Dataset Information

Using less annotation workload to establish a pathological auxiliary diagnosis system for gastric cancer.

ABSTRACT: Pathological diagnosis of gastric cancer requires pathologists to have extensive clinical experience. To help pathologists improve diagnostic accuracy and efficiency, we collected 1,514 cases of stomach H&E-stained specimens with complete diagnostic information to establish a pathological auxiliary diagnosis system based on deep learning. At the slide level, our system achieves a specificity of 0.8878 while maintaining a high sensitivity close to 1.0 on 269 biopsy specimens (147 malignancies) and 163 surgical specimens (80 malignancies). The classified accuracy of our system is 0.9034 at the slide level for 352 biopsy specimens (201 malignancies) from 50 medical centers. With the help of our system, the pathologists' average false-negative rate and average false-positive rate on 100 biopsy specimens (50 malignancies) are reduced to 1/5 and 1/2 of the original rates, respectively. At the same time, the average uncertainty rate and the average diagnosis time are reduced by approximately 22% and 20%, respectively.

SUBMITTER: Lan J

PROVIDER: S-EPMC10140598 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature

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Using less annotation workload to establish a pathological auxiliary diagnosis system for gastric cancer.

Lan Junlin J Chen Musheng M Wang Jianchao J Du Min M Wu Zhida Z Zhang Hejun H Xue Yuyang Y Wang Tao T Chen Lifan L Xu Chaohui C Han Zixin Z Hu Ziwei Z Zhou Yuanbo Y Zhou Xiaogen X Tong Tong T Chen Gang G

Cell reports. Medicine 20230411 4

Pathological diagnosis of gastric cancer requires pathologists to have extensive clinical experience. To help pathologists improve diagnostic accuracy and efficiency, we collected 1,514 cases of stomach H&E-stained specimens with complete diagnostic information to establish a pathological auxiliary diagnosis system based on deep learning. At the slide level, our system achieves a specificity of 0.8878 while maintaining a high sensitivity close to 1.0 on 269 biopsy specimens (147 malignancies) an ...[more]

PMID: 37044091

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Project description:Background and aimMelasma (ML), naevus fusco-caeruleus zygomaticus (NZ), freckles (FC), cafe-au-lait spots (CS), nevus of ota (NO), and lentigo simplex (LS), are common skin diseases causing hyperpigmentation. Deep learning algorithms learn the inherent laws and representation levels of sample data and can analyze the internal details of the image and classify it objectively to be used for image diagnosis. However, deep learning algorithms that can assist clinicians in diagnosing skin hyperpigmentation conditions are lacking.MethodsThe optimal deep-learning image recognition algorithm was explored for the auxiliary diagnosis of hyperpigmented skin disease. Pretrained models, such as VGG-19, GoogLeNet, InceptionV3, ResNet50V2, ResNet101V2, ResNet152V2, InceptionResNetV2, DesseNet201, MobileNet, and NASNetMobile were used to classify images of six common hyperpigmented skin diseases. The best deep learning algorithm for developing an online clinical diagnosis system was selected by using accuracy and area under curve (AUC) as evaluation indicators.ResultsIn this research, the parameters of the above-mentioned ten deep learning algorithms were 18333510, 5979702, 21815078, 23577094, 42638854, 58343942, 54345958, 18333510, 3235014, and 4276058, respectively, and their training time was 380, 162, 199, 188, 315, 511, 471, 697, 101, and 144 min respectively. The respective accuracies of the training set were 85.94%, 99.72%, 99.61%, 99.52%, 99.52%, 98.84%, 99.61%, 99.13%, 99.52%, and 99.61%. The accuracy rates of the test set data were 73.28%, 57.40%, 70.04%, 71.48%, 68.23%, 71.11%, 71.84%, 73.28%, 70.39%, and 43.68%, respectively. Finally, the areas of AUC curves were 0.93, 0.86, 0.93, 0.91, 0.91, 0.92, 0.93, 0.92, 0.93, and 0.82, respectively.ConclusionsThe experimental parameters, training time, accuracy, and AUC of the above models suggest that MobileNet provides a good clinical application prospect in the auxiliary diagnosis of hyperpigmented skin.

Project description:BackgroundCurrently, pathological examination of gastroscopy biopsy specimens is the gold standard for gastric cancer (GC) diagnosis. However, it has a false-negative rate of 10-20% due to inaccurate sampling locations and/or insufficient sampling amount. A signature should be developed to aid the early diagnosis of GC using biopsy specimens even when they are sampled from inaccurate locations.MethodsWe extracted a robust qualitative transcriptional signature, based on the within-sample relative expression orderings (REOs) of gene pairs, to discriminate both GC tissues and adjacent-normal tissues from non-GC gastritis, intestinal metaplasia and normal gastric tissues.ResultsA signature consisting of two gene pairs for GC diagnosis was identified and validated in data of both biopsy specimens and surgical resection specimens pooled from publicly available datasets measured by different laboratories with different platforms. For gastroscopy biopsy specimens, 96.20% of 79 non-GC tissues were correctly identified as non-GC, and 96.84% of 158 GC tissues and six of seven adjacent-normal tissues were correctly identified as GC. For surgical resection specimens, 98.37% of 2560 GC tissues and 97.28% of 221 adjacent-normal tissues were correctly identified as GC. Especially, 97.67% of the 257 GC patients at stage I were exactly diagnosed as GC. We additionally measured 21 GC tissues from seven different GC patients, each with three specimens sampled from three tumor locations with different proportions of the tumor epithelial cell. All these GC tissues were correctly identified as GC, even when the proportion of the tumor epithelial cell was as low as 14%.ConclusionsThe qualitative transcriptional signature can distinguish both GC and adjacent-normal tissues from normal, gastritis and intestinal metaplasia tissues of non-GC patients even using inaccurately sampled biopsy specimens, which can be applied robustly at the individual level to aid the early GC diagnosis.

Dataset Information

Using less annotation workload to establish a pathological auxiliary diagnosis system for gastric cancer.

Publications

Using less annotation workload to establish a pathological auxiliary diagnosis system for gastric cancer.

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