Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.

SCI Publications

2024


A.M. Chalifoux, L. Gibb, K.N. Wurth, T. Tenner, T. Tasdizen, L. MacDonald. “Morphology of uranium oxides reduced from magnesium and sodium diuranate,” In Radiochimica Acta, Vol. 112, No. 2, pp. 73-84. 2024.

ABSTRACT

Morphological analysis of uranium materials has proven to be a key signature for nuclear forensic purposes. This study examines the morphological changes to magnesium diuranate (MDU) and sodium diuranate (SDU) during reduction in a 10 % hydrogen atmosphere with and without steam present. Impurity concentrations of the materials were also examined pre and post reduction using energy dispersive X-ray spectroscopy combined with scanning electron microscopy (SEM-EDX). The structures of the MDU, SDU, and UO x samples were analyzed using powder X-ray diffraction (p-XRD). Using this method, UO x from MDU was found to be a mixture of UO2, U4O9, and MgU2O6 while UO x from SDU were combinations of UO2, U4O9, U3O8, and UO3. By SEM, the MDU and UO x from MDU had identical morphologies comprised of large agglomerates of rounded particles in an irregular pattern. SEM-EDX revealed pockets of high U and high Mg content distributed throughout the materials. The SDU and UO x from SDU had slightly different morphologies. The SDU consisted of massive agglomerates of platy sheets with rough surfaces. The UO x from SDU was comprised of massive agglomerates of acicular and sub-rounded particles that appeared slightly sintered. Backscatter images of SDU and related UO x materials showed sub-rounded dark spots indicating areas of high Na content, especially in UO x materials created in the presence of steam. SEM-EDX confirmed the presence of high sodium concentration spots in the SDU and UO x from SDU. Elemental compositions were found to not change between pre and post reduction of MDU and SDU indicating that reduction with or without steam does not affect Mg or Na concentrations. The identification of Mg and Na impurities using SEM analysis presents a readily accessible tool in nuclear material analysis with high Mg and Na impurities likely indicating processing via MDU or SDU, respectively. Machine learning using convolutional neural networks (CNNs) found that the MDU and SDU had unique morphologies compared to previous publications and that there are distinguishing features between materials created with and without steam.



A. Ferrero, E. Ghelichkhan, H. Manoochehri, M.M. Ho, D.J. Albertson, B.J. Brintz, T. Tasdizen, R.T. Whitaker, B. Knudsen. “HistoEM: A Pathologist-Guided and Explainable Workflow Using Histogram Embedding for Gland Classification,” In Modern Pathology, Vol. 37, No. 4, 2024.

ABSTRACT

Pathologists have, over several decades, developed criteria for diagnosing and grading prostate cancer. However, this knowledge has not, so far, been included in the design of convolutional neural networks (CNN) for prostate cancer detection and grading. Further, it is not known whether the features learned by machine-learning algorithms coincide with diagnostic features used by pathologists. We propose a framework that enforces algorithms to learn the cellular and subcellular differences between benign and cancerous prostate glands in digital slides from hematoxylin and eosin–stained tissue sections. After accurate gland segmentation and exclusion of the stroma, the central component of the pipeline, named HistoEM, utilizes a histogram embedding of features from the latent space of the CNN encoder. Each gland is represented by 128 feature-wise histograms that provide the input into a second network for benign vs cancer classification of the whole gland. Cancer glands are further processed by a U-Net structured network to separate low-grade from high-grade cancer. Our model demonstrates similar performance compared with other state-of-the-art prostate cancer grading models with gland-level resolution. To understand the features learned by HistoEM, we first rank features based on the distance between benign and cancer histograms and visualize the tissue origins of the 2 most important features. A heatmap of pixel activation by each feature is generated using Grad-CAM and overlaid on nuclear segmentation outlines. We conclude that HistoEM, similar to pathologists, uses nuclear features for the detection of prostate cancer. Altogether, this novel approach can be broadly deployed to visualize computer-learned features in histopathology images.



S. Ghorbany, M. Hu, S. Yao, C. Wang, Q.C. Nguyen, X. Yue, M. Alirezaei, T. Tasdizen, M Sisk. “Examining the role of passive design indicators in energy burden reduction: Insights from a machine learning and deep learning approach,” In Building and Environment, Elsevier, 2024.

