In this work, we present a fully automated lung computed tomography (CT) cancer diagnosis system, DeepLung. DeepLung consists of two components, nodule detection (identifying the locations of candidate nodules) and classification (classifying candidate nodules into benign or malignant). Considering the 3D nature of lung CT data and the compactness of dual path networks (DPN), two deep 3D DPN are designed for nodule detection and classification respectively. Specifically, a 3D Faster Regions with Convolutional Neural Net (R-CNN) is designed for nodule detection with 3D dual path blocks and a U-net-like encoder-decoder structure to effectively learn nodule features. For nodule classification, gradient boosting machine (GBM) with 3D dual path network features is proposed. The nodule classification subnetwork was validated on a public dataset from LIDC-IDRI, on which it achieved better performance than state-of-the-art approaches and surpassed the performance of experienced doctors based on image modality. Within the DeepLung system, candidate nodules are detected first by the nodule detection subnetwork, and nodule diagnosis is conducted by the classification subnetwork. Extensive experimental results demonstrate that DeepLung has performance comparable to experienced doctors both for the nodule-level and patient-level diagnosis on the LIDC-IDRI dataset.\footnote{https://github.com/uci-cbcl/DeepLung.git}
In this paper, we study the application of GIST SVM in disease prediction (detection of cancer). Pattern classification problems can be effectively solved by Support vector machines. Here we propose a classifier which can differentiate patients having benign and malignant cancer cells. To improve the accuracy of classification, we propose to determine the optimal size of the training set and perform feature selection. To find the optimal size of the training set, different sizes of training sets are experimented and the one with highest classification rate is selected. The optimal features are selected through their F-Scores.
Early detection of breast cancer is a powerful tool towards decreasing its socioeconomic burden. Although, artificial intelligence (AI) methods have shown remarkable results towards this goal, their "black box" nature hinders their wide adoption in clinical practice. To address the need for AI guided breast cancer diagnosis, interpretability methods can be utilized. In this study, we used AI methods, i.e., Random Forests (RF), Neural Networks (NN) and Ensembles of Neural Networks (ENN), towards this goal and explained and optimized their performance through interpretability techniques, such as the Global Surrogate (GS) method, the Individual Conditional Expectation (ICE) plots and the Shapley values (SV). The Wisconsin Diagnostic Breast Cancer (WDBC) dataset of the open UCI repository was used for the training and evaluation of the AI algorithms. The best performance for breast cancer diagnosis was achieved by the proposed ENN (96.6% accuracy and 0.96 area under the ROC curve), and its predictions were explained by ICE plots, proving that its decisions were compliant with current medical knowledge and can be further utilized to gain new insights in the pathophysiological mechanisms of breast cancer. Feature selection based on features' importance according to the GS model improved the performance of the RF (leading the accuracy from 96.49% to 97.18% and the area under the ROC curve from 0.96 to 0.97) and feature selection based on features' importance according to SV improved the performance of the NN (leading the accuracy from 94.6% to 95.53% and the area under the ROC curve from 0.94 to 0.95). Compared to other approaches on the same dataset, our proposed models demonstrated state of the art performance while being interpretable.
Mitotic count (MC) is an important histological parameter for cancer diagnosis and grading, but the manual process for obtaining MC from whole-slide histopathological images is very time-consuming and prone to error. Therefore, deep learning models have been proposed to facilitate this process. Existing approaches utilize a two-stage pipeline: the detection stage for identifying the locations of potential mitotic cells and the classification stage for refining prediction confidences. However, this pipeline formulation can lead to inconsistencies in the classification stage due to the poor prediction quality of the detection stage and the mismatches in training data distributions between the two stages. In this study, we propose a Refine Cascade Network (ReCasNet), an enhanced deep learning pipeline that mitigates the aforementioned problems with three improvements. First, window relocation was used to reduce the number of poor quality false positives generated during the detection stage. Second, object re-cropping was performed with another deep learning model to adjust poorly centered objects. Third, improved data selection strategies were introduced during the classification stage to reduce the mismatches in training data distributions. ReCasNet was evaluated on two large-scale mitotic figure recognition datasets, canine cutaneous mast cell tumor (CCMCT) and canine mammary carcinoma (CMC), which resulted in up to 4.8% percentage point improvements in the F1 scores for mitotic cell detection and 44.1% reductions in mean absolute percentage error (MAPE) for MC prediction. Techniques that underlie ReCasNet can be generalized to other two-stage object detection networks and should contribute to improving the performances of deep learning models in broad digital pathology applications.
