An accurate and detailed account of patient medications, including medication changes within the patient timeline, is essential for healthcare providers to provide appropriate patient care. Healthcare providers or the patients themselves may initiate changes to patient medication. Medication changes take many forms, including prescribed medication and associated dosage modification. These changes provide information about the overall health of the patient and the rationale that led to the current care. Future care can then build on the resulting state of the patient. This work explores the automatic extraction of medication change information from free-text clinical notes. The Contextual Medication Event Dataset (CMED) is a corpus of clinical notes with annotations that characterize medication changes through multiple change-related attributes, including the type of change (start, stop, increase, etc.), initiator of the change, temporality, change likelihood, and negation. Using CMED, we identify medication mentions in clinical text and propose three novel high-performing BERT-based systems that resolve the annotated medication change characteristics. We demonstrate that our proposed systems improve medication change classification performance over the initial work exploring CMED.
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In the United States, more than 5 million patients are admitted annually to ICUs, with ICU mortality of 10%-29% and costs over $82 billion. Acute brain dysfunction status, delirium, is often underdiagnosed or undervalued. This study's objective was to develop automated computable phenotypes for acute brain dysfunction states and describe transitions among brain dysfunction states to illustrate the clinical trajectories of ICU patients. We created two single-center, longitudinal EHR datasets for 48,817 adult patients admitted to an ICU at UFH Gainesville (GNV) and Jacksonville (JAX). We developed algorithms to quantify acute brain dysfunction status including coma, delirium, normal, or death at 12-hour intervals of each ICU admission and to identify acute brain dysfunction phenotypes using continuous acute brain dysfunction status and k-means clustering approach. There were 49,770 admissions for 37,835 patients in UFH GNV dataset and 18,472 admissions for 10,982 patients in UFH JAX dataset. In total, 18% of patients had coma as the worst brain dysfunction status; every 12 hours, around 4%-7% would transit to delirium, 22%-25% would recover, 3%-4% would expire, and 67%-68% would remain in a coma in the ICU. Additionally, 7% of patients had delirium as the worst brain dysfunction status; around 6%-7% would transit to coma, 40%-42% would be no delirium, 1% would expire, and 51%-52% would remain delirium in the ICU. There were three phenotypes: persistent coma/delirium, persistently normal, and transition from coma/delirium to normal almost exclusively in first 48 hours after ICU admission. We developed phenotyping scoring algorithms that determined acute brain dysfunction status every 12 hours while admitted to the ICU. This approach may be useful in developing prognostic and decision-support tools to aid patients and clinicians in decision-making on resource use and escalation of care.
The goal of continual learning is to improve the performance of recognition models in learning sequentially arrived data. Although most existing works are established on the premise of learning from scratch, growing efforts have been devoted to incorporating the benefits of pre-training. However, how to adaptively exploit the pre-trained knowledge for each incremental task while maintaining its generalizability remains an open question. In this work, we present an extensive analysis for continual learning on a pre-trained model (CLPM), and attribute the key challenge to a progressive overfitting problem. Observing that selectively reducing the learning rate can almost resolve this issue in the representation layer, we propose a simple but extremely effective approach named Slow Learner with Classifier Alignment (SLCA), which further improves the classification layer by modeling the class-wise distributions and aligning the classification layers in a post-hoc fashion. Across a variety of scenarios, our proposal provides substantial improvements for CLPM (e.g., up to 49.76%, 50.05%, 44.69% and 40.16% on Split CIFAR-100, Split ImageNet-R, Split CUB-200 and Split Cars-196, respectively), and thus outperforms state-of-the-art approaches by a large margin. Based on such a strong baseline, critical factors and promising directions are analyzed in-depth to facilitate subsequent research.
