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2019 IEEE 32nd International Symposium on Computer-Based Medical Systems (CBMS)最新文献

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Obtaining Tractable and Interpretable Descriptions for Cases with Complications from a Colorectal Cancer Database 从结直肠癌数据库中获取并发症病例的可处理和可解释的描述
Pub Date : 2019-06-01 DOI: 10.1109/CBMS.2019.00095
José A. Delgado-Osuna, C. García-Martínez, S. Ventura, J. G. Barbadillo
Colorectal cancer affects to a significant portion of the population and is one of the leading causes of cancer-related deaths in many countries. Professionals of the Reina Sofia University Hospital have fed a database about this pathology for more than 10 years. In this work, we apply classification and association rule learning tools, including a new methodology, to obtain tractable and interpretable descriptions of those cases where complications appeared, which is one of the attributes.
结直肠癌影响到很大一部分人口,是许多国家癌症相关死亡的主要原因之一。雷纳索非亚大学医院的专业人员已经为这个病理数据库提供了10多年的数据。在这项工作中,我们应用分类和关联规则学习工具,包括一种新的方法,来获得那些出现复杂性的情况的可处理和可解释的描述,这是属性之一。
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引用次数: 1
Latent Class Multi-Label Classification to Identify Subclasses of Disease for Improved Prediction 潜在类多标签分类识别疾病亚类以改进预测
Pub Date : 2019-06-01 DOI: 10.1109/CBMS.2019.00109
A. A. Alyousef, S. Nihtyanova, C. Denton, Pietro Bosoni, R. Bellazzi, A. Tucker
Disease subtyping can assist the development of precision medicine but remains a challenge in data analysis by reason of the many different methods to group individuals depending on their data. However, identification of subclasses of disease will help to produce better models which are more specific to patients and will improve prediction and interpretation of underlying characteristics of disease. This paper presents a novel algorithm that integrates latent class models with supervised learning. The new algorithm uses latent class models to cluster patients within groups that results in improved classification as well as aiding the understanding of the dissimilarities of the discovered groups. The methods are tested on data from patients with Systemic Sclerosis (SSc), a rare potentially fatal condition. Results show that the "Latent Class Multi-Label Classification Model" improves accuracy when compared with competitive similar methods.
疾病分型有助于精准医学的发展,但在数据分析中仍然是一个挑战,因为根据数据对个体进行分组的方法有许多不同。然而,确定疾病的亚类将有助于产生对患者更具体的更好的模型,并将改进对疾病潜在特征的预测和解释。本文提出了一种将潜在类模型与监督学习相结合的新算法。新算法使用潜在类模型将患者聚类到组内,从而改进分类,并帮助理解所发现组的差异。这些方法是在系统性硬化症(一种罕见的潜在致命疾病)患者的数据上进行测试的。结果表明,与同类方法相比,“潜在类别多标签分类模型”提高了分类准确率。
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引用次数: 1
Facilitators and Barriers to Using Alternative and Augmentative Communication Systems by Aphasic: Therapists Perceptions 失语症患者使用替代和辅助沟通系统的促进因素和障碍:治疗师的看法
Pub Date : 2019-06-01 DOI: 10.1109/CBMS.2019.00077
Jayr Alencar Pereira, Carolline Pena, Mariana de Melo, Bruno Cartaxo, R. Fidalgo, S. Soares
Previous research identifies facilitators and barriers related to the use of Alternative and Augmentative Communication Systems, however, more evidence is needed to understand aspects related to introduction of such systems in an outpatient setting. This paper aims to analyze theses aspects by identifying the facilitators and barriers that comprise systems' use by aphasic people at a University Clinic in Brazil. Semi-structured interviews were conducted and the collected data were analyzed based on qualitative techniques like open coding and constant comparison. In addition to the factors found in previous research, this study identified new factors such as: cost, infantilized systems and sentences' quality produced, that can be considered as facilitators or barriers in using AAC systems. The results of this research can be used to improve the current and new AAC systems.
