A Weakly Supervised Adaptive DenseNet for Classifying Thoracic Diseases and Identifying Abnormalities
We present a weakly supervised deep learning model for classifying diseases and identifying abnormalities based on medical imaging data. In this work, instead of learning from medical imaging data with region-level annotations, our model was trained on imaging data with image-level labels to classify diseases, and is able to identify abnormal image regions simultaneously. Our model consists of a customized pooling structure and an adaptive DenseNet front-end, which can effectively recognize possible disease features for classification and localization tasks. Our method has been validated on the publicly available ChestX-ray14 dataset. Experimental results have demonstrated that our classification and localization prediction performance achieved significant improvement over the previous models on the ChestX-ray14 dataset. In summary, our network can produce accurate disease classification and localization, which can potentially support clinical decisions. ††† Both authors equally contributed to this work
Large scale annotated visual datasets have boosted performance of deep learning methods on many challenging computer vision problems [1, 2, 3]. Tasks like object detection, classification, tracking, and segmentation have been successfully tackled by techniques built on top of these large-scale dataset with annotations [4, 5, 6]. There are increasing numbers of applications utilizing deep learning methods in medical imaging analysis over the last decade . In clinical procedures, visual evidence such as segmentation or spatial localization of abnormal regions that supports the diagnosis results, is an vital part of clinical diagnosis. This provides a comprehensive interpretation of diagnosis results and potentially decreases the false positive rate.
In this work, we focus on the automatic disease diagnosis and localization in chest radiography released by  named ChestX-ray 14, which is one of the largest public chest radiography dataset with image-level disease labels and contains a small subset of region-level disease localizations (bounding boxes). Our goal is to develop a deep learning scheme capable of both classifying the disease and localizing the associated lesion sites. Divergent from standard strongly supervised object detection, our model does not require ground truth localization annotations during training. Firstly, we adopted and modified a pre-trained classification CNN as our front-end feature extractor . The pre-trained front-end encodes the information from a large perceptive field. Then, after passing through a simple bridging structure, the extracted feature from the front-end are fed into a customized two-stage pooling network structure, which produces both classification and associated localization simultaneously.
Both quantitative and qualitative visual evaluations show that our proposed model obtains significant improvement over the previous published state-of-the-art results on disease classification and localization. Visual evaluations indicate a strong alignment and correspondence between the clinical annotations and the predicted disease candidate regions shown in figure 12.
In summary, the contributions of this work are two-folds:
We developed a weakly supervised end-to-end learning structure that learns from chest radiography images containing multiple common thoracic diseases by explicitly searching over possible disease features and locations in the image.
We performed an extensive experimental analysis of our modelâs classification and localization performance on the large-scale ChestX-ray14 datasets. We found that our model (i) outputs more accurate image-level labels than current state-of-the-art; (ii) predicts better lesion localization than previous published methods.
2 Related Work
CAD for chest radiography: The chest radiography is the most ordered and common radiological examination for chest diseases. It is a low-cost, low radiation and fast imaging exam. Recent studies also demonstrated the chest radiography’s application on detection and evaluation of coronary artery diseases, which are usually evaluated using Computed Tomography (CT) with expensive cost and high radiation dose [10, 11, 12]. CAD techniques have been widely applied in chest radiography for task such as automatic diagnosis and patient image retrieval. Previously, Bar et al. adapted the Decaf-Net for 8 thoracic diseases classification on a relatively small chest x-ray dataset . Lajhani et al. proposed the DCNN for tuberculosis classification task. Their model ensembled both Alex-Net and Google-Net and achieved impressive results . Anavi et al. has worked on image retrieval in medicine, specifically for chest radiography given the pathology . All the aforementioned research showed promising results. However, they only conducted their experiments on relatively small dataset, ranging from 10 to 500 images.
