Pub Date : 2023-09-10eCollection Date: 2023-12-01DOI: 10.1007/s41666-023-00144-3
Pratibha Harrison, Rakib Hasan, Kihan Park
Early detection of breast cancer is crucial for a better prognosis. Various studies have been conducted where tumor lesions are detected and localized on images. This is a narrative review where the studies reviewed are related to five different image modalities: histopathological, mammogram, magnetic resonance imaging (MRI), ultrasound, and computed tomography (CT) images, making it different from other review studies where fewer image modalities are reviewed. The goal is to have the necessary information, such as pre-processing techniques and CNN-based diagnosis techniques for the five modalities, readily available in one place for future studies. Each modality has pros and cons, such as mammograms might give a high false positive rate for radiographically dense breasts, while ultrasounds with low soft tissue contrast result in early-stage false detection, and MRI provides a three-dimensional volumetric image, but it is expensive and cannot be used as a routine test. Various studies were manually reviewed using particular inclusion and exclusion criteria; as a result, 91 recent studies that classify and detect tumor lesions on breast cancer images from 2017 to 2022 related to the five image modalities were included. For histopathological images, the maximum accuracy achieved was around 99 , and the maximum sensitivity achieved was 97.29 by using DenseNet, ResNet34, and ResNet50 architecture. For mammogram images, the maximum accuracy achieved was 96.52 using a customized CNN architecture. For MRI, the maximum accuracy achieved was 98.33 using customized CNN architecture. For ultrasound, the maximum accuracy achieved was around 99 by using DarkNet-53, ResNet-50, G-CNN, and VGG. For CT, the maximum sensitivity achieved was 96 by using Xception architecture. Histopathological and ultrasound images achieved higher accuracy of around 99 by using ResNet34, ResNet50, DarkNet-53, G-CNN, and VGG compared to other modalities for either of the following reasons: use of pre-trained architectures with pre-processing techniques, use of modified architectures with pre-processing techniques, use of two-stage CNN, and higher number of studies available for Artificial Intelligence (AI)/machine learning (ML) researchers to reference. One of the gaps we found is that only a single image modality is used for CNN-based diagnosis; in the future, a multiple image modality approach can be used to design a CNN architecture with higher accuracy.
{"title":"State-of-the-Art of Breast Cancer Diagnosis in Medical Images via Convolutional Neural Networks (CNNs).","authors":"Pratibha Harrison, Rakib Hasan, Kihan Park","doi":"10.1007/s41666-023-00144-3","DOIUrl":"10.1007/s41666-023-00144-3","url":null,"abstract":"<p><p>Early detection of breast cancer is crucial for a better prognosis. Various studies have been conducted where tumor lesions are detected and localized on images. This is a narrative review where the studies reviewed are related to five different image modalities: histopathological, mammogram, magnetic resonance imaging (MRI), ultrasound, and computed tomography (CT) images, making it different from other review studies where fewer image modalities are reviewed. The goal is to have the necessary information, such as pre-processing techniques and CNN-based diagnosis techniques for the five modalities, readily available in one place for future studies. Each modality has pros and cons, such as mammograms might give a high false positive rate for radiographically dense breasts, while ultrasounds with low soft tissue contrast result in early-stage false detection, and MRI provides a three-dimensional volumetric image, but it is expensive and cannot be used as a routine test. Various studies were manually reviewed using particular inclusion and exclusion criteria; as a result, 91 recent studies that classify and detect tumor lesions on breast cancer images from 2017 to 2022 related to the five image modalities were included. For histopathological images, the maximum accuracy achieved was around 99 <math><mo>%</mo></math>, and the maximum sensitivity achieved was 97.29 <math><mo>%</mo></math> by using DenseNet, ResNet34, and