先前的研究确定了与使用替代和辅助通信系统相关的促进因素和障碍,然而,需要更多的证据来了解在门诊环境中引入此类系统的相关方面。本文旨在通过确定在巴西大学诊所的失语症患者使用系统的促进因素和障碍来分析这些方面。采用半结构化访谈,并采用开放式编码、恒常比较等定性技术对收集到的数据进行分析。除了之前研究中发现的因素外,本研究还发现了一些新的因素,如成本、幼稚化的系统和句子的质量,这些因素可以被认为是使用AAC系统的促进因素或障碍。研究结果可用于改进现有和新型的AAC系统。
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引用次数: 5
Beyond MeSH: Fine-Grained Semantic Indexing of Biomedical Literature Based on Weak Supervision 超越MeSH:基于弱监督的生物医学文献细粒度语义标引
Pub Date : 2019-06-01 DOI: 10.1109/CBMS.2019.00045
A. Nentidis, Anastasia Krithara, Grigorios Tsoumakas, G. Paliouras
Biomedical literature in MEDLINE/PubMed is semantically indexed with MeSH thesaurus entries (subject annotations) which may correspond to more than one related but distinct domain concepts. In such cases, the subject annotations do not follow the level of detail available in the domain and do not always suffice to meet the information needs of domain experts. In this work, we propose a method to automatically refine subject annotations at the level of concepts and employ it in the case of the MeSH descriptor for Alzheimer's Disease, which corresponds to six different concepts representing disease sub-types. The results indicate that the use of concept-occurrence as weak supervision can improve upon the predictive performance of literal string matching alone. The refined annotations can support more precise concept-based search, enable the integration of subject annotations with other semantic information and facilitate the maintenance of subject annotation consistency, as the MeSH thesaurus evolves with the addition of more detailed entries.
MEDLINE/PubMed中的生物医学文献使用MeSH词库条目(主题注释)进行语义索引,这些条目可能对应于多个相关但不同的领域概念。在这种情况下,主题注释没有遵循领域中可用的详细级别,并且并不总是足以满足领域专家的信息需求。在这项工作中,我们提出了一种在概念层面上自动改进主题注释的方法,并将其应用于阿尔茨海默病的MeSH描述符中,该描述符对应于代表疾病亚型的六个不同概念。结果表明,使用概念出现作为弱监督可以提高单独的字串匹配的预测性能。随着MeSH同义词表的发展,添加了更多的详细条目,精细化的注释可以支持更精确的基于概念的搜索,使主题注释与其他语义信息集成,并便于维护主题注释的一致性。
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引用次数: 10
MiNerDoc: a Semantically Enriched Text Mining System to Transform Clinical Text into Knowledge MiNerDoc:一个语义丰富的文本挖掘系统,将临床文本转换为知识
Pub Date : 2019-06-01 DOI: 10.1109/CBMS.2019.00142
Carmen Luque, J. M. Luna, S. Ventura
Existing systems to support the daily decisiontaking process carried out by health professionals need to be used independently to perform different text mining subtasks. In practice, there are few systems that unify all the subtasks into an unique framework, easing therefore the clinical work by automating complex clinical tasks such as the detection of clinical alerts as well as clinical information coding. In this sense, the MiNerDoc system is proposed, whose main objective is to support clinical decision-taking process by analysing tons of textual clinical reports in an unified framework. MiNerDoc performs two basic functions that are of great importance in the medical field: detection of risk factors based on the recognition of five medical entities (Disease, Pharmacologic, Region/Part Body, Procedure/Test, Finding/Sign), and automatic prediction of standardized diagnostic codes (MeSH descriptors). A major feature of MiNerDoc is it includes external knowledge sources such as MetaMap and UMLS to terminologically and semantically enrich the interpretation of clinical texts. Some study cases are considered in this work to demonstrate the power of MiNerDoc.
