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PubMed1990

Expert systems as a diagnostic aid in otoneurology.

Expert systems (ES) are a new tool for information processing developed by the branch of computer science known as artificial intelligence. ES are capable of solving problems in a given domain by using the knowledge and emulating the behaviour of specialists in that field. ES can be used as powerful tools for education since they are able to justify their own conclusions and to make the underlying reasoning explicit. This paper presents 'Vertigo', an ES aimed at the classification and diagnosis of different forms of dizziness. It has been conceived mainly as a teaching tool in otoneurological departments. The rationale of this project, its development, the structure and the use of the system are described. So far, 'Vertigo' has been tested on more than 200 cases of dizziness and is presently being used by ENT residents during their otoneurology stage.

Diagnosis, Computer-Assisted↗
PubMed1995

[Linear accelerator radiosurgery].

Radiosurgery is the precise radiation of a known intracranial target with a high dose of energy, sparing the adjacent nervous tissue. Technological advances in the construction of linear accelerators, stereotactic instruments and in computer sciences made this technique easier to perform and affordable. The main indications for radiosurgery are inoperable cerebral vascular malformations, vestibular and other cranial schwannomas, skull base meningiomas, deep seated gliomas and cerebral metastases. More recently, the development of fraccionated stereotactic radiotherapy increased the spectrum of indications to bigger lesions and to those adjacent to critical nervous structures. We present our initial experience in the treatment of 31 patients. An adequate control of the neoplastic lesions was obtained and the adequate time of observation is still needed to evaluate the results in arteriovenous malformations.

Adolescent↗
PubMed1992

Proficiency of the Tradescantia-micronucleus image analysis system for scoring micronucleus frequencies and data analysis.

The Tradescantia-micronucleus (Trad-MCN) bioassay is an efficient short-term test for genotoxicity of pollutants. In order to increase the efficiency and to standardize the micronucleus (MCN) scoring process, an automated scoring system was developed using the principle of image analysis in computer science. This assemblage is called the Tradescantia-micronucleus image analysis (Trad-MCNIA) system. The MCN frequencies scored by this system were compared with those scored by human observation for its proficiency. A set of low MCN frequency (around 5 MCN/100 tetrads) slides prepared from a control group, a set of medium MCN frequency (around 20 MCN/100 tetrads) slides prepared from sodium azide treated plant cuttings and a set of high MCN frequency (around 50 MCN/100 tetrads) slides prepared from X-ray treated materials were used for this study. In the low MCN frequency slides, the Trad-MCNIA system scored about the same value as human observation. In the medium and high frequency slides, MCN frequencies scored by the system were lower than those scored by human observers. This discrepancy was corrected by increasing the power of the objective of the microscope in the system. The MCN frequencies scored by the system attained 90% congruity with those scored by human observers after the correction. The scoring speed of the system was about 3.5 times as fast as that by human observers, and the data could be statistically analyzed immediately after the data scores were recorded. Further improvements can be made by upgrading the video camera and the computer speed.

Azides↗
PubMed2006

Combining results of microarray experiments: a rank aggregation approach.

As technology for microarray analysis becomes widespread, it is becoming increasingly important to be able to compare and combine the results of experiments that explore the same scientific question. In this article, we present a rank-aggregation approach for combining results from several microarray studies. The motivation for this approach is twofold; first, the final results of microarray studies are typically expressed as lists of genes, rank-ordered by a measure of the strength of evidence that they are functionally involved in the disease process, and second, using the information on this rank-ordered metric means that we do not have to concern ourselves with data on the actual expression levels, which may not be comparable across experiments. Our approach draws on methods for combining top-k lists from the computer science literature on meta-search. The meta-search problem shares several important features with that of combining microarray experiments, including the fact that there are typically few lists with many elements and the elements may not be common to all lists. We implement two meta-search algorithms, which use a Markov chain framework to convert pairwise preferences between list elements into a stationary distribution that represents an aggregate ranking (Dwork et al, 2001). We explore the behavior of the algorithms in hypothetical examples and a simulated dataset and compare their performance with that of an algorithm based on the order-statistics model of Thurstone (Thurstone, 1927). We apply all three algorithms to aggregate the results of five microarray studies of prostate cancer.

Algorithms↗
PubMed2002

Clinical data retrieval: 25 years of temporal query management at the University of Vienna Medical School.

