Audrey G. Chung

Maya Pavlova, Naomi Terhljan, Audrey G. Chung et al.

As the COVID-19 pandemic continues to devastate globally, the use of chest X-ray (CXR) imaging as a complimentary screening strategy to RT-PCR testing continues to grow given its routine clinical use for respiratory complaint. As part of the COVID-Net open source initiative, we introduce COVID-Net CXR-2, an enhanced deep convolutional neural network design for COVID-19 detection from CXR images built using a greater quantity and diversity of patients than the original COVID-Net. To facilitate this, we also introduce a new benchmark dataset composed of 19,203 CXR images from a multinational cohort of 16,656 patients from at least 51 countries, making it the largest, most diverse COVID-19 CXR dataset in open access form. The COVID-Net CXR-2 network achieves sensitivity and positive predictive value of 95.5%/97.0%, respectively, and was audited in a transparent and responsible manner. Explainability-driven performance validation was used during auditing to gain deeper insights in its decision-making behaviour and to ensure clinically relevant factors are leveraged for improving trust in its usage. Radiologist validation was also conducted, where select cases were reviewed and reported on by two board-certified radiologists with over 10 and 19 years of experience, respectively, and showed that the critical factors leveraged by COVID-Net CXR-2 are consistent with radiologist interpretations. While not a production-ready solution, we hope the open-source, open-access release of COVID-Net CXR-2 and the respective CXR benchmark dataset will encourage researchers, clinical scientists, and citizen scientists to accelerate advancements and innovations in the fight against the pandemic.

Audrey Chung, Francis Li, Jeremy Ward et al.

As electronics manufacturers continue to face pressure to increase production efficiency amid difficulties with supply chains and labour shortages, many printed circuit board assembly (PCBA) manufacturers have begun to invest in automation and technological innovations to remain competitive. One such method is to leverage artificial intelligence (AI) to greatly augment existing manufacturing processes. In this paper, we present the DarwinAI Visual Quality Inspection (DVQI) system, a hardware-integration artificial intelligence system for the automated inspection of printed circuit board assembly defects in an electronics manufacturing environment. The DVQI system enables multi-task inspection via minimal programming and setup for manufacturing engineers while improving cycle time relative to manual inspection. We also present a case study of the deployed DVQI system's performance and impact for a top electronics manufacturer.

Kaylen J. Pfisterer, Robert Amelard, Jennifer Boger et al.

Half of long-term care (LTC) residents are malnourished increasing hospitalization, mortality, morbidity, with lower quality of life. Current tracking methods are subjective and time consuming. This paper presents the automated food imaging and nutrient intake tracking (AFINI-T) technology designed for LTC. We propose a novel convolutional autoencoder for food classification, trained on an augmented UNIMIB2016 dataset and tested on our simulated LTC food intake dataset (12 meal scenarios; up to 15 classes each; top-1 classification accuracy: 88.9%; mean intake error: -0.4 mL$\pm$36.7 mL). Nutrient intake estimation by volume was strongly linearly correlated with nutrient estimates from mass ($r^2$ 0.92 to 0.99) with good agreement between methods ($σ$= -2.7 to -0.01; zero within each of the limits of agreement). The AFINI-T approach is a deep-learning powered computational nutrient sensing system that may provide a novel means for more accurately and objectively tracking LTC resident food intake to support and prevent malnutrition tracking strategies.

Audrey Chung, Mahmoud Famouri, Andrew Hryniowski et al.

The COVID-19 pandemic continues to have a devastating global impact, and has placed a tremendous burden on struggling healthcare systems around the world. Given the limited resources, accurate patient triaging and care planning is critical in the fight against COVID-19, and one crucial task within care planning is determining if a patient should be admitted to a hospital's intensive care unit (ICU). Motivated by the need for transparent and trustworthy ICU admission clinical decision support, we introduce COVID-Net Clinical ICU, a neural network for ICU admission prediction based on patient clinical data. Driven by a transparent, trust-centric methodology, the proposed COVID-Net Clinical ICU was built using a clinical dataset from Hospital Sirio-Libanes comprising of 1,925 COVID-19 patient records, and is able to predict when a COVID-19 positive patient would require ICU admission with an accuracy of 96.9% to facilitate better care planning for hospitals amidst the on-going pandemic. We conducted system-level insight discovery using a quantitative explainability strategy to study the decision-making impact of different clinical features and gain actionable insights for enhancing predictive performance. We further leveraged a suite of trust quantification metrics to gain deeper insights into the trustworthiness of COVID-Net Clinical ICU. By digging deeper into when and why clinical predictive models makes certain decisions, we can uncover key factors in decision making for critical clinical decision support tasks such as ICU admission prediction and identify the situations under which clinical predictive models can be trusted for greater accountability.