ChestX-ray14: Recently, National Institute of Health (NIH) released one of the largest public chest radiography dataset, consisting of 108,948 posterior-anterior view images from 32,797 patients with eight major chest diseases . A small subset of this dataset is provided with hand labeled bounding boxes for evaluation. Lately, NIH further expanded this dataset to 112,120 frontal-view images with 6 additional thoracic diseases, named ChestX-ray14. Several deep learning methods have been addressed the application of CNN on this dataset for thoracic disease classification and localization [16, 17, 18]. Wang et al.  applied a pre-trained Res-Net as the backbone to generate heatmap as localization, and subsequently used a global max pooling to obtain classification. However, most of the localizations generated by their network mismatched with the ground-truth bounding boxes. Yao et al.  used DenseNet  to extract features. To harness the correlation between some of the diseases, they used a LSTM module to repeatedly decode the feature vector from a DenseNet  front end and produced one disease prediction at each step. They achieved improved results compared to the baseline in . One of the most recent work from Rajpurkar et al. achieved a good multi-label classification results by fine-tuning a pre-trained DenseNet-121 [9, 18]. Their classification results outperformed the previous state-of-the-art methods [8, 16, 17]. However, there was no quantification localization analysis from their work. Another most recent work from Li et al.  used a pre-trained Res-Net to extract features and divided them into patches. They passed the extracted patches through a fully-convolutional classification CNN to obtain a disease probability map. In the mean time, a classification score was acquired by multiplying all probability values together. They achieved significantly better classification and localization result than the baseline  for certain diseases.
Weakly supervised learning: The ChestX-ray14 dataset  contains mostly classification labels but few bounding boxes annotations. Therefore, we seek a model that is capable of localizing the diseased regions given only image wise labels. This falls into category of weakly supervise learning (WSL), which often refers as the task of capturing object location through a customized deep learning model that trained with only image-level labels. Oquab et al.  proposed a WSL scheme. They used a pre-trained CNN to generate class probability map across spatial locations and applied max-pooling across spatial locations to get a single binary score vector. With their strategy, they were able to get both decent classification accuracy and localization mAP on the benchmark dataset [20, 3]. Recently, Durand et al. proposed a more sophisticated WSL approach . They presented the idea of class pooling based on the assumption that an object inherently can be decomposed into different sub-maps to capture better semantic segmentation in WSL. Their experimental results tested on PASCAL 2007, PASCAL 2012, MS COCO, 15 Scene, MIT67 [22, 20, 3, 23, 24] indicated the advantage of such design and achieve significant improvement over  ’s model.
In this work, we aim to use chest radiographs as input with only image-wise labels to train a model that generates classification for thoracic disease along with the localization heatmaps. The architecture of our proposed network can be summarized into three parts: 1) using an Adaptive DenseNet to generate feature maps and 2) using a bridging layer to convert the feature maps into class-specific sub-maps 3) using a WSL pooling structure to pool the sub-maps into class-specific heatmaps and single probability score for each disease.
3.1 Adaptive DenseNet
The Adaptive DenseNet inherits the basic structure from DenseNet . The dense block of DenseNet consists of direct connections from preceding layers to all subsequent layers which pass image information in deep model’s training. We maintained the DenseNet structures before the fully connected classification layers as our basic structure. However, the output feature map size after the final dense block is greatly decreased (), losing too much spatial resolution as compared to the input image (), which is not suitable for our localization task. To overcome this, firstly, we took out the average pooling operation at the third transition layer to achieve a fine resolution. Secondly, in order to maintain the same receptive field of each convolution kernel, we dilated all kernels in the fourth dense block. The Adaptive DenseNet outputs a feature map with spatial size of . Details of our Adaptive Densenet is shown in Figure 2. In this work, we chose the DenseNet-169 as our basic structure. Our adaptation can be applied to other DenseNet structures as well, such as DenseNet-121 and Densenet-201. With the Adaptive DenseNet, we were able to acquire a fine resolution feature map.
3.2 Bridging layer
To connect the output of the Adaptive DenseNet and the pooling structure described in section 3.3, a bridging layer is proposed and used here. Specifically, the output of the Adaptive DenseNet is transformed by a convolutional layer, which learns the mapping from the Adaptive DenseNet’s output feature maps to class specific sub-maps. Through the bridging layer, the channel size of the feature map is transferred from (channel size of Adaptive DenseNet’s output) to , as shown in Figure 3. This bridging layer connects the Adaptive DenseNet and the WSL pooling structure together to form the overall network.
