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Faster sequential genetic linkage computations.

Linkage analysis using maximum-likelihood estimation is a powerful tool for locating genes. As available data sets have grown, the computation required for analysis has grown exponentially and become a significant impediment. Others have previously shown that parallel computation is applicable to linkage analysis and can yield order-of-magnitude improvements in speed. In this paper, we demonstrate that algorithmic modifications can also yield order-of-magnitude improvements, and sometimes much more. Using the software package LINKAGE, we describe a variety of algorithmic improvements that we have implemented, demonstrating both how these techniques are applied and their power. Experiments show that these improvements speed up the programs by an order of magnitude, on problems of moderate and large size. All improvements were made only in the combinatorial part of the code, without restoring to parallel computers. These improvements synthesize biological principles with computer science techniques, to effectively restructure the time-consuming computations in genetic linkage analysis.

Algorithms↗

[Program for the development and storing of images].

This procedure has been carried out on the bases of the most updated computer science technologies. This program aims at making use of the computer both as a storing and date processor instrument and as an examination aid with a visual result. Promed Phlebology makes it possible to carry out the test starting straight from the patients medical filing card. The storing system has been simplified at most, all the obliged steps being eliminated. The user will be able to choose the file according to his own needs, as well as avoid the intermediate steps by creating practical and synthetic files. This procedure allows enclosing of data to patient related images (photographs, instrumental text, X-rays, intraoperatory images, etc.), directly drawn by any video source (camera or still video camera). With this way, it is possible to use data storing to practical and statistical goals and to look quickly through the file.

Humans↗

Computational tools for the modern andrologist.

With such a wide array of computational tools to solve inference problems, andrologists and their mathematical or statistical collaborators face perhaps bewildering choices. It is tempting to criticize a method with which one is unfamiliar for its apparent complexity. Yet, many methods are quite elegant; neural computation uses nature's own best biological classifier, for example, and genetic algorithms apply rules of natural selection. Computer scientists will likely find no one single best inference engine to solve all classification problems. Rather, the modeler should choose the most appropriate computational tool based on the specific nature of a problem. If the problem can be separated into obvious components, a Markov chain may be useful. If the andrologist would like to encode a well-known clinical algorithm into the computer, the programmer may use an expert system. Once a modeler builds an inference engine, that engine is not truly useful until other andrologists use it to make inferences with their own data. Because a wide variety of computer hardware and software exists, it is a significant endeavor to translate, or "port," software designed and built on one machine to many other different computers. Fortunately, the World Wide Web offers a means by which computational tools may be made directly available to multiple users on many different systems, or "platforms." The World Wide Web refers to a standardization of information traffic on the global computer network, the Internet. The Internet is simply the linkage of many computers worldwide by computer operators who have chosen to allow other users access to their systems. Because many different types of computers exist, until recently only communication in very rudimentary form, such as text, or between select compatible machines, was available. Within the last half-decade, computer scientists and operators began to use standard means of communication between computers. Interpreters of these standard languages, such as Mosaic and Netscape, are now widely available, and they allow the casual user to access the most sophisticated multimedia aspects of computer information on a variety of different systems. Andrologists may thus use the World Wide Web to make inference engines that they have programmed available to other clinicians and researchers. For example, we programmed a World Wide Web interface to the neural networks that we trained in order to solve a number of andrology classification problems. Interested users connect to our address (at this writing http:@godot.urol.uic.edu), and they may fill out electronic forms with their own patient data, press a "predict" button, and nearly immediately view the results of our neural networks' prediction on their own computers. With the explosion in computer hardware technology, mathematics and computer science that once seemed esoteric can now be investigated on computers available to nearly all andrologists. Rapid advances in computer network technology now render a tool developed by one andrologist immediately available to many. Clearly, andrologists may expect that computational investigations in their field will be a productive ground in the near and far future.

Algorithms↗

Recombination, rationality, reductionism and romantic reactions: culture, computers, and the genetic algorithm.

The genetic algorithm (GA) is a computational procedure that 'evolves' solutions to optimization problems by generating populations of possible solutions, and then by treating these solutions metaphorically as individuals that can 'mate' and 'compete' to 'survive' and 'reproduce'. In this paper, I explore how culturally specific notions of evolution, population, reproduction, sex/gender, and kinship inflect the ways GAs are assembled and understood. Combining the results of fieldwork among GA workers with analysis of GA texts, I contend that the picture of 'nature' embedded in GAs is resonant with the values of secularized Judeo-Christian white middle-class US-American and European heterosexual culture. I also maintain that GA formulations are accented by languages inherited from sociobiology. I argue that examining GAs can help us track how dominant meanings of 'nature' are being stabilized and refigured in an age in which exchanges of metaphor between biology and computer science are increasingly common.

