Deep Learning for Automated Medical Image Analysis

Medical imaging is an essential tool in many areas of medical applications, used for both diagnosis and treatment. However, reading medical images and making diagnosis or treatment recommendations require specially trained medical specialists. The current practice of reading medical images is labor-intensive, time-consuming, costly, and error-prone. It would be more desirable to have a computer-aided system that can automatically make diagnosis and treatment recommendations. Recent advances in deep learning enable us to rethink the ways of clinician diagnosis based on medical images. In this thesis, we will introduce 1) mammograms for detecting breast cancers, the most frequently diagnosed solid cancer for U.S. women, 2) lung CT images for detecting lung cancers, the most frequently diagnosed malignant cancer, and 3) head and neck CT images for automated delineation of organs at risk in radiotherapy. First, we will show how to employ the adversarial concept to generate the hard examples improving mammogram mass segmentation. Second, we will demonstrate how to use the weakly labeled data for the mammogram breast cancer diagnosis by efficiently design deep learning for multi-instance learning. Third, the thesis will walk through DeepLung system which combines deep 3D ConvNets and GBM for automated lung nodule detection and classification. Fourth, we will show how to use weakly labeled data to improve existing lung nodule detection system by integrating deep learning with a probabilistic graphic model. Lastly, we will demonstrate the AnatomyNet which is thousands of times faster and more accurate than previous methods on automated anatomy segmentation.Comment: PhD Thesi

Adversarial Deep Structured Nets for Mass Segmentation from Mammograms

Mass segmentation provides effective morphological features which are important for mass diagnosis. In this work, we propose a novel end-to-end network for mammographic mass segmentation which employs a fully convolutional network (FCN) to model a potential function, followed by a CRF to perform structured learning. Because the mass distribution varies greatly with pixel position, the FCN is combined with a position priori. Further, we employ adversarial training to eliminate over-fitting due to the small sizes of mammogram datasets. Multi-scale FCN is employed to improve the segmentation performance. Experimental results on two public datasets, INbreast and DDSM-BCRP, demonstrate that our end-to-end network achieves better performance than state-of-the-art approaches. \footnote{https://github.com/wentaozhu/adversarial-deep-structural-networks.git}Comment: Accepted by ISBI2018. arXiv admin note: substantial text overlap with arXiv:1612.0597

Automated Lensing Learner: Automated Strong Lensing Identification with a Computer Vision Technique

Forthcoming surveys such as the Large Synoptic Survey Telescope (LSST) and Euclid necessitate automatic and efficient identification methods of strong lensing systems. We present a strong lensing identification approach that utilizes a feature extraction method from computer vision, the Histogram of Oriented Gradients (HOG), to capture edge patterns of arcs. We train a supervised classifier model on the HOG of mock strong galaxy-galaxy lens images similar to observations from the Hubble Space Telescope (HST) and LSST. We assess model performance with the area under the curve (AUC) of a Receiver Operating Characteristic (ROC) curve. Models trained on 10,000 lens and non-lens containing images images exhibit an AUC of 0.975 for an HST-like sample, 0.625 for one exposure of LSST, and 0.809 for 10-year mock LSST observations. Performance appears to continually improve with the training set size. Models trained on fewer images perform better in absence of the lens galaxy light. However, with larger training data sets, information from the lens galaxy actually improves model performance, indicating that HOG captures much of the morphological complexity of the arc finding problem. We test our classifier on data from the Sloan Lens ACS Survey and find that small scale image features reduces the efficiency of our trained model. However, these preliminary tests indicate that some parameterizations of HOG can compensate for differences between observed mock data. One example best-case parameterization results in an AUC of 0.6 in the F814 filter image with other parameterization results equivalent to random performance.Comment: 18 pages, 14 figures, summarizing results in figure