3.3 WSL pooling
To obtain accurate disease classification along with disease localization heatmap, we integrated a customized weakly supervised learning strategy into our network. Similar to , we implemented two types of global pooling layers to summarize all information for each class in feature map outputted from the Adaptive DenseNet, which include: 1) a class-wise pooling within the same class, and 2) a spatial pooling along different classes. The class-wise pooling summarizes submaps into final localization heatmap, and spatial-wise pooling summarizes heatmap into classification. Details of the pooling designs are demonstrated in Figure 4.
class-wise pooling: The class-wise pooling combines the submaps from each of the classes from the bridging layer. In specific, our class-wise pooling combines the maps for all disease classes independently through Equation 1.
where is the number of sub-maps that contains partial information for each disease class. , , are feature map’s height, width, and the number of class, respectively. The input feature with size of is divided into branches with each size of . Then, the sub-maps information are composed into one final feature map for each class through an average pooling. This results in a transformed class heatmap of size .
spatial-wise pooling: Given a class heatmap with size of , we used a spatial-wise pooling to generate our final classification output. Our spatial-wise pooling extracts a classification vector () from the class heatmap outputted from class-wise pooling shown above. The most common strategy for spatial-wise pooling is maxpooling, which might potentially ignore most of the feature information, generate localization heatmap only in small regions, and cause insufficient pass of gradient for training.
Therefore, we proposed to use a customized spatial-wise pooling strategy for both training and testing of our network, as shown in Figure 4. During the training phase, we firstly selected top scores from heatmaps and randomly chose one among the k numbers for each class. Because the class heatmap may not be perfect, the highest score may not correctly correspond to the disease location. Thus, random sampling from top spatial locations instead of simply choosing the max gives the network higher probability to capture the correct spatial location of the disease and generate the correct gradient. During the testing phase, we looked at regions with the highest()/lowest() activation from the heatmap . The highest activation indicates presence of classes while the lowest activation indicates absence of classes. Thus both are incorporated to the prediction layer to achieve a robust classification performance. We introduced a weighting factor to control the relative importance between these two terms.
Formally, let be the heatmap for class , let / be the set of top /bottom scores in , and let be the final class score. During training phase, we have:
where is a single element uniformly random sampled from . During testing phase, we have:
where / are elements in /. and is the weighting factor added on bottom scores.
3.4 Network’s training
For network initialization, we transfered the weights from the pre-trained models on ImageNet for our Adaptive DenseNet. Then, we randomly initialized parameters for bridging and WSL pooling layers. We used learning rate of 0.002 with weight decay of 0.1 for every 10 epochs during training. Our model were implemented with Pytorch (https://pytorch.org/) on a Nvidia GTX 1080Ti. We added batch normalization  after each convolution and additional drop out of rate of 0.1 for each DenseBlock inside Adaptive DenseNet  to prevent overfitting. Since there is a large data imbalance between each class, we trained our model with weighted binary cross entropy loss:
where represents percent of positive sample and represents percent of negative sample among all dataset.
3.5 Disease classification and localization
The heatmap obtained from our class-wise pooling is further used as a reference map to generate disease bounding boxes. A thresholding followed by connected component analysis are applied for each disease class to generate bounding boxes. Empirically, we used a threshold value of 0.8 for ”Cardiomegaly” and threshold values of 0.9 for the rest of classes to obtain the best results. The disease classification score is acquired from the spatial-wise pooling on the heatmap. In short, our network structure is designed for both disease classification and localization tasks, yet only use chest radiographs along with image-level annotations for our training.
4 Experiments and Results
4.1 Data for experiments
We performed our experiment using the ChestX-ray14 dataset. The diseases in the corresponding chest radiograph are diagnosed by radiologists and the labeled ground truth are obtained through text mining on the patients’ diagnostic reports. We used exactly same published data split as in [18, 8, 16]. The dataset is divided into training (70%), validation (10%) and testing (20%). The original resolution of image is and was downscaled to . In order to fit dataset into ImageNet  pre-trained models, we normalized the image by mean and standard deviation of the images from ImageNet. We used random crop of size from the downscaled image as the network input for training and we used center crop of same size for testing. For localization validation, the ChestX-ray14 dataset contains 880 images with 983 disease bounding boxes annotated by board-certified radiologists. We calculated the intersection over union (IoU) between our prediction and the ground truth bounding boxes.
4.2 Disease classification
|Pathology||Wang ||Yao ||Li ||Rajpurkar* ||Ours|
We calculated the Area under Receiver Operating Characteristic curve (AUROC) for each class to evaluate the classification performance of our model. Our results are selected based on the best performance of classifier for each class throughout our training iterations. Our classification performance is compared with other state-of-the-art results [8, 16, 17, 18]. The experiment is tested with the same dataset splitting as demonstrated in [8, 16, 18].
