... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics最新文献_第6页

Integration of Multi-Modal Biomedical Data to Predict Cancer Grade and Patient Survival. 整合多模式生物医学数据预测癌症分级和患者生存。

... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics Pub Date : 2016-02-01 DOI: 10.1109/BHI.2016.7455963

John H Phan, Ryan Hoffman, Sonal Kothari, Po-Yen Wu, May D Wang

{"title":"Integration of Multi-Modal Biomedical Data to Predict Cancer Grade and Patient Survival.","authors":"John H Phan, Ryan Hoffman, Sonal Kothari, Po-Yen Wu, May D Wang","doi":"10.1109/BHI.2016.7455963","DOIUrl":"10.1109/BHI.2016.7455963","url":null,"abstract":"The Big Data era in Biomedical research has resulted in large-cohort data repositories such as The Cancer Genome Atlas (TCGA). These repositories routinely contain hundreds of matched patient samples for genomic, proteomic, imaging, and clinical data modalities, enabling holistic and multi-modal integrative analysis of human disease. Using TCGA renal and ovarian cancer data, we conducted a novel investigation of multi-modal data integration by combining histopathological image and RNA-seq data. We compared the performances of two integrative prediction methods: majority vote and stacked generalization. Results indicate that integration of multiple data modalities improves prediction of cancer grade and outcome. Specifically, stacked generalization, a method that integrates multiple data modalities to produce a single prediction result, outperforms both single-data-modality prediction and majority vote. Moreover, stacked generalization reveals the contribution of each data modality (and specific features within each data modality) to the final prediction result and may provide biological insights to explain prediction performance.","PeriodicalId":72024,"journal":{"name":"... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics","volume":"2016 ","pages":"577-580"},"PeriodicalIF":0.0,"publicationDate":"2016-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/BHI.2016.7455963","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34734499","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}

引用次数: 13

Supporting novice clinicians cognitive strategies: System design perspective. 支持临床新手认知策略:系统设计视角。

... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics Pub Date : 2016-02-01 DOI: 10.1109/BHI.2016.7455946

Roosan Islam, Jeanmarie Mayer, Justin Clutter

{"title":"Supporting novice clinicians cognitive strategies: System design perspective.","authors":"Roosan Islam, Jeanmarie Mayer, Justin Clutter","doi":"10.1109/BHI.2016.7455946","DOIUrl":"https://doi.org/10.1109/BHI.2016.7455946","url":null,"abstract":"Infections occur among all clinical domains. The changing nature of microbes, viruses and infections poses a great threat to the overall well-being in medicine. Clinicians in the infectious disease (ID) domain deal with diagnostic as well as treatment uncertainty in their everyday practice. Our current health information technology (HIT) systems do not consider the level of clinician expertise into the system design process. Thus, information is presented to both novice and expert ID clinicians in identical ways. The purpose of this study was to identify the cognitive strategies novice ID clinicians use in managing complex cases to make better recommendations for system design. In the process, we interviewed 14 ID experts and asked them to give us a detailed description of how novice clinicians would have dealt with complex cases. From the interview transcripts, we identified four major themes that expert clinicians suggested about novices' cognitive strategies including: A) dealing with uncertainty, B) lack of higher macrocognition, C) oversimplification of problems through heuristics and D) dealing with peer pressure. Current and future innovative decision support tools embedded in the electronic health record that can match these cognitive strategies may hold the key to cognitively supporting novice clinicians. The results of this study may open up avenues for future research and suggest design directions for better healthcare systems.","PeriodicalId":72024,"journal":{"name":"... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics","volume":"2016 ","pages":"509-512"},"PeriodicalIF":0.0,"publicationDate":"2016-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/BHI.2016.7455946","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34557607","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}

引用次数: 14

Automated Risk Prediction for Esophageal Optical Endomicroscopic Images. 食管光学内镜图像的自动风险预测。

... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics Pub Date : 2016-02-01 DOI: 10.1109/BHI.2016.7455859

Sonal Kothari, Hang Wu, Li Tong, Kevin E Woods, May D Wang

引用次数: 2

A Fully Implantable, NFC Enabled, Continuous Interstitial Glucose Monitor. 一种完全植入式、近场通信功能、连续间质血糖监测仪。

... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics Pub Date : 2016-02-01 Epub Date: 2016-04-21 DOI: 10.1109/BHI.2016.7455973

