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Radiology reporting is a crucial part of the communication between radiologists and other medical professionals, but it can be time-consuming and error-prone. One approach to alleviate this is structured reporting, which saves time and enables a more accurate evaluation than free-text reports. However, there is limited research on automating structured reporting, and no public benchmark is available for evaluating and comparing different methods. To close this gap, we introduce Rad-ReStruct, a new benchmark dataset that provides fine-grained, hierarchically ordered annotations in the form of structured reports for X-Ray images. We model the structured reporting task as hierarchical visual question answering (VQA) and propose hi-VQA, a novel method that considers prior context in the form of previously asked questions and answers for populating a structured radiology report. Our experiments show that hi-VQA achieves competitive performance to the state-of-the-art on the medical VQA benchmark VQARad while performing best among methods without domain-specific vision-language pretraining and provides a strong baseline on Rad-ReStruct. Our work represents a significant step towards the automated population of structured radiology reports and provides a valuable first benchmark for future research in this area. Our dataset and code is available at //github.com/ChantalMP/Rad-ReStruct.

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視覺問答(Visual Question Answering,VQA),是一種涉及計算機視覺和自然語言處理的學習任務。這一任務的定義如下: A VQA system takes as input an image and a free-form, open-ended, natural-language question about the image and produces a natural-language answer as the output[1]。 翻譯為中文:一個VQA系統以一張圖片和一個關于這張圖片形式自由、開放式的自然語言問題作為輸入,以生成一條自然語言答案作為輸出。簡單來說,VQA就是給定的圖片進行問答。

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Contrastive representation learning is crucial in medical time series analysis as it alleviates dependency on labor-intensive, domain-specific, and scarce expert annotations. However, existing contrastive learning methods primarily focus on one single data level, which fails to fully exploit the intricate nature of medical time series. To address this issue, we present COMET, an innovative hierarchical framework that leverages data consistencies at all inherent levels in medical time series. Our meticulously designed model systematically captures data consistency from four potential levels: observation, sample, trial, and patient levels. By developing contrastive loss at multiple levels, we can learn effective representations that preserve comprehensive data consistency, maximizing information utilization in a self-supervised manner. We conduct experiments in the challenging patient-independent setting. We compare COMET against six baselines using three diverse datasets, which include ECG signals for myocardial infarction and EEG signals for Alzheimer's and Parkinson's diseases. The results demonstrate that COMET consistently outperforms all baselines, particularly in setup with 10% and 1% labeled data fractions across all datasets. These results underscore the significant impact of our framework in advancing contrastive representation learning techniques for medical time series. The source code is available at //github.com/DL4mHealth/COMET.

The detailed clinical records drafted by doctors after each patient's visit are crucial for medical practitioners and researchers. Automating the creation of these notes with language models can reduce the workload of doctors. However, training such models can be difficult due to the limited public availability of conversations between patients and doctors. In this paper, we introduce NoteChat, a cooperative multi-agent framework leveraging Large Language Models (LLMs) for generating synthetic doctor-patient conversations conditioned on clinical notes. NoteChat consists of Planning, Roleplay, and Polish modules. We provide a comprehensive automatic and human evaluation of NoteChat, comparing it with state-of-the-art models, including OpenAI's ChatGPT and GPT-4. Results demonstrate that NoteChat facilitates high-quality synthetic doctor-patient conversations, underscoring the untapped potential of LLMs in healthcare. This work represents the first instance of multiple LLMs cooperating to complete a doctor-patient conversation conditioned on clinical notes, offering promising avenues for the intersection of AI and healthcare

In the absence of readily available labeled data for a given sequence labeling task and language, annotation projection has been proposed as one of the possible strategies to automatically generate annotated data. Annotation projection has often been formulated as the task of transporting, on parallel corpora, the labels pertaining to a given span in the source language into its corresponding span in the target language. In this paper we present T-Projection, a novel approach for annotation projection that leverages large pretrained text-to-text language models and state-of-the-art machine translation technology. T-Projection decomposes the label projection task into two subtasks: (i) A candidate generation step, in which a set of projection candidates using a multilingual T5 model is generated and, (ii) a candidate selection step, in which the generated candidates are ranked based on translation probabilities. We conducted experiments on intrinsic and extrinsic tasks in 5 Indo-European and 8 low-resource African languages. We demostrate that T-projection outperforms previous annotation projection methods by a wide margin. We believe that T-Projection can help to automatically alleviate the lack of high-quality training data for sequence labeling tasks. Code and data are publicly available.

Despite the state-of-the-art performance of deep convolutional neural networks, they are susceptible to bias and malfunction in unseen situations. Moreover, the complex computation behind their reasoning is not human-understandable to develop trust. External explainer methods have tried to interpret network decisions in a human-understandable way, but they are accused of fallacies due to their assumptions and simplifications. On the other side, the inherent self-interpretability of models, while being more robust to the mentioned fallacies, cannot be applied to the already trained models. In this work, we propose a new attention-based pooling layer, called Local Attention Pooling (LAP), that accomplishes self-interpretability and the possibility for knowledge injection without performance loss. The module is easily pluggable into any convolutional neural network, even the already trained ones. We have defined a weakly supervised training scheme to learn the distinguishing features in decision-making without depending on experts' annotations. We verified our claims by evaluating several LAP-extended models on two datasets, including ImageNet. The proposed framework offers more valid human-understandable and faithful-to-the-model interpretations than the commonly used white-box explainer methods.

