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Artificial intelligence defines protein-based classification of thyroid nodules.

ABSTRACT: Determination of malignancy in thyroid nodules remains a major diagnostic challenge. Here we report the feasibility and clinical utility of developing an AI-defined protein-based biomarker panel for diagnostic classification of thyroid nodules: based initially on formalin-fixed paraffin-embedded (FFPE), and further refined for fine-needle aspiration (FNA) tissue specimens of minute amounts which pose technical challenges for other methods. We first developed a neural network model of 19 protein biomarkers based on the proteomes of 1724 FFPE thyroid tissue samples from a retrospective cohort. This classifier achieved over 91% accuracy in the discovery set for classifying malignant thyroid nodules. The classifier was externally validated by blinded analyses in a retrospective cohort of 288 nodules (89% accuracy; FFPE) and a prospective cohort of 294 FNA biopsies (85% accuracy) from twelve independent clinical centers. This study shows that integrating high-throughput proteomics and AI technology in multi-center retrospective and prospective clinical cohorts facilitates precise disease diagnosis which is otherwise difficult to achieve by other methods.

SUBMITTER: Sun Y

PROVIDER: S-EPMC9448820 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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Artificial intelligence defines protein-based classification of thyroid nodules.

Sun Yaoting Y Selvarajan Sathiyamoorthy S Zang Zelin Z Liu Wei W Zhu Yi Y Zhang Hao H Chen Wanyuan W Chen Hao H Li Lu L Cai Xue X Gao Huanhuan H Wu Zhicheng Z Zhao Yongfu Y Chen Lirong L Teng Xiaodong X Mantoo Sangeeta S Lim Tony Kiat-Hon TK Hariraman Bhuvaneswari B Yeow Serene S Alkaff Syed Muhammad Fahmy SMF Lee Sze Sing SS Ruan Guan G Zhang Qiushi Q Zhu Tiansheng T Hu Yifan Y Dong Zhen Z Ge Weigang W Xiao Qi Q Wang Weibin W Wang Guangzhi G Xiao Junhong J He Yi Y Wang Zhihong Z Sun Wei W Qin Yuan Y Zhu Jiang J Zheng Xu X Wang Linyan L Zheng Xi X Xu Kailun K Shao Yingkuan Y Zheng Shu S Liu Kexin K Aebersold Ruedi R Guan Haixia H Wu Xiaohong X Luo Dingcun D Tian Wen W Li Stan Ziqing SZ Kon Oi Lian OL Iyer Narayanan Gopalakrishna NG Guo Tiannan T

Cell discovery 20220906 1

Determination of malignancy in thyroid nodules remains a major diagnostic challenge. Here we report the feasibility and clinical utility of developing an AI-defined protein-based biomarker panel for diagnostic classification of thyroid nodules: based initially on formalin-fixed paraffin-embedded (FFPE), and further refined for fine-needle aspiration (FNA) tissue specimens of minute amounts which pose technical challenges for other methods. We first developed a neural network model of 19 protein ...[more]

PMID: 36068205

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Project description:ObjectivesThis study aimed to explore and develop artificial intelligence approaches for efficient classification of pulmonary nodules based on CT scans.Materials and methodsA number of 1007 nodules were obtained from 551 patients of LIDC-IDRI dataset. All nodules were cropped into 64 × 64 PNG images , and preprocessing was carried out to clean the image from surrounding non-nodular structure. In machine learning method, texture Haralick and local binary pattern features were extracted. Four features were selected using principal component analysis (PCA) algorithm before running classifiers. In deep learning, a simple CNN model was constructed and transfer learning was applied using VGG-16 and VGG-19, DenseNet-121 and DenseNet-169 and ResNet as pre-trained models with fine tuning.ResultsIn statistical machine learning method, the optimal AUROC was 0.885 ± 0.024 with random forest classifier and the best accuracy was 0.819 ± 0.016 with support vector machine. In deep learning, the best accuracy reached 90.39% with DenseNet-121 model and the best AUROC was 96.0%, 95.39% and 95.69% with simple CNN, VGG-16 and VGG-19, respectively. The best sensitivity reached 90.32% using DenseNet-169 and the best specificity attained was 93.65% when applying the DenseNet-121 and ResNet-152V2.ConclusionDeep learning methods with transfer learning showed several benefits over statistical learning in terms of nodule prediction performance and saving efforts and time in training large datasets. SVM and DenseNet-121 showed the best performance when compared with their counterparts. There is still more room for improvement, especially when more data can be trained and lesion volume is represented in 3D.Clinical relevance statementMachine learning methods offer unique opportunities and open new venues in clinical diagnosis of lung cancer. The deep learning approach has been more accurate than statistical learning methods. SVM and DenseNet-121 showed superior performance in pulmonary nodule classification.