ResNet50 architecture. For mammogram images, the maximum accuracy achieved was 96.52 <math><mo>%</mo></math> using a customized CNN architecture. For MRI, the maximum accuracy achieved was 98.33 <math><mo>%</mo></math> using customized CNN architecture. For ultrasound, the maximum accuracy achieved was around 99 <math><mo>%</mo></math> by using DarkNet-53, ResNet-50, G-CNN, and VGG. For CT, the maximum sensitivity achieved was 96 <math><mo>%</mo></math> by using Xception architecture. Histopathological and ultrasound images achieved higher accuracy of around 99 <math><mo>%</mo></math> by using ResNet34, ResNet50, DarkNet-53, G-CNN, and VGG compared to other modalities for either of the following reasons: use of pre-trained architectures with pre-processing techniques, use of modified architectures with pre-processing techniques, use of two-stage CNN, and higher number of studies available for Artificial Intelligence (AI)/machine learning (ML) researchers to reference. One of the gaps we found is that only a single image modality is used for CNN-based diagnosis; in the future, a multiple image modality approach can be used to design a CNN architecture with higher accuracy.</p>","PeriodicalId":101413,"journal":{"name":"Journal of healthcare informatics research","volume":"7 4","pages":"387-432"},"PeriodicalIF":5.4,"publicationDate":"2023-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10620373/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71490989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-01-31eCollection Date: 2020-06-01DOI: 10.1007/s41666-020-00070-8
Salifu Yusif, Abdul Hafeez-Baig, Jeffrey Soar
There are myriad of factors used in assessing health information technology (HIT)/e-Health of healthcare institutions in developing countries and beyond. In this paper, we intended to identify and gain a deeper understanding of factors used in assessing HIT/e-Health readiness in developing countries through the identification of contextual attributes using Ghana as an exemplary developing country. Through in-depth interviews using aide memoire as interview guide, we explored Core readiness, Engagement readiness, Technological readiness, HIT funding readiness, Regulatory and policy readiness, Workforce readiness and Change Management readiness. We adapted the systematic thematic analysis of qualitative data guide suggested by Braun and Clarke (2013) and O'Connor and Gibson (Pimatisiwin 1: 63-90, 2003) in order to generate codes and build over-arching themes. While Organizational cultural readiness was found to be a more applicable theme/factor in place of Engagement readiness and Change management readiness, Resource readiness wasalso deemed a more appropriate theme for HIT funding readiness and Workforce readiness respectively. A total of 23 factors likely to promote HIT adoption in Ghana and 29 factors capable of impeding HIT adoption in Ghana and potentially in other developing countries were identified. For effective assessment of HIT readiness factors, there is a critical need for a deeper understanding of their applicability in differing settings. The outcome of this study offers a valuable insight into improving circumstances under which HIT/e-Health is adopted. When effectually carried out, assessment of this nature could be help side-step losses on large money, effort, time, delay and importantly, dissatisfaction among stakeholders while enabling change processes healthcare institutions and communities involved. This study also contributes to the limited literature on HIT/e-Health implementation scenarios while offering basis for theory-building.
在评估发展中国家及其他国家医疗保健机构的卫生信息技术(HIT)/电子健康状况时,使用的因素不胜枚举。在本文中,我们打算以加纳为典范,通过识别环境属性,确定并深入了解用于评估发展中国家 HIT/e-He-Health 就绪程度的因素。通过使用备忘录作为访谈指南的深入访谈,我们探讨了核心准备程度、参与准备程度、技术准备程度、HIT 资金准备程度、监管和政策准备程度、劳动力准备程度和变革管理准备程度。我们采用了 Braun 和 Clarke(2013 年)以及 O'Connor 和 Gibson(Pimatisiwin 1: 63-90, 2003 年)建议的定性数据系统主题分析指南,以生成代码并构建总体主题。研究发现,组织文化就绪程度是一个更适用的主题/因素,可替代参与就绪程度和变革管理就绪程度,而资源就绪程度也被认为是一个更适用的主题,可分别替代 HIT 资金就绪程度和劳动力就绪程度。共确定了 23 个可能促进加纳采用 HIT 的因素和 29 个可能阻碍加纳以及其他发展中国家采用 HIT 的因素。为了有效评估 HIT 就绪程度因素,亟需深入了解这些因素在不同环境中的适用性。这项研究的结果为改善采用 HIT/e-Health 的环境提供了宝贵的见解。如果能有效地开展这种性质的评估,将有助于避免大量资金、精力、时间、延误以及重要的利益相关者不满等方面的损失,同时促进相关医疗机构和社区的变革进程。本研究还为有限的关于 HIT/e-Health 实施情况的文献做出了贡献,同时为理论建设提供了基础。