Multi-modal medical image fusion is essential for the precise clinical diagnosis and surgical navigation since it can merge the complementary information in multi-modalities into a single image. The quality of the fused image depends on the extracted single modality features as well as the fusion rules for multi-modal information. Existing deep learning-based fusion methods can fully exploit the semantic features of each modality, they cannot distinguish the effective low and high frequency information of each modality and fuse them adaptively. To address this issue, we propose AdaFuse, in which multimodal image information is fused adaptively through frequency-guided attention mechanism based on Fourier transform. Specifically, we propose the cross-attention fusion (CAF) block, which adaptively fuses features of two modalities in the spatial and frequency domains by exchanging key and query values, and then calculates the cross-attention scores between the spatial and frequency features to further guide the spatial-frequential information fusion. The CAF block enhances the high-frequency features of the different modalities so that the details in the fused images can be retained. Moreover, we design a novel loss function composed of structure loss and content loss to preserve both low and high frequency information. Extensive comparison experiments on several datasets demonstrate that the proposed method outperforms state-of-the-art methods in terms of both visual quality and quantitative metrics. The ablation experiments also validate the effectiveness of the proposed loss and fusion strategy.

Dual use, the intentional, harmful reuse of technology and scientific artefacts, is a problem yet to be well-defined within the context of Natural Language Processing (NLP). However, as NLP technologies continue to advance and become increasingly widespread in society, their inner workings have become increasingly opaque. Therefore, understanding dual use concerns and potential ways of limiting them is critical to minimising the potential harms of research and development. In this paper, we conduct a survey of NLP researchers and practitioners to understand the depth and their perspective of the problem as well as to assess existing available support. Based on the results of our survey, we offer a definition of dual use that is tailored to the needs of the NLP community. The survey revealed that a majority of researchers are concerned about the potential dual use of their research but only take limited action toward it. In light of the survey results, we discuss the current state and potential means for mitigating dual use in NLP and propose a checklist that can be integrated into existing conference ethics-frameworks, e.g., the ACL ethics checklist.

Timely and accurate extraction of Adverse Drug Events (ADE) from biomedical literature is paramount for public safety, but involves slow and costly manual labor. We set out to improve drug safety monitoring (pharmacovigilance, PV) through the use of Natural Language Processing (NLP). We introduce BioDEX, a large-scale resource for Biomedical adverse Drug Event Extraction, rooted in the historical output of drug safety reporting in the U.S. BioDEX consists of 65k abstracts and 19k full-text biomedical papers with 256k associated document-level safety reports created by medical experts. The core features of these reports include the reported weight, age, and biological sex of a patient, a set of drugs taken by the patient, the drug dosages, the reactions experienced, and whether the reaction was life threatening. In this work, we consider the task of predicting the core information of the report given its originating paper. We estimate human performance to be 72.0% F1, whereas our best model achieves 62.3% F1, indicating significant headroom on this task. We also begin to explore ways in which these models could help professional PV reviewers. Our code and data are available: //github.com/KarelDO/BioDEX.

With the advances of data-driven machine learning research, a wide variety of prediction problems have been tackled. It has become critical to explore how machine learning and specifically deep learning methods can be exploited to analyse healthcare data. A major limitation of existing methods has been the focus on grid-like data; however, the structure of physiological recordings are often irregular and unordered which makes it difficult to conceptualise them as a matrix. As such, graph neural networks have attracted significant attention by exploiting implicit information that resides in a biological system, with interactive nodes connected by edges whose weights can be either temporal associations or anatomical junctions. In this survey, we thoroughly review the different types of graph architectures and their applications in healthcare. We provide an overview of these methods in a systematic manner, organized by their domain of application including functional connectivity, anatomical structure and electrical-based analysis. We also outline the limitations of existing techniques and discuss potential directions for future research.

Applying artificial intelligence techniques in medical imaging is one of the most promising areas in medicine. However, most of the recent success in this area highly relies on large amounts of carefully annotated data, whereas annotating medical images is a costly process. In this paper, we propose a novel method, called FocalMix, which, to the best of our knowledge, is the first to leverage recent advances in semi-supervised learning (SSL) for 3D medical image detection. We conducted extensive experiments on two widely used datasets for lung nodule detection, LUNA16 and NLST. Results show that our proposed SSL methods can achieve a substantial improvement of up to 17.3% over state-of-the-art supervised learning approaches with 400 unlabeled CT scans.

Many tasks in natural language processing can be viewed as multi-label classification problems. However, most of the existing models are trained with the standard cross-entropy loss function and use a fixed prediction policy (e.g., a threshold of 0.5) for all the labels, which completely ignores the complexity and dependencies among different labels. In this paper, we propose a meta-learning method to capture these complex label dependencies. More specifically, our method utilizes a meta-learner to jointly learn the training policies and prediction policies for different labels. The training policies are then used to train the classifier with the cross-entropy loss function, and the prediction policies are further implemented for prediction. Experimental results on fine-grained entity typing and text classification demonstrate that our proposed method can obtain more accurate multi-label classification results.

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