OBJECTIVES: Today, many clinical information systems include analysis components which allow clinicians to apply a selection of predefined statistical functions that satisfy typical cases. They are mostly to inflexible to handle complex, non-standard problems, however. The focus of this paper, therefore, is to present an approach that enables clinicians to autonomously create ad hoc queries including temporal relations in an interactive environment. METHODS: We developed the query language AMAS, which was specifically customized for users from the medical domain to flexibly retrieve and interpret temporal, clinical data. AMAS provides for a significant temporal expressiveness in data retrieval using time-stamped clinical databases and relies on an operator-operand concept for the specification of a query. RESULTS: Within the last 25 years, four different clinical retrieval systems have been implemented at the Department of Medical Computer Sciences, based on the AMAS query language. Currently, these systems allow access to the medical records of more than 2 million patients. Physicians of 46 different departments at the University of Vienna and Graz Medical Schools have made extensive use of these systems in the course of clinical research and patient care, executing more than 10,000 queries per year. CONCLUSIONS: We discuss a list of 20 issues that represent the most essential lessons we have learned in the development of the four systems mentioned above. Amongst others, our experiences indicate that the operator-operand concept allows on intuitive specification of complex, temporal queries. Further, customization to different user classes, based on their statistical background, is essential.

Austria↗
PubMed1993

VISTAnet: interactive real-time calculation and display of 3-dimensional radiation dose: an application of gigabit networking.

Three-dimensional treatment planning can allow the clinician to create plans that are highly individualized for each patient. However, in lifting the constraints traditionally imposed by 2-dimensional planning, the clinician is faced with the need to compare a much larger number of plans. Although methods to automate that process are being developed, it is not yet clear how well they will perform. VISTAnet is a 3 year collaborative effort between the Departments of Radiation Oncology and Computer Science at the University of North Carolina, the North Carolina Supercomputing Center, BellSouth, and GTE with the medical goal of providing real-time 3-dimensional radiation dose calculation and display. With VISTAnet technology and resources, the user can inspect 3-dimensional treatment plans in real-time along with the associated dose volume histograms and can fine tune these plans in real-time with regard to beam position, weighting, wedging, and shape. Thus VISTAnet provides an alternate and, possibly, complementary approach to computerized searches for optimal radiation treatment plans. Building this system has required the development of very fast radiation dose code, methods for simultaneously manipulating and modifying multiple radiation beams, and new visualizations of 3-dimensional dose distributions.

Computer Communication Networks↗
PubMed1992

High-performance computing, high-speed networks, and configurable computing environments: progress toward fully distributed computing.

The next several years will see the maturing of a collection of technologies that will enable fully and transparently distributed computing environments. Networks will be used to configure independent computing, storage, and I/O elements into "virtual systems" that are optimal for solving a particular problem. This environment will make the most powerful computing systems those that are logically assembled from network-based components and will also make those systems available to a widespread audience. Anticipating that the necessary technology and communications infrastructure will be available in the next 3 to 5 years, we are developing and demonstrating prototype applications that test and exercise the currently available elements of this configurable environment. The Lawrence Berkeley Laboratory (LBL) Information and Computing Sciences and Research Medicine Divisions have collaborated with the Pittsburgh Supercomputer Center to demonstrate one distributed application that illuminates the issues and potential of using networks to configure virtual systems. This application allows the interactive visualization of large three-dimensional (3D) scalar fields (voxel data sets) by using a network-based configuration of heterogeneous supercomputers and workstations. The specific test case is visualization of 3D magnetic resonance imaging (MRI) data. The virtual system architecture consists of a Connection Machine-2 (CM-2) that performs surface reconstruction from the voxel data, a Cray Y-MP that renders the resulting geometric data into an image, and a workstation that provides the display of the image and the user interface for specifying the parameters for the geometry generation and 3D viewing. These three elements are configured into a virtual system by using several different network technologies. This paper reviews the current status of the software, hardware, and communications technologies that are needed to enable this configurable environment. These interdependent technologies include: (1) user interface and application program construction methodologies, (2) the interprocess communication (IPC) mechanisms used to connect the software modules of the application, (3) the network protocols and interface hardware used by the IPC for communicating between modules running on separate and independent computing system elements, (4) the telecommunications infrastructure that provides the low-level data transfer functions for the networks that connect the geographically distributed elements used by the application, and (5) the nature of the functional elements that will be connected to form virtual systems.

