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PubMed1993

Specification of models in large expert systems based on causal probabilistic networks.

Problems involved in the specification of large expert systems are discussed. In the specification of causal probabilistic networks conditional probability tables for all nodes have to be provided. These conditional probability tables can often be described by models that specify the nature of interaction between nodes. Various types of models are described and a program that handles such models is presented. Large causal probabilistic networks often contain several copies of identical tables or structures. A header facility that provides common definitions of such repeated elements is proposed. This facility makes specifications much shorter and easier to construct and maintain.

Expert Systems↗

PubMed1994

Methods in the Virtual Wetlab I: rule-based reasoning driven by nearest-neighbor lattice dynamics.

We describe a discrete dynamical systems approach to exploring the hypothesis-trees associated with wetlab experiments. On-going applications of the method to experimental research using a genetically engineered mouse animal model with severe combined immune deficiency (SCID) in the area of HIV infection are outlined as an example. In conclusion, we survey how this method can be used to engineer an informational murine, called Cybermouse [Mus Cyberspacea], that can be experimented upon using current immersion technologies.

Animals↗

PubMed1994

Combining rule-based reasoning and mathematical modelling in diabetes care.

A prototype computer system utilising a model of carbohydrate metabolism linked to an expert system is described. The prototype which integrates quantitative and qualitative computational methodologies can be used to predict blood glucose profiles and adjust insulin doses in insulin-dependent (type I) diabetic subjects. A feedback loop insulin-dosage optimisation procedure which allows quantitative advice to be generated is also described. Possible clinical applications for the system, which is intended for educational use and clinically as a research tool to try and attain normoglycaemia, are discussed.

Algorithms↗

PubMed1995

A case study in ontology library construction.

The goal of our work is to facilitate the development of medical knowledge-based systems by providing a library of reusable ontologies. The availability of such a library reduces the amount of knowledge acquisition required to create knowledge bases of new applications, and makes it easier to connect a knowledge-based system to existing data bases. This article presents a case study in constructing such a library. The emphasis is on studying the principles that underly the internal structure of the library as well as on the process of constructing and using the library. We envision that, in the future, application ontologies can be constructed by the selection and refinement of generic ontologies and domain ontologies from such a library.

Artificial Intelligence↗

PubMed1995

Ontology-based configuration of problem-solving methods and generation of knowledge-acquisition tools: application of PROTEGE-II to protocol-based decision support.

PROTEGE-II is a suite of tools and a methodology for building knowledge-based systems and domain-specific knowledge-acquisition tools. In this paper, we show how PROTEGE-II can be applied to the task of providing protocol-based decision support in the domain of treating HIV-infected patients. To apply PROTEGE-II, (1) we construct a decomposable problem-solving method called episodic skeletal-plan refinement, (2) we build an application ontology that consists of the terms and relations in the domain, and of method-specific distinctions not already captured in the domain terms, and (3) we specify mapping relations that link terms from the application ontology to the domain-independent terms used in the problem-solving method. From the application ontology, we automatically generate a domain-specific knowledge-acquisition tool that is custom-tailored for the application. The knowledge-acquisition tool is used for the creation and maintenance of domain knowledge used by the problem-solving method. The general goal of the PROTEGE-II approach is to produce systems and components that are reusable and easily maintained. This is the rationale for constructing ontologies and problem-solving methods that can be composed from a set of smaller-grained methods and mechanisms. This is also why we tightly couple the knowledge-acquisition tools to the application ontology that specifies the domain terms used in the problem-solving systems. Although our evaluation is still preliminary, for the application task of providing protocol-based decision support, we show that these goals of reusability and easy maintenance can be achieved. We discuss design decisions and the tradeoffs that have to be made in the development of the system.

Artificial Intelligence↗

PubMed1990

Using a pocket computer to calculate monitor units--outline of a program in BASIC.

A pocket computer was programmed in BASIC to calculate monitor units for a dual energy linear accelerator. Because of the relatively large RAM memory, it was possible to input the TMR (or the PDD) tables for both energies as DATA. The program was written with the intention of providing a back-up check of the hand calculations.

Humans↗

PubMed2005

Evidence and diagnostic reporting in the IHE context.

