10 research outputs found

    Privacy-Preserving Dashboard for F.A.I.R Head and Neck Cancer data supporting multi-centered collaborations

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    Research in modern healthcare requires vast volumes of data from various healthcare centers across the globe. It is not always feasible to centralize clinical data without compromising privacy. A tool addressing these issues and facilitating reuse of clinical data is the need of the hour. The Federated Learning approach, governed in a set of agreements such as the Personal Health Train (PHT) manages to tackle these concerns by distributing models to the data centers instead of the traditional approach of centralizing datasets. One of the prerequisites of PHT is using semantically interoperable datasets for the models to be able to find them. FAIR (Findable, Accessible, Interoperable, Reusable) principles help in building interoperable and reusable data by adding knowledge representation and providing descriptive metadata. However, the process of making data FAIR is not always easy and straight-forward. Our main objective is to disentangle this process by using domain and technical expertise and get data prepared for federated learning. This paper introduces applications that are easily deployable as Docker containers, which will automate parts of the aforementioned process and significantly simplify the task of creating FAIR clinical data. Our method bypasses the need for clinical researchers to have a high degree of technical skills. We demonstrate the FAIR-ification process by applying it to five Head and Neck cancer datasets (four public and one private). The PHT paradigm is explored by building a distributed visualization dashboard from the aggregated summaries of the FAIR-ified datasets. Using the PHT infrastructure for exchanging only statistical summaries or model coefficients allows researchers to explore data from multiple centers without breaching privacy

    Automatic classification of dental artifact status for efficient image veracity checks:effects of image resolution and convolutional neural network depth

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    Enabling automated pipelines, image analysis and big data methodology in cancer clinics requires thorough understanding of the data. Automated quality assurance steps could improve the efficiency and robustness of these methods by verifying possible data biases. In particular, in head and neck (H&amp;N) computed-tomography (CT) images, dental artifacts (DA) obscure visualization of structures and the accuracy of Hounsfield units; a challenge for image analysis tasks, including radiomics, where poor image quality can lead to systemic biases. In this work we analyze the performance of three-dimensional convolutional neural networks (CNN) trained to classify DA statuses. 1538 patient images were scored by a single observer as DA positive or negative. Stratified five-fold cross validation was performed to train and test CNNs using various isotropic resampling grids (64(3), 128(3) and 256(3)), with CNN depths designed to produce 32(3), 16(3), and 8(3) machine generated features. These parameters were selected to determine if more computationally efficient CNNs could be utilized to achieve the same performance. The area under the precision recall curve (PR-AUC) was used to assess CNN performance. The highest PR-AUC (0.92 +/- 0.03) was achieved with a CNN depth = 5, resampling grid = 256. The CNN performance with 256(3) resampling grid size is not significantly better than 64(3) and 128(3) after 20 epochs, which had PR-AUC = 0.89 +/- 0.03 (p -value = 0.28) and 0.91 +/- 0.02 (p -value = 0.93) at depths of 3 and 4, respectively. Our experiments demonstrate the potential to automate specific quality assurance tasks required for unbiased and robust automated pipeline and image analysis research. Additionally, we determined that there is an opportunity to simplify CNNs with smaller resampling grids to make the process more amenable to very large datasets that will be available in the future.</p

    Vulnerabilities of radiomic signature development:The need for safeguards

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    Purpose: Refinement of radiomic results and methodologies is required to ensure progression of the field. In this work, we establish a set of safeguards designed to improve and support current radiomic methodologies through detailed analysis of a radiomic signature. Methods: A radiomic model (MW2018) was fitted and externally validated using features extracted from previously reported lung and head and neck (H&N) cancer datasets using gross-tumour-volume contours, as well as from images with randomly permuted voxel index values; i.e. images without meaningful texture. To determine MW2018's added benefit, the prognostic accuracy of tumour volume alone was calculated as a baseline. Results: MW2018 had an external validation concordance index (c-index) of 0.64. However, a similar performance was achieved using features extracted from images with randomized signal intensities (c-index = 0.64 and 0.60 for H&N and lung, respectively). Tumour volume had a c-index = 0.64 and correlated strongly with three of the four model features. It was determined that the signature was a surrogate for tumour volume and that intensity and texture values were not pertinent for prognostication. Conclusion: Our experiments reveal vulnerabilities in radiomic signature development processes and suggest safeguards that can be used to refine methodologies, and ensure productive radiomic development using objective and independent features. (C) 2018 The Author(s). Published by Elsevier B.V

    User-controlled pipelines for feature integration and head and neck radiation therapy outcome predictions

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    Purpose Precision cancer medicine is dependent on accurate prediction of disease and treatment outcome, requiring integration of clinical, imaging and interventional knowledge. User controlled pipelines are capable of feature integration with varied levels of human interaction. In this work we present two pipelines designed to combine clinical, radiomic (quantified imaging), and RTx-omic (quantified radiation therapy (RT) plan) information for prediction of locoregional failure (LRF) in head and neck cancer (HN and 2) a pipeline with minimal user input that utilizes deep learning convolutional neural networks to extract and combine CT imaging, RT dose and clinical features for model development. Results Clinical features with logistic regression in our highly user-driven pipeline had the highest precision recall area under the curve (PR-AUC) of 0.66 (0.33–0.93), where a PR-AUC = 0.11 is considered random. CONCLUSIONS: Our work demonstrates the potential to aggregate features from multiple specialties for conditional-outcome predictions using pipelines with varied levels of human interaction. Most importantly, our results provide insights into the importance of data curation and quality, as well as user, data and methodology bias awareness as it pertains to result interpretation in user controlled pipelines