{"title":"An Exploratory Study of the Readiness of Public Healthcare Facilities in Developing Countries to Adopt Health Information Technology (HIT)/e-Health: the Case of Ghana.","authors":"Salifu Yusif, Abdul Hafeez-Baig, Jeffrey Soar","doi":"10.1007/s41666-020-00070-8","DOIUrl":"https://doi.org/10.1007/s41666-020-00070-8","url":null,"abstract":"<p><p>There are myriad of factors used in assessing health information technology (HIT)/e-Health of healthcare institutions in developing countries and beyond. In this paper, we intended to identify and gain a deeper understanding of factors used in assessing HIT/e-Health readiness in developing countries through the identification of contextual attributes using Ghana as an exemplary developing country. Through in-depth interviews using <i>aide memoire</i> as interview guide, we explored <i>Core readiness</i>, <i>Engagement readiness</i>, <i>Technological readiness</i>, <i>HIT funding readiness</i>, <i>Regulatory and policy readiness</i>, <i>Workforce readiness and Change Management readiness.</i> We adapted the systematic thematic analysis of qualitative data guide suggested by Braun and Clarke (2013) and O'Connor and Gibson (Pimatisiwin 1: 63-90, 2003) in order to generate codes and build over-arching themes. While <i>Organizational cultural readiness</i> was found to be a more applicable theme/factor in place of <i>Engagement readiness</i> and <i>Change management readiness, Resource readiness</i> wasalso deemed a more appropriate theme for <i>HIT funding readiness</i> and <i>Workforce readiness</i> respectively. A total of 23 factors likely to promote HIT adoption in Ghana and 29 factors capable of impeding HIT adoption in Ghana and potentially in other developing countries were identified. For effective assessment of HIT readiness factors, there is a critical need for a deeper understanding of their applicability in differing settings. The outcome of this study offers a valuable insight into improving circumstances under which HIT/e-Health is adopted. When effectually carried out, assessment of this nature could be help side-step losses on large money, effort, time, delay and importantly, dissatisfaction among stakeholders while enabling change processes healthcare institutions and communities involved. This study also contributes to the limited literature on HIT/e-Health implementation scenarios while offering basis for theory-building.</p>","PeriodicalId":101413,"journal":{"name":"Journal of healthcare informatics research","volume":"4 2","pages":"189-214"},"PeriodicalIF":5.4,"publicationDate":"2020-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8982759/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142057791","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
With wearable, relatively unobtrusive health monitors and smartphone sensors, it is increasingly easy to collect continuously streaming physiological data in a passive mode without placing much burden on participants. At the same time, smartphones provide the ability to survey participants to provide "ground-truth" reporting on psychological states, although this comes at an increased cost in participant burden. In this paper, we examined how analytical approaches from the field of machine learning could allow us to distill the collected physiological data into actionable decision rules about each individual's psychological state, with the eventual goal of identifying important psychological states (e.g., risk moments) without the need for ongoing burdensome active assessment (e.g., self-report). As a first step towards this goal, we compared two methods: (1) a k-nearest neighbor classifier that uses dynamic time warping distance, and (2) a random forests classifier to predict low and high states of affective arousal states based on features extracted using the tsfresh python package. Then, we compared random-forest-based predictive models tailored for the individual with individual-general models. Results showed that the individual-specific model outperformed the general one. Our results support the feasibility of using passively collected wearable data to predict psychological states, suggesting that by relying on both types of data, the active collection can be reduced or eliminated.
