COVID-Net Biochem: An Explainability-driven Framework to Building Machine Learning Models for Predicting Survival and Kidney Injury of COVID-19 Patients from Clinical and Biochemistry Data

Ever since the declaration of COVID-19 as a pandemic by the World Health Organization in 2020, the world has continued to struggle in controlling and containing the spread of the COVID-19 pandemic caused by the SARS-CoV-2 virus. This has been especially challenging with the rise of the Omicron variant and its subvariants and recombinants, which has led to a significant increase in patients seeking treatment and has put a tremendous burden on hospitals and healthcare systems. A major challenge faced during the pandemic has been the prediction of survival and the risk for additional injuries in individual patients, which requires significant clinical expertise and additional resources to avoid further complications. In this study we propose COVID-Net Biochem, an explainability-driven framework for building machine learning models to predict patient survival and the chance of developing kidney injury during hospitalization from clinical and biochemistry data in a transparent and systematic manner. In the first "clinician-guided initial design" phase, we prepared a benchmark dataset of carefully selected clinical and biochemistry data based on clinician assessment, which were curated from a patient cohort of 1366 patients at Stony Brook University. A collection of different machine learning models with a diversity of gradient based boosting tree architectures and deep transformer architectures was designed and trained specifically for survival and kidney injury prediction based on the carefully selected clinical and biochemical markers.

ICDBigBird: A Contextual Embedding Model for ICD Code Classification

The International Classification of Diseases (ICD) system is the international standard for classifying diseases and procedures during a healthcare encounter and is widely used for healthcare reporting and management purposes. Assigning correct codes for clinical procedures is important for clinical, operational, and financial decision-making in healthcare. Contextual word embedding models have achieved state-of-the-art results in multiple NLP tasks. However, these models have yet to achieve state-of-the-art results in the ICD classification task since one of their main disadvantages is that they can only process documents that contain a small number of tokens which is rarely the case with real patient notes. In this paper, we introduce ICDBigBird a BigBird-based model which can integrate a Graph Convolutional Network (GCN), that takes advantage of the relations between ICD codes in order to create 'enriched' representations of their embeddings, with a BigBird contextual model that can process larger documents. Our experiments on a real-world clinical dataset demonstrate the effectiveness of our BigBird-based model on the ICD classification task as it outperforms the previous state-of-the-art models.

FenceNet: Fine-grained Footwork Recognition in Fencing

Current data analysis for the Canadian Olympic fencing team is primarily done manually by coaches and analysts. Due to the highly repetitive, yet dynamic and subtle movements in fencing, manual data analysis can be inefficient and inaccurate. We propose FenceNet as a novel architecture to automate the classification of fine-grained footwork techniques in fencing. FenceNet takes 2D pose data as input and classifies actions using a skeleton-based action recognition approach that incorporates temporal convolutional networks to capture temporal information. We train and evaluate FenceNet on the Fencing Footwork Dataset (FFD), which contains 10 fencers performing 6 different footwork actions for 10-11 repetitions each (652 total videos). FenceNet achieves 85.4% accuracy under 10-fold cross-validation, where each fencer is left out as the test set. This accuracy is within 1% of the current state-of-the-art method, JLJA (86.3%), which selects and fuses features engineered from skeleton data, depth videos, and inertial measurement units. BiFenceNet, a variant of FenceNet that captures the "bidirectionality" of human movement through two separate networks, achieves 87.6% accuracy, outperforming JLJA. Since neither FenceNet nor BiFenceNet requires data from wearable sensors, unlike JLJA, they could be directly applied to most fencing videos, using 2D pose data as input extracted from off-the-shelf 2D human pose estimators. In comparison to JLJA, our methods are also simpler as they do not require manual feature engineering, selection, or fusion.

Improving Classification Model Performance on Chest X-Rays through Lung Segmentation

Chest radiography is an effective screening tool for diagnosing pulmonary diseases. In computer-aided diagnosis, extracting the relevant region of interest, i.e., isolating the lung region of each radiography image, can be an essential step towards improved performance in diagnosing pulmonary disorders. Methods: In this work, we propose a deep learning approach to enhance abnormal chest x-ray (CXR) identification performance through segmentations. Our approach is designed in a cascaded manner and incorporates two modules: a deep neural network with criss-cross attention modules (XLSor) for localizing lung region in CXR images and a CXR classification model with a backbone of a self-supervised momentum contrast (MoCo) model pre-trained on large-scale CXR data sets. The proposed pipeline is evaluated on Shenzhen Hospital (SH) data set for the segmentation module, and COVIDx data set for both segmentation and classification modules. Novel statistical analysis is conducted in addition to regular evaluation metrics for the segmentation module. Furthermore, the results of the optimized approach are analyzed with gradient-weighted class activation mapping (Grad-CAM) to investigate the rationale behind the classification decisions and to interpret its choices. Results and Conclusion: Different data sets, methods, and scenarios for each module of the proposed pipeline are examined for designing an optimized approach, which has achieved an accuracy of 0.946 in distinguishing abnormal CXR images (i.e., Pneumonia and COVID-19) from normal ones. Numerical and visual validations suggest that applying automated segmentation as a pre-processing step for classification improves the generalization capability and the performance of the classification models.

Bag of Tricks for Natural Policy Gradient Reinforcement Learning

Natural policy gradient methods are popular reinforcement learning methods that improve the stability of policy gradient methods by preconditioning the gradient with the inverse of the Fisher-information matrix. However, leveraging natural policy gradient methods in an optimal manner can be very challenging as many implementation details must be set to achieve optimal performance. To the best of the authors' knowledge, there has not been a study that has investigated strategies for setting these details for natural policy gradient methods to achieve high performance in a comprehensive and systematic manner. To address this, we have implemented and compared strategies that impact performance in natural policy gradient reinforcement learning across five different second-order approximations. These include varying batch sizes and optimizing the critic network using the natural gradient. Furthermore, insights about the fundamental trade-offs when optimizing for performance (stability, sample efficiency, and computation time) were generated. Experimental results indicate that the proposed collection of strategies for performance optimization can improve results by 86% to 181% across the MuJuCo control benchmark, with TENGraD exhibiting the best approximation performance amongst the tested approximations. Code in this study is available at https://github.com/gebob19/natural-policy-gradient-reinforcement-learning.

MetaGraspNet: A Large-Scale Benchmark Dataset for Vision-driven Robotic Grasping via Physics-based Metaverse Synthesis

There has been increasing interest in smart factories powered by robotics systems to tackle repetitive, laborious tasks. One impactful yet challenging task in robotics-powered smart factory applications is robotic grasping: using robotic arms to grasp objects autonomously in different settings. Robotic grasping requires a variety of computer vision tasks such as object detection, segmentation, grasp prediction, pick planning, etc. While significant progress has been made in leveraging of machine learning for robotic grasping, particularly with deep learning, a big challenge remains in the need for large-scale, high-quality RGBD datasets that cover a wide diversity of scenarios and permutations. To tackle this big, diverse data problem, we are inspired by the recent rise in the concept of metaverse, which has greatly closed the gap between virtual worlds and the physical world. Metaverses allow us to create digital twins of real-world manufacturing scenarios and to virtually create different scenarios from which large volumes of data can be generated for training models. In this paper, we present MetaGraspNet: a large-scale benchmark dataset for vision-driven robotic grasping via physics-based metaverse synthesis. The proposed dataset contains 100,000 images and 25 different object types and is split into 5 difficulties to evaluate object detection and segmentation model performance in different grasping scenarios. We also propose a new layout-weighted performance metric alongside the dataset for evaluating object detection and segmentation performance in a manner that is more appropriate for robotic grasp applications compared to existing general-purpose performance metrics. Our benchmark dataset is available open-source on Kaggle, with the first phase consisting of detailed object detection, segmentation, layout annotations, and a layout-weighted performance metric script.

Performance or Trust? Why Not Both. Deep AUC Maximization with Self-Supervised Learning for COVID-19 Chest X-ray Classifications

Effective representation learning is the key in improving model performance for medical image analysis. In training deep learning models, a compromise often must be made between performance and trust, both of which are essential for medical applications. Moreover, models optimized with cross-entropy loss tend to suffer from unwarranted overconfidence in the majority class and over-cautiousness in the minority class. In this work, we integrate a new surrogate loss with self-supervised learning for computer-aided screening of COVID-19 patients using radiography images. In addition, we adopt a new quantification score to measure a model's trustworthiness. Ablation study is conducted for both the performance and the trust on feature learning methods and loss functions. Comparisons show that leveraging the new surrogate loss on self-supervised models can produce label-efficient networks that are both high-performing and trustworthy.

Enhancing Food Intake Tracking in Long-Term Care with Automated Food Imaging and Nutrient Intake Tracking Technology

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 ($\sigma$= -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.

MAPLE: Microprocessor A Priori for Latency Estimation

Modern deep neural networks must demonstrate state-of-the-art accuracy while exhibiting low latency and energy consumption. As such, neural architecture search (NAS) algorithms take these two constraints into account when generating a new architecture. However, efficiency metrics such as latency are typically hardware dependent requiring the NAS algorithm to either measure or predict the architecture latency. Measuring the latency of every evaluated architecture adds a significant amount of time to the NAS process. Here we propose Microprocessor A Priori for Latency Estimation MAPLE that does not rely on transfer learning or domain adaptation but instead generalizes to new hardware by incorporating a prior hardware characteristics during training. MAPLE takes advantage of a novel quantitative strategy to characterize the underlying microprocessor by measuring relevant hardware performance metrics, yielding a fine-grained and expressive hardware descriptor. Moreover, the proposed MAPLE benefits from the tightly coupled I/O between the CPU and GPU and their dependency to predict DNN latency on GPUs while measuring microprocessor performance hardware counters from the CPU feeding the GPU hardware. Through this quantitative strategy as the hardware descriptor, MAPLE can generalize to new hardware via a few shot adaptation strategy where with as few as 3 samples it exhibits a 3% improvement over state-of-the-art methods requiring as much as 10 samples. Experimental results showed that, increasing the few shot adaptation samples to 10 improves the accuracy significantly over the state-of-the-art methods by 12%. Furthermore, it was demonstrated that MAPLE exhibiting 8-10% better accuracy, on average, compared to relevant baselines at any number of adaptation samples.

TinyDefectNet: Highly Compact Deep Neural Network Architecture for High-Throughput Manufacturing Visual Quality Inspection

A critical aspect in the manufacturing process is the visual quality inspection of manufactured components for defects and flaws. Human-only visual inspection can be very time-consuming and laborious, and is a significant bottleneck especially for high-throughput manufacturing scenarios. Given significant advances in the field of deep learning, automated visual quality inspection can lead to highly efficient and reliable detection of defects and flaws during the manufacturing process. However, deep learning-driven visual inspection methods often necessitate significant computational resources, thus limiting throughput and act as a bottleneck to widespread adoption for enabling smart factories. In this study, we investigated the utilization of a machine-driven design exploration approach to create TinyDefectNet, a highly compact deep convolutional network architecture tailored for high-throughput manufacturing visual quality inspection. TinyDefectNet comprises of just ~427K parameters and has a computational complexity of ~97M FLOPs, yet achieving a detection accuracy of a state-of-the-art architecture for the task of surface defect detection on the NEU defect benchmark dataset. As such, TinyDefectNet can achieve the same level of detection performance at 52$\times$ lower architectural complexity and 11x lower computational complexity. Furthermore, TinyDefectNet was deployed on an AMD EPYC 7R32, and achieved 7.6x faster throughput using the native Tensorflow environment and 9x faster throughput using AMD ZenDNN accelerator library. Finally, explainability-driven performance validation strategy was conducted to ensure correct decision-making behaviour was exhibited by TinyDefectNet to improve trust in its usage by operators and inspectors.