A fully automatic deep learning system for COVID-19 diagnostic and prognostic analysis.

Coronavirus disease 2019 (COVID-19) has spread globally, and medical resources become insufficient in many regions. Fast diagnosis of COVID-19 and finding high-risk patients with worse prognosis for early prevention and medical resource optimisation is important. Here, we proposed a fully automatic deep learning system for COVID-19 diagnostic and prognostic analysis by routinely used computed tomography.We retrospectively collected 5372 patients with computed tomography images from seven cities or provinces. Firstly, 4106 patients with computed tomography images were used to pre-train the deep learning system, making it learn lung features. Following this, 1266 patients (924 with COVID-19 (471 had follow-up for >5 days) and 342 with other pneumonia) from six cities or provinces were enrolled to train and externally validate the performance of the deep learning system.In the four external validation sets, the deep learning system achieved good performance in identifying COVID-19 from other pneumonia (AUC 0.87 and 0.88, respectively) and viral pneumonia (AUC 0.86). Moreover, the deep learning system succeeded to stratify patients into high- and low-risk groups whose hospital-stay time had significant difference (p=0.013 and p=0.014, respectively). Without human assistance, the deep learning system automatically focused on abnormal areas that showed consistent characteristics with reported radiological findings.Deep learning provides a convenient tool for fast screening of COVID-19 and identifying potential high-risk patients, which may be helpful for medical resource optimisation and early prevention before patients show severe symptoms.

Mining whole-lung information by artificial intelligence for predicting EGFR genotype and targeted therapy response in lung cancer: a multicohort study.

BACKGROUND: Epidermal growth factor receptor (EGFR) genotype is crucial for treatment decision making in lung cancer, but it can be affected by tumour heterogeneity and invasive biopsy during gene sequencing. Importantly, not all patients with an EGFR mutation have good prognosis with EGFR-tyrosine kinase inhibitors (TKIs), indicating the necessity of stratifying for EGFR-mutant genotype. In this study, we proposed a fully automated artificial intelligence system (FAIS) that mines whole-lung information from CT images to predict EGFR genotype and prognosis with EGFR-TKI treatment. METHODS: We included 18 232 patients with lung cancer with CT imaging and EGFR gene sequencing from nine cohorts in China and the USA, including a prospective cohort in an Asian population (n=891) and The Cancer Imaging Archive cohort in a White population. These cohorts were divided into thick CT group and thin CT group. The FAIS was built for predicting EGFR genotype and progression-free survival of patients receiving EGFR-TKIs, and it was evaluated by area under the curve (AUC) and Kaplan-Meier analysis. We further built two tumour-based deep learning models as comparison with the FAIS, and we explored the value of combining FAIS and clinical factors (the FAIS-C model). Additionally, we included 891 patients with 56-panel next-generation sequencing and 87 patients with RNA sequencing data to explore the biological mechanisms of FAIS. FINDINGS: FAIS achieved AUCs ranging from 0·748 to 0·813 in the six retrospective and prospective testing cohorts, outperforming the commonly used tumour-based deep learning model. Genotype predicted by the FAIS-C model was significantly associated with prognosis to EGFR-TKIs treatment (log-rank p<0·05), an important complement to gene sequencing. Moreover, we found 29 prognostic deep learning features in FAIS that were able to identify patients with an EGFR mutation at high risk of TKI resistance. These features showed strong associations with multiple genotypes (p<0·05, t test or Wilcoxon test) and gene pathways linked to drug resistance and cancer progression mechanisms. INTERPRETATION: FAIS provides a non-invasive method to detect EGFR genotype and identify patients with an EGFR mutation at high risk of TKI resistance. The superior performance of FAIS over tumour-based deep learning methods suggests that genotype and prognostic information could be obtained from the whole lung instead of only tumour tissues. FUNDING: National Natural Science Foundation of China.

A Quarter-split Domain-adaptive Network for EGFR Gene Mutation Prediction in Lung Cancer by Standardizing Heterogeneous CT image.