ABSTRACT

Passive design characteristics (PDC) play a pivotal role in reducing the energy burden on households without imposing additional financial constraints on project stakeholders. However, the scarcity of PDC data has posed a challenge in previous studies when assessing their energy-saving impact. To tackle this issue, this research introduces an innovative approach that combines deep learning-powered computer vision with machine learning techniques to examine the relationship between PDC and energy burden in residential buildings. In this study, we employ a convolutional neural network computer vision model to identify and measure key indicators, including window-to-wall ratio (WWR), external shading, and operable window types, using Google Street View images within the Chicago metropolitan area as our case study. Subsequently, we utilize the derived passive design features in conjunction with demographic characteristics to train and compare various machine learning methods. These methods encompass Decision Tree Regression, Random Forest Regression, and Support Vector Regression, culminating in the development of a comprehensive model for energy burden prediction. Our framework achieves a 74.2 % accuracy in forecasting the average energy burden. These results yield invaluable insights for policymakers and urban planners, paving the way toward the realization of smart and sustainable cities.



M.M. Ho, S. Dubey, Y. Chong, B. Knudsen, T. Tasdizen. “F2FLDM: Latent Diffusion Models with Histopathology Pre-Trained Embeddings for Unpaired Frozen Section to FFPE Translation,” Subtitled “arXiv:2404.12650v1,” 2024.

ABSTRACT

The Frozen Section (FS) technique is a rapid and efficient method, taking only 15-30 minutes to prepare slides for pathologists' evaluation during surgery, enabling immediate decisions on further surgical interventions. However, FS process often introduces artifacts and distortions like folds and ice-crystal effects. In contrast, these artifacts and distortions are absent in the higher-quality formalin-fixed paraffin-embedded (FFPE) slides, which require 2-3 days to prepare. While Generative Adversarial Network (GAN)-based methods have been used to translate FS to FFPE images (F2F), they may leave morphological inaccuracies with remaining FS artifacts or introduce new artifacts, reducing the quality of these translations for clinical assessments. In this study, we benchmark recent generative models, focusing on GANs and Latent Diffusion Models (LDMs), to overcome these limitations. We introduce a novel approach that combines LDMs with Histopathology Pre-Trained Embeddings to enhance restoration of FS images. Our framework leverages LDMs conditioned by both text and pre-trained embeddings to learn meaningful features of FS and FFPE histopathology images. Through diffusion and denoising techniques, our approach not only preserves essential diagnostic attributes like color staining and tissue morphology but also proposes an embedding translation mechanism to better predict the targeted FFPE representation of input FS images. As a result, this work achieves a significant improvement in classification performance, with the Area Under the Curve rising from 81.99% to 94.64%, accompanied by an advantageous CaseFD. This work establishes a new benchmark for FS to FFPE image translation quality, promising enhanced reliability and accuracy in histopathology FS image analysis.



M.M. Ho, E. Ghelichkhan, Y. Chong, Y. Zhou, B.S. Knudsen, T. Tasdizen. “DISC: Latent Diffusion Models with Self-Distillation from Separated Conditions for Prostate Cancer Grading,” Subtitled “arXiv:2404.13097,” 2024.

ABSTRACT

Latent Diffusion Models (LDMs) can generate high-fidelity images from noise, offering a promising approach for augmenting histopathology images for training cancer grading models. While previous works successfully generated high-fidelity histopathology images using LDMs, the generation of image tiles to improve prostate cancer grading has not yet been explored. Additionally, LDMs face challenges in accurately generating admixtures of multiple cancer grades in a tile when conditioned by a tile mask. In this study, we train specific LDMs to generate synthetic tiles that contain multiple Gleason Grades (GGs) by leveraging pixel-wise annotations in input tiles. We introduce a novel framework named Self-Distillation from Separated Conditions (DISC) that generates GG patterns guided by GG masks. Finally, we deploy a training framework for pixel-level and slide-level prostate cancer grading, where synthetic tiles are effectively utilized to improve the cancer grading performance of existing models. As a result, this work surpasses previous works in two domains: 1) our LDMs enhanced with DISC produce more accurate tiles in terms of GG patterns, and 2) our training scheme, incorporating synthetic data, significantly improves the generalization of the baseline model for prostate cancer grading, particularly in challenging cases of rare GG5, demonstrating the potential of generative models to enhance cancer grading when data is limited.



