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Register a new userThe Pitfalls of Sample Selection: A Case Study on Lung Nodule Classification
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Added by
Vasileios Baltatzis
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Using publicly available data to determine the performance of methodological contributions is important as it facilitates reproducibility and allows scrutiny of the published results. In lung nodule classification, for example, many works report results on the publicly available LIDC dataset. In theory, this should allow a direct comparison of the performance of proposed methods and assess the impact of individual contributions. When analyzing seven recent works, however, we find that each employs a different data selection process, leading to largely varying total number of samples and ratios between benign and malignant cases. As each subset will have different characteristics with varying difficulty for classification, a direct comparison between the proposed methods is thus not always possible, nor fair. We study the particular effect of truthing when aggregating labels from multiple experts. We show that specific choices can have severe impact on the data distribution where it may be possible to achieve superior performance on one sample distribution but not on another. While we show that we can further improve on the state-of-the-art on one sample selection, we also find that on a more challenging sample selection, on the same database, the more advanced models underperform with respect to very simple baseline methods, highlighting that the selected data distribution may play an even more important role than the model architecture. This raises concerns about the validity of claimed methodological contributions. We believe the community should be aware of these pitfalls and make recommendations on how these can be avoided in future work.
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The progression of lung cancer implies the intrinsic ordinal relationship of lung nodules at different stages-from benign to unsure then to malignant. This problem can be solved by ordinal regression methods, which is between classification and regression due to its ordinal label. However, existing convolutional neural network (CNN)-based ordinal regression methods only focus on modifying classification head based on a randomly sampled mini-batch of data, ignoring the ordinal relationship resided in the data itself. In this paper, we propose a Meta Ordinal Weighting Network (MOW-Net) to explicitly align each training sample with a meta ordinal set (MOS) containing a few samples from all classes. During the training process, the MOW-Net learns a mapping from samples in MOS to the corresponding class-specific weight. In addition, we further propose a meta cross-entropy (MCE) loss to optimize the network in a meta-learning scheme. The experimental results demonstrate that the MOW-Net achieves better accuracy than the state-of-the-art ordinal regression methods, especially for the unsure class.
Convolutional Neural Networks (CNNs) are widely used for image classification in a variety of fields, including medical imaging. While most studies deploy cross-entropy as the loss function in such tasks, a growing number of approaches have turned to a family of contrastive learning-based losses. Even though performance metrics such as accuracy, sensitivity and specificity are regularly used for the evaluation of CNN classifiers, the features that these classifiers actually learn are rarely identified and their effect on the classification performance on out-of-distribution test samples is insufficiently explored. In this paper, motivated by the real-world task of lung nodule classification, we investigate the features that a CNN learns when trained and tested on different distributions of a synthetic dataset with controlled modes of variation. We show that different loss functions lead to different features being learned and consequently affect the generalization ability of the classifier on unseen data. This study provides some important insights into the design of deep learning solutions for medical imaging tasks.
While deep learning methods are increasingly being applied to tasks such as computer-aided diagnosis, these models are difficult to interpret, do not incorporate prior domain knowledge, and are often considered as a black-box. The lack of model interpretability hinders them from being fully understood by target users such as radiologists. In this paper, we present a novel interpretable deep hierarchical semantic convolutional neural network (HSCNN) to predict whether a given pulmonary nodule observed on a computed tomography (CT) scan is malignant. Our network provides two levels of output: 1) low-level radiologist semantic features, and 2) a high-level malignancy prediction score. The low-level semantic outputs quantify the diagnostic features used by radiologists and serve to explain how the model interprets the images in an expert-driven manner. The information from these low-level tasks, along with the representations learned by the convolutional layers, are then combined and used to infer the high-level task of predicting nodule malignancy. This unified architecture is trained by optimizing a global loss function including both low- and high-level tasks, thereby learning all the parameters within a joint framework. Our experimental results using the Lung Image Database Consortium (LIDC) show that the proposed method not only produces interpretable lung cancer predictions but also achieves significantly better results compared to common 3D CNN approaches.
Though large-scale datasets are essential for training deep learning systems, it is expensive to scale up the collection of medical imaging datasets. Synthesizing the objects of interests, such as lung nodules, in medical images based on the distribu
tion of annotated datasets can be helpful for improving the supervised learning tasks, especially when the datasets are limited by size and class balance. In this paper, we propose the class-aware adversarial synthesis framework to synthesize lung nodules in CT images. The framework is built with a coarse-to-fine patch in-painter (generator) and two class-aware discriminators. By conditioning on the random latent variables and the target nodule labels, the trained networks are able to generate diverse nodules given the same context. By evaluating on the public LIDC-IDRI dataset, we demonstrate an example application of the proposed framework for improving the accuracy of the lung nodule malignancy estimation as a binary classification problem, which is important in the lung screening scenario. We show that combining the real image patches and the synthetic lung nodules in the training set can improve the mean AUC classification score across different network architectures by 2%.
Computed tomography imaging is a standard modality for detecting and assessing lung cancer. In order to evaluate the malignancy of lung nodules, clinical practice often involves expert qualitative ratings on several criteria describing a nodules appearance and shape. Translating these features for computer-aided diagnostics is challenging due to their subjective nature and the difficulties in gaining a complete description. In this paper, we propose a computerized approach to quantitatively evaluate both appearance distinctions and 3D surface variations. Nodule shape was modeled and parameterized using spherical harmonics, and appearance features were extracted using deep convolutional neural networks. Both sets of features were combined to estimate the nodule malignancy using a random forest classifier. The proposed algorithm was tested on the publicly available Lung Image Database Consortium dataset, achieving high accuracy. By providing lung nodule characterization, this method can provide a robust alternative reference opinion for lung cancer diagnosis.
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