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Weakly supervised learning with noisy data has drawn attention in the medical imaging community due to the sparsity of high-quality disease labels. However, little is known about the limitations of such weakly supervised learning and the effect of these constraints on disease classification performance. In this paper, we test the effects of such weak supervision by examining model tolerance for three conditions. First, we examined model tolerance for noisy data by incrementally increasing error in the labels within the training data. Second, we assessed the impact of dataset size by varying the amount of training data. Third, we compared performance differences between binary and multi-label classification. Results demonstrated that the model could endure up to 10% added label error before experiencing a decline in disease classification performance. Disease classification performance steadily rose as the amount of training data was increased for all disease classes, before experiencing a plateau in performance at 75% of training data. Last, the binary model outperformed the multilabel model in every disease category. However, such interpretations may be misleading, as the binary model was heavily influenced by co-occurring diseases and may not have learned the specific features of the disease in the image. In conclusion, this study may help the medical imaging community understand the benefits and risks of weak supervision with noisy labels. Such studies demonstrate the need to build diverse, large-scale datasets and to develop explainable and responsible AI., Comment: 16 pages , 8 figures. arXiv admin note: text overlap with arXiv:2202.11709

Despite the potential of weakly supervised learning to automatically annotate massive amounts of data, little is known about its limitations for use in computer-aided diagnosis (CAD). For CT specifically, interpreting the performance of CAD algorithms can be challenging given the large number of co-occurring diseases. This paper examines the effect of co-occurring diseases when training classification models by weakly supervised learning, specifically by comparing multi-label and multiple binary classifiers using the same training data. Our results demonstrated that the binary model outperformed the multi-label classification in every disease category in terms of AUC. However, this performance was heavily influenced by co-occurring diseases in the binary model, suggesting it did not always learn the correct appearance of the specific disease. For example, binary classification of lung nodules resulted in an AUC of < 0.65 when there were no other co-occurring diseases, but when lung nodules co-occurred with emphysema, the performance reached AUC > 0.80. We hope this paper revealed the complexity of interpreting disease classification performance in weakly supervised models and will encourage researchers to examine the effect of co-occurring diseases on classification performance in the future., Comment: 5 pages, 4 figures, Accepted at SPIE Medical Imaging Conference 2022

Purpose: To develop high throughput multi-label annotators for body (chest, abdomen, and pelvis) Computed Tomography (CT) reports that can be applied across a variety of abnormalities, organs, and disease states. Approach: We used a dictionary approach to develop rule-based algorithms (RBA) for extraction of disease labels from radiology text reports. We targeted three organ systems (lungs/pleura, liver/gallbladder, kidneys/ureters) with four diseases per system based on their prevalence in our dataset. To expand the algorithms beyond pre-defined keywords, attention-guided recurrent neural networks (RNN) were trained using the RBA-extracted labels to classify reports as being positive for one or more diseases or normal for each organ system. Confounding effects on model performance were evaluated using random initialization or pre-trained embedding as well as different sizes of training datasets. Performance was evaluated using the receiver operating characteristic (ROC) area under the curve (AUC) against 2,158 manually obtained labels. Results: Our models extracted disease labels from 261,229 radiology reports of 112,501 unique subjects. Pre-trained models outperformed random initialization across all diseases. As the training dataset size was reduced, performance was robust except for a few diseases with relatively small number of cases. Pre-trained classification AUCs achieved > 0.95 for all five disease outcomes across all three organ systems. Conclusions: Our label-extracting pipeline was able to encompass a variety of cases and diseases by generalizing beyond strict rules with exceptional accuracy. This method can be easily adapted to enable automated labeling of hospital-scale medical data sets for training image-based disease classifiers.

