Diagnostic evaluation of a deep learning model for optical diagnosis of colorectal cancer.
Ontology highlight
ABSTRACT:
SUBMITTER: Zhou D
PROVIDER: S-EPMC7289893 | biostudies-literature | 2020 Jun
REPOSITORIES: biostudies-literature
Publications
Diagnostic evaluation of a deep learning model for optical diagnosis of colorectal cancer.
Zhou Dejun D Tian Fei F Tian Xiangdong X Sun Lin L Huang Xianghui X Zhao Feng F Zhou Nan N Chen Zuoyu Z Zhang Qiang Q Yang Meng M Yang Yichen Y Guo Xuexi X Li Zhibin Z Liu Jia J Wang Jiefu J Wang Junfeng J Wang Bangmao B Zhang Guoliang G Sun Baocun B Zhang Wei W Kong Dalu D Chen Kexin K Li Xiangchun X
Nature communications 20200611 1
Colonoscopy is commonly used to screen for colorectal cancer (CRC). We develop a deep learning model called CRCNet for optical diagnosis of CRC by training on 464,105 images from 12,179 patients and test its performance on 2263 patients from three independent datasets. At the patient-level, CRCNet achieves an area under the precision-recall curve (AUPRC) of 0.882 (95% CI: 0.828-0.931), 0.874 (0.820-0.926) and 0.867 (0.795-0.923). CRCNet exceeds average endoscopists performance on recall rate acr ...[more]
Similar Datasets
Project description:BackgroundAccurate assessment of the percentage total body surface area (%TBSA) of burn wounds is crucial in the management of burn patients. The resuscitation fluid and nutritional needs of burn patients, their need for intensive unit care, and probability of mortality are all directly related to %TBSA. It is difficult to estimate a burn area of irregular shape by inspection. Many articles have reported discrepancies in estimating %TBSA by different doctors.ObjectiveWe propose a method, based on deep learning, for burn wound detection, segmentation, and calculation of %TBSA on a pixel-to-pixel basis.MethodsA 2-step procedure was used to convert burn wound diagnosis into %TBSA. In the first step, images of burn wounds were collected from medical records and labeled by burn surgeons, and the data set was then input into 2 deep learning architectures, U-Net and Mask R-CNN, each configured with 2 different backbones, to segment the burn wounds. In the second step, we collected and labeled images of hands to create another data set, which was also input into U-Net and Mask R-CNN to segment the hands. The %TBSA of burn wounds was then calculated by comparing the pixels of mask areas on images of the burn wound and hand of the same patient according to the rule of hand, which states that one's hand accounts for 0.8% of TBSA.ResultsA total of 2591 images of burn wounds were collected and labeled to form the burn wound data set. The data set was randomly split into training, validation, and testing sets in a ratio of 8:1:1. Four hundred images of volar hands were collected and labeled to form the hand data set, which was also split into 3 sets using the same method. For the images of burn wounds, Mask R-CNN with ResNet101 had the best segmentation result with a Dice coefficient (DC) of 0.9496, while U-Net with ResNet101 had a DC of 0.8545. For the hand images, U-Net and Mask R-CNN had similar performance with DC values of 0.9920 and 0.9910, respectively. Lastly, we conducted a test diagnosis in a burn patient. Mask R-CNN with ResNet101 had on average less deviation (0.115% TBSA) from the ground truth than burn surgeons.ConclusionsThis is one of the first studies to diagnose all depths of burn wounds and convert the segmentation results into %TBSA using different deep learning models. We aimed to assist medical staff in estimating burn size more accurately, thereby helping to provide precise care to burn victims.
| S-EPMC8686480 | biostudies-literature
Project description:Deep learning facilitates complex medical data analysis and is increasingly being explored in colorectal cancer diagnostics. However, the training cost of the deep learning model limits its real-world medical utility. In this study, we present a composite network that combines deep learning and unsupervised K-means clustering algorithm (RK-net) for automatic processing of medical images. RK-net was more efficient in image refinement compared with manual screening and annotation. The training of a deep learning model for colorectal cancer diagnosis was accelerated by two times with utilization of RK-net-processed images. Better performance was observed in training loss and accuracy achievement as well. RK-net could be useful to refine medical images of the ever-expanding quantity and assist in subsequent construction of the artificial intelligence model.
