Biomedical ontologies are huge. It is not possible for any one person to manage and engineer a complete ontology. They would need the help of research assistants and other people to develop and maintain the ontology. In the process of developing and maintaining the ontology the research assistants may enter incorrect data, resulting in low quality of the ontology. In this paper we will propose a conceptual framework to solve these ontology management and ontology development issues. There can be N assistants entering data into the ontology. All the data entered initially is stored in an intermediate ontology. The administrator of the ontology has a set of rules, which makes a checklist that checks and validates the data in intermediate ontology for correctness according to the ontology schema. We use the case study of protein ontology for this proposed approach to develop interfaces for assistants and administrators. The proposed approach can easily be extended to other biomedical ontologies just by tweaking the administrator rule set according to the ontology
{"title":"Engineering Trustworthy Ontologies: Case Study of Protein Ontology","authors":"F. Hussain, A. Sidhu, T. Dillon, E. Chang","doi":"10.1109/CBMS.2006.83","DOIUrl":"https://doi.org/10.1109/CBMS.2006.83","url":null,"abstract":"Biomedical ontologies are huge. It is not possible for any one person to manage and engineer a complete ontology. They would need the help of research assistants and other people to develop and maintain the ontology. In the process of developing and maintaining the ontology the research assistants may enter incorrect data, resulting in low quality of the ontology. In this paper we will propose a conceptual framework to solve these ontology management and ontology development issues. There can be N assistants entering data into the ontology. All the data entered initially is stored in an intermediate ontology. The administrator of the ontology has a set of rules, which makes a checklist that checks and validates the data in intermediate ontology for correctness according to the ontology schema. We use the case study of protein ontology for this proposed approach to develop interfaces for assistants and administrators. The proposed approach can easily be extended to other biomedical ontologies just by tweaking the administrator rule set according to the ontology","PeriodicalId":208693,"journal":{"name":"19th IEEE Symposium on Computer-Based Medical Systems (CBMS'06)","volume":"172 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133447730","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}
E. Filho, Y. Saijo, T. Yambe, A. Tanaka, M. Yoshizawa
An innovative application of adaptive thresholding is used for calcification regions detection in intravascular ultrasound images. A priori knowledge about the acoustic shadow that usually follows the calcification regions is used as discriminant of other bright regions of the image. Tests were carried out with 20 in vivo coronary artery images obtained from different patients. This proposed algorithm presented specificity of 88% and sensitivity of 84%. A ROC curve, whose AUC was equal to 0.87, was plotted for evaluation of the algorithm performance
{"title":"Segmentation of Calcification Regions in Intravascular Ultrasound Images by Adaptive Thresholding","authors":"E. Filho, Y. Saijo, T. Yambe, A. Tanaka, M. Yoshizawa","doi":"10.1109/CBMS.2006.142","DOIUrl":"https://doi.org/10.1109/CBMS.2006.142","url":null,"abstract":"An innovative application of adaptive thresholding is used for calcification regions detection in intravascular ultrasound images. A priori knowledge about the acoustic shadow that usually follows the calcification regions is used as discriminant of other bright regions of the image. Tests were carried out with 20 in vivo coronary artery images obtained from different patients. This proposed algorithm presented specificity of 88% and sensitivity of 84%. A ROC curve, whose AUC was equal to 0.87, was plotted for evaluation of the algorithm performance","PeriodicalId":208693,"journal":{"name":"19th IEEE Symposium on Computer-Based Medical Systems (CBMS'06)","volume":"13 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132537161","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}
Sachin Wasnik, Paul Donachy, T. Harmer, R. Perrott, P. Jithesh, M. McCurley, J. Johnston, M. Townsley, S. McKee
One of the challenges for the grid community is to develop services to support both shared computation and shared information. As apart of this development, it is necessary to convert laboratories to pervasive computing environments (smart laboratories) where data generated in the laboratories can be captured and published automatically; where information generated can be combined and compound with other laboratories' data on demand. In this paper, we describe one such initiative to capture and consume the data generated by the nucleotide sequencer in the grid enabled automated analysis system called GeneGrid developed at the Belfast e-Science Centre
