Shikha Chaganti

Vivek Singh, Shikha Chaganti, Matthias Siebert et al.

Early screening for cancer has proven to improve the survival rate and spare patients from intensive and costly treatments due to late diagnosis. Cancer screening in the healthy population involves an initial risk stratification step to determine the screening method and frequency, primarily to optimize resource allocation by targeting screening towards individuals who draw most benefit. For most screening programs, age and clinical risk factors such as family history are part of the initial risk stratification algorithm. In this paper, we focus on developing a blood marker-based risk stratification approach, which could be used to identify patients with elevated cancer risk to be encouraged for taking a diagnostic test or participate in a screening program. We demonstrate that the combination of simple, widely available blood tests, such as complete blood count and complete metabolic panel, could potentially be used to identify patients at risk for colorectal, liver, and lung cancers with areas under the ROC curve of 0.76, 0.85, 0.78, respectively. Furthermore, we hypothesize that such an approach could not only be used as pre-screening risk assessment for individuals but also as population health management tool, for example to better interrogate the cancer risk in certain sub-populations.

Eduardo Jose Mortani Barbosa, Bogdan Georgescu, Shikha Chaganti et al.

Objectives: To investigate machine-learning classifiers and interpretable models using chest CT for detection of COVID-19 and differentiation from other pneumonias, ILD and normal CTs. Methods: Our retrospective multi-institutional study obtained 2096 chest CTs from 16 institutions (including 1077 COVID-19 patients). Training/testing cohorts included 927/100 COVID-19, 388/33 ILD, 189/33 other pneumonias, and 559/34 normal (no pathologies) CTs. A metric-based approach for classification of COVID-19 used interpretable features, relying on logistic regression and random forests. A deep learning-based classifier differentiated COVID-19 via 3D features extracted directly from CT attenuation and probability distribution of airspace opacities. Results: Most discriminative features of COVID-19 are percentage of airspace opacity and peripheral and basal predominant opacities, concordant with the typical characterization of COVID-19 in the literature. Unsupervised hierarchical clustering compares feature distribution across COVID-19 and control cohorts. The metrics-based classifier achieved AUC=0.83, sensitivity=0.74, and specificity=0.79 of versus respectively 0.93, 0.90, and 0.83 for the DL-based classifier. Most of ambiguity comes from non-COVID-19 pneumonia with manifestations that overlap with COVID-19, as well as mild COVID-19 cases. Non-COVID-19 classification performance is 91% for ILD, 64% for other pneumonias and 94% for no pathologies, which demonstrates the robustness of our method against different compositions of control groups. Conclusions: Our new method accurately discriminates COVID-19 from other types of pneumonia, ILD, and no pathologies CTs, using quantitative imaging features derived from chest CT, while balancing interpretability of results and classification performance, and therefore may be useful to facilitate diagnosis of COVID-19.

Siqi Liu, Bogdan Georgescu, Zhoubing Xu et al.

The Coronavirus Disease (COVID-19) has affected 1.8 million people and resulted in more than 110,000 deaths as of April 12, 2020. Several studies have shown that tomographic patterns seen on chest Computed Tomography (CT), such as ground-glass opacities, consolidations, and crazy paving pattern, are correlated with the disease severity and progression. CT imaging can thus emerge as an important modality for the management of COVID-19 patients. AI-based solutions can be used to support CT based quantitative reporting and make reading efficient and reproducible if quantitative biomarkers, such as the Percentage of Opacity (PO), can be automatically computed. However, COVID-19 has posed unique challenges to the development of AI, specifically concerning the availability of appropriate image data and annotations at scale. In this paper, we propose to use synthetic datasets to augment an existing COVID-19 database to tackle these challenges. We train a Generative Adversarial Network (GAN) to inpaint COVID-19 related tomographic patterns on chest CTs from patients without infectious diseases. Additionally, we leverage location priors derived from manually labeled COVID-19 chest CTs patients to generate appropriate abnormality distributions. Synthetic data are used to improve both lung segmentation and segmentation of COVID-19 patterns by adding 20% of synthetic data to the real COVID-19 training data. We collected 2143 chest CTs, containing 327 COVID-19 positive cases, acquired from 12 sites across 7 countries. By testing on 100 COVID-19 positive and 100 control cases, we show that synthetic data can help improve both lung segmentation (+6.02% lesion inclusion rate) and abnormality segmentation (+2.78% dice coefficient), leading to an overall more accurate PO computation (+2.82% Pearson coefficient).