Computer Communication Networks↗
PubMed2001

Case study: how to apply data mining techniques in a healthcare data warehouse.

Healthcare provider organizations are faced with a rising number of financial pressures. Both administrators and physicians need help analyzing large numbers of clinical and financial data when making decisions. To assist them, Rush-Presbyterian-St. Luke's Medical Center and Hitachi America, Ltd. (HAL), Inc., have partnered to build an enterprise data warehouse and perform a series of case study analyses. This article focuses on one analysis, which was performed by a team of physicians and computer science researchers, using a commercially available on-line analytical processing (OLAP) tool in conjunction with proprietary data mining techniques developed by HAL researchers. The initial objective of the analysis was to discover how to use data mining techniques to make business decisions that can influence cost, revenue, and operational efficiency while maintaining a high level of care. Another objective was to understand how to apply these techniques appropriately and to find a repeatable method for analyzing data and finding business insights. The process used to identify opportunities and effect changes is described.

Chicago↗
PubMed2025

CSGL: chemical synthesis graph learning for molecule representation.

MOTIVATION: Molecule representation learning (MRL) translates molecules into a real vector space, serving as input to downstream tasks in biology, chemistry, and computer science. This article introduces a chemical synthesis graph learning (CSGL) framework, which enhances MRL by considering both the atomic structures of molecules and their roles in chemical reactions through a hierarchical graph representation. Specifically, molecules are first modeled based on their molecular graphs, which capture atomic-level structural information. They are then further refined using a chemical synthesis graph, where nodes represent reactant and product molecule sets, and edges encode chemical transformations between reactants and products (e.g. changes in molecular structures). CSGL optimizes molecular embeddings of reactant and product nodes in a fashion that ensures the embeddings conform to a chemical balance constraint. RESULTS: Experimental results show that our method CSGL achieves strong performance on a variety of tasks, including product prediction, reaction classification, and molecular property prediction. AVAILABILITY AND IMPLEMENTATION: https://github.com/li-2023/CSGL.

Machine Learning↗
PubMedDate not supplied

Streamline predicates.

Predicates are functions that return Boolean values. They are an essential tool in computer science. A close look at flow feature definitions reveals that they can be seen as point predicates that tell if a specific feature exists at a certain point. Besides the information about features, scientists and engineers like to know the overall behavior of all streamlines in the flow, typically in the connection with the important features in their application domain. We call this a structure definition for the flow. A successful example for a structure definition is flow topology. In this paper, we present streamline predicates as functions that tell the user about the connection between streamlines and features selected by the user. This means answers to questions like: Which streamlines flow through a given vortex, separation bubble, or shock wave? It can be shown that streamline predicates may refine flow topology so that it also reveals questions about vortices in 3D.

Algorithms↗
PubMed2001

Automatic analysis of agarose gel images.

MOTIVATION: Automatic tools to speed up routine biological processes are very much sought after in bio-medical research. Much repetitive work in molecular biology, such as allele calling in genetic analysis, can be made semi-automatic or task specific automatic by using existing techniques from computer science and signal processing. Computerized analysis is reproducible and avoids various forms of human error. Semi-automatic techniques with an interactive check on the results speed up the analysis and reduce the error. RESULTS: We have successfully implemented an image processing software package to automatically analyze agarose gel images of polymorphic DNA markers. We have obtained up to 90% accuracy for the classification of alleles in good quality images and up to 70% accuracy in average quality images. These results are obtained within a few seconds. Even after subsequent interactive checking to increase the accuracy of allele classification to 100%, the overall speed with which the data can be processed is greatly increased, compared to manual allele classification. AVAILABILITY: The IDL source code of the software is available on request from jonathan.flint@well.ox.ac.uk

Animals↗
PubMedDate not supplied

Bioinformatics and genomic medicine.

Bioinformatics is a rapidly emerging field of biomedical research. A flood of large-scale genomic and postgenomic data means that many of the challenges in biomedical research are now challenges in computational science. Clinical informatics has long developed methodologies to improve biomedical research and clinical care by integrating experimental and clinical information systems. The informatics revolution in both bioinformatics and clinical informatics will eventually change the current practice of medicine, including diagnostics, therapeutics, and prognostics. Postgenome informatics, powered by high-throughput technologies and genomic-scale databases, is likely to transform our biomedical understanding forever, in much the same way that biochemistry did a generation ago. This paper describes how these technologies will impact biomedical research and clinical care, emphasizing recent advances in biochip-based functional genomics and proteomics. Basic data preprocessing with normalization and filtering, primary pattern analysis, and machine-learning algorithms are discussed. Use of integrative biochip informatics technologies, including multivariate data projection, gene-metabolic pathway mapping, automated biomolecular annotation, text mining of factual and literature databases, and the integrated management of biomolecular databases, are also discussed.