Project description:BackgroundUltrasonography (US) is the most common method of identifying thyroid nodules, but US images require an experienced surgeon for identification. Many artificial intelligence (AI) techniques such as computer-aided diagnostic systems (CAD), deep learning (DL), and machine learning (ML) have been used to assist in the diagnosis of thyroid nodules, but whether AI techniques can improve the diagnostic accuracy of thyroid nodules still needs to be explored.ObjectiveTo clarify the accuracy of AI-based thyroid nodule US images for differentiating benign and malignant thyroid nodules.MethodsA search strategy of "subject terms + key words" was used to search PubMed, Cochrane Library, Embase, Web of Science, China Biology Medicine (CBM), and China National Knowledge Infrastructure (CNKI) for studies on AI-assisted diagnosis of thyroid nodules based on US images. The summarized receiver operating characteristic (SROC) curve and the pooled sensitivity and specificity were used to assess the performance of the diagnostic tests. The quality assessment of diagnostics accuracy studies-2 (QUADAS-2) tool was used to assess the methodological quality of the included studies. The Review Manager 5.3 and Stata 15 were used to process the data. Subgroup analysis was based on the integrity of data collection.ResultsA total of 25 studies with 17,429 US images of thyroid nodules were included. AI-assisted diagnostic techniques had better diagnostic efficacy in the diagnosis of benign and malignant thyroid nodules: sensitivity 0.88 (95% CI: (0.85-0.90)), specificity 0.81 (95% CI: 0.74-0.86), diagnostic odds ratio (DOR) 30 (95% CI: 19-46). The SROC curve indicated that the area under the curve (AUC) was 0.92 (95% CI: 0.89-0.94). Threshold effect analysis showed a Spearman correlation coefficient: 0.17 < 0.5, suggesting no threshold effect for the included studies. After a meta-regression analysis of 4 different subgroups, the results showed a statistically significant effect of mean age ≥50 years on heterogeneity. Compared with studies with an average age of ≥50 years, AI-assisted diagnostic techniques had higher diagnostic performance in studies with an average age of <50 years (0.89 (95% CI: 0.87-0.92) vs. 0.80 (95% CI: 0.73-0.88)), (0.83 (95% CI: 0.77-0.88) vs. 0.73 (95% CI: 0.60-0.87)).ConclusionsAI-assisted diagnostic techniques had good diagnostic efficacy for thyroid nodules. For the diagnosis of <50 year olds, AI-assisted diagnostic technology was more effective in diagnosis.

Project description:PurposeThyroid nodules are highly prevalent in the general population, posing a clinical challenge in accurately distinguishing between benign and malignant cases. This study aimed to investigate the diagnostic performance of different strategies, utilizing a combination of a computer-aided diagnosis system (AmCAD) and shear wave elastography (SWE) imaging, to effectively differentiate benign and malignant thyroid nodules in ultrasonography.MethodsA total of 126 thyroid nodules with pathological confirmation were prospectively included in this study. The AmCAD was utilized to analyze the ultrasound imaging characteristics of the nodules, while the SWE was employed to measure their stiffness in both transverse and longitudinal thyroid scans. Twelve diagnostic patterns were formed by combining AmCAD diagnosis and SWE values, including isolation, series, parallel, and integration. The diagnostic performance was assessed using the receiver operating characteristic curve and area under the curve (AUC). Sensitivity, specificity, accuracy, missed malignancy rate, and unnecessary biopsy rate were also determined.ResultsVarious diagnostic schemes have shown specific advantages in terms of diagnostic performance. Overall, integrating AmCAD with SWE imaging in the transverse scan yielded the most favorable diagnostic performance, achieving an AUC of 72.2% (95% confidence interval (CI): 63.0-81.5%), outperforming other diagnostic schemes. Furthermore, in the subgroup analysis of nodules measuring <2 cm or 2-4 cm, the integrated scheme consistently exhibited promising diagnostic performance, with AUCs of 74.2% (95% CI: 61.9-86.4%) and 77.4% (95% CI: 59.4-95.3%) respectively, surpassing other diagnostic schemes. The integrated scheme also effectively addressed thyroid nodule management by reducing the missed malignancy rate to 9.5% and unnecessary biopsy rate to 22.2%.ConclusionThe integration of AmCAD and SWE imaging in the transverse thyroid scan significantly enhances the diagnostic performance for distinguishing benign and malignant thyroid nodules. This strategy offers clinicians the advantage of obtaining more accurate clinical diagnoses and making well-informed decisions regarding patient management.

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Artificial intelligence defines protein-based classification of thyroid nodules.

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Artificial intelligence defines protein-based classification of thyroid nodules.

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