Medical report generation is the task of generating reports based on medical images, such as radiology and pathology images. Given that this task is time-consuming and cumbersome, researchers endeavor to relieve the burden of physicians by automatically generating the findings and descriptions from medical images with machine learning techniques.
Existing studies can be roughly divided into two categories, i.e., generation-based and retrieval-based approaches. Generation-based methods, including LRCN Donahue et al. (2015), CoAtt Jing et al. (2018), and MvH+AttL Yuan et al. (2019), focus on generating image captions with a encoder-decoder model that leverage image features. However, they are unable to produce linguistically diverse descriptions and depict rare but prominent medical findings. On the other hand, Retrieval-based methods such as HRGR-Agent Li et al. (2018) and KEPP Li et al. (2019), pay attention to memorizing templates to generate standardized reports from a predefined retrieval database. However, the quality of generated reports significantly depends on the manually curated template database. Besides, they only use sentence-level templates for the generation but ignore to learn the report-level templates, which prevent them from generating more accurate reports.
To address the aforementioned issues, we propose a new framework called MedWriter as shown in Figure 1. MedWriter introduces a novel hierarchical retrieval mechanism working with a hierarchical language decoder to automatically learn the dynamic report and sentence templates from the data for generating accurate and professional medical reports. MedWriter is inspired by the process of how physicians write medical reports in real life. They keep report templates in mind and then generate reports for new images by using the key information that they find in the medical images to update the templates sentence by sentence.
In particular, we use three modules to mimic this process. First, MedWriter generates report-level templates from the Visual-Language Retrieval (VLR) module using the visual features as the queries. To generate accurate reports, MedWriter also predicts disease labels based on the visual features and extracts medical keywords from the retrieved reports. We propose a multi-query attention mechanism to learn the report-level template representations. Second, to make the generated reports more coherent and fluent, we propose a Language-Language Retrieval (LLR) module, which aims to learn sentence-level templates for the next sentence generation by analyzing between-sentence correlation in the retrieved reports. Finally, a hierarchical language decoder is adopted to generate the full report using visual features, report-level and sentence-level template representations. The designed two-level retrieval mechanism for memorization is helpful in generating accurate and diverse medical reports. To sum up, our contributions are:
To the best of our knowledge, we are the first to model the memory retrieval mechanism in both report and sentence levels. By imitating the standardized medical report generation in real life, our memory retrieval mechanism effectively utilizes existing templates in the two-layer hierarchy in medical texts. This design allows MedWriter to generate more clinically accurate and standardized reports.
On top of the retrieval modules, we design a new multi-query attention mechanism to fuse the retrieved information for medical report generation. The fused information can be well incorporated with the existing image and report-level information, which can improve the quality of generated report .
Experiments conducted on two large-scale medical report generation datasets, i.e., Open-i and MIMIC-CXR show that MedWriter achieves better performance compared with state-of-the-art baselines measured by CIDEr, ROUGE-L, and BLEUs. Besides, case studies show that MedWriter provides more accurate and natural descriptions for medical images through domain expert evaluation.
2 Related work
Generation-based report generation
Visual captioning is the process of generating a textual description given an image or a video. The dominant neural network architecture of the captioning task is based on the encoder-decoder frameworkBahdanau et al. (2014); Vinyals et al. (2015); Mao et al. (2014), with attention mechanism Xu et al. (2015); You et al. (2016); Lu et al. (2017); Anderson et al. (2018); Wang et al. (2019). As a sub-task in the medical domain, early studies directly apply state-of-the-art encoder-decoder models as CNN-RNN Vinyals et al. (2015), LRCN Donahue et al. (2015) and AdaAtt Lu et al. (2017)
to medical report generation task. To further improve long text generation with domain-specific knowledge, later generation-based methods introduce hierarchical LSTM with co-attentionJing et al. (2018) or use the medical concept features Yuan et al. (2019)
to attentively guide the report generation. On the other hand, the concept of reinforcement learningLiu et al. (2019) is utilized to ensure the generated radiology reports correctly describe the clinical findings.
