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Open Access Publications from the University of California

Scholarly Works (7 results)

  • Thesis
  • Peer Reviewed
UCLA Electronic Theses and Dissertations (2018)

Low-dose computed tomography (CT) screening has been widely used to detect and diagnose early stage lung cancer. Clinical trials have shown that low-dose CT reduced lung cancer mortality by 20% relative to plain chest radiography; however, challenges exist in current low-dose CT screening programs including high over-diagnosis rates, high cost and increased radiation exposure. This dissertation attempts to overcome these challenges by developing machine and deep learning models for automated lung cancer diagnosis and disease progression estimation. A novel lung segmentation approach was first developed using a bidirectional chain code method and machine learning framework. This method is designed to include the lung nodules attached to lung wall while minimizing over-segmentation error. Second, a hybrid ensemble convolutional neural network has been developed to classify lung nodule vs. non-nodule objects. The ensemble model combines the VGG, residual and densely connected module designs to improve the model classification robustness for external datasets collected with different acquisition parameters. Third, a hierarchical semantic convolutional neural network (HSCNN) has been described to classify lung nodule malignancy. Semantic characteristic features, predicted in parallel with the malignancy for each nodule, enable the interpretation of the model and improvement of malignancy prediction. Finally, a Bayesian framework combined with a continuous-time Markov model was developed to estimate the multi-state disease progression of lung cancer. The resulting model estimates individual lung cancer state transition information, providing the basis for personalized screening recommendations. Extensive experiments and results have proved the effectiveness of these methods paving the way to optimize and improve the effectiveness of existing low-dose CT screening programs.