{"title":"GeneGrid: From \"Virtual\" Bioinformatics Laboratory to \"Smart\" Bioinformatics Laboratory","authors":"Sachin Wasnik, Paul Donachy, T. Harmer, R. Perrott, P. Jithesh, M. McCurley, J. Johnston, M. Townsley, S. McKee","doi":"10.1109/CBMS.2006.90","DOIUrl":"https://doi.org/10.1109/CBMS.2006.90","url":null,"abstract":"One of the challenges for the grid community is to develop services to support both shared computation and shared information. As apart of this development, it is necessary to convert laboratories to pervasive computing environments (smart laboratories) where data generated in the laboratories can be captured and published automatically; where information generated can be combined and compound with other laboratories' data on demand. In this paper, we describe one such initiative to capture and consume the data generated by the nucleotide sequencer in the grid enabled automated analysis system called GeneGrid developed at the Belfast e-Science Centre","PeriodicalId":208693,"journal":{"name":"19th IEEE Symposium on Computer-Based Medical Systems (CBMS'06)","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115169326","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}
Markov chain modelling, in particular phase type modelling, has been previously used for hospital and community care systems, where we describe hospital care as a series of phases, such as acute, rehabilitation, or long-stay and likewise social care in the community may be modelled using phases such as dependent, convalescent, or nursing home. Such an approach allows us to adopt a holistic systems approach to health and community care modelling and management rather than focusing on the improvement of part of the system to the possible detriment of other components. We here extend this approach by showing how the general Markov framework can be exploited to extract various metrics of interest. In particular, we derive formulae for the mean and variance of the number of spells spent by a patient in hospital and in the community, and the expected total length of time in hospital and in community care, subsequent to first admission. Results are obtained for geriatric patients who have been admitted to hospital care. Finally we discuss how covariates, particularly time dependent covariates such as age, can be incorporated into the analysis
{"title":"Using Markov Models to Assess the Performance of a Health and Community Care System","authors":"S. McClean, M. Faddy, P. Millard","doi":"10.1109/CBMS.2006.164","DOIUrl":"https://doi.org/10.1109/CBMS.2006.164","url":null,"abstract":"Markov chain modelling, in particular phase type modelling, has been previously used for hospital and community care systems, where we describe hospital care as a series of phases, such as acute, rehabilitation, or long-stay and likewise social care in the community may be modelled using phases such as dependent, convalescent, or nursing home. Such an approach allows us to adopt a holistic systems approach to health and community care modelling and management rather than focusing on the improvement of part of the system to the possible detriment of other components. We here extend this approach by showing how the general Markov framework can be exploited to extract various metrics of interest. In particular, we derive formulae for the mean and variance of the number of spells spent by a patient in hospital and in the community, and the expected total length of time in hospital and in community care, subsequent to first admission. Results are obtained for geriatric patients who have been admitted to hospital care. Finally we discuss how covariates, particularly time dependent covariates such as age, can be incorporated into the analysis","PeriodicalId":208693,"journal":{"name":"19th IEEE Symposium on Computer-Based Medical Systems (CBMS'06)","volume":"16 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116727475","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}
Radio frequency identification (RFlD) is a technology for automatically tracking the location of persons and objects tagged with a small radio transceiver. Its use in retail and security applications has received widespread attention in the popular press, RFID's application in hospital business processes is increasing rapidly, and a number of safety-critical clinical applications have been prototyped. In order to determine RFID 's fitness for use in safety-critical as well as more mundane perioperative processes, the operating room of the future project at the University of Maryland Medical Center evaluated six active-RFID systems. The evaluation consisted of hands-on testing of a variety of COTS systems employing the leading active-RFID technologies-802.11 RF, proprietary RF, ultra-wideband, infrared and ultrasound. In this paper we report the results of those tests and discuss their implications for the application of active-RFID technology to clinical applications