To avoid generating clinically non-informative reports, external domain knowledge like knowledge graphsZhang et al. (2020); Li et al. (2019) and anchor words Biswal et al. (2020) are utilized to promote the medical values of diagnostic reports. CLARA Biswal et al. (2020) also provides an interactive solution that integrates the doctors’ judgment into the generation process.
Retrieval-based report generation
Retrieval-based approaches are usually hybridized with generation-based ones to improve the readability of generated medical reports. For example, KERP Li et al. (2019) uses abnormality graphs to retrieve most related sentence templates during the generation. HRGR-AgentLi et al. (2018) incorporates retrieved sentences in a reinforcement learning framework for medical report generation. However, they all require a template database as the model input. Different from these models, MedWriter is able to automatically learn both report-level and sentence-level templates from the data, which significantly enhances the model applicability.
As shown in Figure 2, we propose a new framework called MedWriter, which consists of three modules. The Visual-Language Retrieval (VLR) module works on the report level and uses visual features to find the most relevant template reports based on a multi-view image query. The Language-Language Retrieval (LLR) module works on the sentence level and retrieves a series of candidates that are most likely to be the next sentence from the retrieval pool given the generated language context. Finally, MedWriter generates accurate, diverse, and disease-specified medical reports by a hierarchical language decoder that fuses the visual, linguistics and pathological information obtained by VLR and LLR modules. To improve the effectiveness and efficiency of retrieval, we first pretrain VLR and LLR modules to build up a retrieval pool for medical report generation as follows.
3.1 VLR module pretraining
The VLR module aims to retrieve the most relevant medical reports from the training report corpus for the given medical images. The retrieved reports are further used to learn an abstract template for generating new high-quality reports. Towards this goal, we introduce a self-supervised pretraining task by judging whether an image-report pair come from the same subject, i.e., image-report matching. It is based on an intuitive assumption that an image-report pair from the same subject shares certain common semantics. More importantly, the disease types associated with images and the report should be similar. Thus, in the pretraining task, we also take disease categories into consideration.
3.1.1 Disease classification
The input of the VLR module is a series of multi-modal images and the corresponding report where the set consists of images, and
denotes the report. We employ a Convolutional Neural Network (CNN)as the image encoder to obtain the feature of a given image , i.e., , where is the visual feature for the -th image .
With all the extracted features , we add them together as the inputs of the disease classification task, which is further used to learn the disease type representation as follows,
where and are the weight and bias terms of a linear model, AvgPool is the operation of average pooling, is the number of disease classes, and.
3.1.2 Image-report matching
The next training task for VLR is to predict whether an image-report pair belongs to the same subject. In this subtask, after obtaining the image features and the disease type representation
, we extract a context visual vectorby the pathological attention.
First, for each image feature , we use the disease type representation
to learn the spatial attention score through a linear transformation,
where , , and are the linear transformation matrices. After that, we use the normalized spatial attention score to add visual features over all locations across the feature map,
Then, we compute the context vector of the input image set using a linear layer on the concatenation of all the representation , , where is the learnable parameter.
For the image-report matching task, we also need a language representation, which is extracted by a BERT Devlin et al. (2018) model as the language encoder. converts the medical report into a semantic vector . Finally, the probability of the input pair coming from the same subject can be computed as
Given these two sub-tasks, we simultaneously optimize the cross-entropy losses for both disease classification and image-report matching to train the VLR module.
3.2 LLR module pretraining
A medical report usually has some logical characteristics such as describing the patient’s medical images in a from-top-to-bottom order. Besides, the preceding and following sentences in a medical report may provide explanations for the same object or concept, or they may have certain juxtaposition, transition and progressive relations. Automatically learning such characteristics should be helpful for MedWriter to generate high-quality medical reports. Towards this end, we propose to pretrain a language-language retrieval (LLR) module to search for the most relevant sentences for the next sentence generation. In particular, we introduce a self-supervised pretraining task for LLR to determine if two sentences come from the same report, i.e., sentence-sentence matching.
Similar to the VLR module, we use a BERT model as the sentence encoder to embed the sentence inputs into feature vectors . Then the probability that two sentences come from the same medical report is measure by
Again, the cross-entropy loss is used to optimize the learning objective given probability and the ground-truth label of whether and belong to the same medical report or not.
