Dataset Information

Automatic deep learning-based colorectal adenoma detection system and its similarities with pathologists.

ABSTRACT: OBJECTIVES:The microscopic evaluation of slides has been gradually moving towards all digital in recent years, leading to the possibility for computer-aided diagnosis. It is worthwhile to know the similarities between deep learning models and pathologists before we put them into practical scenarios. The simple criteria of colorectal adenoma diagnosis make it to be a perfect testbed for this study. DESIGN:The deep learning model was trained by 177 accurately labelled training slides (156 with adenoma). The detailed labelling was performed on a self-developed annotation system based on iPad. We built the model based on DeepLab v2 with ResNet-34. The model performance was tested on 194 test slides and compared with five pathologists. Furthermore, the generalisation ability of the learning model was tested by extra 168 slides (111 with adenoma) collected from two other hospitals. RESULTS:The deep learning model achieved an area under the curve of 0.92 and obtained a slide-level accuracy of over 90% on slides from two other hospitals. The performance was on par with the performance of experienced pathologists, exceeding the average pathologist. By investigating the feature maps and cases misdiagnosed by the model, we found the concordance of thinking process in diagnosis between the deep learning model and pathologists. CONCLUSIONS:The deep learning model for colorectal adenoma diagnosis is quite similar to pathologists. It is on-par with pathologists' performance, makes similar mistakes and learns rational reasoning logics. Meanwhile, it obtains high accuracy on slides collected from different hospitals with significant staining configuration variations.

SUBMITTER: Song Z

PROVIDER: S-EPMC7485250 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Automatic deep learning-based colorectal adenoma detection system and its similarities with pathologists.

Song Zhigang Z Yu Chunkai C Zou Shuangmei S Wang Wenmiao W Huang Yong Y Ding Xiaohui X Liu Jinhong J Shao Liwei L Yuan Jing J Gou Xiangnan X Jin Wei W Wang Zhanbo Z Chen Xin X Chen Huang H Liu Cancheng C Xu Gang G Sun Zhuo Z Ku Calvin C Zhang Yongqiang Y Dong Xianghui X Wang Shuhao S Xu Wei W Lv Ning N Shi Huaiyin H

BMJ open 20200910 9

<h4>Objectives</h4>The microscopic evaluation of slides has been gradually moving towards all digital in recent years, leading to the possibility for computer-aided diagnosis. It is worthwhile to know the similarities between deep learning models and pathologists before we put them into practical scenarios. The simple criteria of colorectal adenoma diagnosis make it to be a perfect testbed for this study.<h4>Design</h4>The deep learning model was trained by 177 accurately labelled training slide ...[more]

PMID: 32912980

Similar Datasets

Project description:Rib fracture detection is time-consuming and demanding work for radiologists. This study aimed to introduce a novel rib fracture detection system based on deep learning which can help radiologists to diagnose rib fractures in chest computer tomography (CT) images conveniently and accurately. A total of 1707 patients were included in this study from a single center. We developed a novel rib fracture detection system on chest CT using a three-step algorithm. According to the examination time, 1507, 100 and 100 patients were allocated to the training set, the validation set and the testing set, respectively. Free Response ROC analysis was performed to evaluate the sensitivity and false positivity of the deep learning algorithm. Precision, recall, F1-score, negative predictive value (NPV) and detection and diagnosis were selected as evaluation metrics to compare the diagnostic efficiency of this system with radiologists. The radiologist-only study was used as a benchmark and the radiologist-model collaboration study was evaluated to assess the model's clinical applicability. A total of 50,170,399 blocks (fracture blocks, 91,574; normal blocks, 50,078,825) were labelled for training. The F1-score of the Rib Fracture Detection System was 0.890 and the precision, recall and NPV values were 0.869, 0.913 and 0.969, respectively. By interacting with this detection system, the F1-score of the junior and the experienced radiologists had improved from 0.796 to 0.925 and 0.889 to 0.970, respectively; the recall scores had increased from 0.693 to 0.920 and 0.853 to 0.972, respectively. On average, the diagnosis time of radiologist assisted with this detection system was reduced by 65.3 s. The constructed Rib Fracture Detection System has a comparable performance with the experienced radiologist and is readily available to automatically detect rib fracture in the clinical setting with high efficacy, which could reduce diagnosis time and radiologists' workload in the clinical practice.

