The uncovered biases and errors in clinical determination of bone age by using deep learning models.

OBJECTIVES: To evaluate AI biases and errors in estimating bone age (BA) by comparing AI and radiologists' clinical determinations of BA. METHODS: We established three deep learning models from a Chinese private dataset (CHNm), an American public dataset (USAm), and a joint dataset combining the above two datasets (JOIm). The test data CHNt (n = 1246) were labeled by ten senior pediatric radiologists. The effects of data site differences, interpretation bias, and interobserver variability on BA assessment were evaluated. The differences between the AI models' and radiologists' clinical determinations of BA (normal, advanced, and delayed BA groups by using the Brush data) were evaluated by the chi-square test and Kappa values. The heatmaps of CHNm-CHNt were generated by using Grad-CAM. RESULTS: We obtained an MAD value of 0.42 years on CHNm-CHNt; this result indicated an appropriate accuracy for the whole group but did not indicate an accurate estimation of individual BA because with a kappa value of 0.714, the agreement between AI and human clinical determinations of BA was significantly different. The features of the heatmaps were not fully consistent with the human vision on the X-ray films. Variable performance in BA estimation by different AI models and the disagreement between AI and radiologists' clinical determinations of BA may be caused by data biases, including patients' sex and age, institutions, and radiologists. CONCLUSIONS: The deep learning models outperform external validation in predicting BA on both internal and joint datasets. However, the biases and errors in the models' clinical determinations of child development should be carefully considered. KEY POINTS: • With a kappa value of 0.714, clinical determinations of bone age by using AI did not accord well with clinical determinations by radiologists. • Several biases, including patients' sex and age, institutions, and radiologists, may cause variable performance by AI bone age models and disagreement between AI and radiologists' clinical determinations of bone age. • AI heatmaps of bone age were not fully consistent with human vision on X-ray films.

CT-Based Risk Factors for Mortality of Patients With COVID-19 Pneumonia in Wuhan, China: A Retrospective Study.

Purpose: Computed tomography (CT) characteristics associated with critical outcomes of patients with coronavirus disease 2019 (COVID-19) have been reported. However, CT risk factors for mortality have not been directly reported. We aim to determine the CT-based quantitative predictors for COVID-19 mortality. Methods: In this retrospective study, laboratory-confirmed COVID-19 patients at Wuhan Central Hospital between December 9, 2019, and March 19, 2020, were included. A novel prognostic biomarker, V-HU score, depicting the volume (V) of total pneumonia infection and the average Hounsfield unit (HU) of consolidation areas was automatically quantified from CT by an artificial intelligence (AI) system. Cox proportional hazards models were used to investigate risk factors for mortality. Results: The study included 238 patients (women 136/238, 57%; median age, 65 years, IQR 51-74 years), 126 of whom were survivors. The V-HU score was an independent predictor (hazard ratio [HR] 2.78, 95% confidence interval [CI] 1.50-5.17; p = 0.001) after adjusting for several COVID-19 prognostic indicators significant in univariable analysis. The prognostic performance of the model containing clinical and outpatient laboratory factors was improved by integrating the V-HU score (c-index: 0.695 vs. 0.728; p < 0.001). Older patients (age ≥ 65 years; HR 3.56, 95% CI 1.64-7.71; p < 0.001) and younger patients (age < 65 years; HR 4.60, 95% CI 1.92-10.99; p < 0.001) could be further risk-stratified by the V-HU score. Conclusions: A combination of an increased volume of total pneumonia infection and high HU value of consolidation areas showed a strong correlation to COVID-19 mortality, as determined by AI quantified CT.

From community-acquired pneumonia to COVID-19: a deep learning-based method for quantitative analysis of COVID-19 on thick-section CT scans.