3.3 Retrieval-based report generation
Using the pretrained VLR and LLR modules, MedWriter generates a medical report given a sequence of input images using a novel hierarchical retrieval mechanism with a hierarchical language decoder.
3.3.1 VLR module for report-level retrieval
Let denote the set of all the training reports, where is the number of reports in the training dataset. For each report , MedWriter first obtain its vector representation using in the VLR module, which is denoted as . Let denote the set of training report representations. Given the multi-modal medical images of a subject, the VLR module aims to return the top medical reports as well as medical keywords within in the retrieved reports.
Specifically, MedWriter extracts the image feature for using the pathological attention mechanism as described in Section 3.1. According to Eq. (4), MedWriter then computes a image-report matching sore between and each . The top reports with the largest scores are considered as the most relevant medical reports corresponding to the images, and they are selected as the template descriptions. From these templates, we identify medical keywords using a dictionary as a summarization of the template information. The medical keyword dictionary includes disease phenotype, human organ, and tissue, which consists of 36 medical keywords extracted from the training data with the highest frequency.
Report template representation learning
The retrieved reports are highly related to the given images, which should be helpful for the report generation. To make full use of them, we need to learn a report template representation using the image feature , the features of retrieved reports , medical keywords embeddings for learned from the pretrained word embeddings, and the disease embeddings from predicted disease labels using Disease Classification in Section 3.1.1.
We propose a new multi-query attention mechanism to learn the report template representation. To specify, we use the image features as the key vector , the retrieved report features as the value matrix , and the embeddings of both medical keywords and disease labels as the query vectors . We modify the original self-attention Vaswani et al. (2017) into a multi-query attention. For each query vector in , we first get a corresponding attended feature and then transform them into the report template vector after concatenation,
where , and , and are the transformation matrices. Generally, the Attention function is calculated by
where are queries, keys and values in general case, and is the dimension of the query vector.
3.3.2 LLR module for sentence-level retrieval
Since retrieved reports are highly associated with the input images, the sentence within those reports must contain some instructive pathological information that is helpful for sentence-level generation. Towards this end, we first select sentences from the retrieved reports and then learn sentence-level template representation.
We first divide the retrieved reports into candidate sentences as the retrieval pool in the LLR module. Given the pretrained LLR language encoder , we can obtain the sentence-level feature pool, which is . Assume that the generated sentence at time is denoted as , and its embedding is , which is used to find sentences with the highest probabilities from the candidate sentence pool using Eq. (5) in Section 3.2.
Sentence template representation learning
Similar to the report template representation, we still use the multi-query attention mechanism. From the retrieved sentences, we extract the medical keywords . Besides, we have the predicted disease labels . Their embeddings are considered as the query vectors. The embeddings of the extracted sentence, i.e., , are treated as the value vectors. The key vector is the current sentence (word) hidden state (), which will be introduced in Section 3.3.3. According to Eq. (6), we can obtain the sentence template representation at time , which is denoted as ( used for word-level generation).
3.3.3 Hierarchical language decoder
With the extracted features by the retrieval mechanism described above, we apply a hierarchical decoder to generate radiology reports according to the hierarchical linguistics structure of the medical reports. The decoder contains two layers, i.e., a sentence LSTM decoder that outputs sentence hidden states, and a word LSTM decoder which decodes the sentence hidden states into natural languages. In this way, reports are generated sentence by sentence.
For generating the -th sentence, MedWriter first uses the previous sentences to learn the sentence-level hidden state . Specifically, MedWriter learns the image feature based on Eq. (3). When calculating the attention score with Eq. (2), we consider both the information obtained from the previous sentences (the hidden state ) and the predicted disease representation from Eq. (1), i.e., replacing with . Then the concatenation of the image feature , the report template representation from Eq. (6), and the sentence template representation is used as the input of the sentence LSTM to learn the hidden state
where is obtained using the multi-query attention, the key vector is the hidden state , the value vectors are the representations of the retrieved sentences according to the -th sentence, and the query vectors are the embeddings of both medical keywords extracted from the retrieved sentences and the predicted disease labels.