In all 14 diseases, our model achieved better classification AUROC than [8, 16] as shown in Table 1. In comparison to , our model achieved better classification AUROC in 13 out of 14 diseases. In particular, our model obtained more than 2% higher AUROC in ”Cardiomegaly”, ”Nodule”, ”Pneumonia”, ”Fibrosis” and ”Hernia”. Comparing our results with ’s work, our model outperformed theirs in 11 out of 14 diseases. We observed significant improvements over ’s work, especially for ”Nodule”, ”Pneumonia”, ”Consolidation”, ”Emphysema” and ”Hernia”.
As shown in table 1, our network performed better on diseases classification with large lesions than one with smaller lesions. ”Cardiomegaly” and ”Emphysema” are the representative classes for disease with large lesion and our model achieved classification score over 90% on both. Although our network performed less accurate on identifying smaller lesions such as mass and nodule, our model is significantly improved from [8, 16, 17, 18] on these classes.
In addition, we performed hyper-parameter searching for best classification performance (details shown in Supplemental Materials). In class-wise pooling, we tested number of sub-maps () from number 2 to 18 and found 14 sub-maps yielded best result. We then kept this setting for the rest of experiment. In spatial pooling, we tested hyper-parameters on two different strategies separately. During training, we tested our model using top scores, ranging from 1 to 20. We found that at 10 yielded best network. During testing, we tested from 1 to 20 and from 1 to 25. We found that both and at 15 yielded best classification result. We tested ranging from 0.25 to 1 and equals at 1 gave the best importance balance between and .
4.3 Disease localization
We generated our predicted bounding boxes by applying a thresholding on the heatmap obtained from our class-wise pooling layer. Examples are shown in Figure 5. No localization annotation was used during training process. The heatmaps were generated by network with training only from image-level labels. All 880 images with bounding boxes ground truth were used for evaluation.
In Table 2, we compared our results with . Our model achieved significantly higher IoU score over  on diseases with large lesion, such as ”Cardiomegaly” (abnormally large heart). The heatmap is well-fitted with the ground truth bounding box. Disease such as ”Infiltration” (substance such as blood infiltrates through vessel into lung) and ”Pneumonia” (inflammation in lung) that affect large area of lungs manifest as visually more prominent patterns, which are learned by our network. Moreover, the localization for small disease region such as ”Atelectasis” (partially collapsed lung) and Mass (an abnormal lump 3cm) can also be well captured by our network. Noted that for ”Effusion” (liquid occupying lung space), our network detects the disease that covers whole lesion while the ground truth includes some extra parts such as the shoulder.
We presents 5 ambiguous cases on 5 diseases in Figure 6, which represents bias in localization annotations that leads to lower IoU score. In the case of ”Effusion”, the annotation outlined the liquid-lung boundary. Instead, our network includes the full liquid rinsed area. In the cases of ”Infiltration” and ”Pneumonia” that spread both lungs, the ground truth annotations only includes single lung, whereas our network captures both lungs. For cases like ”Mass” and ”Nodule”, the ground truth bounding box only highlights one of many instances of ”Mass” and ”Nodule”, but our localization highlights all instances.
Observing annotation ambiguity, we attempted to quantify the effect. We expanded the annotations by having a certified radiologist manually re-labeled bounding boxes on lesion on 80 ambiguous cases. We evaluated our model with the expanded annotations and the updated localization IoU is shown in Table 2. The updated IoU score on expanded annotations is significantly improved for certain classes, such as ”Effusion”, ”Nodule”, ”Atelectasis”, ”Infiltration”, ”Mass”, and ”Pneumonia”.
In clinical procedures, visual evidence such as segmentation or spatial localization of disease lesions, in support of disease classification results, is a vital part of clinical diagnosis. It provides a comprehensive insight into the disease and potentially decreases the false positive of diagnosis. In this work, we proposed a weakly supervised adaptive DenseNet architecture. It only trains on image-level annotation, yet is able to provide both disease classification and corresponding visual evidence, making it potentially valuable in clinical setting.
In our experiment, we specifically looked at 14 different thoracic diseases. Our network demonstrated its ability to precisely identify disease patterns which generated accurate disease classification and corresponding heatmaps for disease localization. In our classification experiments, our network outperformed the current state-of-the-art method on 10 out of 14 diseases. Specifically, our network has shown significant classification improvements on diseases with large lesion such as ”Pneumonia” and ”Emphysema”. Our model also gave robust classification results on diseases with small lesions such as ”Nodule”. In our localization experiments, our network achieved significant better localization performance on 5 out of 8 diseases with mean T(IoU)=, as compared to the NIH baseline . The possible reason for our network to achieve higher classification accuracy is two-fold. First of all, the use of a two-stage pooling allows the network to capture complex intra-class variations. Secondly, the removal of average pooling helps to improve spatial resolution and maintain more image details.
