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Publications in this journal

• Machine learning models for lung cancer classification using array comparative genomic hybridization.

  Authors: C. F. Aliferis, D. Hardin, P. P. Massion

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  Array CGH is a recently introduced technology that measures changes in the gene copy number of hundreds of genes in a single experiment. The primary goal of this study was to develop machine learningArray CGH is a recently introduced technology that measures changes in the gene copy number of hundreds of genes in a single experiment. The primary goal of this study was to develop machine learning models that classify non-small Lung Cancers according to histopathology types and to compare several machine learning methods in this learning task. DNA from tumors of 37 patients (21 squamous carcinomas, and 16 adenocarcinomas) were extracted and hybridized onto a 452 BAC clone array. The following algorithms were used: KNN, Decision Tree Induction, Support Vector Machines and Feed-Forward Neural Networks. Performance was measured via leave-one-out classification accuracy. The best multi-gene model found had a leave-one-out accuracy of 89.2%. Decision Trees performed poorer than the other methods in this learning task and dataset. We conclude that gene copy numbers as measured by array CGH are, collectively, an excellent indicator of histological subtype. Several interesting research directions are discussed.

• Information model and terminology model issues related to goals.

  Authors: Suzanne Bakken, Judith J Warren, Anne Casey, Debra Konicek, Cynthia Lundberg, Marcel Pooke

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  Goal statements are a significant component of structures that support the process of health care delivery such as practice guidelines, standards of care, critical pathways, disease management plans,Goal statements are a significant component of structures that support the process of health care delivery such as practice guidelines, standards of care, critical pathways, disease management plans, patient education plans, and nursing care plans. Although these structures are increasingly computer-based, there has been little attention to the formal representation of goal statements. This is a necessary prerequisite for enabling semantic interoperability. Existing and evolving information model and terminology model standards offer some approaches that may be applicable to goal statements, however, a number of issues require resolution

• Controlling the vocabulary for anatomy.

  Authors: R H Baud, C Lovis, A M Rassinoux, P Ruch, A Geissbuhler

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  When confronted with the representation of human anatomy, natural language processing (NLP) system designers are facing an unsolved and frequent problem: the lack of a suitable global reference. TheWhen confronted with the representation of human anatomy, natural language processing (NLP) system designers are facing an unsolved and frequent problem: the lack of a suitable global reference. The available sources in electronic format are numerous, but none fits adequately all the constraints and needs of language analysis. These sources are usually incomplete, difficult to use or tailored to specific needs. The anatomist's or ontologist's view does not necessarily match that of the linguist. The purpose of this paper is to review most recognized sources of knowledge in anatomy usable for linguistic analysis. Their potential and limits are emphasized according to this point of view. Focus is given on the role of the consensus work of the International Federation of Associations of Anatomists (IFAA) giving the Terminologia Anatomica.

• The helpful patient record system: problem oriented and knowledge based.

  Authors: Elisabeth Bayegan, Samson Tu

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  In contrast to existing computerized patient record systems, which merely offer static functionality for storage and presentation, a helpful patient record system is a problem-oriented,In contrast to existing computerized patient record systems, which merely offer static functionality for storage and presentation, a helpful patient record system is a problem-oriented, knowledge-based system which provides the clinician with situation-specific information from the patient record, relevant to the activity within the patient care process. We suggest extending the data model of current patient record systems with (1) knowledge for recognizing and interpreting care situations, (2) knowledge of how clinicians work and what information they need, and (3) means to rank information according to its relevance in a given situation. We present a framework that enables representation of three prerequisite features for a future helpful patient record system: the primary care workflow process, the problem-oriented information model, and means to identify relevant information to the care process and medical decisions.

• A rapid usability assessment methodology to support the choice of clinical information systems: a case study.