OBJECTIVE: To develop a fully automated AI system to quantitatively assess the disease severity and disease progression of COVID-19 using thick-section chest CT images. METHODS: In this retrospective study, an AI system was developed to automatically segment and quantify the COVID-19-infected lung regions on thick-section chest CT images. Five hundred thirty-one CT scans from 204 COVID-19 patients were collected from one appointed COVID-19 hospital. The automatically segmented lung abnormalities were compared with manual segmentation of two experienced radiologists using the Dice coefficient on a randomly selected subset (30 CT scans). Two imaging biomarkers were automatically computed, i.e., the portion of infection (POI) and the average infection HU (iHU), to assess disease severity and disease progression. The assessments were compared with patient status of diagnosis reports and key phrases extracted from radiology reports using the area under the receiver operating characteristic curve (AUC) and Cohen's kappa, respectively. RESULTS: The dice coefficient between the segmentation of the AI system and two experienced radiologists for the COVID-19-infected lung abnormalities was 0.74 ± 0.28 and 0.76 ± 0.29, respectively, which were close to the inter-observer agreement (0.79 ± 0.25). The computed two imaging biomarkers can distinguish between the severe and non-severe stages with an AUC of 0.97 (p value < 0.001). Very good agreement (κ = 0.8220) between the AI system and the radiologists was achieved on evaluating the changes in infection volumes. CONCLUSIONS: A deep learning-based AI system built on the thick-section CT imaging can accurately quantify the COVID-19-associated lung abnormalities and assess the disease severity and its progressions. KEY POINTS: • A deep learning-based AI system was able to accurately segment the infected lung regions by COVID-19 using the thick-section CT scans (Dice coefficient ≥ 0.74). • The computed imaging biomarkers were able to distinguish between the non-severe and severe COVID-19 stages (area under the receiver operating characteristic curve 0.97). • The infection volume changes computed by the AI system were able to assess the COVID-19 progression (Cohen's kappa 0.8220).

IDRiD: Diabetic Retinopathy - Segmentation and Grading Challenge.

Diabetic Retinopathy (DR) is the most common cause of avoidable vision loss, predominantly affecting the working-age population across the globe. Screening for DR, coupled with timely consultation and treatment, is a globally trusted policy to avoid vision loss. However, implementation of DR screening programs is challenging due to the scarcity of medical professionals able to screen a growing global diabetic population at risk for DR. Computer-aided disease diagnosis in retinal image analysis could provide a sustainable approach for such large-scale screening effort. The recent scientific advances in computing capacity and machine learning approaches provide an avenue for biomedical scientists to reach this goal. Aiming to advance the state-of-the-art in automatic DR diagnosis, a grand challenge on "Diabetic Retinopathy - Segmentation and Grading" was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI - 2018). In this paper, we report the set-up and results of this challenge that is primarily based on Indian Diabetic Retinopathy Image Dataset (IDRiD). There were three principal sub-challenges: lesion segmentation, disease severity grading, and localization of retinal landmarks and segmentation. These multiple tasks in this challenge allow to test the generalizability of algorithms, and this is what makes it different from existing ones. It received a positive response from the scientific community with 148 submissions from 495 registrations effectively entered in this challenge. This paper outlines the challenge, its organization, the dataset used, evaluation methods and results of top-performing participating solutions. The top-performing approaches utilized a blend of clinical information, data augmentation, and an ensemble of models. These findings have the potential to enable new developments in retinal image analysis and image-based DR screening in particular.

Fast sequence analysis based on diamond sampling.

Both in DNA and protein contexts, an important method for modelling motifs is to utilize position weight matrix (PWM) in biological sequences. With the development of genome sequencing technology, the quantity of the sequence data is increasing explosively, so the faster searching algorithms which have the ability to meet the increasingly need are desired to develop. In this paper, we proposed a method for speeding up the searching process of candidate transcription factor binding sites (TFBS), and the users can be allowed to specify p threshold to get the desired trade-off between speed and sensitivity for a particular sequence analysis. Moreover, the proposed method can also be generalized to large-scale annotation and sequence projects.