Based on the learned , MedWriter conducts the word-by-word generation using a word-level LSTM. For generating the -th word, MedWriter first learns the image feature using Eq. (2) by replacing with in Eq. (2), where is the hidden state of the -th word. MedWriter then learns the sentence template representation using the multi-query attention, where the key vector is the hidden state , value and query vectors are the same as those used for calculating . Finally, the concatenation of , , , and is taken as the input of the word-level LSTM to generate the -th word as follows:
where is the feed-forward network.
Note that for the first sentence generation, we set as 0, and is the randomly initialized vector, to learn the sentence-level hidden state . When generating the words of the first sentence, we set as the 0 vector.
4.1 Datasets and baselines
Open-i111https://openi.nlm.nih.gov/faq#collection Demner-Fushman et al. (2016) (a.k.a IU X-Ray) provides 7,470 chest X-rays with 3,955 radiology reports. In our experiments, we only utilize samples with both frontal and lateral views, and with complete findings and impression sections in the reports. This results in totally 2,902 cases and 5,804 images. MIMIC-CXR222https://physionet.org/content/mimic-cxr/2.0.0/ Johnson et al. (2019) contains 377,110 chest X-rays associated with 227,827 radiology reports, divided into subsets. We use the same criterion to select samples, which results in 71,386 reports and 142,772 images.
For both datasets, we tokenize all words with more than 3 occurrences and obtain 1,252 tokens on the Open-i dataset and 4,073 tokens on the MIMIC-CXR dataset, including four special tokens , , , and . The findings and impression sections are concatenated as the ground-truth reports. We randomly divide the whole datasets into train/validation/test sets with a ratio of 0.7/0.1/0.2. To conduct the disease classification task, we include 20 most frequent finding keywords extracted from MeSH tags as disease categories on the Open-i dataset and 14 CheXpert categories on the MIMIC-CXR dataset.
On both datasets, we compare with four state-of-the-art image captioning models: CNN-RNNVinyals et al. (2015), CoAttn Jing et al. (2018), MvH+AttL Yuan et al. (2019), and V-L Retrieval. V-L Retrieval only uses the retrieved report templates with the highest probability as prediction without the generation part based on our pretrained VLR module. Due to the lack of the opensource code for Wang et al. (2018); Li et al. (2019, 2018); Donahue et al. (2015) and the template databases for Li et al. (2019, 2018), we only include the reported results on the Open-i dataset in our experiments.
|Open-i||Generation||CNN-RNN Vinyals et al. (2015)||0.294||0.307||0.216||0.124||0.087||0.066||0.426|
|LRCN Donahue et al. (2015)*||0.285||0.307||0.223||0.128||0.089||0.068||–|
|Tie-Net Wang et al. (2018)*||0.279||0.226||0.286||0.160||0.104||0.074||–|
|CoAtt Jing et al. (2018)||0.277||0.369||0.455||0.288||0.205||0.154||0.707|
|MvH+AttL Yuan et al. (2019)||0.229||0.351||0.452||0.311||0.223||0.162||0.725|
|HRGR-Agent Li et al. (2018)*||0.343||0.322||0.438||0.298||0.208||0.151||–|
|KERP Li et al. (2019)*||0.280||0.339||0.482||0.325||0.226||0.162||–|
|MIMIC-CXR||Generation||CNN-RNN Vinyals et al. (2015)||0.245||0.314||0.247||0.165||0.124||0.098||0.472|
|CoAtt Jing et al. (2018)||0.234||0.274||0.410||0.267||0.189||0.144||0.745|
|MvH+AttL Yuan et al. (2019)||0.264||0.309||0.424||0.282||0.203||0.153||0.738|
4.2 Experimental setup
All input images are resized to , and the feature map from DenseNet-121 Huang et al. (2017) is . During training, we use random cropping and color histogram equalization for data augmentation.