{"title":"Active-RFID System Accuracy and Its Implications for Clinical Applications","authors":"Duncan Clarke, Adrian Park","doi":"10.1109/CBMS.2006.33","DOIUrl":"https://doi.org/10.1109/CBMS.2006.33","url":null,"abstract":"Radio frequency identification (RFlD) is a technology for automatically tracking the location of persons and objects tagged with a small radio transceiver. Its use in retail and security applications has received widespread attention in the popular press, RFID's application in hospital business processes is increasing rapidly, and a number of safety-critical clinical applications have been prototyped. In order to determine RFID 's fitness for use in safety-critical as well as more mundane perioperative processes, the operating room of the future project at the University of Maryland Medical Center evaluated six active-RFID systems. The evaluation consisted of hands-on testing of a variety of COTS systems employing the leading active-RFID technologies-802.11 RF, proprietary RF, ultra-wideband, infrared and ultrasound. In this paper we report the results of those tests and discuss their implications for the application of active-RFID technology to clinical applications","PeriodicalId":208693,"journal":{"name":"19th IEEE Symposium on Computer-Based Medical Systems (CBMS'06)","volume":"43 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132809728","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}
We proposed a distributed service oriented system with Web-based interface for medical information to promote the practical prediction of clinical prognosis. The proposed system provided hospitals secure access for medical information and processing simulations to examine effects of surgical treatments. Through a Web interface, users could operate the system in order to execute the simulations, access data from/to distributed storage, and display the medical information. These functions were combined by Web services technique, and ontology mapping based on ICD10 was applied to combine various types of medical information. A client-side volume display using GPU was developed to visualize the result volumetric data interactively, and the system adjusted data precision dynamically to maintain the rendering speed. Being based on standardized mechanism, our framework can be applied to similar complex problems with different types of and quantities of information, such as microscopy or geography
{"title":"Web-Based Distributed Simulation and Data Management Services for Medical Applications","authors":"M. Nakagawa, K. Nozaki, S. Shimojo","doi":"10.1109/CBMS.2006.170","DOIUrl":"https://doi.org/10.1109/CBMS.2006.170","url":null,"abstract":"We proposed a distributed service oriented system with Web-based interface for medical information to promote the practical prediction of clinical prognosis. The proposed system provided hospitals secure access for medical information and processing simulations to examine effects of surgical treatments. Through a Web interface, users could operate the system in order to execute the simulations, access data from/to distributed storage, and display the medical information. These functions were combined by Web services technique, and ontology mapping based on ICD10 was applied to combine various types of medical information. A client-side volume display using GPU was developed to visualize the result volumetric data interactively, and the system adjusted data precision dynamically to maintain the rendering speed. Being based on standardized mechanism, our framework can be applied to similar complex problems with different types of and quantities of information, such as microscopy or geography","PeriodicalId":208693,"journal":{"name":"19th IEEE Symposium on Computer-Based Medical Systems (CBMS'06)","volume":"46 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125739215","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}
C. O. Rolim, F. Koch, M. Assunção, Carlos Becker Westphall
In this article, we describe a grid of sensors to collect patients' vital data and to allow real time monitoring of patients in heath-care centres. We analyse the problem scenario and identify the components involved towards the construction of an integrated and homogeneous management system. Finally, we present a case study to demonstrate the applicability of our approach
{"title":"Towards a Grid of Sensors for Telemedicine","authors":"C. O. Rolim, F. Koch, M. Assunção, Carlos Becker Westphall","doi":"10.1109/CBMS.2006.159","DOIUrl":"https://doi.org/10.1109/CBMS.2006.159","url":null,"abstract":"In this article, we describe a grid of sensors to collect patients' vital data and to allow real time monitoring of patients in heath-care centres. We analyse the problem scenario and identify the components involved towards the construction of an integrated and homogeneous management system. Finally, we present a case study to demonstrate the applicability of our approach","PeriodicalId":208693,"journal":{"name":"19th IEEE Symposium on Computer-Based Medical Systems (CBMS'06)","volume":"295 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124233973","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}
In this paper, we propose a novel gene clustering method named TGmix through integrated analysis on two types of datasets, namely the time-series and two-group microarray datasets. The goal of the proposed method is to discover genes as biomarkers that have similar expression profiles in time-series conditions and are also significantly differentially expressed in two-group conditions. We applied the proposed method to microarray datasets for rat's wound healing experiment, and the genes discovered in the same cluster conform to the analysis goal with related biological functions
