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Biomedical subjects

Antoine Geissbuhler

Publications and source records attributed to Antoine Geissbuhler.

At least 19 recordsLinked to original sources
PubMed2006

Acceptance and cognitive load in a clinical setting of a novel device allowing natural real-time data acquisition.

INTRODUCTION: This paper reports the findings of an evaluation study in the field of human-computer interaction about the use of a new data acquisition device, the digital pen. It focuses on specific aspects of the interaction between the users and the technology: the cognitive burden induced by the design of the tool in real conditions of use and its impact on user acceptance. METHODOLOGY: Human cognition is embedded in a complex sociocultural world. Therefore, we opted for ethnographically informed investigations reinforced by a satisfaction survey. The work context chosen for these investigations was the emergency room triage process. RESULTS: The technology meets a high acceptance (median 3 on a [-5,5] scale) shaded by unexpected additional cognitive burdens. These burdens originate in several technological and ergonomic flaws that have been discovered during the observations. These results have been used to improve the technology. CONCLUSION: We demonstrate the importance of this kind of field study to uncover unexpected possible sources of failure of acceptance of a new technology. Such kind of study should be held prior to the introduction of a new technology to lower the common failure rate encountered in the field of medical informatics.

Attitude to Computers↗
PubMed2006

Comprehensive management of the access to the electronic patient record: towards trans-institutional networks.

BACKGROUND: A system ensuring tight control access is used since 5 years at the University Geneva Hospitals (HUG) over a four campuses health care system with ambulatory care settings behaving like a small community care network. Access to identified clinical information is limited to care providers that have a therapeutic relationship with the patient and to those data needed for that relation. The same policy applies to administrative or scientific research accesses. This paper presents how the HUG met the challenging goal of protecting patient privacy within regulatory limits while keeping the system operational in terms of use and management. SOLUTION: The main characteristics of the system are: (a) an institution-wide policy for access rights to the computerized patient record; (b) an institutional management of the contracts of the collaborators; (c) access profiles based on application-independent, fine-grained access rights; (d) a decentralized attribution of profession-specific access profiles; (e) a complete, centralized log of all accesses to the clinical information system; and (f) a decentralized verification of the accesses. Many of these characteristics can be maintained when evolving towards a trans-institutional computerized patient record, but new constraints need to be taken into account.

Access to Information↗
PubMed2006

Assessment of Internet-based tele-medicine in Africa (the RAFT project).

The objectives of this paper on the Réseau Afrique Francophone de Télémédecine (RAFT) project are the evaluation of feasibility, potential, problems and risks of an Internet-based tele-medicine network in developing countries of Africa. The RAFT project was started in Western African countries 5 years ago and has now extended to other regions of Africa as well (i.e. Madagascar, Rwanda). A project for the development of a national tele-medicine network in Mali was initiated in 2001, extended to Mauritania in 2002 and to Morocco in 2003. By 2006, a total of nine countries are connected. The entire technical infrastructure is based on Internet technologies for medical distance learning and tele-consultations. The results are a tele-medicine network that has been in productive use for over 5 years and has enabled various collaboration channels, including North-to-South (from Europe to Africa), South-to-South (within Africa), and South-to-North (from Africa to Europe) distance learning and tele-consultations, plus many personal exchanges between the participating hospitals and Universities. It has also unveiled a set of potential problems: (a) the limited importance of North-to-South collaborations when there are major differences in the available resources or the socio-cultural contexts between the collaborating parties; (b) the risk of an induced digital divide if the periphery of the health system in developing countries is not involved in the development of the network; and (c) the need for the development of local medical content management skills. Particularly point (c) is improved through the collaboration between the various countries as professionals from the medical and the computer science field are sharing courses and resources. Personal exchanges between partners in the project are frequent, and several persons received an education at one of the partner Universities. As conclusion, we can say that the identified risks have to be taken into account when designing large-scale tele-medicine projects in developing countries. These problems can be mitigated by fostering South-South collaboration channels, by the use of satellite-based Internet connectivity in remote areas, the appreciation of local knowledge and its publication on-line. The availability of such an infrastructure also facilitates the development of other projects, courses, and local content creation.