{"title":"Individualized Modeling to Distinguish Between High and Low Arousal States Using Physiological Data.","authors":"Ame Osotsi, Zita Oravecz, Qunhua Li, Joshua Smyth, Timothy R Brick","doi":"10.1007/s41666-019-00064-1","DOIUrl":"10.1007/s41666-019-00064-1","url":null,"abstract":"<p><p>With wearable, relatively unobtrusive health monitors and smartphone sensors, it is increasingly easy to collect continuously streaming physiological data in a passive mode without placing much burden on participants. At the same time, smartphones provide the ability to survey participants to provide \"ground-truth\" reporting on psychological states, although this comes at an increased cost in participant burden. In this paper, we examined how analytical approaches from the field of machine learning could allow us to distill the collected physiological data into actionable decision rules about each individual's psychological state, with the eventual goal of identifying important psychological states (e.g., risk moments) without the need for ongoing burdensome active assessment (e.g., self-report). As a first step towards this goal, we compared two methods: (1) a k-nearest neighbor classifier that uses dynamic time warping distance, and (2) a random forests classifier to predict low and high states of affective arousal states based on features extracted using the <i>tsfresh</i> python package. Then, we compared random-forest-based predictive models tailored for the individual with individual-general models. Results showed that the individual-specific model outperformed the general one. Our results support the feasibility of using passively collected wearable data to predict psychological states, suggesting that by relying on both types of data, the active collection can be reduced or eliminated.</p>","PeriodicalId":101413,"journal":{"name":"Journal of healthcare informatics research","volume":"4 1","pages":"91-109"},"PeriodicalIF":3.7,"publicationDate":"2020-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8982753/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144755592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-09-01Epub Date: 2018-11-06DOI: 10.1007/s41666-018-0042-9
Feichen Shen, David W Larson, James M Naessens, Elizabeth B Habermann, Hongfang Liu, Sunghwan Sohn
Postsurgical complications (PSCs) are known as a deviation from the normal postsurgical course and categorized by severity and treatment requirements. Surgical site infection (SSI) is one of major PSCs and the most common healthcare-associated infection, resulting in increased length of hospital stay and cost. In this work, we proposed an automated way to generate keyword features using sublanguage analysis with heuristics to detect SSI from cohort in clinical notes and evaluated these keywords with medical experts. To further valid our approach, we also applied different machine learning algorithms on cohort using automatically generated keywords. The results showed that our approach was able to identify SSI keywords from clinical narratives and can be used as a foundation to develop an information extraction system or support search-based natural language processing (NLP) approaches by augmenting search queries.
{"title":"Detection of Surgical Site Infection Utilizing Automated Feature Generation in Clinical Notes.","authors":"Feichen Shen, David W Larson, James M Naessens, Elizabeth B Habermann, Hongfang Liu, Sunghwan Sohn","doi":"10.1007/s41666-018-0042-9","DOIUrl":"https://doi.org/10.1007/s41666-018-0042-9","url":null,"abstract":"<p><p>Postsurgical complications (PSCs) are known as a deviation from the normal postsurgical course and categorized by severity and treatment requirements. Surgical site infection (SSI) is one of major PSCs and the most common healthcare-associated infection, resulting in increased length of hospital stay and cost. In this work, we proposed an automated way to generate keyword features using sublanguage analysis with heuristics to detect SSI from cohort in clinical notes and evaluated these keywords with medical experts. To further valid our approach, we also applied different machine learning algorithms on cohort using automatically generated keywords. The results showed that our approach was able to identify SSI keywords from clinical narratives and can be used as a foundation to develop an information extraction system or support search-based natural language processing (NLP) approaches by augmenting search queries.</p>","PeriodicalId":101413,"journal":{"name":"Journal of healthcare informatics research","volume":"3 3","pages":"267-282"},"PeriodicalIF":3.7,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6855398/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145126750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-03-21eCollection Date: 2019-09-01DOI: 10.1007/s41666-019-00050-7
Ebrahim Oshni Alvandi, George Van Doorn, Mark Symmons
Emotional awareness has been previously investigated among clinicians. In this work, we bring to the fore of research the interest to uncover emotional awareness of clinicians during the tele-mental health session. The study reported here aimed at determining whether clinicians process their own emotions, as well as those of the client, in a computer-mediated context. Also, clinicians' decision-making process was assessed because such action appears to be related to the way they feel and recognise how those emotions may change their thinking and impact their interaction with clients. We estimated that such ability in clinicians' would be contrasted when the psychotherapy-session level is conducted via various technologies. Participant of the study were presented by stimuli in different modes of delivery (e.g. text, audio, and video). The experiment indicates that the ability to manage, perceive, and utilise emotions was as being satisfactory during all modes of delivery. In essence, the findings contribute to the field of remote therapy suggesting emotional awareness as a key cognitive factor in diagnosis.