Nijad Anabtawi, Sabrina Freeman, Rony Ferzli

引用次数: 0

Toward patient-tailored summarization of lung cancer literature. 针对患者的肺癌文献综述。

... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics Pub Date : 2016-02-01 Epub Date: 2016-04-21 DOI: 10.1109/BHI.2016.7455931

Jean I Garcia-Gathright, Nicholas J Matiasz, Edward B Garon, Denise R Aberle, Ricky K Taira, Alex A T Bui

{"title":"Toward patient-tailored summarization of lung cancer literature.","authors":"Jean I Garcia-Gathright, Nicholas J Matiasz, Edward B Garon, Denise R Aberle, Ricky K Taira, Alex A T Bui","doi":"10.1109/BHI.2016.7455931","DOIUrl":"https://doi.org/10.1109/BHI.2016.7455931","url":null,"abstract":"As the volume of biomedical literature increases, it can be challenging for clinicians to stay up-to-date. Graphical summarization systems help by condensing knowledge into networks of entities and relations. However, existing systems present relations out of context, ignoring key details such as study population. To better support precision medicine, summarization systems should include such information to contextualize and tailor results to individual patients. This paper introduces \"contextualized semantic maps\" for patient-tailored graphical summarization of published literature. These efforts are demonstrated in the domain of driver mutations in non-small cell lung cancer (NSCLC). A representation for relations and study population context in NSCLC was developed. An annotated gold standard for this representation was created from a set of 135 abstracts; F1-score annotator agreement was 0.78 for context and 0.68 for relations. Visualizing the contextualized relations demonstrated that context facilitates the discovery of key findings that are relevant to patient-oriented queries.","PeriodicalId":72024,"journal":{"name":"... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics","volume":"2016 ","pages":"449-452"},"PeriodicalIF":0.0,"publicationDate":"2016-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/BHI.2016.7455931","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35180951","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}

引用次数: 3

An Auditory Nerve Stimulation Chip with Integrated AFE, Sound Processing, and Power Management for Fully Implantable Cochlear Implants. 一种集成了AFE、声音处理和电源管理的听觉神经刺激芯片，用于完全植入式耳蜗植入。

... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics Pub Date : 2016-02-01 Epub Date: 2016-04-21 DOI: 10.1109/BHI.2016.7455974

Nijad Anabtawi, Sabrina Freeman, Rony Ferzli

引用次数: 0

Predicting Lung Cancer Incidence from Air Pollution Exposures Using Shapelet-based Time Series Analysis. 基于shapelet的时间序列分析预测空气污染暴露的肺癌发病率。

... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics Pub Date : 2016-02-01 Epub Date: 2016-04-21 DOI: 10.1109/BHI.2016.7455960

Hong-Jun Yoon, Songhua Xu, Georgia Tourassi

{"title":"Predicting Lung Cancer Incidence from Air Pollution Exposures Using Shapelet-based Time Series Analysis.","authors":"Hong-Jun Yoon, Songhua Xu, Georgia Tourassi","doi":"10.1109/BHI.2016.7455960","DOIUrl":"https://doi.org/10.1109/BHI.2016.7455960","url":null,"abstract":"In this paper we investigated whether the geographical variation of lung cancer incidence can be predicted through examining the spatiotemporal trend of particulate matter air pollution levels. Regional trends of air pollution levels were analyzed by a novel shapelet-based time series analysis technique. First, we identified U.S. counties with reportedly high and low lung cancer incidence between 2008 and 2012 via the State Cancer Profiles provided by the National Cancer Institute. Then, we collected particulate matter exposure levels (PM2.5 and PM10) of the counties for the previous decade (1998-2007) via the AirData dataset provided by the Environmental Protection Agency. Using shapelet-based time series pattern mining, regional environmental exposure profiles were examined to identify frequently occurring sequential exposure patterns. Finally, a binary classifier was designed to predict whether a U.S. region is expected to experience high lung cancer incidence based on the region's PM2.5 and PM10 exposure the decade prior. The study confirmed the association between prolonged PM exposure and lung cancer risk. In addition, the study findings suggest that not only cumulative exposure levels but also the temporal variability of PM exposure influence lung cancer risk.","PeriodicalId":72024,"journal":{"name":"... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics","volume":"2016 ","pages":"565-568"},"PeriodicalIF":0.0,"publicationDate":"2016-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/BHI.2016.7455960","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34974381","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}