  Authors: M C Beuscart-Zéphir, L Watbled, A M Carpentier, M Degroisse, O Alao

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  We present here an adapted methodology integrating usability engineering and early evaluation procedures to support the choice of a Clinical Information System in the context of a standard Call forWe present here an adapted methodology integrating usability engineering and early evaluation procedures to support the choice of a Clinical Information System in the context of a standard Call for Tender. We illustrate the application of this methodology with a case study. We integrated a standard 'contextual task and activity analysis' into the choice process and then drew up usability recommendations for the choice of an application. We organized a one-week on-site exhibition and test for each candidate company. During the test sessions, we performed a rapid usability assessment. The final choice of the application is strongly and positively influenced by the results of the usability assessment.

• A modern optical character recognition system in a real world clinical setting: some accuracy and feasibility observations.

  Authors: Paul G Biondich, J Marc Overhage, Paul R Dexter, Stephen M Downs, Larry Lemmon, Clement J McDonald

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  Advances in optical character recognition (OCR) software and computer hardware have stimulated a reevaluation of the technology and its ability to capture structured clinical data from preexistingAdvances in optical character recognition (OCR) software and computer hardware have stimulated a reevaluation of the technology and its ability to capture structured clinical data from preexisting paper forms. In our pilot evaluation, we measured the accuracy and feasibility of capturing vitals data from a pediatric encounter form that has been in use for over twenty years. We found that the software had a digit recognition rate of 92.4% (95% confidence interval: 91.6 to 93.2) overall. More importantly, this system was approximately three times as fast as our existing method of data entry. These preliminary results suggest that with further refinements in the approach and additional development, we may be able to incorporate OCR as another method for capturing structured clinical data.

• Automatic generation of a metamodel from an existing knowledge base to assist the development of a new analogous knowledge base.

  Authors: J Bouaud, B Séroussi

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  Knowledge acquisition is a key step in the development of knowledge-based systems and methods have been proposed to help elicitating a domain-specific task model from a generic task model. WeKnowledge acquisition is a key step in the development of knowledge-based systems and methods have been proposed to help elicitating a domain-specific task model from a generic task model. We explored how an existing validated knowledge base (KB) represented by a decision tree could be automatically processed to infer a higher level domain-specific task model. On-codoc is a guideline-based decision support system applied to breast cancer therapy. Assuming task identity and ontological proximity between breast and lung cancer domains, the generalization of the breast can-cer KB should allow to build a metamodel to serve as a guide for the elaboration of a new specific KB on lung cancer. Two types of parametrized generalization methods based on tree structure simplification and ontological abstraction were used. We defined a similarity distance and a generalization coefficient to select the best metamodel identified as the closest to the original decision tree of the most generalized metamodels.

• Representation of roles in biomedical ontologies: a case study in functional genomics.

  Authors: Anita Burgun, Olivier Bodenreider, Franck Le Duff, Fouzia Moussouni, Olivier Loreal

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  OBJECTIVE: Representing roles, i.e. functions of proteins, sequences and structures, is the cornerstone of knowledge representation in functional genomics. The objective of this study is toOBJECTIVE: Representing roles, i.e. functions of proteins, sequences and structures, is the cornerstone of knowledge representation in functional genomics. The objective of this study is to investigate representation of roles as functional categories or associative relations. We focus on GeneOntology (GO) and the UMLS and take examples from iron metabolism. METHODS: The terms corresponding to the main proteins involved in iron metabolism were mapped to GO (including the annotations) and the UMLS. The representation of their biological roles was then analyzed. RESULTS: Functional aspects are represented in both GO and the UMLS. However, the granularity may not be appropriate. DISCUSSION: Advantages and limits of functional categories and associative relations are discussed.

• Knowledge-based bioterrorism surveillance.