{"title":"Emotional Awareness and Decision-Making in the Context of Computer-Mediated Psychotherapy.","authors":"Ebrahim Oshni Alvandi, George Van Doorn, Mark Symmons","doi":"10.1007/s41666-019-00050-7","DOIUrl":"https://doi.org/10.1007/s41666-019-00050-7","url":null,"abstract":"<p><p>Emotional awareness has been previously investigated among clinicians. In this work, we bring to the fore of research the interest to uncover emotional awareness of clinicians during the tele-mental health session. The study reported here aimed at determining whether clinicians process their own emotions, as well as those of the client, in a computer-mediated context. Also, clinicians' decision-making process was assessed because such action appears to be related to the way they feel and recognise how those emotions may change their thinking and impact their interaction with clients. We estimated that such ability in clinicians' would be contrasted when the psychotherapy-session level is conducted via various technologies. Participant of the study were presented by stimuli in different modes of delivery (e.g. text, audio, and video). The experiment indicates that the ability to manage, perceive, and utilise emotions was as being satisfactory during all modes of delivery. In essence, the findings contribute to the field of remote therapy suggesting emotional awareness as a key cognitive factor in diagnosis.</p>","PeriodicalId":101413,"journal":{"name":"Journal of healthcare informatics research","volume":"3 3","pages":"345-370"},"PeriodicalIF":5.4,"publicationDate":"2019-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8982805/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142057789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-02-08eCollection Date: 2019-12-01DOI: 10.1007/s41666-019-00045-4
Gaurav N Pradhan, Jamie M Bogle, Michael J Cevette, Jan Stepanek
In this paper, we focus on the application of oculometric patterns extracted from raw eye movements during a mental workload task to assess changes in cognitive performance in healthy youth athletes over the course of a typical sport season. Oculometric features pertaining to fixations and saccades were measured on 116 athletes in pre- and post-season testing. Participants were between 7 and 14 years of age at pre-season testing. Due to varied developmental rates, there were large interindividual performance differences during a mental workload task consisting of reading numbers. Based on different reading speeds, we classified three profiles (slow, moderate, and fast) and established their corresponding baselines for oculometric data. Within each profile, we describe changes in oculomotor function based on changes in cognitive performance during the season. To visualize these changes in multidimensional oculometric data, we also present a multidimensional visualization tool named DiViTo (diagnostic visualization tool). These experimental, computational informatics and visualization methodologies may serve to utilize oculometric information to detect changes in cognitive performance due to mild or severe cognitive impairment such as concussion/mild traumatic brain injury, as well as possibly other disorders such as attention deficit hyperactivity disorders, learning/reading disabilities, impairment of alertness, and neurocognitive function.
{"title":"Discovering Oculometric Patterns to Detect Cognitive Performance Changes in Healthy Youth Football Athletes.","authors":"Gaurav N Pradhan, Jamie M Bogle, Michael J Cevette, Jan Stepanek","doi":"10.1007/s41666-019-00045-4","DOIUrl":"https://doi.org/10.1007/s41666-019-00045-4","url":null,"abstract":"<p><p>In this paper, we focus on the application of oculometric patterns extracted from raw eye movements during a mental workload task to assess changes in cognitive performance in healthy youth athletes over the course of a typical sport season. Oculometric features pertaining to fixations and saccades were measured on 116 athletes in pre- and post-season testing. Participants were between 7 and 14 years of age at pre-season testing. Due to varied developmental rates, there were large interindividual performance differences during a mental workload task consisting of reading numbers. Based on different reading speeds, we classified three profiles (slow, moderate, and fast) and established their corresponding baselines for oculometric data. Within each profile, we describe changes in oculomotor function based on changes in cognitive performance during the season. To visualize these changes in multidimensional oculometric data, we also present a multidimensional visualization tool named DiViTo (diagnostic visualization tool). These experimental, computational informatics and visualization methodologies may serve to utilize oculometric information to detect changes in cognitive performance due to mild or severe cognitive impairment such as concussion/mild traumatic brain injury, as well as possibly other disorders such as attention deficit hyperactivity disorders, learning/reading disabilities, impairment of alertness, and neurocognitive function.</p>","PeriodicalId":101413,"journal":{"name":"Journal of healthcare informatics research","volume":"3 4","pages":"371-392"},"PeriodicalIF":5.4,"publicationDate":"2019-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8982780/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142057790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-01-28eCollection Date: 2019-06-01DOI: 10.1007/s41666-019-00044-5
Sungrim Moon, Sijia Liu, David Chen, Yanshan Wang, Douglas L Wood, Rajeev Chaudhry, Hongfang Liu, Paul Kingsbury