Audrey G. Chung, Maya Pavlova, Hayden Gunraj et al.

As the COVID-19 pandemic continues to devastate globally, one promising field of research is machine learning-driven computer vision to streamline various parts of the COVID-19 clinical workflow. These machine learning methods are typically stand-alone models designed without consideration for the integration necessary for real-world application workflows. In this study, we take a machine learning and systems (MLSys) perspective to design a system for COVID-19 patient screening with the clinical workflow in mind. The COVID-Net system is comprised of the continuously evolving COVIDx dataset, COVID-Net deep neural network for COVID-19 patient detection, and COVID-Net S deep neural networks for disease severity scoring for COVID-19 positive patient cases. The deep neural networks within the COVID-Net system possess state-of-the-art performance, and are designed to be integrated within a user interface (UI) for clinical decision support with automatic report generation to assist clinicians in their treatment decisions.

Alexander Wong, Zhong Qiu Lin, Linda Wang et al.

Background: A critical step in effective care and treatment planning for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of the COVID-19 pandemic, is the assessment of the severity of disease progression. Chest x-rays (CXRs) are often used to assess SARS-CoV-2 severity, with two important assessment metrics being extent of lung involvement and degree of opacity. In this proof-of-concept study, we assess the feasibility of computer-aided scoring of CXRs of SARS-CoV-2 lung disease severity using a deep learning system. Materials and Methods: Data consisted of 396 CXRs from SARS-CoV-2 positive patient cases. Geographic extent and opacity extent were scored by two board-certified expert chest radiologists (with 20+ years of experience) and a 2nd-year radiology resident. The deep neural networks used in this study, which we name COVID-Net S, are based on a COVID-Net network architecture. 100 versions of the network were independently learned (50 to perform geographic extent scoring and 50 to perform opacity extent scoring) using random subsets of CXRs from the study, and we evaluated the networks using stratified Monte Carlo cross-validation experiments. Findings: The COVID-Net S deep neural networks yielded R$^2$ of 0.664 $\pm$ 0.032 and 0.635 $\pm$ 0.044 between predicted scores and radiologist scores for geographic extent and opacity extent, respectively, in stratified Monte Carlo cross-validation experiments. The best performing networks achieved R$^2$ of 0.739 and 0.741 between predicted scores and radiologist scores for geographic extent and opacity extent, respectively. Interpretation: The results are promising and suggest that the use of deep neural networks on CXRs could be an effective tool for computer-aided assessment of SARS-CoV-2 lung disease severity, although additional studies are needed before adoption for routine clinical use.

Kaylen J Pfisterer, Robert Amelard, Audrey G Chung et al.

Malnutrition is a multidomain problem affecting 54% of older adults in long-term care (LTC). Monitoring nutritional intake in LTC is laborious and subjective, limiting clinical inference capabilities. Recent advances in automatic image-based food estimation have not yet been evaluated in LTC settings. Here, we describe a fully automatic imaging system for quantifying food intake. We propose a novel deep convolutional encoder-decoder food network with depth-refinement (EDFN-D) using an RGB-D camera for quantifying a plate's remaining food volume relative to reference portions in whole and modified texture foods. We trained and validated the network on the pre-labelled UNIMIB2016 food dataset and tested on our two novel LTC-inspired plate datasets (689 plate images, 36 unique foods). EDFN-D performed comparably to depth-refined graph cut on IOU (0.879 vs. 0.887), with intake errors well below typical 50% (mean percent intake error: -4.2%). We identify how standard segmentation metrics are insufficient due to visual-volume discordance, and include volume disparity analysis to facilitate system trust. This system provides improved transparency, approximates human assessors with enhanced objectivity, accuracy, and precision while avoiding hefty semi-automatic method time requirements. This may help address short-comings currently limiting utility of automated early malnutrition detection in resource-constrained LTC and hospital settings.

Audrey Chung, Paul Fieguth, Alexander Wong

Evolutionary deep intelligence has recently shown great promise for producing small, powerful deep neural network models via the organic synthesis of increasingly efficient architectures over successive generations. Existing evolutionary synthesis processes, however, have allowed the mating of parent networks independent of architectural alignment, resulting in a mismatch of network structures. We present a preliminary study into the effects of architectural alignment during evolutionary synthesis using a gene tagging system. Surprisingly, the network architectures synthesized using the gene tagging approach resulted in slower decreases in performance accuracy and storage size; however, the resultant networks were comparable in size and performance accuracy to the non-gene tagging networks. Furthermore, we speculate that there is a noticeable decrease in network variability for networks synthesized with gene tagging, indicating that enforcing a like-with-like mating policy potentially restricts the exploration of the search space of possible network architectures.

Xiaodan Hu, Audrey G. Chung, Paul Fieguth et al.