Algorithms↗

Entropy-based analysis of the number partitioning problem.

In this paper we apply the multicanonical method of statistical physics on the number partitioning problem (NPP). This problem is a basic NP-hard problem from computer science, and can be formulated as a spin-glass problem. We compute the spectral degeneracy, which gives us information about the number of solutions for a given cost E and cardinality difference m. We also study an extension of this problem for Q partitions. We show that a fundamental difference on the spectral degeneracy of the generalized (Q>2) NPP exists, which could explain why it is so difficult to find good solutions for this case.

Journal Article↗

John von Neumann: the founding father of artificial life.

Aside from being known for his contributions to mathematics and physics, John von Neumann is considered one of the founding fathers of computer science and engineering. Not only did he do pioneering work on sequential computing systems, but he also carried out a major investigation of parallel architectures, leading to his work on cellular automata. His exceptional vision and daring, borrowing from biology the concept of genomic information even before the discovery of DNA's double helix, led him to propose the concept of self-reproducing automata.

Artificial Intelligence↗

Computers and occupational therapy.

The benefits and applications of computer science for occupational therapy are explored and a basic, functional description of the computer and computer programming is presented. Potential problems and advantages of computer utilization are compared and examples of existing computer systems in health fields are cited. Methods for successfully introducing computers are discussed.

Computers↗

An overview of neural networks.

Some of the world's leading researchers in neural networks submitted their most recent results concerning their research in neural networks to the author for inclusion in this survey. Descriptive accounts of their collective papers are presented as well as a list of sources of information concerning neural networks, such as journals, books, and technical reports. The material is broken into categories related to established areas in computer science, robotics, neural modeling, and engineering.

Algorithms↗

A vision of hand surgery over the next 25 years.

Predictions for hand surgery advances over the first 25 years of the new millennium are made. Anticipated changes are categorized as societal, technologic, and research with clinical applications. Certainly advances in computer science and molecular biology will affect all aspects of our lives. Within hand surgery, tissue engineering, materials science, and nanotechnology offer great promise.

Computers↗

A primer on aspects of cognition for medical informatics.

As a multidisciplinary field, medical informatics draws on a range of disciplines, such as computer science, information science, and the social and cognitive sciences. The cognitive sciences can provide important insights into the nature of the processes involved in human- computer interaction and help improve the design of medical information systems by providing insight into the roles that knowledge, memory, and strategies play in a variety of cognitive activities. In this paper, the authors survey literature on aspects of medical cognition and provide a set of claims that they consider to be important in medical informatics.

Cognition↗

Interactive computer technology, behavioral science, and family practice.

In this paper we discuss conceptual and practical uses for interactive computer applications (ICAs) for family practice, with an emphasis on implications for patient self-management, physician-patient relationships, primary care research, and health care systems quality improvement. We discuss recent behavioral science advances in patient self-management and the advantages and potential limitations of ICAs for medicine. We describe the benefits and risks of using ICAs for providing information, coping-skills training, and social support for patients and for improving the consistency and quality of care given by physicians. There are currently many effective ICAs, and they will play a central role in future health care. There is also the risk of inappropriate use of ICAs. We provide a summary of the empirical literature examining the use of ICAs to aid patients and providers in behavioral change and guidelines adherence efforts. We advise those people researching and applying ICAs in health care to be bold in what they attempt, but cautious in what they claim. Rigorous scientific evaluation and standardized reporting criteria can help quicken this advance, and there are important policy and ethical issues to consider. We conclude with a list of issues for family practices to consider when selecting and using ICAs.

Ambulatory Care Information Systems↗

Computer-based learning materials for medical education: a model production.

Computer-based learning materials (CBL or courseware) have the potential to be valuable learning resources for medical education. However, CBL has failed to realize its potential primarily because of unstructured approaches towards design and development. This paper describes the courseware development model (CDM), a conceptual model produced and used by the Medical Education Unit at The University of Liverpool. The model describes a structured multi-disciplinary approach to the design and production of CBL materials. It promotes meticulous planning, communication and organization. The CDM draws on three areas of expertise: (1) education; (2) computer science; and (3) medical content.

Computer Systems↗

Dissemination of computer skills among physicians: the infectious process model.