Outside medical records (OMRs) accompanying referred patients are frequently sent as faxes from external healthcare providers. Accessing useful and relevant information from these OMRs in a timely manner is a challenging task due to a combination of the presence of machine-illegible information and the limited system interoperability inherent in healthcare. Little research has been done on investigating information in OMRs. This paper evaluated overlapping and non-overlapping medical concepts captured from digitally faxed OMRs for patients transferring to the Department of Cardiovascular Medicine and from clinical consultant notes generated at the Mayo Clinic. We used optical character recognition (OCR) techniques to make faxed OMRs machine-readable and used natural language processing (NLP) techniques to capture clinical concepts from both machine-readable OMRs and Mayo clinical notes. We measured the level of overlap in medical concepts between OMRs and Mayo clinical narratives in the quantitative approaches and assessed the salience of concepts specific to Cardiovascular Medicine by calculating the ratio of those mentioned concepts relative to an independent clinical corpus. Among the concepts collected from the OMRs, 11.19% of those were also present in the Mayo clinical narratives that were generated within the 3 months after their initial encounter at the Mayo Clinic. For those common concepts, 73.97% were identified in initial consultant notes (ICNs) and 26.03% were captured over subsequent follow-up consultant notes (FCNs). These findings implied that information collected from the OMRs is potentially informative for patient care, but some valuable information (additionally identified in FCNs) collected from the OMRs is not fully used in an earlier stage of the care process. The concepts collected from the ICNs have the highest salience to Cardiovascular Medicine (0.112) compared to concepts in OMRs and concepts in FCNs. Additionally, unique concepts captured in ICNs (unseen in OMRs or FCNs) carried the most salient information (0.094), which demonstrated that ICNs provided the most informative concepts for the care of transferred patients.
{"title":"Salience of Medical Concepts of Inside Clinical Texts and Outside Medical Records for Referred Cardiovascular Patients.","authors":"Sungrim Moon, Sijia Liu, David Chen, Yanshan Wang, Douglas L Wood, Rajeev Chaudhry, Hongfang Liu, Paul Kingsbury","doi":"10.1007/s41666-019-00044-5","DOIUrl":"https://doi.org/10.1007/s41666-019-00044-5","url":null,"abstract":"<p><p>Outside medical records (OMRs) accompanying referred patients are frequently sent as faxes from external healthcare providers. Accessing useful and relevant information from these OMRs in a timely manner is a challenging task due to a combination of the presence of machine-illegible information and the limited system interoperability inherent in healthcare. Little research has been done on investigating information in OMRs. This paper evaluated overlapping and non-overlapping medical concepts captured from digitally faxed OMRs for patients transferring to the Department of Cardiovascular Medicine and from clinical consultant notes generated at the Mayo Clinic. We used optical character recognition (OCR) techniques to make faxed OMRs machine-readable and used natural language processing (NLP) techniques to capture clinical concepts from both machine-readable OMRs and Mayo clinical notes. We measured the level of overlap in medical concepts between OMRs and Mayo clinical narratives in the quantitative approaches and assessed the salience of concepts specific to Cardiovascular Medicine by calculating the ratio of those mentioned concepts relative to an independent clinical corpus. Among the concepts collected from the OMRs, 11.19% of those were also present in the Mayo clinical narratives that were generated within the 3 months after their initial encounter at the Mayo Clinic. For those common concepts, 73.97% were identified in initial consultant notes (ICNs) and 26.03% were captured over subsequent follow-up consultant notes (FCNs). These findings implied that information collected from the OMRs is potentially informative for patient care, but some valuable information (additionally identified in FCNs) collected from the OMRs is not fully used in an earlier stage of the care process. The concepts collected from the ICNs have the highest salience to Cardiovascular Medicine (0.112) compared to concepts in OMRs and concepts in FCNs. Additionally, unique concepts captured in ICNs (unseen in OMRs or FCNs) carried the most salient information (0.094), which demonstrated that ICNs provided the most informative concepts for the care of transferred patients.</p>","PeriodicalId":101413,"journal":{"name":"Journal of healthcare informatics research","volume":"3 2","pages":"200-219"},"PeriodicalIF":0.0,"publicationDate":"2019-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8982748/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140913664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-10-12eCollection Date: 2019-03-01DOI: 10.1007/s41666-018-0036-7
Sabita Acharya, Andrew D Boyd, Richard Cameron, Karen Dunn Lopez, Pamela Martyn-Nemeth, Carolyn Dickens, Amer Ardati, Jose D Flores, Matt Baumann, Betty Welland, Barbara Di Eugenio
Comprehending medical information is a challenging task, especially for people who have not received formal medical education. When patients are discharged from the hospital, they are provided with lengthy medical documents that contain intricate terminologies. Studies have shown that if people do not understand the content of their health documents, they will neither look for new information regarding their illness nor will they take actions to prevent or recover from their health issue. In this article, we highlight the need for generating personalized hospital-stay summaries and several research challenges associated with this task. The proposed directions are directly informed by our ongoing work in generating concise and comprehensible hospitalization summaries that are tailored to suit the patient's understanding of medical terminologies and level of engagement in improving their own health. Our preliminary evaluation shows that our summaries effectively present required medical concepts.