| S-EPMC9762730 | biostudies-literature
Project description:Prior reports have shown optical coherence tomography (OCT) can differentiate normal colonic mucosa from neoplasia, potentially offering an alternative technique to endoscopic biopsy - the current gold-standard colorectal cancer screening and surveillance modality. To help clinical translation limited by processing the large volume of generated data, we designed a deep learning-based pattern recognition (PR) OCT system that automates image processing and provides accurate diagnosis potentially in real-time. Method: OCT is an emerging imaging technique to obtain 3-dimensional (3D) "optical biopsies" of biological samples with high resolution. We designed a convolutional neural network to capture the structure patterns in human colon OCT images. The network is trained and tested using around 26,000 OCT images acquired from 20 tumor areas, 16 benign areas, and 6 other abnormal areas. Results: The trained network successfully detected patterns that identify normal and neoplastic colorectal tissue. Experimental diagnoses predicted by the PR-OCT system were compared to the known histologic findings and quantitatively evaluated. A sensitivity of 100% and specificity of 99.7% can be reached. Further, the area under the receiver operating characteristic (ROC) curves (AUC) of 0.998 is achieved. Conclusions: Our results demonstrate that PR-OCT can be used to give an accurate real-time computer-aided diagnosis of colonic neoplastic mucosa. Future development of this system as an "optical biopsy" tool to assist doctors in real-time for early mucosal neoplasms screening and treatment evaluation following initial oncologic therapy is planned.
| S-EPMC7052898 | biostudies-literature
Project description:We aimed to develop a computer-aided diagnostic system (CAD) for predicting colorectal polyp histology using deep-learning technology and to validate its performance. Near-focus narrow-band imaging (NBI) pictures of colorectal polyps were retrieved from the database of our institution. Of these, 12480 image patches of 624 polyps were used as a training set to develop the CAD. The CAD performance was validated with two test datasets of 545 polyps. Polyps were classified into three histological groups: serrated polyp (SP), benign adenoma (BA)/mucosal or superficial submucosal cancer (MSMC), and deep submucosal cancer (DSMC). The overall kappa value measuring the agreement between the true polyp histology and the expected histology by the CAD was 0.614-0.642, which was higher than that of trainees (n = 6, endoscopists with experience of 100 NBI colonoscopies in <6 months; 0.368-0.401) and almost comparable with that of the experts (n = 3, endoscopists with experience of 2,500 NBI colonoscopies in ≥5 years) (0.649-0.735). The areas under the receiver operating curves for CAD were 0.93-0.95, 0.86-0.89, and 0.89-0.91 for SP, BA/MSMC, and DSMC, respectively. The overall diagnostic accuracy of the CAD was 81.3-82.4%, which was significantly higher than that of the trainees (63.8-71.8%, P < 0.01) and comparable with that of experts (82.4-87.3%). The kappa value and diagnostic accuracies of the trainees improved with CAD assistance: that is, the kappa value increased from 0.368 to 0.655, and the overall diagnostic accuracy increased from 63.8-71.8% to 82.7-84.2%. CAD using a deep-learning model can accurately assess polyp histology and may facilitate the diagnosis of colorectal polyps by endoscopists.