To pretrain the VLR module, the maximum length of the report is restricted to 128 words. We train VLR module for 100 epochs with an AdamKingma and Ba (2014) optimizer with 1e-5 as the initial learning rate, 1e-5 for L2 regularization, and 16 as the mini-batch size. To pretrain the LLR module, the maximum length of each sentence is set to 32 words. We optimize the LLR module for 100 epochs with an Adam Kingma and Ba (2014) optimizer with the initial learning rate of 1e-5 and a mini-batch size of 64. The learning rate is multiplied by 0.2 every 20 epochs.
To train the full model for MedWriter, we set the retrieved reports number and sentences number . Extracting medical keywords and predicting disease labels are used for report generation. Both sentence and word LSTM have 512 hidden units. We freeze the weights for the pretrained VLR and LLR modules and only optimize on the language decoder. We set the initial learning rate as 3e-4 and mini-batch size as 32. MedWriter takes 10 hours to train on the Open-i dataset and 3 days on the MIMIC-CXR dataset with four GeForce GTX 1080 Ti GPUs.
4.3 Quantitative and qualitative results
Table 1 shows the CIDEr, ROUGE-L, BLUE, and AUC scores achieved by different methods on the test sets of Open-i and MIMIC-CXR.
From Table 1, we make the following observations. First, compared with Generation-based model, Retrieval-based model that uses the template reports as results has set up a relatively strong baseline for medical report generation. Second, compared with V-L retrieval, other Retrieval-based approaches perform much better in terms of all the metrics. This again shows that that by integrating the information retrieval method into the deep sequence generation framework, we can not only use the retrieved language information as templates to help generate long sentences, but also overcome the monotony of only using the templates as the generations. Finally, we see that the proposed MedWriter achieves the highest language scores on 5/6 metrics on Open-i datasets and all metrics on MIMIC-CXR among all methods. MedWriter not only improves current SOTA model CoAttn Jing et al. (2018) by 5% and MvH+AttL Yuan et al. (2019) by 4% on Open-i in average, but also goes beyond SOAT retrieval-based approaches like KERP Li et al. (2019) and HRGR-Agent Li et al. (2018) and significantly improves the performance, even without using manually curated template databases. This illustrates the effectiveness of automatically learning templates and adopting hierarchical retrieval in writing medical reports.
We train two report classification BERT models on both datasets and use it to judge whether the generated reports correctly reflect the ground-truth findings. We show the mean ROC-AUC scores achieved by generated reports from different baselines in the last column of Table 1. We can observe that MedWriter achieves the highest AUC scores compared with other baselines. In addition, our method achieves the AUC scores that are very close to those of professional doctors’ reports, with 0.814/0.915 and 0.833/0.923 on two datasets. This shows that the generation performance of MedWriter has approached the level of human domain experts, and it embraces great medical potentials in identifying disease-related medical findings.
We also qualitatively evaluate the quality of the generated reports via a user study. We randomly select 50 samples from the Open-i test set and collect ground-truth reports and the generated reports from both MvH+AttL Yuan et al. (2019) and MedWriter to conduct the human evaluation. Two experienced radiologists were asked to give ratings for each selected report, in terms of whether the generated reports are realistic and relevant to the X-ray images. The ratings are integers from one to five. The higher, the better.
Table 2 shows average human evaluation results on MedWriter compared with Ground Truth reports and generations of MvH+AttL Yuan et al. (2019) on Open-i, evaluated in terms of realistic scores and relevant scores. MedWriter achieves much higher human preference than the baseline model, even approaching the performance of Ground Truth reports that wrote by experienced radiologists. It shows that MedWriter is able to generate accurate clinical reports that are comparable to domain experts.