J Johnson, L McDonald, T Tasdizen. “Improving uranium oxide pathway discernment and generalizability using contrastive self-supervised learning,” In Computational Materials Science, Vol. 223, Elsevier, 2024.

ABSTRACT

In the field of Nuclear Forensics, there exists a plethora of different tools to aid investigators when performing analysis of unknown nuclear materials. Many of these tools offer visual representations of the uranium ore concentrate (UOC) materials that include complimentary and contrasting information. In this paper, we present a novel technique drawing from state-of-the-art machine learning methods that allows information from scanning electron microscopy images (SEM) to be combined to create digital encodings of the material that can be used to determine the material’s processing route. Our technique can classify UOC processing routes with greater than 96% accuracy in a fraction of a second and can be adapted to unseen samples at similarly high accuracy. The technique’s high accuracy and speed allow forensic investigators to quickly get preliminary results, while generalization allows the model to be adapted to new materials or processing routes quickly without the need for complete retraining of the model.



Q.C. Nguyen, T. Tasdizen, M. Alirezaei, H. Mane, X. Yue, J.S. Merchant, W. Yu, L. Drew, D. Li, T.T. Nguyen. “Neighborhood built environment, obesity, and diabetes: A Utah siblings study,” In SSM - Population Health, Vol. 26, 2024.

ABSTRACT

Background

This study utilizes innovative computer vision methods alongside Google Street View images to characterize neighborhood built environments across Utah.

Methods

Convolutional Neural Networks were used to create indicators of street greenness, crosswalks, and building type on 1.4 million Google Street View images. The demographic and medical profiles of Utah residents came from the Utah Population Database (UPDB). We implemented hierarchical linear models with individuals nested within zip codes to estimate associations between neighborhood built environment features and individual-level obesity and diabetes, controlling for individual- and zip code-level characteristics (n = 1,899,175 adults living in Utah in 2015). Sibling random effects models were implemented to account for shared family attributes among siblings (n = 972,150) and twins (n = 14,122).

Results

Consistent with prior neighborhood research, the variance partition coefficients (VPC) of our unadjusted models nesting individuals within zip codes were relatively small (0.5%–5.3%), except for HbA1c (VPC = 23%), suggesting a small percentage of the outcome variance is at the zip code-level. However, proportional change in variance (PCV) attributable to zip codes after the inclusion of neighborhood built environment variables and covariates ranged between 11% and 67%, suggesting that these characteristics account for a substantial portion of the zip code-level effects. Non-single-family homes (indicator of mixed land use), sidewalks (indicator of walkability), and green streets (indicator of neighborhood aesthetics) were associated with reduced diabetes and obesity. Zip codes in the third tertile for non-single-family homes were associated with a 15% reduction (PR: 0.85; 95% CI: 0.79, 0.91) in obesity and a 20% reduction (PR: 0.80; 95% CI: 0.70, 0.91) in diabetes. This tertile was also associated with a BMI reduction of −0.68 kg/m2 (95% CI: −0.95, −0.40)

Conclusion

We observe associations between neighborhood characteristics and chronic diseases, accounting for biological, social, and cultural factors shared among siblings in this large population-based study.



Q.C. Nguyen, M. Alirezaei, X. Yue, H. Mane, D. Li, L. Zhao, T.T. Nguyen, R. Patel, W. Yu, M. Hu, D. Quistberg, T. Tasdizen. “Leveraging computer vision for predicting collision risks: a cross-sectional analysis of 2019–2021 fatal collisions in the USA,” In Injury Prevention, BMJ, 2024.

ABSTRACT

Objective The USA has higher rates of fatal motor vehicle collisions than most high-income countries. Previous studies examining the role of the built environment were generally limited to small geographic areas or single cities. This study aims to quantify associations between built environment characteristics and traffic collisions in the USA.

Methods Built environment characteristics were derived from Google Street View images and summarised at the census tract level. Fatal traffic collisions were obtained from the 2019–2021 Fatality Analysis Reporting System. Fatal and non-fatal traffic collisions in Washington DC were obtained from the District Department of Transportation. Adjusted Poisson regression models examined whether built environment characteristics are related to motor vehicle collisions in the USA, controlling for census tract sociodemographic characteristics.

