Chronic obstructive pulmonary disease (COPD) is a lung disease where early detection benefits the survival rate. COPD can be quantified by classifying patches of computed tomography images, and combining patch labels into an overall diagnosis for the image. As labeled patches are often not available, image labels are propagated to the patches, incorrectly labeling healthy patches in COPD patients as being affected by the disease. We approach quantification of COPD from lung images as a multiple instance learning (MIL) problem, which is more suitable for such weakly labeled data. We investigate various MIL assumptions in the context of COPD and show that although a concept region with COPD-related disease patterns is present, considering the whole distribution of lung tissue patches improves the performance. The best method is based on averaging instances and obtains an AUC of 0.742, which is higher than the previously reported best of 0.713 on the same dataset. Using the full training set further increases performance to 0.776, which is significantly higher (DeLong test) than previous results.

Classification of COPD with Multiple Instance Learning

Intracranial hemorrhage (ICH) is a life-threatening emergency with high rates of mortality and morbidity. Rapid and accurate detection of ICH is crucial for patients to get a timely treatment. In order to achieve the automatic diagnosis of ICH, most deep learning models rely on huge amounts of slice labels for training. Unfortunately, the manual annotation of CT slices by radiologists is time-consuming and costly. To diagnose ICH, in this work, we propose to use an attention-based multiple instance learning (Att-MIL) approach implemented through the combination of an attention-based convolutional neural network (Att-CNN) and a variational Gaussian process for multiple instance learning (VGP-MIL). Only labels at scan-level are necessary for training. Our method trains the model using scan labels and assigns each slice with an attention weight, which can be used to provide slice-level predictions, and uses the VGPMIL model based on low-dimensional features extracted by the Att-CNN to obtain improved predictions both at slice and scan levels. To analyze the performance of the proposed approach, our model has been trained on 1150 scans from an RSNA dataset and evaluated on 490 scans from an external CQ500 dataset. Our method outperforms other methods using the same scan-level training and is able to achieve comparable or even better results than other methods relying on slicelevel annotations.

/pdf/combining-attention-based-multiple-instance-learning-and-47wliahjo0.pdf

Combining Attention-based Multiple Instance Learning and Gaussian Processes for CT Hemorrhage Detection

Intracranial hemorrhage (ICH) is a life-threatening emergency with high rates of mortality and morbidity. Rapid and accurate detection of ICH is crucial for patients to get a timely treatment. In order to achieve the automatic diagnosis of ICH, most deep learning models rely on huge amounts of slice labels for training. Unfortunately, the manual annotation of CT slices by radiologists is time-consuming and costly. To diagnose ICH, in this work, we propose to use an attention-based multiple instance learning (Att-MIL) approach implemented through the combination of an attention-based convolutional neural network (Att-CNN) and a variational Gaussian process for multiple instance learning (VGPMIL). Only labels at scan-level are necessary for training. Our method (a) trains the model using scan labels and assigns each slice with an attention weight, which can be used to provide slice-level predictions, and (b) uses the VGPMIL model based on low-dimensional features extracted by the Att-CNN to obtain improved predictions both at slice and scan levels. To analyze the performance of the proposed approach, our model has been trained on 1150 scans from an RSNA dataset and evaluated on 490 scans from an external CQ500 dataset. Our method outperforms other methods using the same scan-level training and is able to achieve comparable or even better results than other methods relying on slice-level annotations.