{"title":"What Happened to Me while I Was in the Hospital? Challenges and Opportunities for Generating Patient-Friendly Hospitalization Summaries.","authors":"Sabita Acharya, Andrew D Boyd, Richard Cameron, Karen Dunn Lopez, Pamela Martyn-Nemeth, Carolyn Dickens, Amer Ardati, Jose D Flores, Matt Baumann, Betty Welland, Barbara Di Eugenio","doi":"10.1007/s41666-018-0036-7","DOIUrl":"10.1007/s41666-018-0036-7","url":null,"abstract":"<p><p>Comprehending medical information is a challenging task, especially for people who have not received formal medical education. When patients are discharged from the hospital, they are provided with lengthy medical documents that contain intricate terminologies. Studies have shown that if people do not understand the content of their health documents, they will neither look for new information regarding their illness nor will they take actions to prevent or recover from their health issue. In this article, we highlight the need for generating personalized hospital-stay summaries and several research challenges associated with this task. The proposed directions are directly informed by our ongoing work in generating concise and comprehensible hospitalization summaries that are tailored to suit the patient's understanding of medical terminologies and level of engagement in improving their own health. Our preliminary evaluation shows that our summaries effectively present required medical concepts.</p>","PeriodicalId":101413,"journal":{"name":"Journal of healthcare informatics research","volume":"3 1","pages":"107-123"},"PeriodicalIF":3.7,"publicationDate":"2018-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8982693/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145093425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-10-10eCollection Date: 2019-03-01DOI: 10.1007/s41666-018-0035-8
Thomas R Kirchner, Hong Gao, Daniel J Lewis, Andrew Anesetti-Rothermel, Heather A Carlos, Brian House
There is growing interest in the way exposure to neighborhood risk and protective factors affects the health of residents. Although multiple approaches have been reported, empirical methods for contrasting the spatial uncertainty of exposure estimates are not well established. The objective of this paper was to contrast real-time versus neighborhood approximated exposure to the landscape of tobacco outlets across the contiguous US. A nationwide density surface of tobacco retail outlet locations was generated using kernel density estimation (KDE). This surface was linked to participants' (Np = 363) inferred residential location, as well as to their real-time geographic locations, recorded every 10 min over 180 days. Real-time exposure was estimated as the hourly product of radius of gyration and average tobacco outlet density (Nhour = 304, 164 h). Ordinal logit modeling was used to assess the distribution of real-time exposure estimates as a function of each participant's residential exposure. Overall, 61.3% of real-time, hourly exposures were of relatively low intensity, and after controlling for temporal and seasonal variation, 72.8% of the variance among these low-level exposures was accounted for by residence in one of the two lowest residential exposure quintiles. Most moderate to high intensity exposures (38.7% of all real-time, hourly exposures) were no more likely to have been contributed by subjects from any single residential exposure cluster than another. Altogether, 55.2% of the variance in real-time exposures was not explained by participants' residential exposure cluster. Calculating hourly exposure estimates made it possible to directly contrast real-time observations with static residential exposure estimates. Results document the substantial degree that real-time exposures can be misclassified by residential approximations, especially in residential areas characterized by moderate to high retail density levels.
