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Register a new userUnifying Relational Sentence Generation and Retrieval for Medical Image Report Composition
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Added by
Liang Lin
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Beyond generating long and topic-coherent paragraphs in traditional captioning tasks, the medical image report composition task poses more task-oriented challenges by requiring both the highly-accurate medical term diagnosis and multiple heterogeneous forms of information including impression and findings. Current methods often generate the most common sentences due to dataset bias for individual case, regardless of whether the sentences properly capture key entities and relationships. Such limitations severely hinder their applicability and generalization capability in medical report composition where the most critical sentences lie in the descriptions of abnormal diseases that are relatively rare. Moreover, some medical terms appearing in one report are often entangled with each other and co-occurred, e.g. symptoms associated with a specific disease. To enforce the semantic consistency of medical terms to be incorporated into the final reports and encourage the sentence generation for rare abnormal descriptions, we propose a novel framework that unifies template retrieval and sentence generation to handle both common and rare abnormality while ensuring the semantic-coherency among the detected medical terms. Specifically, our approach exploits hybrid-knowledge co-reasoning: i) explicit relationships among all abnormal medical terms to induce the visual attention learning and topic representation encoding for better topic-oriented symptoms descriptions; ii) adaptive generation mode that changes between the template retrieval and sentence generation according to a contextual topic encoder. Experimental results on two medical report benchmarks demonstrate the superiority of the proposed framework in terms of both human and metrics evaluation.
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Medical report generation is one of the most challenging tasks in medical image analysis. Although existing approaches have achieved promising results, they either require a predefined template database in order to retrieve sentences or ignore the hierarchical nature of medical report generation. To address these issues, we propose MedWriter that incorporates a novel hierarchical retrieval mechanism to automatically extract both report and sentence-level templates for clinically accurate report generation. MedWriter first employs the Visual-Language Retrieval~(VLR) module to retrieve the most relevant reports for the given images. To guarantee the logical coherence between sentences, the Language-Language Retrieval~(LLR) module is introduced to retrieve relevant sentences based on the previous generated description. At last, a language decoder fuses image features and features from retrieved reports and sentences to generate meaningful medical reports. We verified the effectiveness of our model by automatic evaluation and human evaluation on two datasets, i.e., Open-I and MIMIC-CXR.
Medical images can be decomposed into normal and abnormal features, which is considered as the compositionality. Based on this idea, we propose an encoder-decoder network to decompose a medical image into two discrete latent codes: a normal anatomy code and an abnormal anatomy code. Using these latent codes, we demonstrate a similarity retrieval by focusing on either normal or abnormal features of medical images.
We introduce two pre-trained retrieval focused multilingual sentence encoding models, respectively based on the Transformer and CNN model architectures. The models embed text from 16 languages into a single semantic space using a multi-task trained dual-encoder that learns tied representations using translation based bridge tasks (Chidambaram al., 2018). The models provide performance that is competitive with the state-of-the-art on: semantic retrieval (SR), translation pair bitext retrieval (BR) and retrieval question answering (ReQA). On English transfer learning tasks, our sentence-level embeddings approach, and in some cases exceed, the performance of monolingual, English only, sentence embedding models. Our models are made available for download on TensorFlow Hub.
Pre-training models such as BERT have achieved great success in many natural language processing tasks. However, how to obtain better sentence representation through these pre-training models is still worthy to exploit. Previous work has shown that the anisotropy problem is an critical bottleneck for BERT-based sentence representation which hinders the model to fully utilize the underlying semantic features. Therefore, some attempts of boosting the isotropy of sentence distribution, such as flow-based model, have been applied to sentence representations and achieved some improvement. In this paper, we find that the whitening operation in traditional machine learning can similarly enhance the isotropy of sentence representations and achieve competitive results. Furthermore, the whitening technique is also capable of reducing the dimensionality of the sentence representation. Our experimental results show that it can not only achieve promising performance but also significantly reduce the storage cost and accelerate the model retrieval speed.
Processing medical data to find abnormalities is a time-consuming and costly task, requiring tremendous efforts from medical experts. Therefore, Ai has become a popular tool for the automatic processing of medical data, acting as a supportive tool for doctors. AI tools highly depend on data for training the models. However, there are several constraints to access to large amounts of medical data to train machine learning algorithms in the medical domain, e.g., due to privacy concerns and the costly, time-consuming medical data annotation process. To address this, in this paper we present a novel synthetic data generation pipeline called SinGAN-Seg to produce synthetic medical data with the corresponding annotated ground truth masks. We show that these synthetic data generation pipelines can be used as an alternative to bypass privacy concerns and as an alternative way to produce artificial segmentation datasets with corresponding ground truth masks to avoid the tedious medical data annotation process. As a proof of concept, we used an open polyp segmentation dataset. By training UNet++ using both the real polyp segmentation dataset and the corresponding synthetic dataset generated from the SinGAN-Seg pipeline, we show that the synthetic data can achieve a very close performance to the real data when the real segmentation datasets are large enough. In addition, we show that synthetic data generated from the SinGAN-Seg pipeline improving the performance of segmentation algorithms when the training dataset is very small. Since our SinGAN-Seg pipeline is applicable for any medical dataset, this pipeline can be used with any other segmentation datasets.
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