Results Census tracts in the highest tertile of sidewalks, single-lane roads, streetlights and street greenness had 70%, 50%, 30% and 26% fewer fatal vehicle collisions compared with those in the lowest tertile. Street greenness and single-lane roads were associated with 37% and 38% fewer pedestrian-involved and cyclist-involved fatal collisions. Analyses with fatal and non-fatal collisions in Washington DC found streetlights and stop signs were associated with fewer pedestrians and cyclists-involved vehicle collisions while road construction had an adverse association.

Conclusion This study demonstrates the utility of using data algorithms that can automatically analyse street segments to create indicators of the built environment to enhance understanding of large-scale patterns and inform interventions to decrease road traffic injuries and fatalities.



H.Y. Zewdie, O.L. Sarmiento, J.D. Pinzón, M.A. Wilches-Mogollon, P. A. Arbelaez, L. Baldovino-Chiquillo, D. Hidalgo, L. Guzman, S.J. Mooney, Q.C. Nguyen, T. Tasdizen, D.A. Quistberg . “Road Traffic Injuries and the Built Environment in Bogotá, Colombia, 2015–2019: A Cross-Sectional Analysis,” In Journal of Urban Health, Springer, 2024.

ABSTRACT

Nine in 10 road traffic deaths occur in low- and middle-income countries (LMICs). Despite this disproportionate burden, few studies have examined built environment correlates of road traffic injury in these settings, including in Latin America. We examined road traffic collisions in Bogotá, Colombia, occurring between 2015 and 2019, and assessed the association between neighborhood-level built environment features and pedestrian injury and death. We used descriptive statistics to characterize all police-reported road traffic collisions that occurred in Bogotá between 2015 and 2019. Cluster detection was used to identify spatial clustering of pedestrian collisions. Adjusted multivariate Poisson regression models were fit to examine associations between several neighborhood-built environment features and rate of pedestrian road traffic injury and death. A total of 173,443 police-reported traffic collisions occurred in Bogotá between 2015 and 2019. Pedestrians made up about 25% of road traffic injuries and 50% of road traffic deaths in Bogotá between 2015 and 2019. Pedestrian collisions were spatially clustered in the southwestern region of Bogotá. Neighborhoods with more street trees (RR, 0.90; 95% CI, 0.82–0.98), traffic signals (0.89, 0.81–0.99), and bus stops (0.89, 0.82–0.97) were associated with lower pedestrian road traffic deaths. Neighborhoods with greater density of large roads were associated with higher pedestrian injury. Our findings highlight the potential for pedestrian-friendly infrastructure to promote safer interactions between pedestrians and motorists in Bogotá and in similar urban contexts globally.


2023


M. Hu, K. Zhang, Q. Nguyen, T. Tasdizen. “The effects of passive design on indoor thermal comfort and energy savings for residential buildings in hot climates: A systematic review,” In Urban Climate, Vol. 49, pp. 101466. 2023.
DOI: https://doi.org/10.1016/j.uclim.2023.101466

ABSTRACT

In this study, a systematic review and meta-analysis were conducted to identify, categorize, and investigate the effectiveness of passive cooling strategies (PCSs) for residential buildings. Forty-two studies published between 2000 and 2021 were reviewed; they examined the effects of PCSs on indoor temperature decrease, cooling load reduction, energy savings, and thermal comfort hour extension. In total, 30 passive strategies were identified and classified into three categories: design approach, building envelope, and passive cooling system. The review found that using various passive strategies can achieve, on average, (i) an indoor temperature decrease of 2.2 °C, (ii) a cooling load reduction of 31%, (iii) energy savings of 29%, and (v) a thermal comfort hour extension of 23%. Moreover, the five most effective passive strategies were identified as well as the differences between hot and dry climates and hot and humid climates.



C. Ly, C. Nizinski, A. Hagen, L. McDonald IV, T. Tasdizen. “Improving Robustness for Model Discerning Synthesis Process of Uranium Oxide with Unsupervised Domain Adaptation,” In Frontiers in Nuclear Engineering, 2023.