引用次数: 6

Assessing Variability in Brain Tumor Segmentation to Improve Volumetric Accuracy and Characterization of Change. 评估脑肿瘤分割的可变性以提高体积准确性和变化特征。

... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics Pub Date : 2016-02-01 Epub Date: 2016-04-21 DOI: 10.1109/BHI.2016.7455914

Edgar A Rios Piedra, Ricky K Taira, Suzie El-Saden, Benjamin M Ellingson, Alex A T Bui, William Hsu

{"title":"Assessing Variability in Brain Tumor Segmentation to Improve Volumetric Accuracy and Characterization of Change.","authors":"Edgar A Rios Piedra, Ricky K Taira, Suzie El-Saden, Benjamin M Ellingson, Alex A T Bui, William Hsu","doi":"10.1109/BHI.2016.7455914","DOIUrl":"https://doi.org/10.1109/BHI.2016.7455914","url":null,"abstract":"Brain tumor analysis is moving towards volumetric assessment of magnetic resonance imaging (MRI), providing a more precise description of disease progression to better inform clinical decision-making and treatment planning. While a multitude of segmentation approaches exist, inherent variability in the results of these algorithms may incorrectly indicate changes in tumor volume. In this work, we present a systematic approach to characterize variability in tumor boundaries that utilizes equivalence tests as a means to determine whether a tumor volume has significantly changed over time. To demonstrate these concepts, 32 MRI studies from 8 patients were segmented using four different approaches (statistical classifier, region-based, edge-based, knowledge-based) to generate different regions of interest representing tumor extent. We showed that across all studies, the average Dice coefficient for the superset of the different methods was 0.754 (95% confidence interval 0.701-0.808) when compared to a reference standard. We illustrate how variability obtained by different segmentations can be used to identify significant changes in tumor volume between sequential time points. Our study demonstrates that variability is an inherent part of interpreting tumor segmentation results and should be considered as part of the interpretation process.","PeriodicalId":72024,"journal":{"name":"... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics","volume":"2016 ","pages":"380-383"},"PeriodicalIF":0.0,"publicationDate":"2016-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/BHI.2016.7455914","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35136956","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}

引用次数: 7

Evaluating the impact of sequencing error correction for RNA-seq data with ERCC RNA spike-in controls. 用ERCC RNA刺入对照评估测序错误校正对RNA-seq数据的影响。

... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics Pub Date : 2016-02-01 DOI: 10.1109/BHI.2016.7455838

Li Tong, Cheng Yang, Po-Yen Wu, May D Wang

{"title":"Evaluating the impact of sequencing error correction for RNA-seq data with ERCC RNA spike-in controls.","authors":"Li Tong, Cheng Yang, Po-Yen Wu, May D Wang","doi":"10.1109/BHI.2016.7455838","DOIUrl":"https://doi.org/10.1109/BHI.2016.7455838","url":null,"abstract":"Sequencing errors are a major issue for several next-generation sequencing-based applications such as de novo assembly and single nucleotide polymorphism detection. Several error-correction methods have been developed to improve raw data quality. However, error-correction performance is hard to evaluate because of the lack of a ground truth. In this study, we propose a novel approach which using ERCC RNA spike-in controls as the ground truth to facilitate error-correction performance evaluation. After aligning raw and corrected RNA-seq data, we characterized the quality of reads by three metrics: mismatch patterns (i.e., the substitution rate of A to C) of reads aligned with one mismatch, mismatch patterns of reads aligned with two mismatches and the percentage increase of reads aligned to reference. We observed that the mismatch patterns for reads aligned with one mismatch are significantly correlated between ERCC spike-ins and real RNA samples. Based on such observations, we conclude that ERCC spike-ins can serve as ground truths for error correction beyond their previous applications for validation of dynamic range and fold-change response. Also, the mismatch patterns for ERCC reads aligned with one mismatch can serve as a novel and reliable metric to evaluate the performance of error-correction tools.","PeriodicalId":72024,"journal":{"name":"... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics","volume":"2016 ","pages":"74-77"},"PeriodicalIF":0.0,"publicationDate":"2016-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/BHI.2016.7455838","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34313367","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}

引用次数: 6

Vital Signs Analysis for Oceanauts in Deep Sea Submerged Environment: A Case Study 深海潜水环境下海洋生物生命体征分析

... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics Pub Date : 2015-10-09 DOI: 10.1007/978-981-10-4505-9_39

F. Miao, Ye Li, Lu Shi

引用次数: 1