支持卫生专业人员日常决策过程的现有系统需要独立使用,以执行不同的文本挖掘子任务。在实践中,很少有系统将所有子任务统一到一个独特的框架中,从而通过自动化复杂的临床任务(如临床警报检测和临床信息编码)来简化临床工作。从这个意义上说,MiNerDoc系统被提出,其主要目标是通过在统一的框架中分析大量文本临床报告来支持临床决策过程。MiNerDoc实现了在医疗领域非常重要的两个基本功能:基于对五个医疗实体(疾病、药理学、区域/部分身体、程序/测试、发现/标志)的识别来检测风险因素,以及对标准化诊断代码(MeSH描述符)的自动预测。MiNerDoc的一个主要特点是它包含了外部知识来源,如MetaMap和UMLS,从术语和语义上丰富了临床文本的解释。在这项工作中考虑了一些研究案例来展示MiNerDoc的功能。
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引用次数: 2
Interpretability in HealthCare A Comparative Study of Local Machine Learning Interpretability Techniques 医疗保健中的可解释性:本地机器学习可解释性技术的比较研究
Pub Date : 2019-06-01 DOI: 10.1109/CBMS.2019.00065
Radwa El Shawi, Youssef Mohamed, M. Al-Mallah, S. Sakr
Although complex machine learning models (e.g., Random Forest, Neural Networks) are commonly outperforming the traditional simple interpretable models (e.g., Linear Regression, Decision Tree), in the healthcare domain, clinicians find it hard to understand and trust these complex models due to the lack of intuition and explanation of their predictions. With the new General Data Protection Regulation (GDPR), the importance for plausibility and verifiability of the predictions made by machine learning models has become essential. To tackle this challenge, recently, several machine learning interpretability techniques have been developed and introduced. In general, the main aim of these interpretability techniques is to shed light and provide insights into the predictions process of the machine learning models and explain how the model predictions have resulted. However, in practice, assessing the quality of the explanations provided by the various interpretability techniques is still questionable. In this paper, we present a comprehensive experimental evaluation of three recent and popular local model agnostic interpretability techniques, namely, LIME, SHAP and Anchors on different types of real-world healthcare data. Our experimental evaluation covers different aspects for its comparison including identity, stability, separability, similarity, execution time and bias detection. The results of our experiments show that LIME achieves the lowest performance for the identity metric and the highest performance for the separability metric across all datasets included in this study. On average, SHAP has the smallest average time to output explanation across all datasets included in this study. For detecting the bias, SHAP enables the participants to better detect the bias.
尽管复杂的机器学习模型(例如随机森林、神经网络)通常优于传统的简单可解释模型(例如线性回归、决策树),但在医疗保健领域,由于缺乏直觉和对其预测的解释,临床医生发现很难理解和信任这些复杂的模型。随着新的通用数据保护条例(GDPR)的实施,机器学习模型所做预测的合理性和可验证性变得至关重要。为了应对这一挑战,最近已经开发并引入了几种机器学习可解释性技术。一般来说,这些可解释性技术的主要目的是阐明和提供对机器学习模型的预测过程的见解,并解释模型预测的结果。然而,在实践中,评估各种可解释性技术提供的解释的质量仍然存在问题。在本文中,我们对三种最近流行的局部模型不可知可解释性技术(即LIME、SHAP和anchor)在不同类型的现实世界医疗数据上进行了全面的实验评估。我们的实验评估涵盖了同一性、稳定性、可分离性、相似性、执行时间和偏差检测等多个方面进行比较。我们的实验结果表明,LIME在本研究中包含的所有数据集上实现了身份度量的最低性能和可分性度量的最高性能。平均而言,在本研究中包含的所有数据集中,SHAP的平均输出解释时间最短。对于偏倚的检测,SHAP使参与者能够更好地检测偏倚。
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引用次数: 94
Opening the Black Box: Exploring Temporal Pattern of Type 2 Diabetes Complications in Patient Clustering Using Association Rules and Hidden Variable Discovery 打开黑箱:利用关联规则和隐藏变量发现探索患者聚类中2型糖尿病并发症的时间模式
Pub Date : 2019-06-01 DOI: 10.1109/CBMS.2019.00048
Leila Yousefi, S. Swift, Mahir Arzoky, L. Sacchi, L. Chiovato, A. Tucker