  Authors: David L Buckeridge, Justin Graham, Martin J O'Connor, Michael K Choy, Samson W. Tu, Mark A. Musen

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  An epidemic resulting from an act of bioterrorism could be catastrophic. However, if an epidemic can be detected and characterized early on, prompt public health intervention may mitigate its impact.An epidemic resulting from an act of bioterrorism could be catastrophic. However, if an epidemic can be detected and characterized early on, prompt public health intervention may mitigate its impact. Current surveillance approaches do not perform well in terms of rapid epidemic detection or epidemic monitoring. One reason for this shortcoming is their failure to bring existing knowledge and data to bear on the problem in a coherent manner. Knowledge-based methods can integrate surveillance data and knowledge, and allow for careful evaluation of problem-solving methods. This paper presents an argument for knowledge-based surveillance, describes a prototype of BioSTORM, a system for real-time epidemic surveillance, and shows an initial evaluation of this system applied to a simulated epidemic from a bioterrorism attack.

• The internet and locus of control in older adults.

  Authors: Robert J Campbell, Kimberly D Harris, James Wabby

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  OBJECTIVE: To investigate how training older adults to find medical information using the Internet affects their locus of control. METHODS: Quantitative methods were utilized. Specifically, theOBJECTIVE: To investigate how training older adults to find medical information using the Internet affects their locus of control. METHODS: Quantitative methods were utilized. Specifically, the Multidimensional Health Locus of Control survey was distributed at the onset of each seminar and again at the conclusion. RESULTS: Paired t-tests revealed that the subjects did not change their locus of control regarding their health beliefs over the period of the seminar. However, there was statistical significance with regard to eight specific questions. CONCLUSION: Subjects scored high on their level of internal locus of control coming into the study. The majority of subjects had already learned to use the computer, owned a home computer, and had access to the Internet, but had not used the Internet to search for healthcare information. The challenge continues to be reaching those older adults who have not encountered the computer and the Internet.

• Using medication list--problem list mismatches as markers of potential error.

  Authors: James D Carpenter, Paul N Gorman

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  The goal of this project was to specify and develop an algorithm that will check for drug and problem list mismatches in an electronic medical record (EMR). The algorithm is based on the premise thatThe goal of this project was to specify and develop an algorithm that will check for drug and problem list mismatches in an electronic medical record (EMR). The algorithm is based on the premise that a patient's problem list and medication list should agree, and a mismatch may indicate medication error. Successful development of this algorithm could mean detection of some errors, such as medication orders entered into a wrong patient record, or drug therapy omissions, that are not otherwise detected via automated means. Additionally, mismatches may identify opportunities to improve problem list integrity. To assess the concept's feasibility, this study compared medications listed in a pharmacy information system with findings in an online nursing adult admission assessment, serving as a proxy for the problem list. Where drug and problem list mismatches were discovered, examination of the patient record confirmed the mismatch, and identified any potential causes. Evaluation of the algorithm in diabetes treatment indicates that it successfully detects both potential medication error and opportunities to improve problem list completeness. This algorithm, once fully developed and deployed, could prove a valuable way to improve the patient problem list, and could decrease the risk of medication error.

• Initializing the VA medication reference terminology using UMLS metathesaurus co-occurrences.

  Authors: John S Carter, Steven H Brown, Mark S. Erlbaum, William Gregg, Peter L Elkin, Ted Speroff, Mark S. Tuttle

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  We developed and evaluated a UMLS Metathesaurus Co-occurrence mining algorithm to connect medications and diseases they may treat. Based on 16 years of co-occurrence data, we created 977 candidateWe developed and evaluated a UMLS Metathesaurus Co-occurrence mining algorithm to connect medications and diseases they may treat. Based on 16 years of co-occurrence data, we created 977 candidate drug-disease pairs for a sample of 100 ingredients (50 commonly prescribed and 50 selected at random). Our evaluation showed that more than 80% of the candidate drug-disease pairs were rated "APPROPRIATE" by physician raters. Additionally, there was a highly significant correlation between the overall frequency of citation and the likelihood that the connection was rated "APPROPRIATE." The drug-disease pairs were used to initialize term definitions in an ongoing effort to build a medication reference terminology for the Veterans Health Administration. Co-occurrence mining is a valuable technique for initializing term definitions in a large-scale reference terminology creation project.