We also evaluated the effect of localization label ambiguity. We collaborated with a certified radiologist to expand the ground truth bounding box annotations on 80 cases. We found that our localization has significantly better overlap with the bounding box in the expanded annotation than the one provided in ChestX-ray14 dataset on certain cases. Examples of the ambiguity cases are illustrated in our Supplemental Materials with detailed explanations.
It is worth noting that the annotations in the ChestX-ray14 dataset is generated by text mining instead of manual annotation, which guarantees 90% correctness of labeling. Given that manual annotation is laborious, text mining is a viable way to automatically extract large amount of image-level label from existing clinical text corpus. In this case, the labels can potentially be further improved. The model should be able to achieve enhanced performance if such data is available. Furthermore, a dataset with more disease categories included will be favorable as it is closer to real life clinic settings. Future works include expanding the current ChestX-ray14 dataset with more manual label and more disease categories such as coronary artery disease [10, 11] for evaluation. Applications of our model on different medical imaging dataset that targeting multiple diseases should also be evaluated in the future.
Currently, our localization result is on the level of bounding box. Another future improvement of our network is to produce a fine-grain instance segmentation of object given the probability map (heatmap). Fully-connected CRF (FC-CRF) is a post-processing technique that can produce such segmentation. One downfall of FC-CRF is it requires objects in the image with a clear boundary. In our dataset, chest radiography generates a projective images where objects overlay, so the objects tends to be blurry and FC-CRF is hardly applicable. However, extensive studies have shown FC-CRF’s successful applications on other medical imaging modalities, such as CT and MRI, which capture medical images with clear organ/disease boundary. [27, 28, 29]. Thus, our model can also be applied to other medical image dataset and further produce object segmentation given only image-level annotation for training.
In summary, we presented a weakly supervised adaptive DenseNet to classify and localize 14 thoracic diseases by using only image-level annotation during training. Extensive experiments demonstrated the effectiveness of our network which achieved both the best classification and localization results among the previous published state-of-the-art approaches on the ChestX-ray14 dataset.
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Appendix A Analysis of Model Parameters
Appendix B Detailed Model Discussion
Figure 12 shows cases where our localization results are preferred over the given ground truth by a certified radiologist. In example ”Mass”, ”Nodule”, ”Pneumonia”, our localization covered more instances of lesions than the ground truth. In example ”Effusion”, ”Infiltration”, our model defined more precise bounding boxes than the ground truth. In example ”Atelectasis”, our model captured more likely lesion region than the ground truth.
Localization of ”Atelectasis” and ”Pneumothorax” is often complicated by associated medical complexity. Figure 13 shows two example cases. ”Atelectasis” (partially collapsed lung) is a disease of heterogeneous appearances, whose appearances is affected by locale, extent and cause of the pathology. Two common sub-types of atelectasis is plate-like atelectasis and lobar atelectasis. Plate-like atelectasis manifests as a visible white dense strip on lower lung, while atelectasis on lower lobe can lead to shrink up of the lobe and disrupts the right interlobar artery. In this case our network mis-classifies a disrupted right interlobar artery as lobar atelectasis and misses the plate-like atelectasis. ”Pneumothorax” (air enter chest cavity) is an acute symptom which must be promptly treated in clinical setting. The treatment vacuums the excessive air in chest cavity by inserting a tube. Therefore pneumothroax X-ray image tends to manifests as a restored lung with the vacuum tube presenting. This misleads the network to associate the tube, instead of the actual pathology, to pneumothorax label.
Appendix C Artifacts from Dilated Kernel
Despite the performance of our network, there is a design that potentially can further improve the network’s performance. In specific, we removed average pooling in the last transition block and introduced dilated convolution in sub-sequent dense block. This doubles the size of output feature map and provides better localization. Empirically this also boosts up classification accuracy. However, the dilated convolution introduces griding artifact in the heatmap. An example is shown in Figure 14. This is caused by high frequency components in the convolution inputs, as explained in . We suspect the high frequency components in inputs comes from dense connection from shallow layers, where features are still raw and noisy. One of our future improvement is to remove the griding artifact while still making use of pre-trained convolution weights.