There is a great deal of debate over the importance of explanation in AI models inferred from health data. In particular, there is a balance that needs to be made between the accuracy of complex 'deep' models such as convolutional neural networks and the transparency of models that aim to model data in a more 'human' way such as expert systems. In this paper, we explore the use of temporal association rules to validate and uncover the meaning behind discrete hidden variables that have been inferred from clinical diabetes data. We use a recently published technique based upon the IC* (Induction Causation) algorithm that limits the number of hidden variables and places them within a network structure. Here, we take the hidden variables and compare their underlying discrete states to clusters that have been generated from temporal association rules. This allows us to characterise the hidden states based upon different sequences of complications. Results are very promising, with many hidden states aligning with the discovered clusters giving us a direct interpretation.
关于从健康数据推断出的人工智能模型中解释的重要性,存在大量争论。特别是,需要在复杂的“深度”模型(如卷积神经网络)的准确性和旨在以更“人性化”的方式(如专家系统)建模数据的模型(如专家系统)的透明度之间取得平衡。在本文中,我们探索使用时间关联规则来验证和揭示从临床糖尿病数据推断出的离散隐藏变量背后的含义。我们使用了最近发表的一种基于IC*(归纳因果关系)算法的技术,该算法限制了隐藏变量的数量并将它们置于网络结构中。在这里,我们采用隐藏变量,并将其潜在的离散状态与从时间关联规则生成的集群进行比较。这使我们能够根据不同的复杂序列来描述隐藏状态。结果非常有希望,许多隐藏状态与发现的星团一致,给了我们一个直接的解释。
{"title":"Opening the Black Box: Exploring Temporal Pattern of Type 2 Diabetes Complications in Patient Clustering Using Association Rules and Hidden Variable Discovery","authors":"Leila Yousefi, S. Swift, Mahir Arzoky, L. Sacchi, L. Chiovato, A. Tucker","doi":"10.1109/CBMS.2019.00048","DOIUrl":"https://doi.org/10.1109/CBMS.2019.00048","url":null,"abstract":"There is a great deal of debate over the importance of explanation in AI models inferred from health data. In particular, there is a balance that needs to be made between the accuracy of complex 'deep' models such as convolutional neural networks and the transparency of models that aim to model data in a more 'human' way such as expert systems. In this paper, we explore the use of temporal association rules to validate and uncover the meaning behind discrete hidden variables that have been inferred from clinical diabetes data. We use a recently published technique based upon the IC* (Induction Causation) algorithm that limits the number of hidden variables and places them within a network structure. Here, we take the hidden variables and compare their underlying discrete states to clusters that have been generated from temporal association rules. This allows us to characterise the hidden states based upon different sequences of complications. Results are very promising, with many hidden states aligning with the discovered clusters giving us a direct interpretation.","PeriodicalId":311634,"journal":{"name":"2019 IEEE 32nd International Symposium on Computer-Based Medical Systems (CBMS)","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122260885","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
GenericCDSS - A Generic Clinical Decision Support System GenericCDSS -一个通用临床决策支持系统
Pub Date : 2019-06-01 DOI: 10.1109/CBMS.2019.00046
João Rafael Almeida, J. Oliveira
Clinical decision support systems (CDSS) are currently essential tools to guide medical diagnostics and patients' treatments, and they are specially important for the better care management of chronic diseases, such as cancer and diabetes. These systems help to decide on the best treatment solution, namely in centres where there is a shortage of medical experts. CDSS tools are often integrated into the Electronic Health Record (EHR) to facilitate the reuse of patient data. However, many times, creating new and intuitive protocols that are disease-specific is still a challenge. In this paper we present an open source solution (GenericCDSS) that can be used to streamline the development of autonomous CDSS, avoiding the dependency on third-party tools to manage patient data and clinical protocols. The software tool provides a modern user interface, supporting multi-platforms such as mobile and desktop devices. GenericCDSS is publicly available at https://github.com/bioinformatics-ua/GenericCDSS, under a GNU GPL license.