| S-EPMC6949236 | biostudies-literature
Project description:The aim of this study was to develop a novel deep learning (DL) model without requiring large-annotated training datasets for detecting pancreatic cancer (PC) using computed tomography (CT) images. This retrospective diagnostic study was conducted using CT images collected from 2004 and 2019 from 4287 patients diagnosed with PC. We proposed a self-supervised learning algorithm (pseudo-lesion segmentation (PS)) for PC classification, which was trained with and without PS and validated on randomly divided training and validation sets. We further performed cross-racial external validation using open-access CT images from 361 patients. For internal validation, the accuracy and sensitivity for PC classification were 94.3% (92.8-95.4%) and 92.5% (90.0-94.4%), and 95.7% (94.5-96.7%) and 99.3 (98.4-99.7%) for the convolutional neural network (CNN) and transformer-based DL models (both with PS), respectively. Implementing PS on a small-sized training dataset (randomly sampled 10%) increased accuracy by 20.5% and sensitivity by 37.0%. For external validation, the accuracy and sensitivity were 82.5% (78.3-86.1%) and 81.7% (77.3-85.4%) and 87.8% (84.0-90.8%) and 86.5% (82.3-89.8%) for the CNN and transformer-based DL models (both with PS), respectively. PS self-supervised learning can increase DL-based PC classification performance, reliability, and robustness of the model for unseen, and even small, datasets. The proposed DL model is potentially useful for PC diagnosis.
| S-EPMC10340780 | biostudies-literature
Project description:BackgroundStratification of DNA mismatch repair (MMR) status in patients with colorectal cancer (CRC) enables individual clinical treatment decision making. The present study aimed to develop and validate a deep learning (DL) model based on the pre-treatment CT images for predicting MMR status in CRC.Methods1812 eligible participants (training cohort: n = 1124; internal validation cohort: n = 482; external validation cohort: n = 206) with CRC were enrolled from two institutions. All pretherapeutic CT images from three dimensions were trained by the ResNet101, then integrated by Gaussian process regression (GPR) to develop a full-automatic DL model for MMR status prediction. The predictive performance of the DL model was evaluated using the area under the receiver operating characteristic curve (AUC) and then tested in the internal and external validation cohorts. Additionally, the participants from institution 1 were sub-grouped by various clinical factors for subgroup analysis, then the predictive performance of the DL model for identifying MMR status between participants in different groups were compared.ResultsThe full-automatic DL model was established in the training cohort to stratify the MMR status, which presented promising discriminative ability with the AUCs of 0.986 (95% CI 0.971-1.000) in the internal validation cohort and 0.915 (95% CI 0.870-0.960) in the external validation cohort. In addition, the subgroup analysis based on the thickness of CT images, clinical T and N stages, gender, the longest diameter, and the location of tumors revealed that the DL model showed similar satisfying prediction performance.ConclusionsThe DL model may potentially serve as a noninvasive tool to facilitate the pre-treatment individualized prediction of MMR status in patients with CRC, which could promote the personalized clinical-making decision.
| S-EPMC10035255 | biostudies-literature
Project description:Colorectal cancer (CRC) is a common cancer with a high mortality rate and a rising incidence rate in the developed world. Molecular profiling techniques have been used to better understand the variability between tumors and disease models such as cell lines. To maximize the translatability and clinical relevance of in vitro studies, the selection of optimal cancer models is imperative. We have developed a deep learning-based method to measure the similarity between CRC tumors and disease models such as cancer cell lines. Our method efficiently leverages multiomics data sets containing copy number alterations, gene expression, and point mutations and learns latent factors that describe data in lower dimensions. These latent factors represent the patterns that are clinically relevant and explain the variability of molecular profiles across tumors and cell lines. Using these, we propose refined CRC subtypes and provide best-matching cell lines to different subtypes. These findings are relevant to patient stratification and selection of cell lines for early-stage drug discovery pipelines, biomarker discovery, and target identification.