Africa↗
PubMed2006

Comprehensive management of the access to a component-based healthcare information system.

OBJECTIVE: to describe the key concepts and elements used to implement a comprehensive access management system to a distributed, component-based healthcare information system. METHODS: the a priori access is based on an institution-wide policy for access rights coupled to proximity process for the granting of such rights. Access rights are explicit and externalized from the information systems components. A posteriori control is based on a centralized, exhaustive journal of accesses to all components coupled to a decentralized verification process for suspicious accesses. RESULTS: the system has been operational for three years, initially used for the access to the computerized patient record components, and now extending to all the components of the hospital information system. The same architecture will be used for the development of the trans-institutional community health information network.

Access to Information↗
PubMed2005

Health search engine with e-document analysis for reliable search results.

OBJECTIVE: After a review of the existing practical solution available to the citizen to retrieve eHealth document, the paper describes an original specialized search engine WRAPIN. METHOD: WRAPIN uses advanced cross lingual information retrieval technologies to check information quality by synthesizing medical concepts, conclusions and references contained in the health literature, to identify accurate, relevant sources. Thanks to MeSH terminology [1] (Medical Subject Headings from the U.S. National Library of Medicine) and advanced approaches such as conclusion extraction from structured document, reformulation of the query, WRAPIN offers to the user a privileged access to navigate through multilingual documents without language or medical prerequisites. RESULTS: The results of an evaluation conducted on the WRAPIN prototype show that results of the WRAPIN search engine are perceived as informative 65% (59% for a general-purpose search engine), reliable and trustworthy 72% (41% for the other engine) by users. But it leaves room for improvement such as the increase of database coverage, the explanation of the original functionalities and an audience adaptability. CONCLUSION: Thanks to evaluation outcomes, WRAPIN is now in exploitation on the HON web site (http://www.healthonnet.org), free of charge. Intended to the citizen it is a good alternative to general-purpose search engines when the user looks up trustworthy health and medical information or wants to check automatically a doubtful content of a Web page.

Europe↗
PubMed2005

Learning from imbalanced data in surveillance of nosocomial infection.

OBJECTIVE: An important problem that arises in hospitals is the monitoring and detection of nosocomial or hospital acquired infections (NIs). This paper describes a retrospective analysis of a prevalence survey of NIs done in the Geneva University Hospital. Our goal is to identify patients with one or more NIs on the basis of clinical and other data collected during the survey. METHODS AND MATERIAL: Standard surveillance strategies are time-consuming and cannot be applied hospital-wide; alternative methods are required. In NI detection viewed as a classification task, the main difficulty resides in the significant imbalance between positive or infected (11%) and negative (89%) cases. To remedy class imbalance, we explore two distinct avenues: (1) a new re-sampling approach in which both over-sampling of rare positives and under-sampling of the noninfected majority rely on synthetic cases (prototypes) generated via class-specific sub-clustering, and (2) a support vector algorithm in which asymmetrical margins are tuned to improve recognition of rare positive cases. RESULTS AND CONCLUSION: Experiments have shown both approaches to be effective for the NI detection problem. Our novel re-sampling strategies perform remarkably better than classical random re-sampling. However, they are outperformed by asymmetrical soft margin support vector machines which attained a sensitivity rate of 92%, significantly better than the highest sensitivity (87%) obtained via prototype-based re-sampling.

Algorithms↗
PubMed2005

Design of a Multi Dimensional Database for the Archimed DataWarehouse.

