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Background: X-ray dark-field imaging (XDFI) has been explored to provide superior performance over the conventional X-ray imaging for the diagnosis of many pathologic conditions. A simulation tool to reliably predict clinical XDFI images at a human scale, however, is currently missing. Purpose: In this paper, we demonstrate XDFI simulation at a human scale for the first time to the best of our knowledge. Using the developed simulation tool, we demonstrate the strengths and limitations of XDFI for the diagnosis of emphysema, fibrosis, atelectasis, edema, and pneumonia. Methods: We augment the XCAT phantom with Voronoi grids to simulate alveolar substructure, responsible for the dark-field signal from lungs, assign material properties to each tissue type, and simulate X-ray wave propagation through the augmented XCAT phantom using a multi-layer wave-optics propagation. Altering the density and thickness of the Voronoi grids as well as the material properties, we simulate XDFI images of normal and diseased lungs. Results: Our simulation framework can generate realistic XDFI images of a human chest with normal or diseased lungs. The simulation confirms that the normal, emphysematous, and fibrotic lungs show clearly distinct dark-field signals. It also shows that alveolar fluid accumulation in pneumonia, wall thickening in interstitial edema, and deflation in atelectasis result in a similar reduction in dark-field signal. Conclusions: It is feasible to augment XCAT with pulmonary substructure and generate realistic XDFI images using multi-layer wave optics. By providing the most realistic XDFI images of lung pathologies, the developed simulation framework will enable in-silico clinical trials and the optimization of both hardware and software for XDFI.

We consider the problem of graph analytics on evolving graphs. In this scenario, a query typically needs to be applied to different snapshots of the graph over an extended time window. We propose CommonGraph, an approach for efficient processing of queries on evolving graphs. We first observe that edge deletions are significantly more expensive than addition operations. CommonGraph converts all deletions to additions by finding a common graph that exists across all snapshots. After computing the query on this graph, to reach any snapshot, we simply need to add the missing edges and incrementally update the query results. CommonGraph also allows sharing of common additions among snapshots that require them, and breaks the sequential dependency inherent in the traditional streaming approach where snapshots are processed in sequence, enabling additional opportunities for parallelism. We incorporate the CommonGraph approach by extending the KickStarter streaming framework. CommonGraph achieves 1.38x-8.17x improvement in performance over Kickstarter across multiple benchmarks.

Purpose: Despite the potential of machine learning models, the lack of generalizability has hindered their widespread adoption in clinical practice. We investigate three methodological pitfalls: (1) violation of independence assumption, (2) model evaluation with an inappropriate performance indicator or baseline for comparison, and (3) batch effect. Materials and Methods: Using several retrospective datasets, we implement machine learning models with and without the pitfalls to quantitatively illustrate these pitfalls' effect on model generalizability. Results: Violation of independence assumption, more specifically, applying oversampling, feature selection, and data augmentation before splitting data into train, validation, and test sets, respectively, led to misleading and superficial gains in F1 scores of 71.2% in predicting local recurrence and 5.0% in predicting 3-year overall survival in head and neck cancer as well as 46.0% in distinguishing histopathological patterns in lung cancer. Further, randomly distributing data points for a subject across training, validation, and test sets led to a 21.8% superficial increase in F1 score. Also, we showed the importance of the choice of performance measures and baseline for comparison. In the presence of batch effect, a model built for pneumonia detection led to F1 score of 98.7%. However, when the same model was applied to a new dataset of normal patients, it only correctly classified 3.86% of the samples. Conclusions: These methodological pitfalls cannot be captured using internal model evaluation, and the inaccurate predictions made by such models may lead to wrong conclusions and interpretations. Therefore, understanding and avoiding these pitfalls is necessary for developing generalizable models., Comment: 18 pages, 7 Figures

Urinalysis is a standard diagnostic test to detect urinary system related problems. The automation of urinalysis will reduce the overall diagnostic time. Recent studies used urine microscopic datasets for designing deep learning based algorithms to classify and detect urine cells. But these datasets are not publicly available for further research. To alleviate the need for urine datsets, we prepare our urine sediment microscopic image (UMID) dataset comprising of around 3700 cell annotations and 3 categories of cells namely RBC, pus and epithelial cells. We discuss the several challenges involved in preparing the dataset and the annotations. We make the dataset publicly available., Comment: 7 pages, 1 image

Containment, the key strategy in quickly halting an epidemic, requires rapid identification and quarantine of the infected individuals, determination of whom they have had close contact with in the previous days and weeks, and decontamination of locations the infected individual has visited. Achieving containment demands accurate and timely collection of the infected individual's location and contact history. Traditionally, this process is labor intensive, susceptible to memory errors, and fraught with privacy concerns. With the recent almost ubiquitous availability of smart phones, many people carry a tool which can be utilized to quickly identify an infected individual's contacts during an epidemic, such as the current 2019 novel Coronavirus crisis. Unfortunately, the very same first-generation contact tracing tools have been used to expand mass surveillance, limit individual freedoms and expose the most private details about individuals. We seek to outline the different technological approaches to mobile-phone based contact-tracing to date and elaborate on the opportunities and the risks that these technologies pose to individuals and societies. We describe advanced security enhancing approaches that can mitigate these risks and describe trade-offs one must make when developing and deploying any mass contact-tracing technology. With this paper, our aim is to continue to grow the conversation regarding contact-tracing for epidemic and pandemic containment and discuss opportunities to advance this space. We invite feedback and discussion., Comment: 15 pages

Shortage of labeled data has been holding the surge of deep learning in healthcare back, as sample sizes are often small, patient information cannot be shared openly, and multi-center collaborative studies are a burden to set up. Distributed machine learning methods promise to mitigate these problems. We argue for a split learning based approach and apply this distributed learning method for the first time in the medical field to compare performance against (1) centrally hosted and (2) non collaborative configurations for a range of participants. Two medical deep learning tasks are used to compare split learning to conventional single and multi center approaches: a binary classification problem of a data set of 9000 fundus photos, and multi-label classification problem of a data set of 156,535 chest X-rays. The several distributed learning setups are compared for a range of 1-50 distributed participants. Performance of the split learning configuration remained constant for any number of clients compared to a single center study, showing a marked difference compared to the non collaborative configuration after 2 clients (p < 0.001) for both sets. Our results affirm the benefits of collaborative training of deep neural networks in health care. Our work proves the significant benefit of distributed learning in healthcare, and paves the way for future real-world implementations., Comment: Workshop paper: 8 pages, 2 figures, 1 table