• Machine learning for sub-population assessment: evaluating the C-section rate of different physician practices.

  Authors: Rich Caruana, Radu S Niculescu, R Bharat Rao, Cynthia Simms

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  We apply machine learning to the problem of subpopulation assessment for Caesarian Section. In subpopulation assessment, we are interested in making predictions not for a single patient, but forWe apply machine learning to the problem of subpopulation assessment for Caesarian Section. In subpopulation assessment, we are interested in making predictions not for a single patient, but for groups of patients. Typically, in any large population, different subpopulations will have different "outcome" rates. In our example, the C-section rate of a population of 22,176 expectant mothers is 16.8%; yet, the 17 physician groups that serve this population have vastly different group C-section rates, ranging from 11% to 23%. The ultimate goal of subpopulation assessment is to determine if these variations in the observed rates can be attributed to (a) variations in intrinsic risk of the patient sub-populations (i.e. some groups contain more "high-risk C-section" patients), or (b) differences in physician practice (i.e. some groups do more C-sections). Our results indicate that although there is some variation in intrinsic risk, there is also much variation in physician practice.

• Unsupervised imaging, registration and archiving of tissue microarrays.

  Authors: Wenjin Chen, David J Foran, Michael Reiss

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  Tissue microarray (TMA) technology offers several advantages over traditional methods of specimen preparation by maximizing limited tissue resources and providing the means for visualizing molecularTissue microarray (TMA) technology offers several advantages over traditional methods of specimen preparation by maximizing limited tissue resources and providing the means for visualizing molecular targets. Currently, the primary methods used to evaluate arrays involves the interactive review of TMA samples while they are viewed by microscope and are subjectively evaluated and scored. The process is slow, tedious and prone to error. In order to facilitate large-scale, multi-institutional studies a more automated and reliable means for processing tissue microarrays is needed. We have developed a web-based prototype which features automated imaging, registration and intelligent archiving of tissue microarrays in multi-user, network environments.

• Software engineering risk factors in the implementation of a small electronic medical record system: the problem of scalability.

  Authors: Michael F Chiang, Justin B Starren

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  The successful implementation of clinical information systems is difficult. In examining the reasons and potential solutions for this problem, the medical informatics community may benefit from theThe successful implementation of clinical information systems is difficult. In examining the reasons and potential solutions for this problem, the medical informatics community may benefit from the lessons of a rich body of software engineering and management literature about the failure of software projects. Based on previous studies, we present a conceptual framework for understanding the risk factors associated with large-scale projects. However, the vast majority of existing literature is based on large, enterprise-wide systems, and it unclear whether those results may be scaled down and applied to smaller projects such as departmental medical information systems. To examine this issue, we discuss the case study of a delayed electronic medical record implementation project in a small specialty practice at Columbia-Presbyterian Medical Center. While the factors contributing to the delay of this small project share some attributes with those found in larger organizations, there are important differences. The significance of these differences for groups implementing small medical information systems is discussed.

• Test of the technology acceptance model for the internet in pediatrics.

  Authors: William G. Chismar, Sonja Wiley-Patton

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  There is growing recognition of the importance of the Internet and, more generally, information technology to pediatric care. However, acceptance of these technologies has been low. Attitudes ofThere is growing recognition of the importance of the Internet and, more generally, information technology to pediatric care. However, acceptance of these technologies has been low. Attitudes of physicians can play a pivotal role in the adoption session. This study tests the extension to a widely used model in the information systems literature: the Technology Acceptance Model (TAM). Data were collected in a survey of pediatricians to see how well the extended model, TAM2, fits in the medical arena. Our results partially confirm the model; significant parts of the model were not confirmed. The primary factors in pediatricians' acceptance of technology applications relate to their usefulness and job relevance. Little weight is given to ease of use and social factors. We discuss possible explanations for the discrepancies and suggest future research.

• The horizontal and vertical nature of patient phenotype retrieval: new directions for clinical text processing.