The Archimed data warehouse project started in 1993 at the Geneva University Hospital. It has progressively integrated seven data marts (or domains of activity) archiving medical data such as Admission/Discharge/Transfer (ADT) data, laboratory results, radiology exams, diagnoses, and procedure codes. The objective of the Archimed data warehouse is to facilitate the access to an integrated and coherent view of patient medical in order to support analytical activities such as medical statistics, clinical studies, retrieval of similar cases and data mining processes. This paper discusses three principal design aspects relative to the conception of the database of the data warehouse: 1) the granularity of the database, which refers to the level of detail or summarization of data, 2) the database model and architecture, describing how data will be presented to end users and how new data is integrated, 3) the life cycle of the database, in order to ensure long term scalability of the environment. Both, the organization of patient medical data using a standardized elementary fact representation and the use of the multi dimensional model have proved to be powerful design tools to integrate data coming from the multiple heterogeneous database systems part of the transactional Hospital Information System (HIS). Concurrently, the building of the data warehouse in an incremental way has helped to control the evolution of the data content. These three design aspects bring clarity and performance regarding data access. They also provide long term scalability to the system and resilience to further changes that may occur in source systems feeding the data warehouse.

Databases, Factual↗
PubMed2005

SVM Modeling via a Hybrid Genetic Strategy. A Health Care Application.

This paper addresses the model selection problem for Support Vector Machines. A hybrid genetic algorithm guided by Direct Simplex Search to evolves hyperparameter values using an empirical error estimate as a steering criterion. This approach is specificaly tailored and experimentally evaluated on a health care problem which involves discriminating 11 % nosocomially infected patients from 89 % non infected patients. The combination of Direct Search Simplex with GAs is shown to improve the performance of GAs in terms of solution quality and computational efficiency. Unlike most other hyperparameter tuning techniques, our hybrid approach does not require supplementary effort such as computation of derivatives, making them well suited for practical purposes. This method produces encouraging results: it exhibits high performance and good convergence properties.

Algorithms↗
PubMed2005

The digital pen and paper technology: implementation and use in an existing clinical information system.

OBJECTIVE: Evaluation of the technical feasibility of tight integration of the digital pen and paper technology in an existing computerized patient record.Technology: The digital pen is a normal pen able to record all actions of the user and to analyze a micro pattern printed on the paper. The digital paper is a normal paper printed with an almost invisible micro pattern of small dots encoding information such as position and identifiers. We report our experience in the implementation and the use of this technology in an existing large clinical information system for acquiring clinical information. DISCUSSION: It is possible to print uniquely identified forms using the digital paper technology. These forms can be pre-filled with clinical readable information about the patient. When care providers complete these forms using the digital pen, it is possible to acquire the data in a structured computerized patient record. The technology is easy to integrate in a component-based architecture based on Web Services. CONCLUSION: The digital pen and paper is a cost-effective technology that can be integrated in an existing clinical information system and allows fast and easy bedside clinical information acquisition without the need for an expensive infrastructure based on traditional portable devices or wireless devices.

Humans↗
PubMed2005

Lung CT Analysis and Retrieval as a Diagnostic Aid.

Image retrieval is currently a very active research field due to the large amount of visual data being produced in most modern hospitals. Most often, the goal is to aid the diagnostic process. Unfortunately, only very few medical image retrieval systems are currently used in clinical routine. One of the application domains for image retrieval is the analysis and retrieval of lung CTs. A first user study in the United States shows that these systems allow improving the diagnostic quality.This article describes the approach to an aid for lung CT diagnostics. The analysis incorporates several steps and the goal is to automate the process as much as possible for easy integration into diagnostics. Thus, several automatic steps are proposed from a selection of the most characteristic slices, to an automatic segmentation of the lung tissue and a classification on the segmented area into diagnostic classes. Feedback to the MD will be given in the form of marked regions in the images that appear to be different from the norm of healthy tissue. We are currently working on a small set of training images with marked and annotated regions but a larger set of images for the evaluation of our algorithm is in work. For this reason, the article does currently not contain much quantitative evaluation.For several tasks we use existing open source software such as Weka and itk. This allows an easy reproduction of the search results.

Algorithms↗
PubMed2005

Desiderata for representing anatomical knowledge.