Computational Biology↗
PubMed1992

A physician's workstation designed for NASA and earth-based applications.

One of the prime missions for NASA is the safety and care of astronauts. In addressing this challenge, a tool has been developed which has great potential for earth-based applications. The multimedia physician's workstation is the result of 13 years of planning and technical revolution in the field of computer science. Today, we have the hardware and the software to make a major change in the office-based practice of physicians. By offering the online features of a medical library as well as a complete multimedia medical record system, we are now in a position to introduce advance decision support technology that can be used on a daily basis for routine outpatient care. The system supports a new platform for patient education and offers the doctor an opportunity to share his expertise with his patient and their family. Although NASA will need several more years before this technology can be applied to a remote space environment, we plan to introduce this system into the doctor's office as an initial test of its feasibility. The basic design and general specifications of this multimedia workstation/office system are described and illustrated as they currently exist.

Aerospace Medicine↗
PubMed1995

Computerized breast cancer diagnosis and prognosis from fine-needle aspirates.

OBJECTIVE: To use digital image analysis and machine learning to (1) improve breast mass diagnosis based on fine-needle aspirates and (2) improve breast cancer prognostic estimations. DESIGN: An interactive computer system evaluates, diagnoses, and determines prognosis based on cytologic features derived from a digital scan of fine-needle aspirate slides. SETTING: The University of Wisconsin (Madison) Departments of Computer Science and Surgery and the University of Wisconsin Hospital and Clinics. PATIENTS: Five hundred sixty-nine consecutive patients (212 with cancer and 357 with benign masses) provided the data for the diagnostic algorithm, and an additional 118 (31 with malignant masses and 87 with benign masses) consecutive, new patients tested the algorithm. One hundred ninety of these patients with invasive cancer and without distant metastases were used for prognosis. INTERVENTIONS: Surgical biopsy specimens were taken from all cancers and some benign masses. The remaining cytologically benign masses were followed up for a year and surgical biopsy specimens were taken if they changed in size or character. Patients with cancer received standard treatment. OUTCOME MEASURES: Cross validation was used to project the accuracy of the diagnostic algorithm and to determine the importance of prognostic features. In addition, the mean errors were calculated between the actual times of distant disease occurrence and the times predicted using various prognostic features. Statistical analyses were also done. RESULTS: The predicted diagnostic accuracy was 97% and the actual diagnostic accuracy on 118 new samples was 100%. Tumor size and lymph node status were weak prognosticators compared with nuclear features, in particular those measuring nuclear size. Compared with the actual time for recurrence, the mean error of predicted times for recurrence with the nuclear features was 17.9 months and was 20.1 months with tumor size and lymph node status (P = .11). CONCLUSION: Computer technology will improve breast fine-needle aspirate accuracy and prognostic estimations.

Biopsy, Needle↗
PubMed2001

[New knowledge derived from measurement of gene expression with the DNA microarray method].

BACKGROUND: The cDNA microarray method offers the first possibility of obtaining a global understanding of biological processes in living organisms, by simultaneous read-outs of tens of thousands of mRNAs. Initial experiments suggest that genes with similar function have similar expression patterns. MATERIAL AND METHODS: Understanding this level of biological complexity will, however, require completely new approaches to data analysis. Computer science methods, such as data mining and knowledge discovery, can synthesize interpretable if-then rules that model the relation between gene expressions and functions and use the rules to classify unknown genes. The huge body of existing biological and medical knowledge makes it necessary to develop methods for extracting knowledge from such repositories. RESULTS: Models of relations between gene expressions and gene functions in a data set from a publicly available source are synthesized semiautomatically and applied to classify unknown genes. Encouraging results have been achieved. The method is applied in the analysis of data from our microarray system which has recently become operational. INTERPRETATION: The principles are of general importance and will be used to evaluate a wide range of complex data sets like decision support in clinical medicine, for situations in which physicians need to handle a large volume of data for each patient.

Computational Biology↗
PubMed2002

Gene expression profiling by DNA microarrays and its application to dental research.