{"title":"Individual Mobility and Uncertain Geographic Context: Real-time Versus Neighborhood Approximated Exposure to Retail Tobacco Outlets Across the US.","authors":"Thomas R Kirchner, Hong Gao, Daniel J Lewis, Andrew Anesetti-Rothermel, Heather A Carlos, Brian House","doi":"10.1007/s41666-018-0035-8","DOIUrl":"https://doi.org/10.1007/s41666-018-0035-8","url":null,"abstract":"<p><p>There is growing interest in the way exposure to neighborhood risk and protective factors affects the health of residents. Although multiple approaches have been reported, empirical methods for contrasting the spatial uncertainty of exposure estimates are not well established. The objective of this paper was to contrast real-time versus neighborhood approximated exposure to the landscape of tobacco outlets across the contiguous US. A nationwide density surface of tobacco retail outlet locations was generated using kernel density estimation (KDE). This surface was linked to participants' (<i>N</i> <sub><i>p</i></sub> = 363) inferred residential location, as well as to their real-time geographic locations, recorded every 10 min over 180 days. Real-time exposure was estimated as the hourly product of radius of gyration and average tobacco outlet density (<i>N</i> <sub>hour</sub> = 304, 164 h). Ordinal logit modeling was used to assess the distribution of real-time exposure estimates as a function of each participant's residential exposure. Overall, 61.3% of real-time, hourly exposures were of relatively low intensity, and after controlling for temporal and seasonal variation, 72.8% of the variance among these low-level exposures was accounted for by residence in one of the two lowest residential exposure quintiles. Most moderate to high intensity exposures (38.7% of all real-time, hourly exposures) were no more likely to have been contributed by subjects from any single residential exposure cluster than another. Altogether, 55.2% of the variance in real-time exposures was <i>not</i> explained by participants' residential exposure cluster. Calculating hourly exposure estimates made it possible to directly contrast real-time observations with static residential exposure estimates. Results document the substantial degree that real-time exposures can be misclassified by residential approximations, especially in residential areas characterized by moderate to high retail density levels.</p>","PeriodicalId":101413,"journal":{"name":"Journal of healthcare informatics research","volume":"3 1","pages":"70-85"},"PeriodicalIF":5.4,"publicationDate":"2018-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8982724/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142057788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-08-30eCollection Date: 2019-03-01DOI: 10.1007/s41666-018-0032-y
Yan Hu, Rui Wang, Feng Chen
Online health discussion forums as information exchange repository are used by different patient groups for sharing experience and seeking advice. Their accessibility is tremendously expanded in the last decade with the rapid growth of mobile internet. Among many popular topics, "drug-drug interactions" (DDIs) forum embeds a large number of DDIs hazards patient experienced however not published. In this paper, we intend to uncover the potential DDIs from the online forums and formulate the task as a sub-graph detection problem, such that co-mentioned drugs and symptoms are modeled as vertices, along with the occurrences are modeled as weighted edges. Therefore, a connected sub-graph consisting of both symptoms and drug vertices reveals DDIs occurrence. We then propose a novel bi-submodular function to characterize the likelihood of DDI occurrence within a connected sub-graph and apply an approximated algorithm to resolve the bi-submodular optimization (BSMO). The complexity of the algorithm is nearly linear. Our extensive experiments demonstrate the effectiveness and efficiency of the proposed approach.
{"title":"Bi-submodular Optimization (BSMO) for Detecting Drug-Drug Interactions (DDIs) from On-line Health Forums.","authors":"Yan Hu, Rui Wang, Feng Chen","doi":"10.1007/s41666-018-0032-y","DOIUrl":"https://doi.org/10.1007/s41666-018-0032-y","url":null,"abstract":"<p><p>Online health discussion forums as information exchange repository are used by different patient groups for sharing experience and seeking advice. Their accessibility is tremendously expanded in the last decade with the rapid growth of mobile internet. Among many popular topics, \"drug-drug interactions\" (DDIs) forum embeds a large number of DDIs hazards patient experienced however not published. In this paper, we intend to uncover the potential DDIs from the online forums and formulate the task as a sub-graph detection problem, such that co-mentioned drugs and symptoms are modeled as vertices, along with the occurrences are modeled as weighted edges. Therefore, a connected sub-graph consisting of both symptoms and drug vertices reveals DDIs occurrence. We then propose a novel bi-submodular function to characterize the likelihood of DDI occurrence within a connected sub-graph and apply an approximated algorithm to resolve the bi-submodular optimization (BSMO). The complexity of the algorithm is nearly linear. Our extensive experiments demonstrate the effectiveness and efficiency of the proposed approach.</p>","PeriodicalId":101413,"journal":{"name":"Journal of healthcare informatics research","volume":"3 1","pages":"19-42"},"PeriodicalIF":5.4,"publicationDate":"2018-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8982730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142057787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}