Generative Adversarial Networks (GANs) have shown considerable promise for mitigating the challenge of data scarcity when building machine learning-driven analysis algorithms. Specifically, a number of studies have shown that GAN-based image synthesis for data augmentation can aid in improving classification accuracy in a number of medical image analysis tasks, such as brain and liver image analysis. However, the efficacy of leveraging GANs for tackling prostate cancer analysis has not been previously explored. Motivated by this, in this study we introduce ProstateGAN, a GAN-based model for synthesizing realistic prostate diffusion imaging data. More specifically, in order to generate new diffusion imaging data corresponding to a particular cancer grade (Gleason score), we propose a conditional deep convolutional GAN architecture that takes Gleason scores into consideration during the training process. Experimental results show that high-quality synthetic prostate diffusion imaging data can be generated using the proposed ProstateGAN for specified Gleason scores.

Zhong Qiu Lin, Audrey G. Chung, Alexander Wong

Despite showing state-of-the-art performance, deep learning for speech recognition remains challenging to deploy in on-device edge scenarios such as mobile and other consumer devices. Recently, there have been greater efforts in the design of small, low-footprint deep neural networks (DNNs) that are more appropriate for edge devices, with much of the focus on design principles for hand-crafting efficient network architectures. In this study, we explore a human-machine collaborative design strategy for building low-footprint DNN architectures for speech recognition through a marriage of human-driven principled network design prototyping and machine-driven design exploration. The efficacy of this design strategy is demonstrated through the design of a family of highly-efficient DNNs (nicknamed EdgeSpeechNets) for limited-vocabulary speech recognition. Experimental results using the Google Speech Commands dataset for limited-vocabulary speech recognition showed that EdgeSpeechNets have higher accuracies than state-of-the-art DNNs (with the best EdgeSpeechNet achieving ~97% accuracy), while achieving significantly smaller network sizes (as much as 7.8x smaller) and lower computational cost (as much as 36x fewer multiply-add operations, 10x lower prediction latency, and 16x smaller memory footprint on a Motorola Moto E phone), making them very well-suited for on-device edge voice interface applications.

Audrey G. Chung, Paul Fieguth, Alexander Wong

Evolutionary deep intelligence synthesizes highly efficient deep neural networks architectures over successive generations. Inspired by the nature versus nurture debate, we propose a study to examine the role of external factors on the network synthesis process by varying the availability of simulated environmental resources. Experimental results were obtained for networks synthesized via asexual evolutionary synthesis (1-parent) and sexual evolutionary synthesis (2-parent, 3-parent, and 5-parent) using a 10% subset of the MNIST dataset. Results show that a lower environmental factor model resulted in a more gradual loss in performance accuracy and decrease in storage size. This potentially allows significantly reduced storage size with minimal to no drop in performance accuracy, and the best networks were synthesized using the lowest environmental factor models.

Kaylen J. Pfisterer, Robert Amelard, Audrey G. Chung et al.

Dysphagia affects 590 million people worldwide and increases risk for malnutrition. Pureed food may reduce choking, however preparation differences impact nutrient density making quality assurance necessary. This paper is the first study to investigate the feasibility of computational pureed food nutritional density analysis using an imaging system. Motivated by a theoretical optical dilution model, a novel deep neural network (DNN) was evaluated using 390 samples from thirteen types of commercially prepared purees at five dilutions. The DNN predicted relative concentration of the puree sample (20%, 40%, 60%, 80%, 100% initial concentration). Data were captured using same-side reflectance of multispectral imaging data at different polarizations at three exposures. Experimental results yielded an average top-1 prediction accuracy of 92.2+/-0.41% with sensitivity and specificity of 83.0+/-15.0% and 95.0+/-4.8%, respectively. This DNN imaging system for nutrient density analysis of pureed food shows promise as a novel tool for nutrient quality assurance.

Mohammad Javad Shafiee, Audrey G. Chung, Farzad Khalvati et al.

While lung cancer is the second most diagnosed form of cancer in men and women, a sufficiently early diagnosis can be pivotal in patient survival rates. Imaging-based, or radiomics-driven, detection methods have been developed to aid diagnosticians, but largely rely on hand-crafted features which may not fully encapsulate the differences between cancerous and healthy tissue. Recently, the concept of discovery radiomics was introduced, where custom abstract features are discovered from readily available imaging data. We propose a novel evolutionary deep radiomic sequencer discovery approach based on evolutionary deep intelligence. Motivated by patient privacy concerns and the idea of operational artificial intelligence, the evolutionary deep radiomic sequencer discovery approach organically evolves increasingly more efficient deep radiomic sequencers that produce significantly more compact yet similarly descriptive radiomic sequences over multiple generations. As a result, this framework improves operational efficiency and enables diagnosis to be run locally at the radiologist's computer while maintaining detection accuracy. We evaluated the evolved deep radiomic sequencer (EDRS) discovered via the proposed evolutionary deep radiomic sequencer discovery framework against state-of-the-art radiomics-driven and discovery radiomics methods using clinical lung CT data with pathologically-proven diagnostic data from the LIDC-IDRI dataset. The evolved deep radiomic sequencer shows improved sensitivity (93.42%), specificity (82.39%), and diagnostic accuracy (88.78%) relative to previous radiomics approaches.