Epidermal growth factor receptor (EGFR) gene mutation status is crucial for the treatment planning of lung cancer. The gold standard for detecting EGFR mutation status relies on invasive tumor biopsy and expensive gene sequencing. Recently, computed tomography (CT) images and deep learning have shown promising results in non-invasively predicting EGFR mutation in lung cancer. However, CT scanning parameters such as slice thickness vary largely between different scanners and centers, making the deep learning models very sensitive to noise and therefore not robust in clinical practice. In this study, we propose a novel QuarterNetadaptive model to predict EGFR mutation in lung cancer, which is robust to CT images of different thicknesses. We propose two components: 1) a quarter-split network to sequentially learn local lung features from different lung lobes and global lung features; 2) a domain adaptive strategy to learn CT thickness-invariant features. Furthermore, we collected a large dataset including 1413 patients with both EGFR gene sequencing and CT images of various thicknesses to evaluate the performance of the proposed model. Finally, the QuarterNetadaptive model achieved AUC over 0.88 regarding CT images of different thicknesses, which improves largely than state-of-the-art methods.Clinical relevance-We proposed a non-invasive model to detect EGFR gene mutation in lung cancer, which is robust to CT images of different thicknesses and can assist lung cancer treatment planning.

Mix Contrast for COVID-19 Mild-to-Critical Prediction.

OBJECTIVE: In a few patients with mild COVID-19, there is a possibility of the infection becoming severe or critical in the future. This work aims to identify high-risk patients who have a high probability of changing from mild to critical COVID-19 (only account for 5% of cases). METHODS: Using traditional convolutional neural networks for classification may not be suitable to identify this 5% of high risk patients from an entire dataset due to the highly imbalanced label distribution. To address this problem, we propose a Mix Contrast model, which matches original features with mixed features for contrastive learning. Three modules are proposed for training the model: 1) a cumulative learning strategy for synthesizing the mixed feature; 2) a commutative feature combination module for learning the commutative law of feature concatenation; 3) a united pairwise loss assigning adaptive weights for sample pairs with different class anchors based on their current optimization status. RESULTS: We collect a multi-center computed tomography dataset including 918 confirmed COVID-19 patients from four hospitals and evaluate the proposed method on both the COVID-19 mild-to-critical prediction and COVID-19 diagnosis tasks. For mild-to-critical prediction, the experimental results show a recall of 0.80 and a specificity of 0.815. For diagnosis, the model shows comparable results with deep neural networks using a large dataset. Our method demonstrates improvements when the amount of training data is small or imbalanced. SIGNIFICANCE: Identifying mild-to-critical COVID-19 patients is important for early prevention and personalized treatment planning.

Gene signatures predict biochemical recurrence-free survival in primary prostate cancer patients after radical therapy.

BACKGROUND: This study evaluated the predictive value of gene signatures for biochemical recurrence (BCR) in primary prostate cancer (PCa) patients. METHODS: Clinical features and gene expression profiles of PCa patients were attained from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets, which were further classified into a training set (n = 419), a validation set (n = 403). The least absolute shrinkage and selection operator Cox (LASSO-Cox) method was used to select discriminative gene signatures in training set for biochemical recurrence-free survival (BCRFS). Selected gene signatures established a risk score system. Univariate and multivariate analyses of prognostic factors about BCRFS were performed using the Cox proportional hazards regression models. A nomogram based on multivariate analysis was plotted to facilitate clinical application. Kyoto Encyclopedia of Gene and Genomes (KEGG) and Gene Ontology (GO) analyses were then executed for differentially expressed genes (DEGs). RESULTS: Notably, the risk score could significantly identify BCRFS by time-dependent receiver operating characteristic (t-ROC) curves in the training set (3-year area under the curve (AUC) = 0.820, 5-year AUC = 0.809) and the validation set (3-year AUC = 0.723, 5-year AUC = 0.733). CONCLUSIONS: Clinically, the nomogram model, which incorporates Gleason score and the risk score, could effectively predict BCRFS and potentially be utilized as a useful tool for the screening of BCRFS in PCa.