    Cover page: Characterizing Pulmonary Nodules using Machine and Deep Learning Methods to Improve Lung Cancer Diagnosis
    • Article
    • Peer Reviewed
    UCLA Previously Published Works (2015)
    Computer-aided detection and diagnosis (CAD) has been widely investigated to improve radiologists׳ diagnostic accuracy in detecting and characterizing lung disease, as well as to assist with the processing of increasingly sizable volumes of imaging. Lung segmentation is a requisite preprocessing step for most CAD schemes. This paper proposes a parameter-free lung segmentation algorithm with the aim of improving lung nodule detection accuracy, focusing on juxtapleural nodules. A bidirectional chain coding method combined with a support vector machine (SVM) classifier is used to selectively smooth the lung border while minimizing the over-segmentation of adjacent regions. This automated method was tested on 233 computed tomography (CT) studies from the lung imaging database consortium (LIDC), representing 403 juxtapleural nodules. The approach obtained a 92.6% re-inclusion rate. Segmentation accuracy was further validated on 10 randomly selected CT series, finding a 0.3% average over-segmentation ratio and 2.4% under-segmentation rate when compared to manually segmented reference standards done by an expert.
      Cover page: An automated lung segmentation approach using bidirectional chain codes to improve nodule detection accuracy
      • Article
      • Peer Reviewed
      UCLA Previously Published Works (2017)
      A growing number of individuals who are considered at high risk of cancer are now routinely undergoing population screening. However, noted harms such as radiation exposure, overdiagnosis, and overtreatment underscore the need for better temporal models that predict who should be screened and at what frequency. The mean sojourn time (MST), an average duration period when a tumor can be detected by imaging but with no observable clinical symptoms, is a critical variable for formulating screening policy. Estimation of MST has been long studied using continuous Markov model (CMM) with Maximum likelihood estimation (MLE). However, a lot of traditional methods assume no observation error of the imaging data, which is unlikely and can bias the estimation of the MST. In addition, the MLE may not be stably estimated when data is sparse. Addressing these shortcomings, we present a probabilistic modeling approach for periodic cancer screening data. We first model the cancer state transition using a three state CMM model, while simultaneously considering observation error. We then jointly estimate the MST and observation error within a Bayesian framework. We also consider the inclusion of covariates to estimate individualized rates of disease progression. Our approach is demonstrated on participants who underwent chest x-ray screening in the National Lung Screening Trial (NLST) and validated using posterior predictive p-values and Pearson's chi-square test. Our model demonstrates more accurate and sensible estimates of MST in comparison to MLE.
        Cover page: A Bayesian model for estimating multi-state disease progression
        • Article
        • Peer Reviewed
        UCLA Previously Published Works (2019)
        While deep learning methods have demonstrated performance comparable to human readers in tasks such as computer-aided diagnosis, these models are difficult to interpret, do not incorporate prior domain knowledge, and are often considered as a "black-box." The lack of model interpretability hinders them from being fully understood by end users such as radiologists. In this paper, we present a novel interpretable deep hierarchical semantic convolutional neural network (HSCNN) to predict whether a given pulmonary nodule observed on a computed tomography (CT) scan is malignant. Our network provides two levels of output: 1) low-level semantic features; and 2) a high-level prediction of nodule malignancy. The low-level outputs reflect diagnostic features often reported by radiologists and serve to explain how the model interprets the images in an expert-interpretable manner. The information from these low-level outputs, along with the representations learned by the convolutional layers, are then combined and used to infer the high-level output. This unified architecture is trained by optimizing a global loss function including both low- and high-level tasks, thereby learning all the parameters within a joint framework. Our experimental results using the Lung Image Database Consortium (LIDC) show that the proposed method not only produces interpretable lung cancer predictions but also achieves significantly better results compared to using a 3D CNN alone.
          Cover page: An interpretable deep hierarchical semantic convolutional neural network for lung nodule malignancy classification
          • Article
          • Peer Reviewed
          UCLA Previously Published Works (2019)
            • Article
            • Peer Reviewed
            UCLA Previously Published Works (2019)
            Prostate cancer is the most common and second most deadly form of cancer in men in the United States. The classification of prostate cancers based on Gleason grading using histological images is important in risk assessment and treatment planning for patients. Here, we demonstrate a new region-based convolutional neural network framework for multi-task prediction using an epithelial network head and a grading network head. Compared with a single-task model, our multi-task model can provide complementary contextual information, which contributes to better performance. Our model is achieved a state-of-the-art performance in epithelial cells detection and Gleason grading tasks simultaneously. Using fivefold cross-validation, our model is achieved an epithelial cells detection accuracy of 99.07% with an average area under the curve of 0.998. As for Gleason grading, our model is obtained a mean intersection over union of 79.56% and an overall pixel accuracy of 89.40%.
              Cover page: Path R-CNN for Prostate Cancer Diagnosis and Gleason Grading of Histological Images
              • Article
              • Peer Reviewed
              UCLA Previously Published Works (2016)
              A growing number of individuals who are considered at high risk of cancer are now routinely undergoing population screening. However, noted harms such as radiation exposure, overdiagnosis, and overtreatment underscore the need for better temporal models that predict who should be screened and at what frequency. The mean sojourn time (MST), an average duration period when a tumor can be detected by imaging but with no observable clinical symptoms, is a critical variable for formulating screening policy. Estimation of MST has been long studied using continuous Markov model (CMM) with Maximum likelihood estimation (MLE). However, a lot of traditional methods assume no observation error of the imaging data, which is unlikely and can bias the estimation of the MST. In addition, the MLE may not be stably estimated when data is sparse. Addressing these shortcomings, we present a probabilistic modeling approach for periodic cancer screening data. We first model the cancer state transition using a three state CMM model, while simultaneously considering observation error. We then jointly estimate the MST and observation error within a Bayesian framework. We also consider the inclusion of covariates to estimate individualized rates of disease progression. Our approach is demonstrated on participants who underwent chest x-ray screening in the National Lung Screening Trial (NLST) and validated using posterior predictive p-values and Pearson’s chi-square test. Our model demonstrates more accurate and sensible estimates of MST in comparison to MLE.
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