack Fu ◽  
Xiaoxuan Liu ◽  
Edward Korot ◽  
...  
Keyword(s):  
Deep Learning ◽  
Medical Image ◽  
Healthcare Professionals ◽  
External Validation ◽  
Learning Model ◽  
Discriminative Performance ◽  
Classification Tasks ◽  
Medical University ◽  
Deep Learning Model ◽  
Diagnostic Properties

ABSTRACTDeep learning has huge potential to transform healthcare. However, significant expertise is required to train such models and this is a significant blocker for their translation into clinical practice. In this study, we therefore sought to evaluate the use of automated deep learning software to develop medical image diagnostic classifiers by healthcare professionals with limited coding – and no deep learning – expertise.We used five publicly available open-source datasets: (i) retinal fundus images (MESSIDOR); (ii) optical coherence tomography (OCT) images (Guangzhou Medical University/Shiley Eye Institute, Version 3); (iii) images of skin lesions (Human against Machine (HAM)10000) and (iv) both paediatric and adult chest X-ray (CXR) images (Guangzhou Medical University/Shiley Eye Institute, Version 3 and the National Institute of Health (NIH)14 dataset respectively) to separately feed into a neural architecture search framework that automatically developed a deep learning architecture to classify common diseases. Sensitivity (recall), specificity and positive predictive value (precision) were used to evaluate the diagnostic properties of the models. The discriminative performance was assessed using the area under the precision recall curve (AUPRC). In the case of the deep learning model developed on a subset of the HAM10000 dataset, we performed external validation using the Edinburgh Dermofit Library dataset.Diagnostic properties and discriminative performance from internal validations were high in the binary classification tasks (range: sensitivity of 73.3-97.0%, specificity of 67-100% and AUPRC of 0.87-1). In the multiple classification tasks, the diagnostic properties ranged from 38-100% for sensitivity and 67-100% for specificity. The discriminative performance in terms of AUPRC ranged from 0.57 to 1 in the five automated deep learning models. In an external validation using the Edinburgh Dermofit Library dataset, the automated deep learning model showed an AUPRC of 0.47, with a sensitivity of 49% and a positive predictive value of 52%. The quality of the open-access datasets used in this study (including the lack of information about patient flow and demographics) and the absence of measurement for precision, such as confidence intervals, constituted the major limitation of this study.All models, except for the automated deep learning model trained on the multi-label classification task of the NIH CXR14 dataset, showed comparable discriminative performance and diagnostic properties to state-of-the-art performing deep learning algorithms. The performance in the external validation study was low. The availability of automated deep learning may become a cornerstone for the democratization of sophisticated algorithmic modelling in healthcare as it allows the derivation of classification models without requiring a deep understanding of the mathematical, statistical and programming principles. Future studies should compare several application programming interfaces on thoroughly curated datasets.

scholarly journals A deep learning model for detection of cervical spinal cord compression in MRI scans

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zamir Merali ◽  
Justin Z. Wang ◽  
Jetan H. Badhiwala ◽  
Christopher D. Witiw ◽  
Jefferson R. Wilson ◽  
...  
Keyword(s):  
Spinal Cord ◽  
Deep Learning ◽  
Spinal Cord Compression ◽  
Cervical Spinal Cord ◽  
Learning Model ◽  
Cord Compression ◽  
Validation Dataset ◽  
Imaging Data ◽  
Mri Scans ◽  
Deep Learning Model

AbstractMagnetic Resonance Imaging (MRI) evidence of spinal cord compression plays a central role in the diagnosis of degenerative cervical myelopathy (DCM). There is growing recognition that deep learning models may assist in addressing the increasing volume of medical imaging data and provide initial interpretation of images gathered in a primary-care setting. We aimed to develop and validate a deep learning model for detection of cervical spinal cord compression in MRI scans. Patients undergoing surgery for DCM as a part of the AO Spine CSM-NA or CSM-I prospective cohort studies were included in our study. Patients were divided into a training/validation or holdout dataset. Images were labelled by two specialist physicians. We trained a deep convolutional neural network using images from the training/validation dataset and assessed model performance on the holdout dataset. The training/validation cohort included 201 patients with 6588 images and the holdout dataset included 88 patients with 2991 images. On the holdout dataset the deep learning model achieved an overall AUC of 0.94, sensitivity of 0.88, specificity of 0.89, and f1-score of 0.82. This model could improve the efficiency and objectivity of the interpretation of cervical spine MRI scans.

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