Recently, many studies incorporate external knowledge into character-level feature based models to improve the performance of Chinese relation extraction. However, these methods tend to ignore the internal information of the Chinese character and cannot filter out the noisy information of external knowledge. To address these issues, we propose a mixture-of-view-experts framework (MoVE) to dynamically learn multi-view features for Chinese relation extraction. With both the internal and external knowledge of Chinese characters, our framework can better capture the semantic information of Chinese characters. To demonstrate the effectiveness of the proposed framework, we conduct extensive experiments on three real-world datasets in distinct domains. Experimental results show consistent and significant superiority and robustness of our proposed framework. Our code and dataset will be released at: //gitee.com/tmg-nudt/multi-view-of-expert-for-chineserelation-extraction
The speaker extraction technique seeks to single out the voice of a target speaker from the interfering voices in a speech mixture. Typically an auxiliary reference of the target speaker is used to form voluntary attention. Either a pre-recorded utterance or a synchronized lip movement in a video clip can serve as the auxiliary reference. The use of visual cue is not only feasible, but also effective due to its noise robustness, and becoming popular. However, it is difficult to guarantee that such parallel visual cue is always available in real-world applications where visual occlusion or intermittent communication can occur. In this paper, we study the audio-visual speaker extraction algorithms with intermittent visual cue. We propose a joint speaker extraction and visual embedding inpainting framework to explore the mutual benefits. To encourage the interaction between the two tasks, they are performed alternately with an interlacing structure and optimized jointly. We also propose two types of visual inpainting losses and study our proposed method with two types of popularly used visual embeddings. The experimental results show that we outperform the baseline in terms of signal quality, perceptual quality, and intelligibility.
Recent advancements in large language models (LLMs) have led to the development of highly potent models like OpenAI's ChatGPT. These models have exhibited exceptional performance in a variety of tasks, such as question answering, essay composition, and code generation. However, their effectiveness in the healthcare sector remains uncertain. In this study, we seek to investigate the potential of ChatGPT to aid in clinical text mining by examining its ability to extract structured information from unstructured healthcare texts, with a focus on biological named entity recognition and relation extraction. However, our preliminary results indicate that employing ChatGPT directly for these tasks resulted in poor performance and raised privacy concerns associated with uploading patients' information to the ChatGPT API. To overcome these limitations, we propose a new training paradigm that involves generating a vast quantity of high-quality synthetic data with labels utilizing ChatGPT and fine-tuning a local model for the downstream task. Our method has resulted in significant improvements in the performance of downstream tasks, improving the F1-score from 23.37% to 63.99% for the named entity recognition task and from 75.86% to 83.59% for the relation extraction task. Furthermore, generating data using ChatGPT can significantly reduce the time and effort required for data collection and labeling, as well as mitigate data privacy concerns. In summary, the proposed framework presents a promising solution to enhance the applicability of LLM models to clinical text mining.
Clinical needs and technological advances have resulted in increased use of Artificial Intelligence (AI) in clinical decision support. However, such support can introduce new and amplify existing cognitive biases. Through contextual inquiry and interviews, we set out to understand the use of an existing AI support system by ophthalmologists. We identified concerns regarding anchoring bias and a misunderstanding of the AI's capabilities. Following, we evaluated clinicians' perceptions of three bias mitigation strategies as integrated into their existing decision support system. While clinicians recognised the danger of anchoring bias, we identified a concern around the impact of bias mitigation on procedure time. Our participants were divided in their expectations of any positive impact on diagnostic accuracy, stemming from varying reliance on the decision support. Our results provide insights into the challenges of integrating bias mitigation into AI decision support.