{"title":"Discovering Gene Clusters via Integrated Analysis on Time-Series and Group-Comparative Microarray Datasets","authors":"V. Tseng, Lien-Chin Chen, Yao-Dung Hsieh","doi":"10.1109/CBMS.2006.76","DOIUrl":"https://doi.org/10.1109/CBMS.2006.76","url":null,"abstract":"In this paper, we propose a novel gene clustering method named TGmix through integrated analysis on two types of datasets, namely the time-series and two-group microarray datasets. The goal of the proposed method is to discover genes as biomarkers that have similar expression profiles in time-series conditions and are also significantly differentially expressed in two-group conditions. We applied the proposed method to microarray datasets for rat's wound healing experiment, and the genes discovered in the same cluster conform to the analysis goal with related biological functions","PeriodicalId":208693,"journal":{"name":"19th IEEE Symposium on Computer-Based Medical Systems (CBMS'06)","volume":"18 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126479031","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}
We present methods for monitoring a large, diverse, and autonomously modified collection of healthcare documents on the Web. Our methods do not require document-providers to offer any special services. They are based on explicating changes between document versions on a per-user basis by using differencing algorithms. These changes are presented to users in the context of the documents using special XML elements. In order to effectively browse changes in large document collections, we use a variable-resolution XML browser. A noteworthy feature of this browser is that it produces usable displays at any level of detail specified by a user
{"title":"Tracking Changes in Healthcare Documents","authors":"S. Chawathe","doi":"10.1109/CBMS.2006.161","DOIUrl":"https://doi.org/10.1109/CBMS.2006.161","url":null,"abstract":"We present methods for monitoring a large, diverse, and autonomously modified collection of healthcare documents on the Web. Our methods do not require document-providers to offer any special services. They are based on explicating changes between document versions on a per-user basis by using differencing algorithms. These changes are presented to users in the context of the documents using special XML elements. In order to effectively browse changes in large document collections, we use a variable-resolution XML browser. A noteworthy feature of this browser is that it produces usable displays at any level of detail specified by a user","PeriodicalId":208693,"journal":{"name":"19th IEEE Symposium on Computer-Based Medical Systems (CBMS'06)","volume":"393 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122993372","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}
O. Caelen, Gianluca Bontempi, E. Coussaert, L. Barvais, Francois Clement
The growing availability of high throughput measurement devices in the operating room makes possible the collection of a huge amount of data about the state of the patient and the doctors' practice during a surgical operation. This paper explores the possibility of extracting from these data relevant information and pertinent decision rules in order to support the daily anesthesia procedures. In particular we focus on machine learning strategies to design a closed-loop controller that, in a near future, could play the role of a decision support tool and, in a further perspective, the one of automatic pilot of the anesthesia procedure. Two strategies (direct and inverse) for learning a controller from observed data are assessed on the basis of a database of measurements collected in recent years by the ULB Erasme anaesthesiology group. The preliminary results of the learning approach applied to the regulation of hypnosis through the bispectral index (BIS) in a simulated framework appear to be promising and worthy of future investigation
{"title":"Machine Learning Techniques to Enable Closed-Loop Control in Anesthesia","authors":"O. Caelen, Gianluca Bontempi, E. Coussaert, L. Barvais, Francois Clement","doi":"10.1109/CBMS.2006.110","DOIUrl":"https://doi.org/10.1109/CBMS.2006.110","url":null,"abstract":"The growing availability of high throughput measurement devices in the operating room makes possible the collection of a huge amount of data about the state of the patient and the doctors' practice during a surgical operation. This paper explores the possibility of extracting from these data relevant information and pertinent decision rules in order to support the daily anesthesia procedures. In particular we focus on machine learning strategies to design a closed-loop controller that, in a near future, could play the role of a decision support tool and, in a further perspective, the one of automatic pilot of the anesthesia procedure. Two strategies (direct and inverse) for learning a controller from observed data are assessed on the basis of a database of measurements collected in recent years by the ULB Erasme anaesthesiology group. The preliminary results of the learning approach applied to the regulation of hypnosis through the bispectral index (BIS) in a simulated framework appear to be promising and worthy of future investigation","PeriodicalId":208693,"journal":{"name":"19th IEEE Symposium on Computer-Based Medical Systems (CBMS'06)","volume":"94 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115766628","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}
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