Ulcerative colitis (UC) is a chronic inflammatory bowel disease characterized by relapsing inflammation of the large intestine. The severity of UC is often represented by the Mayo Endoscopic Subscore (MES) which quantifies mucosal disease activity from endoscopy videos. In clinical trials, an endoscopy video is assigned an MES based upon the most severe disease activity observed in the video. For this reason, severe inflammation spread throughout the colon will receive the same MES as an otherwise healthy colon with severe inflammation restricted to a small, localized segment. Therefore, the extent of disease activity throughout the large intestine, and overall response to treatment, may not be completely captured by the MES. In this work, we aim to automatically estimate UC severity for each frame in an endoscopy video to provide a higher resolution assessment of disease activity throughout the colon. Because annotating severity at the frame-level is expensive, labor-intensive, and highly subjective, we propose a novel weakly supervised, ordinal classification method to estimate frame severity from video MES labels alone. Using clinical trial data, we first achieved 0.92 and 0.90 AUC for predicting mucosal healing and remission of UC, respectively. Then, for severity estimation, we demonstrate that our models achieve substantial Cohen's Kappa agreement with ground truth MES labels, comparable to the inter-rater agreement of expert clinicians. These findings indicate that our framework could serve as a foundation for novel clinical endpoints, based on a more localized scoring system, to better evaluate UC drug efficacy in clinical trials.

Automatic Estimation of Ulcerative Colitis Severity from Endoscopy Videos using Ordinal Multi-Instance Learning

Weakly supervised learning promises reduced annotation effort while maintaining performance.

Weakly Supervised MRI Slice-Level Deep Learning Classification of Prostate Cancer Approximates Full Voxel- and Slice-Level Annotation: Effect of Increasing Training Set Size.

Multiple instance learning (MIL) is a supervised learning methodology that aims to allow models to learn instance class labels from bag class labels, where a bag is defined to contain multiple instances. MIL is gaining traction for learning from weak labels but has not been widely applied to 3D medical imaging. MIL is well-suited to clinical CT acquisitions since (1) the highly anisotropic voxels hinder application of traditional 3D networks and (2) patch-based networks have limited ability to learn whole volume labels. In this work, we apply MIL with a deep convolutional neural network to identify whether clinical CT head image volumes possess one or more large hemorrhages (>; 20cm3 ), resulting in a learned 2D model without the need for 2D slice annotations. Individual image volumes are considered separate bags, and the slices in each volume are instances. Such a framework sets the stage for incorporating information obtained in clinical reports to help train a 2D segmentation approach. Within this context, we evaluate the data requirements to enable generalization of MIL by varying the amount of training data. Our results show that a training size of at least 400 patient image volumes was needed to achieve accurate per-slice hemorrhage detection. Over a five-fold cross-validation, the leading model, which made use of the maximum number of training volumes, had an average true positive rate of 98.10%, an average true negative rate of 99.36%, and an average precision of 0.9698. The models have been made available along with source code1 to enabled continued exploration and adaption of MIL in CT neuroimaging.

Extracting 2D weak labels from volume labels using multiple instance learning in CT hemorrhage detection.

Multiple instance learning (MIL) is a supervised learning methodology that aims to allow models to learn instance class labels from bag class labels, where a bag is defined to contain multiple instances. MIL is gaining traction for learning from weak labels but has not been widely applied to 3D medical imaging. MIL is well-suited to clinical CT acquisitions since (1) the highly anisotropic voxels hinder application of traditional 3D networks and (2) patch-based networks have limited ability to learn whole volume labels. In this work, we apply MIL with a deep convolutional neural network to identify whether clinical CT head image volumes possess one or more large hemorrhages (> 20cm$^3$), resulting in a learned 2D model without the need for 2D slice annotations. Individual image volumes are considered separate bags, and the slices in each volume are instances. Such a framework sets the stage for incorporating information obtained in clinical reports to help train a 2D segmentation approach. Within this context, we evaluate the data requirements to enable generalization of MIL by varying the amount of training data. Our results show that a training size of at least 400 patient image volumes was needed to achieve accurate per-slice hemorrhage detection. Over a five-fold cross-validation, the leading model, which made use of the maximum number of training volumes, had an average true positive rate of 98.10%, an average true negative rate of 99.36%, and an average precision of 0.9698. The models have been made available along with source code to enabled continued exploration and adaption of MIL in CT neuroimaging.

Extracting 2D weak labels from volume labels using multiple instance learning in CT hemorrhage detection

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Extracting 2D weak labels from volume labels using multiple instance learning in CT hemorrhage detection.

Extracting 2D weak labels from volume labels using multiple instance learning in CT hemorrhage detection