  Authors: Christopher G Chute

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  The author reviews the historical problem of identifying appropriate patients for retrieval from a clinical repository of patient records, compares the competing features of document classificationThe author reviews the historical problem of identifying appropriate patients for retrieval from a clinical repository of patient records, compares the competing features of document classification and natural language processing, and proposes an alternative approach. The alternative approach 1) codes inquiries in an ontology to lend a vertical axis to retrieval knowledge instead of coding the target body of notes, 2) invokes natural language indexing and lexical normalizations on the corpus of notes that is scalable and tractable, and 3) leverages thesauri of word-level synonyms and near-synonyms to expand term searches "horizontally" around the concept spaces drawn from the ontology in which the queries were "coded."

• A generic computerized method for estimate of familial risks.

  Authors: Isabelle Colombet, Yigang Xu, Marie-Christine Jaulent, Daniel Desages, Patrice Degoulet, Gilles Chatellier

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  Most guidelines developed for cancers screening and for cardiovascular risk management use rules to estimate familial risk. These rules are complex, difficult to memorize, and need to collect aMost guidelines developed for cancers screening and for cardiovascular risk management use rules to estimate familial risk. These rules are complex, difficult to memorize, and need to collect a complete pedigree. This paper describes a generic computerized method to estimate familial risks and its implementation in an internet-based application. The program is based on 3 generic models: a model of the family; a model of familial risk; a display model for the pedigree. The model of family allows to represent each member of the family and to construct and display a family tree. The model of familial risk is generic and allows easy update of the program with new diseases or new rules. It was possible to implement guidelines dealing with breast and colorectal cancer and cardiovascular diseases prevention. First evaluation with general practitioners showed that the program was usable. Impact on quality of familial risk estimate should be more documented.

• Towards a sharable numeric and symbolic knowledge base on cerebral cortex anatomy: lessons learned from a prototype.

  Authors: Olivier Dameron, Bernard Gibaud, Anita Burgun, Xavier Morandi

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  We propose a knowledge base that combines numeric and symbolic knowledge about sulco-gyral brain cortex. This knowledge base is implemented using Web technologies. It is intended to be easilyWe propose a knowledge base that combines numeric and symbolic knowledge about sulco-gyral brain cortex. This knowledge base is implemented using Web technologies. It is intended to be easily reusable in various application contexts such as teaching, decision support in neurosurgery and sharing of neuroimaging data for research purposes. Our analysis shows that (1) a formal representation of taxonomy and mereotopology, and (2) use of identity criteria to represent symbolic concepts, are needed to serve those applications.

• SYNCHRONUS: a reusable software module for temporal integration.

  Authors: Amar K. Das, Mark A. Musen

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  Querying time-stamped data in clinical databases is an essential step in the actuation of many decision-support rules. Since previous methods of temporal data management are not readily transferableQuerying time-stamped data in clinical databases is an essential step in the actuation of many decision-support rules. Since previous methods of temporal data management are not readily transferable among legacy databases, developers must create de novo querying methods that allow temporal integration of a decision-support program and existing database. In this paper, we outline four software-engineering principles that support a general, reusable approach to temporal integration. We then describe the design and implementation of SYNCHRONUS, a software module that advances our prior work on temporal querying. We show how this module satisfies the four principles for the task of temporal integration. SYNCHRONUS can help developers to overcome the software-engineering burden of temporal model heterogeneity within decision-support architectures.

• End-to-end performance measurement of Internet based medical applications.

  Authors: P Dev, D Harris, D Gutierrez, A Shah, S Senger

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  We present a method to obtain an end-to-end characterization of the performance of an application over a network. This method is not dependent on any specific application or type of network. TheWe present a method to obtain an end-to-end characterization of the performance of an application over a network. This method is not dependent on any specific application or type of network. The method requires characterization of network parameters, such as latency and packet loss, between the expected server or client endpoints, as well as characterization of the application's constraints on these parameters. A subjective metric is presented that integrates these characterizations and that operates over a wide range of applications and networks. We believe that this method may be of wide applicability as research and educational applications increasingly make use of computation and data servers that are distributed over the Internet.