|Method||Realistic Score||Relevant Score|
|MvH+AttL Yuan et al. (2019)||2.50||2.57|
|Lateral Image||Ground Truth||MvH+AttL||MedWriter|
|3.5cmemphysematous changes. resolution of prior right midlung infiltrate. previous is normal in size and contour. lungs are clear. no focal consolidation pneumothorax or pleural effusion. interval of previously described right midlung opacity suggesting resolved process. lungs are hyperexpanded with flattened diaphragms. and soft tissue are unremarkable.||3cmno acute cardiopulmonary disease. the heart is normal in size. the lungs are clear. there is no pleural effusion or pneumothorax. of the right clavicle. are present. to the glenoid joints.||3cmhyperexpanded lungs. right upper lobe . no focal pneumonia. the cardiomediastinal silhouette is normal in size and contour. negative for focal consolidation pneumothorax or large pleural effusion. negative for acute bone abnormality.|
||3.5cmchest. large nodule at the right lung base that probably represents a granuloma although not it is not calcified. there is a mm nodule in the right lower lobe that is relatively dense but not calcified on the corresponding rib series. there are probably right hilar calcified lymph . lungs otherwise are clear. there is no pleural effusion. left ribs. no fracture or focal bony destruction.||3cmno acute cardiopulmonary disease. the heart is normal in size and contour. are clear without evidence of infiltrate. is no pneumothorax. degenerative changes of the thoracic spine.. head..||3cmright upper lobe pneumonia. consideration may be given for primary or . recommend ct of the chest may be helpful for further diagnosis. in the interval a 3 cm mass has developed in the right lower lobe. no pneumothorax or pleural effusion. the mediastinal contours are normal.|
|Open-i||MedWriter w/o VLRM||0.333||0.373||0.466||0.324||0.229||0.159|
|MedWriter w/o LLRM||0.329||0.354||0.453||0.307||0.215||0.154|
|MedWriter w/o HLD||0.284||0.317||0.434||0.295||0.208||0.149|
|MIMIC-CXR||MedWriter w/o VLRM||0.294||0.317||0.432||0.288||0.209||0.161|
|MedWriter w/o LLRM||0.283||0.305||0.425||0.280||0.204||0.157|
|MedWriter w/o HLD||0.263||0.287||0.418||0.265||0.187||0.146|
Figure 3 shows qualitative results of MedWriter and baseline models on the Open-i dataset. MedWriter not only produces longer reports compared with MvH+AttL but also accurately detects the medical findings in the images (marked in red and bold). On the other hand, we find that MedWriter is able to put forward some supplementary suggestions (marked in blue) and descriptions, which are not in the original report but have diagnostic value. The underlying reason for this merit comes from the memory retrieval mechanism that introduces prior medical knowledge to facilitate the generation process.
4.4 Ablation study
We perform ablation studies on the Open-i and MIMIC-CXR datasets to investigate the effectiveness of each module in MedWriter. In each of the following studies, we change one module with other modules intact.
Removing the VLR module
In this experiment, global report feature is neglected in Eqs. (7) and (8), and the first sentence is generated only based on image features. The LLR module keeps its functionality. However, instead of looking for sentence-level templates from the retrieved reports, it searches for most relevant sentences from all the reports. As can be seen from Table 3, removing VLR module (“w/o VLRM”) leads to performance reduction by 2% on average. This demonstrates that visual-language retrieval is capable in sketching out the linguistic structure of the whole report. The rest of the language generation is largely influenced by report-level context information.
Removing the LLR module
The generation of -th sentence is based on the global report feature and the image feature , without using the retrieved sentences information in Eq. (8). Table 3 shows that removing LLR module (“w/o LLRM”) results in the decease of average evaluation scores by 4% compared with the full model. This verifies that the LLR module plays an essential role in generating long and coherent clinical reports.
Replacing hierarchical language decoder
We use a single layer LSTM that treats the whole report as a long sentence and conduct the generation word-by-word. Table 3 shows that replacing hierarchical language decoder with a single-layer LSTM (“w/o HLD”) introduces dramatic performance reduction. This phenomenon shows that the hierarchical generative model can effectively and greatly improve the performance of long text generation tasks.
Automatically generating accurate reports from medical images is a key challenge in medical image analysis. In this paper, we propose a novel model named MedWriter to solve this problem based on hierarchical retrieval techniques. In particular, MedWriter consists of three main modules, which are the visual-language retrieval (VLR) module, the language-language retrieval (LLR) module, and the hierarchical language decoder. These three modules tightly work with each other to automatically generate medical reports. Experimental results on two datasets demonstrate the effectiveness of the proposed MedWriter. Besides, qualitative studies show that MedWriter is able to generate meaningful and realistic medical reports.
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