A. G. Chung, M. J. Shafiee, A. Wong

The approximation of nonlinear kernels via linear feature maps has recently gained interest due to their applications in reducing the training and testing time of kernel-based learning algorithms. Current random projection methods avoid the curse of dimensionality by embedding the nonlinear feature space into a low dimensional Euclidean space to create nonlinear kernels. We introduce a Layered Random Projection (LaRP) framework, where we model the linear kernels and nonlinearity separately for increased training efficiency. The proposed LaRP framework was assessed using the MNIST hand-written digits database and the COIL-100 object database, and showed notable improvement in object classification performance relative to other state-of-the-art random projection methods.

Mohammad Javad Shafiee, Audrey G. Chung, Devinder Kumar et al.

Radiomics has proven to be a powerful prognostic tool for cancer detection, and has previously been applied in lung, breast, prostate, and head-and-neck cancer studies with great success. However, these radiomics-driven methods rely on pre-defined, hand-crafted radiomic feature sets that can limit their ability to characterize unique cancer traits. In this study, we introduce a novel discovery radiomics framework where we directly discover custom radiomic features from the wealth of available medical imaging data. In particular, we leverage novel StochasticNet radiomic sequencers for extracting custom radiomic features tailored for characterizing unique cancer tissue phenotype. Using StochasticNet radiomic sequencers discovered using a wealth of lung CT data, we perform binary classification on 42,340 lung lesions obtained from the CT scans of 93 patients in the LIDC-IDRI dataset. Preliminary results show significant improvement over previous state-of-the-art methods, indicating the potential of the proposed discovery radiomics framework for improving cancer screening and diagnosis.

Devinder Kumar, Mohammad Javad Shafiee, Audrey G. Chung et al.

Lung cancer is the leading cause for cancer related deaths. As such, there is an urgent need for a streamlined process that can allow radiologists to provide diagnosis with greater efficiency and accuracy. A powerful tool to do this is radiomics: a high-dimension imaging feature set. In this study, we take the idea of radiomics one step further by introducing the concept of discovery radiomics for lung cancer prediction using CT imaging data. In this study, we realize these custom radiomic sequencers as deep convolutional sequencers using a deep convolutional neural network learning architecture. To illustrate the prognostic power and effectiveness of the radiomic sequences produced by the discovered sequencer, we perform cancer prediction between malignant and benign lesions from 97 patients using the pathologically-proven diagnostic data from the LIDC-IDRI dataset. Using the clinically provided pathologically-proven data as ground truth, the proposed framework provided an average accuracy of 77.52% via 10-fold cross-validation with a sensitivity of 79.06% and specificity of 76.11%, surpassing the state-of-the art method.

Audrey G. Chung, Mohammad Javad Shafiee, Devinder Kumar et al.

Prostate cancer is the most diagnosed form of cancer in Canadian men, and is the third leading cause of cancer death. Despite these statistics, prognosis is relatively good with a sufficiently early diagnosis, making fast and reliable prostate cancer detection crucial. As imaging-based prostate cancer screening, such as magnetic resonance imaging (MRI), requires an experienced medical professional to extensively review the data and perform a diagnosis, radiomics-driven methods help streamline the process and has the potential to significantly improve diagnostic accuracy and efficiency, and thus improving patient survival rates. These radiomics-driven methods currently rely on hand-crafted sets of quantitative imaging-based features, which are selected manually and can limit their ability to fully characterize unique prostate cancer tumour phenotype. In this study, we propose a novel \textit{discovery radiomics} framework for generating custom radiomic sequences tailored for prostate cancer detection. Discovery radiomics aims to uncover abstract imaging-based features that capture highly unique tumour traits and characteristics beyond what can be captured using predefined feature models. In this paper, we discover new custom radiomic sequencers for generating new prostate radiomic sequences using multi-parametric MRI data. We evaluated the performance of the discovered radiomic sequencer against a state-of-the-art hand-crafted radiomic sequencer for computer-aided prostate cancer detection with a feedforward neural network using real clinical prostate multi-parametric MRI data. Results for the discovered radiomic sequencer demonstrate good performance in prostate cancer detection and clinical decision support relative to the hand-crafted radiomic sequencer. The use of discovery radiomics shows potential for more efficient and reliable automatic prostate cancer detection.