Project description:Brief fragments of sleep shorter than 15 s are defined as microsleep episodes (MSEs), often subjectively perceived as sleepiness. Their main characteristic is a slowing in frequency in the electroencephalogram (EEG), similar to stage N1 sleep according to standard criteria. The maintenance of wakefulness test (MWT) is often used in a clinical setting to assess vigilance. Scoring of the MWT in most sleep-wake centers is limited to classical definition of sleep (30 s epochs), and MSEs are mostly not considered in the absence of established scoring criteria defining MSEs but also because of the laborious work. We aimed for automatic detection of MSEs with machine learning, i.e., with deep learning based on raw EEG and EOG data as input. We analyzed MWT data of 76 patients. Experts visually scored wakefulness, and according to recently developed scoring criteria MSEs, microsleep episode candidates (MSEc), and episodes of drowsiness (ED). We implemented segmentation algorithms based on convolutional neural networks (CNNs) and a combination of a CNN with a long-short term memory (LSTM) network. A LSTM network is a type of a recurrent neural network which has a memory for past events and takes them into account. Data of 53 patients were used for training of the classifiers, 12 for validation and 11 for testing. Our algorithms showed a good performance close to human experts. The detection was very good for wakefulness and MSEs and poor for MSEc and ED, similar to the low inter-expert reliability for these borderline segments. We performed a visualization of the internal representation of the data by the artificial neuronal network performing best using t-distributed stochastic neighbor embedding (t-SNE). Visualization revealed that MSEs and wakefulness were mostly separable, though not entirely, and MSEc and ED largely intersected with the two main classes. We provide a proof of principle that it is feasible to reliably detect MSEs with deep neuronal networks based on raw EEG and EOG data with a performance close to that of human experts. The code of the algorithms (https://github.com/alexander-malafeev/microsleep-detection) and data (https://zenodo.org/record/3251716) are available.

Project description:BackgroundMedication errors account for a large proportion of all medical errors. In most homes, patients take a variety of medications for a long period. However, medication errors frequently occur because patients often throw away the containers of their medications.ObjectiveWe proposed a deep learning-based system for reducing medication errors by accurately identifying prescription pills. Given the pill images, our system located the pills in the respective pill databases in South Korea and the United States.MethodsWe organized the system into a pill recognition step and pill retrieval step, and we applied deep learning models to train not only images of the pill but also imprinted characters. In the pill recognition step, there are 3 modules that recognize the 3 features of pills and their imprints separately and correct the recognized imprint to fit the actual data. We adopted image classification and text detection models for the feature and imprint recognition modules, respectively. In the imprint correction module, we introduced a language model for the first time in the pill identification system and proposed a novel coordinate encoding technique for effective correction in the language model. We identified pills using similarity scores of pill characteristics with those in the database.ResultsWe collected the open pill database from South Korea and the United States in May 2022. We used a total of 24,404 pill images in our experiments. The experimental results show that the predicted top-1 candidates achieve accuracy levels of 85.6% (South Korea) and 74.5% (United States) for the types of pills not trained on 2 different databases (South Korea and the United States). Furthermore, the predicted top-1 candidate accuracy of our system was 78% with consumer-granted images, which was achieved by training only 1 image per pill. The results demonstrate that our system could identify and retrieve new pills without additional model updates. Finally, we confirmed through an ablation study that the language model that we emphasized significantly improves the pill identification ability of the system.ConclusionsOur study proposes the possibility of reducing medical errors by showing that the introduction of artificial intelligence can identify numerous pills with high precision in real time. Our study suggests that the proposed system can reduce patients' misuse of medications and help medical staff focus on higher-level tasks by simplifying time-consuming lower-level tasks such as pill identification.

Dataset Information

Automatic deep learning-based colorectal adenoma detection system and its similarities with pathologists.

Publications

Automatic deep learning-based colorectal adenoma detection system and its similarities with pathologists.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets