COVID-19 severity is due to complications from SARS-Cov-2 but the clinical course of the infection varies for individuals, emphasizing the need to better understand the disease at the molecular level. We use clinical and multiple molecular data (or views) obtained from patients with and without COVID-19 who were (or not) admitted to the intensive care unit to shed light on COVID-19 severity. Methods for jointly associating the views and separating the COVID-19 groups (i.e., one-step methods) have focused on linear relationships. The relationships between the views and COVID-19 patient groups, however, are too complex to be understood solely by linear methods. Existing nonlinear one-step methods cannot be used to identify signatures to aid in our understanding of the complexity of the disease. We propose Deep IDA (Integrative Discriminant Analysis) to address analytical challenges in our problem of interest. Deep IDA learns nonlinear projections of two or more views that maximally associate the views and separate the classes in each view, and permits feature ranking for interpretable findings. Our applications demonstrate that Deep IDA has competitive classification rates compared to other state-of-the-art methods and is able to identify molecular signatures that facilitate an understanding of COVID-19 severity.
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Continual learning (CL) is under-explored in the video domain. The few existing works contain splits with imbalanced class distributions over the tasks, or study the problem in unsuitable datasets. We introduce vCLIMB, a novel video continual learning benchmark. vCLIMB is a standardized test-bed to analyze catastrophic forgetting of deep models in video continual learning. In contrast to previous work, we focus on class incremental continual learning with models trained on a sequence of disjoint tasks, and distribute the number of classes uniformly across the tasks. We perform in-depth evaluations of existing CL methods in vCLIMB, and observe two unique challenges in video data. The selection of instances to store in episodic memory is performed at the frame level. Second, untrimmed training data influences the effectiveness of frame sampling strategies. We address these two challenges by proposing a temporal consistency regularization that can be applied on top of memory-based continual learning methods. Our approach significantly improves the baseline, by up to 24% on the untrimmed continual learning task. To streamline and foster future research in video continual learning, we will publicly release the code for our benchmark and method.
A critical step in the fight against COVID-19, which continues to have a catastrophic impact on peoples lives, is the effective screening of patients presented in the clinics with severe COVID-19 symptoms. Chest radiography is one of the promising screening approaches. Many studies reported detecting COVID-19 in chest X-rays accurately using deep learning. A serious limitation of many published approaches is insufficient attention paid to explaining decisions made by deep learning models. Using explainable artificial intelligence methods, we demonstrate that model decisions may rely on confounding factors rather than medical pathology. After an analysis of potential confounding factors found on chest X-ray images, we propose a novel method to minimise their negative impact. We show that our proposed method is more robust than previous attempts to counter confounding factors such as ECG leads in chest X-rays that often influence model classification decisions. In addition to being robust, our method achieves results comparable to the state-of-the-art. The source code and pre-trained weights are publicly available (//github.com/tomek1911/POTHER).
Given the impact of health literacy (HL) on patients outcomes, limited health literacy (LHL) is a major barrier in cancer care globally. HL refers to the degree in which an individual is able to acquire, process and comprehend information in a way to be actively involved in their health decisions. Previous research found that almost half of the population in developed countries have difficulties in understanding health related information. With the gradual shift toward the shared decision making (SDM) process and digital transformation in oncology, the need for dealing with low HL issues is more crucial. Decision making in oncology is often accompanied by considerable consequences on patients lives, which requires patients to understand complex information and be able to compare treatment methods by considering their own values. How health information is perceived by patients is influenced by various factors including patients characteristics and the way information is presented to patients. Based on the findings, identifying patients with low HL and using simple data visualizations are the best practice to help patients and clinicians in dealing with LHL. Furthermore, preparing reliable sources of information in tools such as patient decision aids (PDA), as well as involving HL mediators in consultation sessions supports patients to make sense of complex information.
Predictions obtained by, e.g., artificial neural networks have a high accuracy but humans often perceive the models as black boxes. Insights about the decision making are mostly opaque for humans. Particularly understanding the decision making in highly sensitive areas such as healthcare or fifinance, is of paramount importance. The decision-making behind the black boxes requires it to be more transparent, accountable, and understandable for humans. This survey paper provides essential definitions, an overview of the different principles and methodologies of explainable Supervised Machine Learning (SML). We conduct a state-of-the-art survey that reviews past and recent explainable SML approaches and classifies them according to the introduced definitions. Finally, we illustrate principles by means of an explanatory case study and discuss important future directions.
As we seek to deploy machine learning models beyond virtual and controlled domains, it is critical to analyze not only the accuracy or the fact that it works most of the time, but if such a model is truly robust and reliable. This paper studies strategies to implement adversary robustly trained algorithms towards guaranteeing safety in machine learning algorithms. We provide a taxonomy to classify adversarial attacks and defenses, formulate the Robust Optimization problem in a min-max setting and divide it into 3 subcategories, namely: Adversarial (re)Training, Regularization Approach, and Certified Defenses. We survey the most recent and important results in adversarial example generation, defense mechanisms with adversarial (re)Training as their main defense against perturbations. We also survey mothods that add regularization terms that change the behavior of the gradient, making it harder for attackers to achieve their objective. Alternatively, we've surveyed methods which formally derive certificates of robustness by exactly solving the optimization problem or by approximations using upper or lower bounds. In addition, we discuss the challenges faced by most of the recent algorithms presenting future research perspectives.