While the potential utility of computer technology to medicine is often acknowledged, little is known as to the best methods to actually teach physicians about computers. The current variability in physician computer fluency implies there is no accepted minimum required level of computer skills for physicians. Special techniques are needed to instill these skills in the physician and measure their effects within the medical profession. This hypothesis is suggested following the development of a specialized course for the new physician. In a population of physicians where medical computing usage was considered nonexistent, intense interest developed the following exposure to a role model having strong credentials in both medicine and computer science. This produced an atmosphere where there was a perceived benefit in being knowledgeable about the medical computer usage. The subsequent increase in computer systems use was the result of the availability of resources and development of computer skills that could be exchanged among the students and faculty. This growth in computer use is described using the parameters of an infectious process model. While other approaches may also be useful, the infectious process model permits the growth of medical computer usage to be quantitatively described, evaluates specific determinants of use patterns, and allows the future growth of computer utilization in medicine to be predicted.

Computers↗

A versatile mobile clinical microcomputer system.

A microcomputer system is described that has been incorporated into a custom-designed cart for mobility throughout a clinical setting with consequent increased utilization and cost-effectiveness. A library of clinical profiles has been developed that processes and consolidates quantitative clinical data into a bar-graph format for more convenient interpretation and documentation. It is suggested that even a small hospital can acquire a mobile computer system and hire a senior or graduate student in the physical or computer sciences, on a part-time basis, from a neighboring university or technical college, to develop clinical computer software suitable for that particular institution.

Computers↗

An efficient approximation algorithm for finding a maximum clique using Hopfield network learning.

In this article, we present a solution to the maximum clique problem using a gradient-ascent learning algorithm of the Hopfield neural network. This method provides a near-optimum parallel algorithm for finding a maximum clique. To do this, we use the Hopfield neural network to generate a near-maximum clique and then modify weights in a gradient-ascent direction to allow the network to escape from the state of near-maximum clique to maximum clique or better. The proposed parallel algorithm is tested on two types of random graphs and some benchmark graphs from the Center for Discrete Mathematics and Theoretical Computer Science (DIMACS). The simulation results show that the proposed learning algorithm can find good solutions in reasonable computation time.

Algorithms↗

[New horizons in medicine. Chaos and its laws].

We have synthesized the fundamentals that modern technology offers in all areas of research, especially in the field of biomedicine. The theory of systems, cybernetics, synergetics, boolean algebra, communication science (according to modern laws of signal transmission and translation), the solution of non-linear equations by computer science, applied principles of reduction in biological survey, fractal analysis as a representation of dynamic, chaotic, non-linear systems, defined attractors as conditioning elements of biologic function, are just a few of the many instruments that modern science offers as a revolutionary approach to research programming. Borrowing the laws of mathematics, we have defined the fundamental characteristics of linear and non-linear homeostatic systems along with the concept of predictable behavior of a system as a function of its complex structure. Lastly, we have documented, based on personal research and recent findings in biomathematics, and despite current and strong opposition, how the functional death of any dynamic system is identified by the system's absolute state of equilibrium. The operative errors at times caused by different stimuli acting on specific organs and apparatus, are interpreted not as an index of altered function but as an expression of a chaotic response of the deterministic type and therefore an indication of the system's adaptability to the specific functional requirements in that precise moment.

Mathematics↗

Representing clinical guidelines in GLIF: individual and collaborative expertise.

OBJECTIVE: An evaluation of the cognitive processes used in the translation of a clinical guideline from text into an encoded form so that it can be shared among medical institutions. DESIGN: A comparative study at three sites regarding the generation of individual and collaborative representations of a guideline for the management of encephalopathy using the GuideLine Interchange Format (GLIF) developed by members of the InterMed Collaboratory. MEASUREMENTS: Using theories and methods of cognitive science, the study involves a detailed analysis of the cognitive processes used in generating representations in GLIF. The resulting process-outcome measures are used to compare subjects with various types of computer science or clinical expertise and from different institutions. RESULTS: Consistent with prior studies of text comprehension and expertise, the variability in strategies was found to be dependent on the degree of prior experience and knowledge of the domain. Differing both in content and structure, the representations developed by physicians were found to have additional information and organization not explicitly stated in the guidelines, reflecting the physicians' understanding of the underlying pathophysiology. The computer scientists developed more literal representations of the guidelines; addition were mostly limited to specifications mandated by the logic of GLIF itself. Collaboration between physicians and computer scientists resulted in consistent representations that were more than the sum of the separate parts, in that both domain-specific knowledge of medicine and generic knowledge of guideline structure were seamlessly integrated. CONCLUSION: Because of the variable construction of guideline representations, understanding the processes and limitations involved in their generation is important in developing strategies to construct shared representations that are both accurate and efficient. The encoded guidelines developed by teams that include both clinicians and experts in computer-based representations are preferable to those developed by individuals of either type working alone.

Brain Diseases↗