The general problem of knowledge representation for gross anatomy supporting both computers and human is rarely globally solved. Partial solutions are flourishing, but the actual and potential users are left with a lack of satisfaction and uncomfortable feeling of incompleteness. Moreover, these solutions are not ready for a sound evolution and are at risk to disappear at any moment by default of adequate maintenance. In addition, the problem is complicated by the fact that any solutions should be relevant for Natural Language Processing applications in a multilingual environment.This paper tackles with this problem and defines the basic steps for a proper knowledge representation scheme. Taking the subdomain of gross anatomy, it shows how each step has been solved and what performances and benefits are expected by such a solution. A discussion is done on the way to interface from a common source for both computers and humans.

Anatomy↗
PubMed2005

A decade devoted to improving online health information quality.

Created in 1995 in response to consumer enthusiasm for the World Wide Web, Health On the Net FoundationHealth On the Net Foundation: http://www.healthonnet.org/ has developed solutions to address the problem of potentially dangerous online health and medical information. Then as now, no international legal framework regulated online content, and consumers needed to be given the means to check the reliability and the relevance of health information [[1]]. HON was first to introduce a code of conduct for online health and medical publishers, the HONcode [[2],[3],[4]], which was readily adopted by webmasters aware of the need for credibility in the new, competitive online space. HON went on to develop Web applications to enhance access to reliable information, making use of innovative NLP-based and semantic search technologies.This paper describes the implementation of a quality standard for online information (HONcode) based on the information production process; its evolution through nearly 10 years of effectiveness, its challenges and results. Today, over 4,700 HON-accredited websites, respecting minimum standards for disclosure and responsibility in online medical publishing, constitute the largest voluntary accreditation network on the Web.

Consumer Health Information↗
PubMed2004

Experience in implementing inpatient clinical note capture via a provider order entry system.

Care providers' adoption of computer-based health-related documentation ("note capture") tools has been limited, even though such tools have the potential to facilitate information gathering and to promote efficiency of clinical charting. The authors have developed and deployed a computerized note-capture tool that has been made available to end users through a care provider order entry (CPOE) system already in wide use at Vanderbilt. Overall note-capture tool usage between January 1, 1999, and December 31, 2001, increased substantially, both in the number of users and in their frequency of use. This case report is provided as an example of how an existing care provider order entry environment can facilitate clinical end-user adoption of a computer-assisted documentation tool-a concept that may seem counterintuitive to some.

Academic Medical Centers↗
PubMed2004

A reference data set for the evaluation of medical image retrieval systems.

Content-based image retrieval is starting to become an increasingly important factor in medical imaging research and image management systems. Several retrieval systems and methodologies exist and are used in a large variety of applications from automatic labelling of images to diagnostic aid and image classification. Still, it is very hard to compare the performance of these systems as the used databases often contain copyrighted or private images and are thus not interchangeable between research groups, also for patient privacy. Most of the currently used databases for evaluating systems are also fairly small which is partly due to the high cost in obtaining a gold standard or ground truth that is necessary for evaluation. Several large image databases, though without a gold standard, start to be available publicly, for example by the NIH (National Institutes for Health). This article describes the creation of a large medical image database that is used in a teaching file containing more than 8,700 varied medical images. The images are anonymised and can be exchanged free of charge and copyright. Ground truth (a gold standard) has been obtained for a set of 26 images being selected as query topics for content-based query by image example. To reduce the time for the generation of ground truth, pooling methods well known from the text or information retrieval field have been used. Such a database is a good starting point for comparing the current image retrieval systems and to measure the retrieval quality, especially within the context of teaching files, image case databases and the support of teaching. For a comparison of retrieval systems for diagnostic aid, specialised image databases, including the diagnosis and a case description will need to be made available, as well, including gold standards for a proper system evaluation. A first evaluation event for image retrieval is foreseen at the 2004 CLEF conference (Cross Language Evaluation Forum) to compare text-and content-based access mechanism to images.

Databases, Factual↗
PubMed2004

A review of content-based image retrieval systems in medical applications-clinical benefits and future directions.