• Expected value prioritization of prompts and reminders.

  Authors: Stephen M Downs, Hasmet Uner

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  Computer-based prompting and reminder systems have been shown to be highly effective in increasing rates of preventive services delivery. However, there are many more recommended preventive servicesComputer-based prompting and reminder systems have been shown to be highly effective in increasing rates of preventive services delivery. However, there are many more recommended preventive services than can be practically included in a typical clinic visit. Therefore prioritization of preventive services prompts is necessary. We describe two approaches to prioritizing preventive services prompts based on expected value decision making. One method involves a static, global prioritization across all preventive services and has been used in a production system for almost 7 years. The second method uses influence diagrams to prioritize prompts dynamically, based on individual patient data. The latter approach is still under development. Both methods are labor intensive and require a combination of epidemiologic data and expert judgment. Compromises in strictly normative process were necessary to achieve user satisfaction.

• The Stanford MediaServer Project: strategies for building a flexible digital media platform to support biomedical education and research.

  Authors: Jeremy C Durack, Chih-Chien Chao, Derek Stevenson, Katherine P Andriole, Parvati Dev

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  Medical media collections are growing at a pace that exceeds the value they currently provide as research and educational resources. To address this issue, the Stanford MediaServer was designed toMedical media collections are growing at a pace that exceeds the value they currently provide as research and educational resources. To address this issue, the Stanford MediaServer was designed to promote innovative multimedia-based application development. The nucleus of the MediaServer platform is a digital media database strategically designed to meet the information needs of many biomedical disciplines. Key features include an intuitive web-based interface for collaboratively populating the media database, flexible creation of media collections for diverse and specialized purposes, and the ability to construct a variety of end-user applications from the same database to support biomedical education and research.

• Implementation of a classification hierarchy for the GeneTests/GeneClinics genetic testing databases.

  Authors: J Edwards, P Tarczy-Hornoch

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  The combination of a) our changing understanding of genotypic and phenotypic classification of diseases and b) the rapid growth and expansion of the number of entries in two databases targeted towardThe combination of a) our changing understanding of genotypic and phenotypic classification of diseases and b) the rapid growth and expansion of the number of entries in two databases targeted toward clinicians resulted in the need to develop a flexible dynamic hierarchical classification system for genetic disorders. The two databases making use of this classification schemas are the GeneClinics (GC) database - www.geneclinics.org and the GeneTests (GT) database - www.genetests.org The GC and GT databases serve respsectively as the users manual and yellow pages of genetic testing. The GeneTests/GeneClinics (GT/GC) classification hierarchy is maintained as a simple set of parent/child relationships in a relational database. The hierarchy is generated in real time in response to a user request. It is not maintained as a set of members with relationships defined by characters that are parsed to determine the structure of the tree. The GT/GC classification hierarchy entries are handled as objects by the data maintenance and search tools and may have a number of attributes and associations that create a rich tool for defining and examining genetic disorders

• A proposed key escrow system for secure patient information disclosure in biomedical research databases.

  Authors: Todd A Ferris, Gregory M Garrison, Henry J Lowe

  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.

  Access to clinical data is of increasing importance to biomedical research. The pending HIPAA privacy regulations provide specific requirements for the release of protected health information. UnderAccess to clinical data is of increasing importance to biomedical research. The pending HIPAA privacy regulations provide specific requirements for the release of protected health information. Under the regulations, biomedical researchers may utilize anonymized data, or adhere to HIPAA requirements regarding protected health information. In order to provide researchers with anonymized data from a clinical research database, we reviewed several published strategies for de-identification of protected health information. Critical analysis with respect to this project suggests that de-identification alone is problematic when applied to clinical research databases. We propose a hybrid system; utilizing secure key escrow, de-identification, and role-based access for IRB approved researchers.

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