ABSTRACT

The quantitative characterization of surface structures captured in scanning electron microscopy (SEM) images has proven to be effective for discerning provenance of an unknown nuclear material. Recently, many works have taken advantage of the powerful performance of convolutional neural networks (CNNs) to provide faster and more consistent characterization of surface structures. However, one inherent limitation of CNNs is their degradation in performance when encountering discrepancy between training and test datasets, which limits their use widely.The common discrepancy in an SEM image dataset occurs at low-level image information due to user-bias in selecting acquisition parameters and microscopes from different manufacturers.Therefore, in this study, we present a domain adaptation framework to improve robustness of CNNs against the discrepancy in low-level image information. Furthermore, our proposed approach makes use of only unlabeled test samples to adapt a pretrained model, which is more suitable for nuclear forensics application for which obtaining both training and test datasets simultaneously is a challenge due to data sensitivity. Through extensive experiments, we demonstrate that our proposed approach effectively improves the performance of a model by at least 18% when encountering domain discrepancy, and can be deployed in many CNN architectures.



L.W. McDonald IV, K. Sentz, A. Hagen, B.W. Chung, T. Tasdizen, et. al.. “Review of Multi-Faceted Morphologic Signatures of Actinide Process Materials for Nuclear Forensic Science,” In Journal of Nuclear Materials, Elsevier, 2023.

ABSTRACT

Particle morphology is an emerging signature that has the potential to identify the processing history of unknown nuclear materials. Using readily available scanning electron microscopes (SEM), the morphology of nearly any solid material can be measured within hours. Coupled with robust image analysis and classification methods, the morphological features can be quantified and support identification of the processing history of unknown nuclear materials. The viability of this signature depends on developing databases of morphological features, coupled with a rapid data analysis and accurate classification process. With developed reference methods, datasets, and throughputs, morphological analysis can be applied within days to (i) interdicted bulk nuclear materials (gram to kilogram quantities), and (ii) trace amounts of nuclear materials detected on swipes or environmental samples. This review aims to develop validated and verified analytical strategies for morphological analysis relevant to nuclear forensics.



M. Shao, T. Tasdizen, S. Joshi. “Analyzing the Domain Shift Immunity of Deep Homography Estimation,” Subtitled “arXiv:2304.09976v1,” 2023.

ABSTRACT

Homography estimation is a basic image-alignment method in many applications. Recently, with the development of convolutional neural networks (CNNs), some learning based approaches have shown great success in this task. However, the performance across different domains has never been researched. Unlike other common tasks (e.g., classification, detection, segmentation), CNN based homography estimation models show a domain shift immunity, which means a model can be trained on one dataset and tested on another without any transfer learning. To explain this unusual performance, we need to determine how CNNs estimate homography. In this study, we first show the domain shift immunity of different deep homography estimation models. We then use a shallow network with a specially designed dataset to analyze the features used for estimation. The results show that networks use low-level texture information to estimate homography. We also design some experiments to compare the performance between different texture densities and image features distorted on some common datasets to demonstrate our findings. Based on these findings, we provide an explanation of the domain shift immunity of deep homography estimation.



B. Zhang, H. Manoochehri, M.M. Ho, F. Fooladgar, Y. Chong, B. Knudsen, D. Sirohi, T. Tasdizen. “CLASSMix: Adaptive stain separation-based contrastive learning with pseudo labeling for histopathological image classification,” Subtitled “arXiv:2312.06978v2,” 2023.

ABSTRACT

Histopathological image classification is one of the critical aspects in medical image analysis. Due to the high expense associated with the labeled data in model training, semi-supervised learning methods have been proposed to alleviate the need of extensively labeled datasets. In this work, we propose a model for semi-supervised classification tasks on digital histopathological Hematoxylin and Eosin (H&E) images. We call the new model Contrastive Learning with Adaptive Stain Separation and MixUp (CLASS-M). Our model is formed by two main parts: contrastive learning between adaptively stain separated Hematoxylin images and Eosin images, and pseudo-labeling using MixUp. We compare our model with other state-of-the-art models on clear cell renal cell carcinoma (ccRCC) datasets from our institution and The Cancer Genome Atlas Program (TCGA). We demonstrate that our CLASS-M model has the best performance on both datasets. The contributions of different parts in our model are also analyzed.