Content-based visual information retrieval (CBVIR) or content-based image retrieval (CBIR) has been one on the most vivid research areas in the field of computer vision over the last 10 years. The availability of large and steadily growing amounts of visual and multimedia data, and the development of the Internet underline the need to create thematic access methods that offer more than simple text-based queries or requests based on matching exact database fields. Many programs and tools have been developed to formulate and execute queries based on the visual or audio content and to help browsing large multimedia repositories. Still, no general breakthrough has been achieved with respect to large varied databases with documents of differing sorts and with varying characteristics. Answers to many questions with respect to speed, semantic descriptors or objective image interpretations are still unanswered. In the medical field, images, and especially digital images, are produced in ever-increasing quantities and used for diagnostics and therapy. The Radiology Department of the University Hospital of Geneva alone produced more than 12,000 images a day in 2002. The cardiology is currently the second largest producer of digital images, especially with videos of cardiac catheterization ( approximately 1800 exams per year containing almost 2000 images each). The total amount of cardiologic image data produced in the Geneva University Hospital was around 1 TB in 2002. Endoscopic videos can equally produce enormous amounts of data. With digital imaging and communications in medicine (DICOM), a standard for image communication has been set and patient information can be stored with the actual image(s), although still a few problems prevail with respect to the standardization. In several articles, content-based access to medical images for supporting clinical decision-making has been proposed that would ease the management of clinical data and scenarios for the integration of content-based access methods into picture archiving and communication systems (PACS) have been created. This article gives an overview of available literature in the field of content-based access to medical image data and on the technologies used in the field. Section 1 gives an introduction into generic content-based image retrieval and the technologies used. Section 2 explains the propositions for the use of image retrieval in medical practice and the various approaches. Example systems and application areas are described. Section 3 describes the techniques used in the implemented systems, their datasets and evaluations. Section 4 identifies possible clinical benefits of image retrieval systems in clinical practice as well as in research and education. New research directions are being defined that can prove to be useful. This article also identifies explanations to some of the outlined problems in the field as it looks like many propositions for systems are made from the medical domain and research prototypes are developed in computer science departments using medical datasets. Still, there are very few systems that seem to be used in clinical practice. It needs to be stated as well that the goal is not, in general, to replace text-based retrieval methods as they exist at the moment but to complement them with visual search tools.

Databases, Factual↗
PubMed2004

Coping with the variability of medical terms.

OBJECTIVES: To cope with medical terms, which present a high variability of expression through a single natural language, in the sense that any term may be reformulated in hundred of different ways. METHODS: A typology of term variants is presented as a systematic approach in order to favour the implementation of an exhaustive solution. Then, an algorithm able to handle all variants is designed. RESULTS: Using MetaMap, single terms are analyzed with a success rate varying between 68 and 88 %; the algorithm presented in this paper improves this situation. CONCLUSIONS: This experience shows that a semantic driven method, based on a thesaurus, provides a satisfactory solution to the problem of variability of a single term. The presented typology is representative of most variants in a language.

Algorithms↗
PubMed2004

An application of one-class support vector machine to nosocomial infection detection.

Nosocomial infections (NIs)---those acquired in health care settings---are among the major causes of increased mortality among hospitalized patients. They are a significant burden for patients and health authorities alike; it is thus important to monitor and detect them through an effective surveillance system. This paper describes a retrospective analysis of a prevalence survey of NIs done in the Geneva University Hospital. Our goal is to identify patients with one or more NIs on the basis of clinical and other data collected during the survey. In this two-class classification task, the main difficulty lies in the significant imbalance between positive or infected (11%) and negative (89%) cases. To cope with class imbalance, we investigate one-class SVMs which can be trained to distinguish two classes on the basis of examples from a single class (in this case, only "normal" or non infected patients). The infected ones are then identified as "abnormal" cases or outliers that deviate significantly from the normal profile. Experimental results are encouraging: whereas standard 2-class SVMs scored a baseline sensitivity of 50.6% on this problem, the one-class approach increased sensitivity to as much as 92.6%. These results are comparable to those obtained by the authors in a previous study on asymmetrical soft margin SVMs; they suggest that one-class SVMs can provide an effective and efficient way of overcoming data imbalance in classification problems.

Algorithms↗