Lung cancer is a global and dangerous disease, and its early detection is crucial to reducing the risks of mortality. In this regard, it has been of great interest in developing a computer-aided system for pulmonary nodules detection as early as possible on thoracic CT scans. In general, a nodule detection system involves two steps: (i) candidate nodule detection at a high sensitivity, which captures many false positives and (ii) false positive reduction from candidates. However, due to the high variation of nodule morphological characteristics and the possibility of mistaking them for neighboring organs, candidate nodule detection remains a challenge. In this study, we propose a novel Multi-scale Gradual Integration Convolutional Neural Network (MGI-CNN), designed with three main strategies: (1) to use multi-scale inputs with different levels of contextual information, (2) to use abstract information inherent in different input scales with gradual integration, and (3) to learn multi-stream feature integration in an end-to-end manner. To verify the efficacy of the proposed network, we conducted exhaustive experiments on the LUNA16 challenge datasets by comparing the performance of the proposed method with state-of-the-art methods in the literature. On two candidate subsets of the LUNA16 dataset, i.e., V1 and V2, our method achieved an average CPM of 0.908 (V1) and 0.942 (V2), outperforming comparable methods by a large margin. Our MGI-CNN is implemented in Python using TensorFlow and the source code is available from 'https://github.com/ku-milab/MGICNN.'
Objective: Lung cancer is the leading cause of cancer-related death worldwide. Computer-aided diagnosis (CAD) systems have shown significant promise in recent years for facilitating the effective detection and classification of abnormal lung nodules in computed tomography (CT) scans. While hand-engineered radiomic features have been traditionally used for lung cancer prediction, there have been significant recent successes achieving state-of-the-art results in the area of discovery radiomics. Here, radiomic sequencers comprising of highly discriminative radiomic features are discovered directly from archival medical data. However, the interpretation of predictions made using such radiomic sequencers remains a challenge. Method: A novel end-to-end interpretable discovery radiomics-driven lung cancer prediction pipeline has been designed, build, and tested. The radiomic sequencer being discovered possesses a deep architecture comprised of stacked interpretable sequencing cells (SISC). Results: The SISC architecture is shown to outperform previous approaches while providing more insight in to its decision making process. Conclusion: The SISC radiomic sequencer is able to achieve state-of-the-art results in lung cancer prediction, and also offers prediction interpretability in the form of critical response maps. Significance: The critical response maps are useful for not only validating the predictions of the proposed SISC radiomic sequencer, but also provide improved radiologist-machine collaboration for effective diagnosis.
The recent development of imaging and sequencing technologies enables systematic advances in the clinical study of lung cancer. Meanwhile, the human mind is limited in effectively handling and fully utilizing the accumulation of such enormous amounts of data. Machine learning-based approaches play a critical role in integrating and analyzing these large and complex datasets, which have extensively characterized lung cancer through the use of different perspectives from these accrued data. In this article, we provide an overview of machine learning-based approaches that strengthen the varying aspects of lung cancer diagnosis and therapy, including early detection, auxiliary diagnosis, prognosis prediction and immunotherapy practice. Moreover, we highlight the challenges and opportunities for future applications of machine learning in lung cancer.
The recent development of imaging and sequencing technologies enables systematic advances in the clinical study of lung cancer. Meanwhile, the human mind is limited in effectively handling and fully utilizing the accumulation of such enormous amounts of data. Machine learning-based approaches play a critical role in integrating and analyzing these large and complex datasets, which have extensively characterized lung cancer through the use of different perspectives from these accrued data. In this article, we provide an overview of machine learning-based approaches that strengthen the varying aspects of lung cancer diagnosis and therapy, including early detection, auxiliary diagnosis, prognosis prediction and immunotherapy practice. Moreover, we highlight the challenges and opportunities for future applications of machine learning in lung cancer.
Skin cancer is a major public health problem, as is the most common type of cancer and represents more than half of cancer diagnoses worldwide. Early detection influences the outcome of the disease and motivates our work. We investigate the composition of CNN committees and data augmentation for the the ISBI 2017 Melanoma Classification Challenge (named Skin Lesion Analysis towards Melanoma Detection) facing the peculiarities of dealing with such a small, unbalanced, biological database. For that, we explore committees of Convolutional Neural Networks trained over the ISBI challenge training dataset artificially augmented by both classical image processing transforms and image warping guided by specialist knowledge about the lesion axis and improve the final classifier invariance to common melanoma variations.
Oral cancer incidence is rapidly increasing worldwide. The most important determinant factor in cancer survival is early diagnosis. To facilitate large scale screening, we propose a fully automated end-to-end pipeline for oral cancer screening on whole slide cytology images. The pipeline consists of regression based nucleus detection, followed by per cell focus selection, and CNN based classification. We demonstrate that the pipeline provides fast and efficient cancer classification of whole slide cytology images, improving over previous results. The complete source code is made available as open source (https://github.com/MIDA-group/OralScreen).
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