临床决策支持系统(CDSS)是目前指导医学诊断和患者治疗的重要工具,对癌症和糖尿病等慢性病的更好护理管理尤为重要。这些系统有助于确定最佳治疗方案,即在医疗专家短缺的中心。CDSS工具通常集成到电子健康记录(EHR)中,以促进患者数据的重用。然而,很多时候,创建针对特定疾病的新的直观方案仍然是一个挑战。在本文中,我们提出了一个开源解决方案(GenericCDSS),可用于简化自主CDSS的开发,避免依赖第三方工具来管理患者数据和临床协议。该软件工具提供了一个现代化的用户界面,支持多平台,如移动和桌面设备。GenericCDSS在GNU GPL许可下可在https://github.com/bioinformatics-ua/GenericCDSS公开获得。
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引用次数: 4
[Title page iii] [标题页iii]
Pub Date : 2019-06-01 DOI: 10.1109/cbms.2019.00002
{"title":"[Title page iii]","authors":"","doi":"10.1109/cbms.2019.00002","DOIUrl":"https://doi.org/10.1109/cbms.2019.00002","url":null,"abstract":"","PeriodicalId":311634,"journal":{"name":"2019 IEEE 32nd International Symposium on Computer-Based Medical Systems (CBMS)","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133401096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Pervasive Tracking for Time-Dependent Acute Patient Flow: A Case Study in Trauma Management 时间依赖性急性病人流动的普遍跟踪:创伤管理的案例研究
Pub Date : 2019-06-01 DOI: 10.1109/CBMS.2019.00057
Sara Montagna, Angelo Croatti, A. Ricci, V. Agnoletti, Vittorio Albarello
The problem of tracking has gained a central role in healthcare research since it enables the acquisition of the information needed for improving healthcare management and efficiency, alongside patient safety. In literature, it is mainly discussed as an allocation problem that must deal with limited resources (rooms, physicians, equipment) to optimise workflows, and Real-Time Location Systems have been introduced with the main goal of locating and identifying assets and personnel in a healthcare facility. In this paper, we propose a novel perspective of pervasive tracking into Hospital 4.0, devised explicitly for time-dependent acute patient flow. The goal is to develop a tracking system that acquires not only the time and location of entities, exploiting state-of-the-art techniques, but also the main clinical events occurred. As an example application we describe TraumaTracker, a system developed to support the accurate and complete documentation of trauma resuscitation processes from pre-hospital care.
跟踪问题在医疗保健研究中发挥了核心作用,因为它可以获取改善医疗保健管理和效率以及患者安全所需的信息。在文献中,它主要是作为一个分配问题来讨论的,必须处理有限的资源(房间,医生,设备)来优化工作流程,实时定位系统已经被引入,其主要目标是定位和识别医疗机构中的资产和人员。在本文中,我们提出了一个新的视角,普遍跟踪到医院4.0,明确为时间依赖的急性病人流设计。目标是开发一种追踪系统,不仅可以利用最先进的技术获取实体的时间和位置,还可以获取主要的临床事件。作为一个例子应用,我们描述了创伤跟踪器,一个系统开发,以支持准确和完整的记录创伤复苏过程,从院前护理。
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引用次数: 4
期刊
2019 IEEE 32nd International Symposium on Computer-Based Medical Systems (CBMS)
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