UNLABELLED: DNA microarray technology has been used for genome-wide gene expression studies that incorporate molecular genetics and computer science skills on massive levels. The technology permits the simultaneous analysis of tens of thousands of genes for the purposes of gene discovery, disease diagnosis. improved drug development, and therapeutics tailored to specific disease processes. OBJECTIVE: In this review, the two most common microarray technologies and their potential application to dental research will be discussed. The authors review current articles pertaining to the technologies and analysis of mRNA expression using DNA micro-arrays and its application to dental research. Since many genes contribute to normal functioning, research efforts are moving from the search for a disease specific gene to the understanding of the biochemical and molecular functioning of a variety of genes and how complicated networks of interaction can lead to a disease state, such as oral cancer. With the incorporation of DNA micro-array based research, we can look forward to more accurate diagnosis and surgical treatment/drug-delivery therapy based on an individual patient's genetic profile.

Carcinoma, Squamous Cell↗
PubMed1995

Information, intelligence, and interface: the pillars of a successful medical information system.

This paper addresses three key issues facing developers of clinical and/or research medical information systems. 1. INFORMATION. The basic function of every database is to store information about the phenomenon under investigation. There are many ways to organize information in a computer; however only a few will prove optimal for any real life situation. Computer Science theory has developed several approaches to database structure, with relational theory leading in popularity among end users [8]. Strict conformance to the rules of relational database design rewards the user with consistent data and flexible access to that data. A properly defined database structure minimizes redundancy i.e.,multiple storage of the same information. Redundancy introduces problems when updating a database, since the repeated value has to be updated in all locations--missing even a single value corrupts the whole database, and incorrect reports are produced [8]. To avoid such problems, relational theory offers a formal mechanism for determining the number and content of data files. These files not only preserve the conceptual schema of the application domain, but allow a virtually unlimited number of reports to be efficiently generated. 2. INTELLIGENCE. Flexible access enables the user to harvest additional value from collected data. This value is usually gained via reports defined at the time of database design. Although these reports are indispensable, with proper tools more information can be extracted from the database. For example, machine learning, a sub-discipline of artificial intelligence, has been successfully used to extract knowledge from databases of varying size by uncovering a correlation among fields and records[1-6, 9]. This knowledge, represented in the form of decision trees, production rules, and probabilistic networks, clearly adds a flavor of intelligence to the data collection and manipulation system. 3. INTERFACE. Despite the obvious importance of collecting data and extracting knowledge, current systems often impede these processes. Problems stem from the lack of user friendliness and functionality. To overcome these problems, several features of a successful human-computer interface have been identified [7], including the following "golden" rules of dialog design [7]: consistency, use of shortcuts for frequent users, informative feedback, organized sequence of actions, simple error handling, easy reversal of actions, user-oriented focus of control, and reduced short-term memory load. To this list of rules, we added visual representation of both data and query results, since our experience has demonstrated that users react much more positively to visual rather than textual information. In our design of the Orthopaedic Trauma Registry--under development at the Carolinas Medical Center--we have made every effort to follow the above rules. The results were rewarding--the end users actually not only want to use the product, but also to participate in its development.

Artificial Intelligence↗
PubMed2006

Adaptive properties of living beings: proposal for a generic mechanism. (Self-programming machines III).

Living systems are capable to have appropriate responses to unpredictable environment. This kind of self-organization seems to operate as a self-programming machine, i.e. an organization able to modify itself. Until now the models of self-organization of living beings proposed are functions solutions of differential systems or transition functions of automata. These functions are fixed and these models are therefore unable to modify their organization. On the other hand, computer science propose a lot of models having the properties of adaptive systems of living beings, but all these models depend on the comparison between a goal and the results and ingenious choices of parameters by programmers, whereas there are no programmer's intention nor choice in the living systems. From two best known examples of adaptive systems of living beings, nervous system and immune system that have in common that the external signals modify the rewriting of their organization and therefore work as self-organizing machines, we devised machines with a finite set of inputs, based upon a recurrence, are able to rewrite their organization (Self-programming machines or m(sp)) whenever external conditions vary and have striking properties of adaptation. M(sp) have similar properties whatever the operation defining the recurrence maybe. These results bring us to make the following statement: adaptive properties of living systems can be explained by their ability to rewrite their organization whenever external conditions vary under the only assumption that the rewriting mechanism be a deterministic constant recurrence in a finite state set.

Artificial Intelligence↗