Shikha Chaganti, Abishek Balachandran, Guillaume Chabin et al.

Purpose: To present a method that automatically segments and quantifies abnormal CT patterns commonly present in coronavirus disease 2019 (COVID-19), namely ground glass opacities and consolidations. Materials and Methods: In this retrospective study, the proposed method takes as input a non-contrasted chest CT and segments the lesions, lungs, and lobes in three dimensions, based on a dataset of 9749 chest CT volumes. The method outputs two combined measures of the severity of lung and lobe involvement, quantifying both the extent of COVID-19 abnormalities and presence of high opacities, based on deep learning and deep reinforcement learning. The first measure of (PO, PHO) is global, while the second of (LSS, LHOS) is lobewise. Evaluation of the algorithm is reported on CTs of 200 participants (100 COVID-19 confirmed patients and 100 healthy controls) from institutions from Canada, Europe and the United States collected between 2002-Present (April, 2020). Ground truth is established by manual annotations of lesions, lungs, and lobes. Correlation and regression analyses were performed to compare the prediction to the ground truth. Results: Pearson correlation coefficient between method prediction and ground truth for COVID-19 cases was calculated as 0.92 for PO (P < .001), 0.97 for PHO(P < .001), 0.91 for LSS (P < .001), 0.90 for LHOS (P < .001). 98 of 100 healthy controls had a predicted PO of less than 1%, 2 had between 1-2%. Automated processing time to compute the severity scores was 10 seconds per case compared to 30 minutes required for manual annotations. Conclusion: A new method segments regions of CT abnormalities associated with COVID-19 and computes (PO, PHO), as well as (LSS, LHOS) severity scores.

Donghao Zhang, Siqi Liu, Shikha Chaganti et al.

With the injection of contrast material into blood vessels, multi-phase contrasted CT images can enhance the visibility of vessel networks in the human body. Reconstructing the 3D geometric morphology of liver vessels from the contrasted CT images can enable multiple liver preoperative surgical planning applications. Automatic reconstruction of liver vessel morphology remains a challenging problem due to the morphological complexity of liver vessels and the inconsistent vessel intensities among different multi-phase contrasted CT images. On the other side, high integrity is required for the 3D reconstruction to avoid decision making biases. In this paper, we propose a framework for liver vessel morphology reconstruction using both a fully convolutional neural network and a graph attention network. A fully convolutional neural network is first trained to produce the liver vessel centerline heatmap. An over-reconstructed liver vessel graph model is then traced based on the heatmap using an image processing based algorithm. We use a graph attention network to prune the false-positive branches by predicting the presence probability of each segmented branch in the initial reconstruction using the aggregated CNN features. We evaluated the proposed framework on an in-house dataset consisting of 418 multi-phase abdomen CT images with contrast. The proposed graph network pruning improves the overall reconstruction F1 score by 6.4% over the baseline. It also outperformed the other state-of-the-art curvilinear structure reconstruction algorithms.

Cailey I. Kerley, Yuankai Huo, Shikha Chaganti et al.

Brain imaging analysis on clinically acquired computed tomography (CT) is essential for the diagnosis, risk prediction of progression, and treatment of the structural phenotypes of traumatic brain injury (TBI). However, in real clinical imaging scenarios, entire body CT images (e.g., neck, abdomen, chest, pelvis) are typically captured along with whole brain CT scans. For instance, in a typical sample of clinical TBI imaging cohort, only ~15% of CT scans actually contain whole brain CT images suitable for volumetric brain analyses; the remaining are partial brain or non-brain images. Therefore, a manual image retrieval process is typically required to isolate the whole brain CT scans from the entire cohort. However, the manual image retrieval is time and resource consuming and even more difficult for the larger cohorts. To alleviate the manual efforts, in this paper we propose an automated 3D medical image retrieval pipeline, called deep montage-based image retrieval (dMIR), which performs classification on 2D montage images via a deep convolutional neural network. The novelty of the proposed method for image processing is to characterize the medical image retrieval task based on the montage images. In a cohort of 2000 clinically acquired TBI scans, 794 scans were used as training data, 206 scans were used as validation data, and the remaining 1000 scans were used as testing data. The proposed achieved accuracy=1.0, recall=1.0, precision=1.0, f1=1.0 for validation data, while achieved accuracy=0.988, recall=0.962, precision=0.962, f1=0.962 for testing data. Thus, the proposed dMIR is able to perform accurate CT whole brain image retrieval from large-scale clinical cohorts.