Capturing clinical observations and findings during the diagnostic imaging process is increasingly becoming a critical step in diagnostic reporting. Standards developers-notably HL7 and DICOM-are making significant progress toward standards that enable exchanging clinical observations and findings among the various information systems of the healthcare enterprise. DICOM-like the HL7 Clinical Document Architecture (CDA) -uses templates and constrained, coded vocabulary (SNOMED, LOINC, etc.). Such a representation facilitates automated software recognition of findings and observations, intrapatient comparison, correlation to norms, and outcomes research. The scope of DICOM Structured Reporting (SR) includes many findings that products routinely create in digital form (measurements, computed estimates, etc.). In the Integrating the Healthcare Enterprise (IHE) framework, two Integration Profiles are defined for clinical data capture and diagnostic reporting: Evidence Document, and Simple Image and Numeric Report. This report describes these two DICOM SR-based integration profiles in the diagnostic reporting process.

Computer Systems↗

PubMed2004

Memetic algorithms for the unconstrained binary quadratic programming problem.

This paper presents a memetic algorithm, a highly effective evolutionary algorithm incorporating local search for solving the unconstrained binary quadratic programming problem (BQP). To justify the approach, a fitness landscape analysis is conducted experimentally for several instances of the BQP. The results of the analysis show that recombination-based variation operators are well suited for the evolutionary algorithms with local search. Therefore, the proposed approach includes--besides a highly effective randomized k-opt local search--a new variation operator that has been tailored specially for the application in the hybrid evolutionary framework. The operator is called innovative variation and is fundamentally different from traditional crossover operators, since new genetic material is included in the offspring which is not contained in one of the parents. The evolutionary heuristic is tested on 35 publicly available BQP instances, and it is shown experimentally that the algorithm is capable of finding best-known solutions to large BQPs in a short time and with a high frequency. In comparison to other approaches for the BQP, the approach appears to be much more effective, particularly for large instances of 1000 or 2500 binary variables.

Algorithms↗

PubMed2004

A Java software for creation of image mosaics.

Besides the dimensions of the selected image field width, the resolution of the individual objects is also of major importance for automatic reconstruction and other sophisticated histological work. The software solution presented here allows the user to create image mosaics by using a combination of several photographs. Optimum control is achieved by combining two procedures and several control mechanisms. In sample tests involving 50 image pairs, all images were mosaiced without giving rise to error. The program is ready for public download.

Computers↗

PubMed2005

MSurvPow: a FORTRAN program to calculate the sample size and power for cluster-randomized clinical trials with survival outcomes.

Manatunga and Chen [A.K. Manatunga, S. Chen, Sample size estimation for survival outcomes in cluster-randomized studies with small cluster sizes, Biometrics 56 (2000) 616-621] proposed a method to estimate sample size and power for cluster-randomized studies where the primary outcome variable was survival time. The sample size formula was constructed by considering a bivariate marginal distribution (Clayton-Oakes model) with univariate exponential marginal distributions. In this paper, a user-friendly FORTRAN 90 program was provided to implement this method and a simple example was used to illustrate the features of the program.

Cluster Analysis↗

PubMed2005

NONMEMory: a run management tool for NONMEM.

NONMEM is an extremely powerful tool for nonlinear mixed-effect modelling and simulation of pharmacokinetic and pharmacodynamic data. However, it is a console-based application whose output does not lend itself to rapid interpretation or efficient management. NONMEMory has been created to be a comprehensive project manager for NONMEM, providing detailed summary, comparison and overview of the runs comprising a given project, including the display of output data, simple post-run processing, fast diagnostic plots and run output management, complementary to other available modelling aids. Analysis time ought not to be spent on trivial tasks, and NONMEMory's role is to eliminate these as far as possible by increasing the efficiency of the modelling process. NONMEMory is freely available from http://www.uct.ac.za/depts/pha/nonmemory.php.

Computer Simulation↗

PubMed2005

Multiple correspondence analysis in S-PLUS.

Multiple correspondence analysis (MCA) is a multivariate method for analyzing multidimensional contingency tables. General software procedures to perform MCA are available. Among them SAS Proc CORRESP, SPAD CORMU procedure and the mca function of the MASS library in S-PLUS are probably the most used. However, CORRESP and CORMU output is different from that of mca function. The aim of this short note is showing how to obtain from mca function results compatible with those achieved with SAS or SPAD. A modified code is proposed in order to obtain the same coordinate system computed by SAS and SPAD. Moreover, the computation of the contributions of the levels of the factors to the inertia explained by each axis, the squared cosine of each factor level and the re-evaluation of the inertia explained by each axis have been added in order to improve the interpretations of the results of the decomposition.

Programming Languages↗

PubMed2005

Development of an HL7 interface engine, based on tree structure and streaming algorithm, for large-size messages which include image data.

