... 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

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

mHealth Platform for Parkinson’s Disease Management 帕金森病管理移动健康平台

... 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_5

Dimitrios A. Gatsios, G. Rigas, D. Miljković, B. Seljak, M. Bohanec, M. Arredondo, A. Antonini, S. Konitsiotis, D. Fotiadis

引用次数: 10

Reconstruction and in Silico Simulation Towards Electricigens Metabolic Network of Electronic Mediator 电子介质电代谢物网络的重构与计算机模拟

... 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_48

Yuhe Wang, Zhenglin Tong, Jianming Xie

引用次数: 2

Identifying Cancer Subnetwork Markers Using Game Theory Method 用博弈论方法识别癌症子网络标记

... 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_17

Saman Farahmand, S. Goliaei, Z. Kashani, Sina Farahmand

引用次数: 3

Measuring Physiological Stress Using Heart-Related Measures 使用心脏相关测量测量生理应激

... 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_14

AN-YU Luo, Siyi Deng, M. Pesavento, J. Mak

引用次数: 0

Automatic Co-registration of MEG-MRI Data Using Multiple RGB-D Cameras 使用多个RGB-D相机的MEG-MRI数据自动协同配准

... 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_43

Shih-Yen Lin, Chin Han Cheng, Li-Fen Chen, Yong-Sheng Chen

引用次数: 0

High-Speed Intravascular Spectroscopic Photoacoustic Imaging at Two Spectral Bands 两个光谱波段的高速血管内光谱光声成像

... 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_33

Xiaojing Gong, Yan Li, Riqiang Lin, Ji Leng, Liang Song

引用次数: 0

Effectiveness of Evidence-Based Venous Thromboembolism Electronic Order Sets Measured by Health Outcomes 以健康结果衡量的循证静脉血栓栓塞电子订单集的有效性

... 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_9

J. Krive, J. Shoolin, S. Zink

引用次数: 0