2022


M. Alirezaei, T. Tasdizen. “Adversarially Robust Classification by Conditional Generative Model Inversion,” Subtitled “arXiv preprint arXiv:2201.04733,” 2022.

ABSTRACT

Most adversarial attack defense methods rely on obfuscating gradients. These methods are successful in defending against gradient-based attacks; however, they are easily circumvented by attacks which either do not use the gradient or by attacks which approximate and use the corrected gradient. Defenses that do not obfuscate gradients such as adversarial training exist, but these approaches generally make assumptions about the attack such as its magnitude. We propose a classification model that does not obfuscate gradients and is robust by construction without assuming prior knowledge about the attack. Our method casts classification as an optimization problem where we "invert" a conditional generator trained on unperturbed, natural images to find the class that generates the closest sample to the query image. We hypothesize that a potential source of brittleness against adversarial attacks is the high-to-low-dimensional nature of feed-forward classifiers which allows an adversary to find small perturbations in the input space that lead to large changes in the output space. On the other hand, a generative model is typically a low-to-high-dimensional mapping. While the method is related to Defense-GAN, the use of a conditional generative model and inversion in our model instead of the feed-forward classifier is a critical difference. Unlike Defense-GAN, which was shown to generate obfuscated gradients that are easily circumvented, we show that our method does not obfuscate gradients. We demonstrate that our model is extremely robust against black-box attacks and has improved robustness against white-box attacks compared to naturally trained, feed-forward classifiers.



M. Alirezaei, Q.C. Nguyen, R. Whitaker, T. Tasdizen. “Multi-Task Classification for Improved Health Outcome Prediction Based on Environmental Indicators,” In IEEE Access, 2022.
DOI: 10.1109/ACCESS.2023.3295777

ABSTRACT

The influence of the neighborhood environment on health outcomes has been widely recognized in various studies. Google street view (GSV) images offer a unique and valuable tool for evaluating neighborhood environments on a large scale. By annotating the images with labels indicating the presence or absence of certain neighborhood features, we can develop classifiers that can automatically analyze and evaluate the environment. However, labeling GSV images on a large scale is a time-consuming and labor-intensive task. Considering these challenges, we propose using a multi-task classifier to improve training a classifier with limited supervised, GSV data. Our multi-task classifier utilizes readily available, inexpensive online images collected from Flicker as a related classification task. The hypothesis is that a classifier trained on multiple related tasks is less likely to overfit to small amounts of training data and generalizes better to unseen data. We leverage the power of multiple related tasks to improve the classifier’s overall performance and generalization capability. Here we show that, with the proposed learning paradigm, predicted labels for GSV test images are more accurate. Across different environment indicators, the accuracy, F1 score and balanced accuracy increase up to 6 % in the multi-task learning framework compared to its single-task learning counterpart. The enhanced accuracy of the predicted labels obtained through the multi-task classifier contributes to a more reliable and precise regression analysis determining the correlation between predicted built environment indicators and health outcomes. The R2 values calculated for different health outcomes improve by up to 4 % using multi-task learning detected indicators.



M. Grant, M. R. Kunz, K. Iyer, L. I. Held, T. Tasdizen, J. A. Aguiar, P. P. Dholabhai. “Integrating atomistic simulations and machine learning to design multi-principal element alloys with superior elastic modulus,” In Journal of Materials Research, Springer International Publishing, pp. 1--16. 2022.

ABSTRACT

Multi-principal element, high entropy alloys (HEAs) are an emerging class of materials that have found applications across the board. Owing to the multitude of possible candidate alloys, exploration and compositional design of HEAs for targeted applications is challenging since it necessitates a rational approach to identify compositions exhibiting enriched performance. Here, we report an innovative framework that integrates molecular dynamics and machine learning to explore a large chemical-configurational space for evaluating elastic modulus of equiatomic and non-equiatomic HEAs along primary crystallographic directions. Vital thermodynamic properties and machine learning features have been incorporated to establish fundamental relationships correlating Young’s modulus with Gibbs free energy, valence electron concentration, and atomic size difference. In HEAs, as the number of elements increases …



R. Lanfredi, J.D. Schroeder, T. Tasdizen. “Localization supervision of chest x-ray classifiers using label-specific eye-tracking annotation,” Subtitled “arXiv:2207.09771,” 2022.