The amount of medical images stored in hospitals is increasing faster than ever; however, utilizing the accumulated medical images has been limited. This is because existing content-based medical image retrieval (CBMIR) systems usually require example images to construct query vectors; nevertheless, example images cannot always be prepared. Besides, there can be images with rare characteristics that make it difficult to find similar example images, which we call isolated samples. Here, we introduce a novel sketch-based medical image retrieval (SBMIR) system that enables users to find images of interest without example images. The key idea lies in feature decomposition of medical images, whereby the entire feature of a medical image can be decomposed into and reconstructed from normal and abnormal features. By extending this idea, our SBMIR system provides an easy-to-use two-step graphical user interface: users first select a template image to specify a normal feature and then draw a semantic sketch of the disease on the template image to represent an abnormal feature. Subsequently, it integrates the two kinds of input to construct a query vector and retrieves reference images with the closest reference vectors. Using two datasets, ten healthcare professionals with various clinical backgrounds participated in the user test for evaluation. As a result, our SBMIR system enabled users to overcome previous challenges, including image retrieval based on fine-grained image characteristics, image retrieval without example images, and image retrieval for isolated samples. Our SBMIR system achieves flexible medical image retrieval on demand, thereby expanding the utility of medical image databases.
While (1) serverless computing is emerging as a popular form of cloud execution, datacenters are going through major changes: (2) storage dissaggregation in the system infrastructure level and (3) integration of domain-specific accelerators in the hardware level. Each of these three trends individually provide significant benefits; however, when combined the benefits diminish. Specifically, the paper makes the key observation that for serverless functions, the overhead of accessing dissaggregated persistent storage overshadows the gains from accelerators. Therefore, to benefit from all these trends in conjunction, we propose Domain-Specific Computational Storage for Serverless (DSCS-Serverless). This idea contributes a serverless model that leverages a programmable accelerator within computational storage to conjugate the benefits of acceleration and storage disaggregation simultaneously. Our results with eight applications shows that integrating a comparatively small accelerator within the storage (DSCS-Serverless) that fits within its power constrains (15 Watts), significantly outperforms a traditional disaggregated system that utilizes the NVIDIA RTX 2080 Ti GPU (250 Watts). Further, the work highlights that disaggregation, serverless model, and the limited power budget for computation in storage require a different design than the conventional practices of integrating microprocessors and FPGAs. This insight is in contrast with current practices of designing computational storage that are yet to address the challenges associated with the shifts in datacenters. In comparison with two such conventional designs that either use quad-core ARM A57 or a Xilinx FPGA, DSCS-Serverless provides 3.7x and 1.7x end-to-end application speedup, 4.3x and 1.9x energy reduction, and 3.2x and 2.3x higher cost efficiency, respectively.
Following unprecedented success on the natural language tasks, Transformers have been successfully applied to several computer vision problems, achieving state-of-the-art results and prompting researchers to reconsider the supremacy of convolutional neural networks (CNNs) as {de facto} operators. Capitalizing on these advances in computer vision, the medical imaging field has also witnessed growing interest for Transformers that can capture global context compared to CNNs with local receptive fields. Inspired from this transition, in this survey, we attempt to provide a comprehensive review of the applications of Transformers in medical imaging covering various aspects, ranging from recently proposed architectural designs to unsolved issues. Specifically, we survey the use of Transformers in medical image segmentation, detection, classification, reconstruction, synthesis, registration, clinical report generation, and other tasks. In particular, for each of these applications, we develop taxonomy, identify application-specific challenges as well as provide insights to solve them, and highlight recent trends. Further, we provide a critical discussion of the field's current state as a whole, including the identification of key challenges, open problems, and outlining promising future directions. We hope this survey will ignite further interest in the community and provide researchers with an up-to-date reference regarding applications of Transformer models in medical imaging. Finally, to cope with the rapid development in this field, we intend to regularly update the relevant latest papers and their open-source implementations at \url{//github.com/fahadshamshad/awesome-transformers-in-medical-imaging}.
Large, pre-trained transformer-based language models such as BERT have drastically changed the Natural Language Processing (NLP) field. We present a survey of recent work that uses these large language models to solve NLP tasks via pre-training then fine-tuning, prompting, or text generation approaches. We also present approaches that use pre-trained language models to generate data for training augmentation or other purposes. We conclude with discussions on limitations and suggested directions for future research.
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