Weakly supervised disease classification of CT imaging suffers from poor localization owing to case-level annotations, where even a positive scan can hold hundreds to thousands of negative slices along multiple planes. Furthermore, although deep learning segmentation and classification models extract distinctly unique combinations of anatomical features from the same target class(es), they are typically seen as two independent processes in a computer-aided diagnosis (CAD) pipeline, with little to no feature reuse. In this research, we propose a medical classifier that leverages the semantic structural concepts learned via multi-resolution segmentation feature maps, to guide weakly supervised 3D classification of chest CT volumes. Additionally, a comparative analysis is drawn across two different types of feature aggregation to explore the vast possibilities surrounding feature fusion. Using a dataset of 1593 scans labeled on a case-level basis via rule-based model, we train a dual-stage convolutional neural network (CNN) to perform organ segmentation and binary classification of four representative diseases (emphysema, pneumonia/atelectasis, mass and nodules) in lungs. The baseline model, with separate stages for segmentation and classification, results in AUC of 0.791. Using identical hyperparameters, the connected architecture using static and dynamic feature aggregation improves performance to AUC of 0.832 and 0.851, respectively. This study advances the field in two key ways. First, case-level report data is used to weakly supervise a 3D CT classifier of multiple, simultaneous diseases for an organ. Second, segmentation and classification models are connected with two different feature aggregation strategies to enhance the classification performance., Comment: Accepted to 2020 SPIE Medical Imaging: Computer-Aided Diagnosis [oral presentation]

Purpose: To design multi-disease classifiers for body CT scans for three different organ systems using automatically extracted labels from radiology text reports.Materials & Methods: This retrospective study included a total of 12,092 patients (mean age 57 +- 18; 6,172 women) for model development and testing (from 2012-2017). Rule-based algorithms were used to extract 19,225 disease labels from 13,667 body CT scans from 12,092 patients. Using a three-dimensional DenseVNet, three organ systems were segmented: lungs and pleura; liver and gallbladder; and kidneys and ureters. For each organ, a three-dimensional convolutional neural network classified no apparent disease versus four common diseases for a total of 15 different labels across all three models. Testing was performed on a subset of 2,158 CT volumes relative to 2,875 manually derived reference labels from 2133 patients (mean age 58 +- 18;1079 women). Performance was reported as receiver operating characteristic area under the curve (AUC) with 95% confidence intervals by the DeLong method. Results: Manual validation of the extracted labels confirmed 91% to 99% accuracy across the 15 different labels. AUCs for lungs and pleura labels were: atelectasis 0.77 (95% CI: 0.74, 0.81), nodule 0.65 (0.61, 0.69), emphysema 0.89 (0.86, 0.92), effusion 0.97 (0.96, 0.98), and no apparent disease 0.89 (0.87, 0.91). AUCs for liver and gallbladder were: hepatobiliary calcification 0.62 (95% CI: 0.56, 0.67), lesion 0.73 (0.69, 0.77), dilation 0.87 (0.84, 0.90), fatty 0.89 (0.86, 0.92), and no apparent disease 0.82 (0.78, 0.85). AUCs for kidneys and ureters were: stone 0.83 (95% CI: 0.79, 0.87), atrophy 0.92 (0.89, 0.94), lesion 0.68 (0.64, 0.72), cyst 0.70 (0.66, 0.73), and no apparent disease 0.79 (0.75, 0.83). Conclusion: Weakly-supervised deep learning models were able to classify diverse diseases in multiple organ systems., Comment: 22 pages, 6 figures, 2 tables; Accepted for publication at Radiology: Artificial Intelligence

Machine learning models for radiology benefit from large-scale data sets with high quality labels for abnormalities. We curated and analyzed a chest computed tomography (CT) data set of 36,316 volumes from 19,993 unique patients. This is the largest multiply-annotated volumetric medical imaging data set reported. To annotate this data set, we developed a rule-based method for automatically extracting abnormality labels from free-text radiology reports with an average F-score of 0.976 (min 0.941, max 1.0). We also developed a model for multi-organ, multi-disease classification of chest CT volumes that uses a deep convolutional neural network (CNN). This model reached a classification performance of AUROC greater than 0.90 for 18 abnormalities, with an average AUROC of 0.773 for all 83 abnormalities, demonstrating the feasibility of learning from unfiltered whole volume CT data. We show that training on more labels improves performance significantly: for a subset of 9 labels - nodule, opacity, atelectasis, pleural effusion, consolidation, mass, pericardial effusion, cardiomegaly, and pneumothorax - the model's average AUROC increased by 10% when the number of training labels was increased from 9 to all 83. All code for volume preprocessing, automated label extraction, and the volume abnormality prediction model will be made publicly available. The 36,316 CT volumes and labels will also be made publicly available pending institutional approval., Comment: 20 pages, 3 figures, 5 tables (appendices additional). Published in Medical Image Analysis (October 2020)