A basic assumption of Health Level Seven (HL7) protocol is 'No limitation of message length'. However, most existing commercial HL7 interface engines do limit message length because they use the string array method, which is run in the main memory for the HL7 message parsing process. Specifically, messages with image and multi-media data create a long string array and thus cause the computer system to raise critical and fatal problem. Consequently, HL7 messages cannot handle the image and multi-media data necessary in modern medical records. This study aims to solve this problem with the 'streaming algorithm' method. This new method for HL7 message parsing applies the character-stream object which process character by character between the main memory and hard disk device with the consequence that the processing load on main memory could be alleviated. The main functions of this new engine are generating, parsing, validating, browsing, sending, and receiving HL7 messages. Also, the engine can parse and generate XML-formatted HL7 messages. This new HL7 engine successfully exchanged HL7 messages with 10 megabyte size images and discharge summary information between two university hospitals.

Algorithms↗

PubMed2005

An efficient and generic extension to ITK to process arbitrary shaped regions of interest.

The paper describes a software method to extend ITK (Insight ToolKit, supported by the National Library of Medicine), leading to ITK++. This method, which is based on the extension of the iterator design pattern, allows the processing of regions of interest with arbitrary shapes, without modifying the existing ITK code. We experimentally evaluate this work by considering the practical case of the liver vessel segmentation from CT-scan images, where it is pertinent to constrain processings to the liver area. Experimental results clearly prove the interest of this work: for instance, the anisotropic filtering of this area is performed in only 16 s with our proposed solution, while it takes 52 s using the native ITK framework. A major advantage of this method is that only add-ons are performed: this facilitates the further evaluation of ITK++ while preserving the native ITK framework.

Algorithms↗

PubMed2006

A service based approach for medical image distribution in healthcare Intranets.

The Digital Imaging and Communications in Medicine (DICOM) protocol is currently the ubiquitous standard for the communication of medical images and related data within the radiology department. However, seamless image distribution within the healthcare enterprise and especially with research and educational information systems is still hard to achieve, as software developers of such third-party applications have to go through the rather cumbersome task of adapting the DICOM communication model and implementing the DICOM protocol. This paper gives a brief outline of current trends in medical image distribution in the healthcare enterprise, and proposes a new technological approach for distributing DICOM images and related data through commonplace Internet technologies, based on the emerging web services software paradigm. In particular, the paper describes the DICOM Image Management (DIM) web service which acts as a façade for conventional DICOM sources allowing DICOM image data and related information, to be transformed into XML documents encapsulated in SOAP messages, enabling integration at the application level through general purpose standardized web technologies. Implementation issues are discussed and a demonstration of engaging the DIM web service is included.

Computer Communication Networks↗

PubMed2005

Design and implementation of a smart card based healthcare information system.

Smart cards are used in information technologies as portable integrated devices with data storage and data processing capabilities. As in other fields, smart card use in health systems became popular due to their increased capacity and performance. Their efficient use with easy and fast data access facilities leads to implementation particularly widespread in security systems. In this paper, a smart card based healthcare information system is developed. The system uses smart card for personal identification and transfer of health data and provides data communication via a distributed protocol which is particularly developed for this study. Two smart card software modules are implemented that run on patient and healthcare professional smart cards, respectively. In addition to personal information, general health information about the patient is also loaded to patient smart card. Health care providers use their own smart cards to be authenticated on the system and to access data on patient cards. Encryption keys and digital signature keys stored on smart cards of the system are used for secure and authenticated data communication between clients and database servers over distributed object protocol. System is developed on Java platform by using object oriented architecture and design patterns.

Computer Communication Networks↗

PubMed2005

Efficient storage of healthcare data in XML-based smart cards.

In this paper we present storage structures for efficiently processing XML path queries on healthcare data stored in smart cards using XML format. In the design of the storage structures that we present, properties of healthcare data and fundamental types of queries on the healthcare data are taken into account as well as the constraints of the smart cards. We compare the space and time efficiency of the proposed storage structures for various types of queries.

Algorithms↗

PubMed2006

Distributed computing methodology for training neural networks in an image-guided diagnostic application.

Distributed computing is a process through which a set of computers connected by a network is used collectively to solve a single problem. In this paper, we propose a distributed computing methodology for training neural networks for the detection of lesions in colonoscopy. Our approach is based on partitioning the training set across multiple processors using a parallel virtual machine. In this way, interconnected computers of varied architectures can be used for the distributed evaluation of the error function and gradient values, and, thus, training neural networks utilizing various learning methods. The proposed methodology has large granularity and low synchronization, and has been implemented and tested. Our results indicate that the parallel virtual machine implementation of the training algorithms developed leads to considerable speedup, especially when large network architectures and training sets are used.

Algorithms↗