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Register a new userWriting by Memorizing: Hierarchical Retrieval-based Medical Report Generation
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Xingyi Yang
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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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.
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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.
Speech-based image retrieval has been studied as a proxy for joint representation learning, usually without emphasis on retrieval itself. As such, it is unclear how well speech-based retrieval can work in practice -- both in an absolute sense and versus alternative strategies that combine automatic speech recognition (ASR) with strong text encoders. In this work, we extensively study and expand choices of encoder architectures, training methodology (including unimodal and multimodal pretraining), and other factors. Our experiments cover different types of speech in three datasets: Flickr Audio, Places Audio, and Localized Narratives. Our best model configuration achieves large gains over state of the art, e.g., pushing recall-at-one from 21.8% to 33.2% for Flickr Audio and 27.6% to 53.4% for Places Audio. We also show our best speech-based models can match or exceed cascaded ASR-to-text encoding when speech is spontaneous, accented, or otherwise hard to automatically transcribe.
In models to generate program source code from natural language, representing this code in a tree structure has been a common approach. However, existing methods often fail to generate complex code correctly due to a lack of ability to memorize large and complex structures. We introduce ReCode, a method based on subtree retrieval that makes it possible to explicitly reference existing code examples within a neural code generation model. First, we retrieve sentences that are similar to input sentences using a dynamic-programming-based sentence similarity scoring method. Next, we extract n-grams of action sequences that build the associated abstract syntax tree. Finally, we increase the probability of actions that cause the retrieved n-gram action subtree to be in the predicted code. We show that our approach improves the performance on two code generation tasks by up to +2.6 BLEU.
Given a collection of untrimmed and unsegmented videos, video corpus moment retrieval (VCMR) is to retrieve a temporal moment (i.e., a fraction of a video) that semantically corresponds to a given text query. As video and text are from two distinct feature spaces, there are two general approaches to address VCMR: (i) to separately encode each modality representations, then align the two modality representations for query processing, and (ii) to adopt fine-grained cross-modal interaction to learn multi-modal representations for query processing. While the second approach often leads to better retrieval accuracy, the first approach is far more efficient. In this paper, we propose a Retrieval and Localization Network with Contrastive Learning (ReLoCLNet) for VCMR. We adopt the first approach and introduce two contrastive learning objectives to refine video encoder and text encoder to learn video and text representations separately but with better alignment for VCMR. The video contrastive learning (VideoCL) is to maximize mutual information between query and candidate video at video-level. The frame contrastive learning (FrameCL) aims to highlight the moment region corresponds to the query at frame-level, within a video. Experimental results show that, although ReLoCLNet encodes text and video separately for efficiency, its retrieval accuracy is comparable with baselines adopting cross-modal interaction learning.
Automatically inducing high quality knowledge graphs from a given collection of documents still remains a challenging problem in AI. One way to make headway for this problem is through advancements in a related task known as slot filling. In this task, given an entity query in form of [Entity, Slot, ?], a system is asked to fill the slot by generating or extracting the missing value exploiting evidence extracted from relevant passage(s) in the given document collection. The recent works in the field try to solve this task in an end-to-end fashion using retrieval-based language models. In this paper, we present a novel approach to zero-shot slot filling that extends dense passage retrieval with hard negatives and robust training procedures for retrieval augmented generation models. Our model reports large improvements on both T-REx and zsRE slot filling datasets, improving both passage retrieval and slot value generation, and ranking at the top-1 position in the KILT leaderboard. Moreover, we demonstrate the robustness of our system showing its domain adaptation capability on a new variant of the TACRED dataset for slot filling, through a combination of zero/few-shot learning. We release the source code and pre-trained models.
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