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Register a new userImproving Medical Image Classification with Label Noise Using Dual-uncertainty Estimation
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Added by
Lie Ju
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Deep neural networks are known to be data-driven and label noise can have a marked impact on model performance. Recent studies have shown great robustness to classic image recognition even under a high noisy rate. In medical applications, learning from datasets with label noise is more challenging since medical imaging datasets tend to have asymmetric (class-dependent) noise and suffer from high observer variability. In this paper, we systematically discuss and define the two common types of label noise in medical images - disagreement label noise from inconsistency expert opinions and single-target label noise from wrong diagnosis record. We then propose an uncertainty estimation-based framework to handle these two label noise amid the medical image classification task. We design a dual-uncertainty estimation approach to measure the disagreement label noise and single-target label noise via Direct Uncertainty Prediction and Monte-Carlo-Dropout. A boosting-based curriculum training procedure is later introduced for robust learning. We demonstrate the effectiveness of our method by conducting extensive experiments on three different diseases: skin lesions, prostate cancer, and retinal diseases. We also release a large re-engineered database that consists of annotations from more than ten ophthalmologists with an unbiased golden standard dataset for evaluation and benchmarking.
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The classification accuracy of deep learning models depends not only on the size of their training sets, but also on the quality of their labels. In medical image classification, large-scale datasets are becoming abundant, but their labels will be noisy when they are automatically extracted from radiology reports using natural language processing tools. Given that deep learning models can easily overfit these noisy-label samples, it is important to study training approaches that can handle label noise. In this paper, we adapt a state-of-the-art (SOTA) noisy-label multi-class training approach to learn a multi-label classifier for the dataset Chest X-ray14, which is a large scale dataset known to contain label noise in the training set. Given that this dataset also has label noise in the testing set, we propose a new theoretically sound method to estimate the performance of the model on a hidden clean testing data, given the result on the noisy testing data. Using our clean data performance estimation, we notice that the majority of label noise on Chest X-ray14 is present in the class No Finding, which is intuitively correct because this is the most likely class to contain one or more of the 14 diseases due to labelling mistakes.
Among the three main components (data, labels, and models) of any supervised learning system, data and models have been the main subjects of active research. However, studying labels and their properties has received very little attention. Current principles and paradigms of labeling impose several challenges to machine learning algorithms. Labels are often incomplete, ambiguous, and redundant. In this paper we study the effects of various properties of labels and introduce the Label Refinery: an iterative procedure that updates the ground truth labels after examining the entire dataset. We show significant gain using refined labels across a wide range of models. Using a Label Refinery improves the state-of-the-art top-1 accuracy of (1) AlexNet from 59.3 to 67.2, (2) MobileNet from 70.6 to 73.39, (3) MobileNet-0.25 from 50.6 to 55.59, (4) VGG19 from 72.7 to 75.46, and (5) Darknet19 from 72.9 to 74.47.
Multi-label image classification is the task of predicting a set of labels corresponding to objects, attributes or other entities present in an image. In this work we propose the Classification Transformer (C-Tran), a general framework for multi-label image classification that leverages Transformers to exploit the complex dependencies among visual features and labels. Our approach consists of a Transformer encoder trained to predict a set of target labels given an input set of masked labels, and visual features from a convolutional neural network. A key ingredient of our method is a label mask training objective that uses a ternary encoding scheme to represent the state of the labels as positive, negative, or unknown during training. Our model shows state-of-the-art performance on challenging datasets such as COCO and Visual Genome. Moreover, because our model explicitly represents the uncertainty of labels during training, it is more general by allowing us to produce improved results for images with partial or extra label annotations during inference. We demonstrate this additional capability in the COCO, Visual Genome, News500, and CUB image datasets.
Recently, as an effective way of learning latent representations, contrastive learning has been increasingly popular and successful in various domains. The success of constrastive learning in single-label classifications motivates us to leverage this learning framework to enhance distinctiveness for better performance in multi-label image classification. In this paper, we show that a direct application of contrastive learning can hardly improve in multi-label cases. Accordingly, we propose a novel framework for multi-label classification with contrastive learning in a fully supervised setting, which learns multiple representations of an image under the context of different labels. This facilities a simple yet intuitive adaption of contrastive learning into our model to boost its performance in multi-label image classification. Extensive experiments on two benchmark datasets show that the proposed framework achieves state-of-the-art performance in the comparison with the advanced methods in multi-label classification.
Despite the state-of-the-art performance for medical image segmentation, deep convolutional neural networks (CNNs) have rarely provided uncertainty estimations regarding their segmentation outputs, e.g., model (epistemic) and image-based (aleatoric) uncertainties. In this work, we analyze these different types of uncertainties for CNN-based 2D and 3D medical image segmentation tasks. We additionally propose a test-time augmentation-based aleatoric uncertainty to analyze the effect of different transformations of the input image on the segmentation output. Test-time augmentation has been previously used to improve segmentation accuracy, yet not been formulated in a consistent mathematical framework. Hence, we also propose a theoretical formulation of test-time augmentation, where a distribution of the prediction is estimated by Monte Carlo simulation with prior distributions of parameters in an image acquisition model that involves image transformations and noise. We compare and combine our proposed aleatoric uncertainty with model uncertainty. Experiments with segmentation of fetal brains and brain tumors from 2D and 3D Magnetic Resonance Images (MRI) showed that 1) the test-time augmentation-based aleatoric uncertainty provides a better uncertainty estimation than calculating the test-time dropout-based model uncertainty alone and helps to reduce overconfident incorrect predictions, and 2) our test-time augmentation outperforms a single-prediction baseline and dropout-based multiple predictions.
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