The COVID-19 pandemic continues to have a devastating effect on the health and well-being of the global population. A critical step in the fight against COVID-19 is effective screening of infected patients, with one of the key screening approaches being radiological imaging using chest radiography. Motivated by this, a number of artificial intelligence (AI) systems based on deep learning have been proposed and results have been shown to be quite promising in terms of accuracy in detecting patients infected with COVID-19 using chest radiography images. However, to the best of the authors' knowledge, these developed AI systems have been closed source and unavailable to the research community for deeper understanding and extension, and unavailable for public access and use. Therefore, in this study we introduce COVID-Net, a deep convolutional neural network design tailored for the detection of COVID-19 cases from chest radiography images that is open source and available to the general public. We also describe the chest radiography dataset leveraged to train COVID-Net, which we will refer to as COVIDx and is comprised of 5941 posteroanterior chest radiography images across 2839 patient cases from two open access data repositories. Furthermore, we investigate how COVID-Net makes predictions using an explainability method in an attempt to gain deeper insights into critical factors associated with COVID cases, which can aid clinicians in improved screening. By no means a production-ready solution, the hope is that the open access COVID-Net, along with the description on constructing the open source COVIDx dataset, will be leveraged and build upon by both researchers and citizen data scientists alike to accelerate the development of highly accurate yet practical deep learning solutions for detecting COVID-19 cases and accelerate treatment of those who need it the most.
Breast cancer remains a global challenge, causing over 1 million deaths globally in 2018. To achieve earlier breast cancer detection, screening x-ray mammography is recommended by health organizations worldwide and has been estimated to decrease breast cancer mortality by 20-40%. Nevertheless, significant false positive and false negative rates, as well as high interpretation costs, leave opportunities for improving quality and access. To address these limitations, there has been much recent interest in applying deep learning to mammography; however, obtaining large amounts of annotated data poses a challenge for training deep learning models for this purpose, as does ensuring generalization beyond the populations represented in the training dataset. Here, we present an annotation-efficient deep learning approach that 1) achieves state-of-the-art performance in mammogram classification, 2) successfully extends to digital breast tomosynthesis (DBT; "3D mammography"), 3) detects cancers in clinically-negative prior mammograms of cancer patients, 4) generalizes well to a population with low screening rates, and 5) outperforms five-out-of-five full-time breast imaging specialists by improving absolute sensitivity by an average of 14%. Our results demonstrate promise towards software that can improve the accuracy of and access to screening mammography worldwide.
Learning to rank has been intensively studied and widely applied in information retrieval. Typically, a global ranking function is learned from a set of labeled data, which can achieve good performance on average but may be suboptimal for individual queries by ignoring the fact that relevant documents for different queries may have different distributions in the feature space. Inspired by the idea of pseudo relevance feedback where top ranked documents, which we refer as the \textit{local ranking context}, can provide important information about the query's characteristics, we propose to use the inherent feature distributions of the top results to learn a Deep Listwise Context Model that helps us fine tune the initial ranked list. Specifically, we employ a recurrent neural network to sequentially encode the top results using their feature vectors, learn a local context model and use it to re-rank the top results. There are three merits with our model: (1) Our model can capture the local ranking context based on the complex interactions between top results using a deep neural network; (2) Our model can be built upon existing learning-to-rank methods by directly using their extracted feature vectors; (3) Our model is trained with an attention-based loss function, which is more effective and efficient than many existing listwise methods. Experimental results show that the proposed model can significantly improve the state-of-the-art learning to rank methods on benchmark retrieval corpora.
Weakly supervised instance segmentation with image-level labels, instead of expensive pixel-level masks, remains unexplored. In this paper, we tackle this challenging problem by exploiting class peak responses to enable a classification network for instance mask extraction. With image labels supervision only, CNN classifiers in a fully convolutional manner can produce class response maps, which specify classification confidence at each image location. We observed that local maximums, i.e., peaks, in a class response map typically correspond to strong visual cues residing inside each instance. Motivated by this, we first design a process to stimulate peaks to emerge from a class response map. The emerged peaks are then back-propagated and effectively mapped to highly informative regions of each object instance, such as instance boundaries. We refer to the above maps generated from class peak responses as Peak Response Maps (PRMs). PRMs provide a fine-detailed instance-level representation, which allows instance masks to be extracted even with some off-the-shelf methods. To the best of our knowledge, we for the first time report results for the challenging image-level supervised instance segmentation task. Extensive experiments show that our method also boosts weakly supervised pointwise localization as well as semantic segmentation performance, and reports state-of-the-art results on popular benchmarks, including PASCAL VOC 2012 and MS COCO.
Multi-view networks are ubiquitous in real-world applications. In order to extract knowledge or business value, it is of interest to transform such networks into representations that are easily machine-actionable. Meanwhile, network embedding has emerged as an effective approach to generate distributed network representations. Therefore, we are motivated to study the problem of multi-view network embedding, with a focus on the characteristics that are specific and important in embedding this type of networks. In our practice of embedding real-world multi-view networks, we identify two such characteristics, which we refer to as preservation and collaboration. We then explore the feasibility of achieving better embedding quality by simultaneously modeling preservation and collaboration, and propose the mvn2vec algorithms. With experiments on a series of synthetic datasets, an internal Snapchat dataset, and two public datasets, we further confirm the presence and importance of preservation and collaboration. These experiments also demonstrate that better embedding can be obtained by simultaneously modeling the two characteristics, while not over-complicating the model or requiring additional supervision.
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