| S-EPMC6892438 | biostudies-literature
Project description:Deep learning (DL) has been widely investigated in breast ultrasound (US) for distinguishing between benign and malignant breast masses. This systematic review of test diagnosis aims to examine the accuracy of DL, compared to human readers, for the diagnosis of breast cancer in the US under clinical settings. Our literature search included records from databases including PubMed, Embase, Scopus, and Cochrane Library. Test accuracy outcomes were synthesized to compare the diagnostic performance of DL and human readers as well as to evaluate the assistive role of DL to human readers. A total of 16 studies involving 9238 female participants were included. There were no prospective studies comparing the test accuracy of DL versus human readers in clinical workflows. Diagnostic test results varied across the included studies. In 14 studies employing standalone DL systems, DL showed significantly lower sensitivities in 5 studies with comparable specificities and outperformed human readers at higher specificities in another 4 studies; in the remaining studies, DL models and human readers showed equivalent test outcomes. In 12 studies that assessed assistive DL systems, no studies proved the assistive role of DL in the overall diagnostic performance of human readers. Current evidence is insufficient to conclude that DL outperforms human readers or enhances the accuracy of diagnostic breast US in a clinical setting. Standardization of study methodologies is required to improve the reproducibility and generalizability of DL research, which will aid in clinical translation and application.
| S-EPMC10821881 | biostudies-literature
Project description:Automated medical data analysis demonstrated a significant role in modern medicine, and cancer diagnosis/prognosis to achieve highly reliable and generalizable systems. In this study, an automated breast cancer screening method in ultrasound imaging is proposed. A convolutional deep autoencoder model is presented for simultaneous segmentation and radiomic extraction. The model segments the breast lesions while concurrently extracting radiomic features. With our deep model, we perform breast lesion segmentation, which is linked to low-dimensional deep-radiomic extraction (four features). Similarly, we used high dimensional conventional imaging throughputs and applied spectral embedding techniques to reduce its size from 354 to 12 radiomics. A total of 780 ultrasound images-437 benign, 210, malignant, and 133 normal-were used to train and validate the models in this study. To diagnose malignant lesions, we have performed training, hyperparameter tuning, cross-validation, and testing with a random forest model. This resulted in a binary classification accuracy of 78.5% (65.1-84.1%) for the maximal (full multivariate) cross-validated model for a combination of radiomic groups.
| S-EPMC9179519 | biostudies-literature
Project description:In this paper, we first describe the basics of the field of cancer diagnosis, which includes steps of cancer diagnosis followed by the typical classification methods used by doctors, providing a historical idea of cancer classification techniques to the readers. These methods include Asymmetry, Border, Color and Diameter (ABCD) method, seven-point detection method, Menzies method, and pattern analysis. They are used regularly by doctors for cancer diagnosis, although they are not considered very efficient for obtaining better performance. Moreover, considering all types of audience, the basic evaluation criteria are also discussed. The criteria include the receiver operating characteristic curve (ROC curve), Area under the ROC curve (AUC), F1 score, accuracy, specificity, sensitivity, precision, dice-coefficient, average accuracy, and Jaccard index. Previously used methods are considered inefficient, asking for better and smarter methods for cancer diagnosis. Artificial intelligence and cancer diagnosis are gaining attention as a way to define better diagnostic tools. In particular, deep neural networks can be successfully used for intelligent image analysis. The basic framework of how this machine learning works on medical imaging is provided in this study, i.e., pre-processing, image segmentation and post-processing. The second part of this manuscript describes the different deep learning techniques, such as convolutional neural networks (CNNs), generative adversarial models (GANs), deep autoencoders (DANs), restricted Boltzmann's machine (RBM), stacked autoencoders (SAE), convolutional autoencoders (CAE), recurrent neural networks (RNNs), long short-term memory (LTSM), multi-scale convolutional neural network (M-CNN), multi-instance learning convolutional neural network (MIL-CNN). For each technique, we provide Python codes, to allow interested readers to experiment with the cited algorithms on their own diagnostic problems. The third part of this manuscript compiles the successfully applied deep learning models for different types of cancers. Considering the length of the manuscript, we restrict ourselves to the discussion of breast cancer, lung cancer, brain cancer, and skin cancer. The purpose of this bibliographic review is to provide researchers opting to work in implementing deep learning and artificial neural networks for cancer diagnosis a knowledge from scratch of the state-of-the-art achievements.
| S-EPMC6770116 | biostudies-literature