ABSTRACT

Convolutional neural networks (CNNs) have been successfully applied to chest x-ray (CXR) images. Moreover, annotated bounding boxes have been shown to improve the interpretability of a CNN in terms of localizing abnormalities. However, only a few relatively small CXR datasets containing bounding boxes are available, and collecting them is very costly. Opportunely, eye-tracking (ET) data can be collected in a non-intrusive way during the clinical workflow of a radiologist. We use ET data recorded from radiologists while dictating CXR reports to train CNNs. We extract snippets from the ET data by associating them with the dictation of keywords and use them to supervise the localization of abnormalities. We show that this method improves a model's interpretability without impacting its image-level classification.



Q. C. Nguyen, T. Belnap, P. Dwivedi, A. Hossein Nazem Deligani, A. Kumar, D. Li, R. Whitaker, J. Keralis, H. Mane, X. Yue, T. T. Nguyen, T. Tasdizen, K. D. Brunisholz. “Google Street View Images as Predictors of Patient Health Outcomes, 2017–2019,” In Big Data and Cognitive Computing, Vol. 6, No. 1, Multidisciplinary Digital Publishing Institute, 2022.

ABSTRACT

Collecting neighborhood data can both be time- and resource-intensive, especially across broad geographies. In this study, we leveraged 1.4 million publicly available Google Street View (GSV) images from Utah to construct indicators of the neighborhood built environment and evaluate their associations with 2017–2019 health outcomes of approximately one-third of the population living in Utah. The use of electronic medical records allows for the assessment of associations between neighborhood characteristics and individual-level health outcomes while controlling for predisposing factors, which distinguishes this study from previous GSV studies that were ecological in nature. Among 938,085 adult patients, we found that individuals living in communities in the highest tertiles of green streets and non-single-family homes have 10–27% lower diabetes, uncontrolled diabetes, hypertension, and obesity, but higher substance use disorders—controlling for age, White race, Hispanic ethnicity, religion, marital status, health insurance, and area deprivation index. Conversely, the presence of visible utility wires overhead was associated with 5–10% more diabetes, uncontrolled diabetes, hypertension, obesity, and substance use disorders. Our study found that non-single-family and green streets were related to a lower prevalence of chronic conditions, while visible utility wires and single-lane roads were connected with a higher burden of chronic conditions. These contextual characteristics can better help healthcare organizations understand the drivers of their patients’ health by further considering patients’ residential environments, which present both …



C. A. Nizinski, C. Ly, C. Vachet, A. Hagen, T. Tasdizen, L. W. McDonald. “Characterization of uncertainties and model generalizability for convolutional neural network predictions of uranium ore concentrate morphology,” In Chemometrics and Intelligent Laboratory Systems, Vol. 225, Elsevier, pp. 104556. 2022.
ISSN: 0169-7439
DOI: https://doi.org/10.1016/j.chemolab.2022.104556

ABSTRACT

As the capabilities of convolutional neural networks (CNNs) for image classification tasks have advanced, interest in applying deep learning techniques for determining the natural and anthropogenic origins of uranium ore concentrates (UOCs) and other unknown nuclear materials by their surface morphology characteristics has grown. But before CNNs can join the nuclear forensics toolbox along more traditional analytical techniques – such as scanning electron microscopy (SEM), X-ray diffractometry, mass spectrometry, radiation counting, and any number of spectroscopic methods – a deeper understanding of “black box” image classification will be required. This paper explores uncertainty quantification for convolutional neural networks and their ability to generalize to out-of-distribution (OOD) image data sets. For prediction uncertainty, Monte Carlo (MC) dropout and random image crops as variational inference techniques are implemented and characterized. Convolutional neural networks and classifiers using image features from unsupervised vector-quantized variational autoencoders (VQ-VAE) are trained using SEM images of pure, unaged, unmixed uranium ore concentrates considered “unperturbed.” OOD data sets are developed containing perturbations from the training data with respect to the chemical and physical properties of the UOCs or data collection parameters; predictions made on the perturbation sets identify where significant shortcomings exist in the current training data and techniques used to develop models for classifying uranium process history, and provides valuable insights into how datasets and classification models can be improved for better generalizability to out-of-distribution examples.