Deep Metric Learning (DML) provides a crucial tool for visual similarity and zero-shot retrieval applications by learning generalizing embedding spaces, although recent work in DML has shown strong performance saturation across training objectives. However, generalization capacity is known to scale with the embedding space dimensionality. Unfortunately, high dimensional embeddings also create higher retrieval cost for downstream applications. To remedy this, we propose S2SD - Simultaneous Similarity-based Self-distillation. S2SD extends DML with knowledge distillation from auxiliary, high-dimensional embedding and feature spaces to leverage complementary context during training while retaining test-time cost and with negligible changes to the training time. Experiments and ablations across different objectives and standard benchmarks show S2SD offering notable improvements of up to 7% in Recall@1, while also setting a new state-of-the-art. Code available at https://github.com/MLforHealth/S2SD.
A common approach to medical image analysis on volumetric data uses deep 2D convolutional neural networks (CNNs). This is largely attributed to the challenges imposed by the nature of the 3D data: variable volume size, GPU exhaustion during optimization. However, dealing with the individual slices independently in 2D CNNs deliberately discards the depth information which results in poor performance for the intended task. Therefore, it is important to develop methods that not only overcome the heavy memory and computation requirements but also leverage the 3D information. To this end, we evaluate a set of volume uniformizing methods to address the aforementioned issues. The first method involves sampling information evenly from a subset of the volume. Another method exploits the full geometry of the 3D volume by interpolating over the z-axis. We demonstrate performance improvements using controlled ablation studies as well as put this approach to the test on the ImageCLEF Tuberculosis Severity Assessment 2019 benchmark. We report 73% area under curve (AUC) and binary classification accuracy (ACC) of 67.5% on the test set beating all methods which leveraged only image information (without using clinical meta-data) achieving 5-th position overall. All codes and models are made available at https://github.com/hasibzunair/uniformizing-3D.
There is a rise in the use of deep learning for automated medical diagnosis, most notably in medical imaging. Such an automated system uses a set of images from a patient to diagnose whether they have a disease. However, systems trained for one particular domain of images cannot be expected to perform accurately on images of a different domain. These images should be filtered out by an Out-of-Distribution Detection (OoDD) method prior to diagnosis. This paper benchmarks popular OoDD methods in three domains of medical imaging: chest x-rays, fundus images, and histology slides. Our experiments show that despite methods yielding good results on some types of out-of-distribution samples, they fail to recognize images close to the training distribution.
Across the world's coronavirus disease 2019 (COVID-19) hot spots, the need to streamline patient diagnosis and management has become more pressing than ever. As one of the main imaging tools, chest X-rays (CXRs) are common, fast, non-invasive, relatively cheap, and potentially bedside to monitor the progression of the disease. This paper describes the first public COVID-19 image data collection as well as a preliminary exploration of possible use cases for the data. This dataset currently contains hundreds of frontal view X-rays and is the largest public resource for COVID-19 image and prognostic data, making it a necessary resource to develop and evaluate tools to aid in the treatment of COVID-19. It was manually aggregated from publication figures as well as various web based repositories into a machine learning (ML) friendly format with accompanying dataloader code. We collected frontal and lateral view imagery and metadata such as the time since first symptoms, intensive care unit (ICU) status, survival status, intubation status, or hospital location. We present multiple possible use cases for the data such as predicting the need for the ICU, predicting patient survival, and understanding a patient's trajectory during treatment. Data can be accessed here: https://github.com/ieee8023/covid-chestxray-dataset
The need to streamline patient management for COVID-19 has become more pressing than ever. Chest X-rays provide a non-invasive (potentially bedside) tool to monitor the progression of the disease. In this study, we present a severity score prediction model for COVID-19 pneumonia for frontal chest X-ray images. Such a tool can gauge severity of COVID-19 lung infections (and pneumonia in general) that can be used for escalation or de-escalation of care as well as monitoring treatment efficacy, especially in the ICU. Images from a public COVID-19 database were scored retrospectively by three blinded experts in terms of the extent of lung involvement as well as the degree of opacity. A neural network model that was pre-trained on large (non-COVID-19) chest X-ray datasets is used to construct features for COVID-19 images which are predictive for our task. This study finds that training a regression model on a subset of the outputs from an this pre-trained chest X-ray model predicts our geographic extent score (range 0-8) with 1.14 mean absolute error (MAE) and our lung opacity score (range 0-6) with 0.78 MAE. All code, labels, and data are made available at https://github.com/mlmed/torchxrayvision and https://github.com/ieee8023/covid-chestxray-dataset
Visual Similarity plays an important role in many computer vision applications. Deep metric learning (DML) is a powerful framework for learning such similarities which not only generalize from training data to identically distributed test distributions, but in particular also translate to unknown test classes. However, its prevailing learning paradigm is class-discriminative supervised training, which typically results in representations specialized in separating training classes. For effective generalization, however, such an image representation needs to capture a diverse range of data characteristics. To this end, we propose and study multiple complementary learning tasks, targeting conceptually different data relationships by only resorting to the available training samples and labels of a standard DML setting. Through simultaneous optimization of our tasks we learn a single model to aggregate their training signals, resulting in strong generalization and state-of-the-art performance on multiple established DML benchmark datasets.
This paper describes the initial COVID-19 open image data collection. It was created by assembling medical images from websites and publications and currently contains 123 frontal view X-rays.
Deep Metric Learning (DML) is arguably one of the most influential lines of research for learning visual similarities with many proposed approaches every year. Although the field benefits from the rapid progress, the divergence in training protocols, architectures, and parameter choices make an unbiased comparison difficult. To provide a consistent reference point, we revisit the most widely used DML objective functions and conduct a study of the crucial parameter choices as well as the commonly neglected mini-batch sampling process. Based on our analysis, we uncover a correlation between the embedding space compression and the generalization performance of DML models. Exploiting these insights, we propose a simple, yet effective, training regularization to reliably boost the performance of ranking-based DML models on various standard benchmark datasets.