Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “computer sciences”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,009 records · Page 56Linked to original sources
PubMed2004

Robust PCA and classification in biosciences.

MOTIVATION: Principal components analysis (PCA) is a very popular dimension reduction technique that is widely used as a first step in the analysis of high-dimensional microarray data. However, the classical approach that is based on the mean and the sample covariance matrix of the data is very sensitive to outliers. Also, classification methods based on this covariance matrix do not give good results in the presence of outlying measurements. RESULTS: First, we propose a robust PCA (ROBPCA) method for high-dimensional data. It combines projection-pursuit ideas with robust estimation of low-dimensional data. We also propose a diagnostic plot to display and classify the outliers. This ROBPCA method is applied to several bio-chemical datasets. In one example, we also apply a robust discriminant method on the scores obtained with ROBPCA. We show that this combination of robust methods leads to better classifications than classical PCA and quadratic discriminant analysis. AVAILABILITY: All the programs are part of the Matlab Toolbox for Robust Calibration, available at http://www.wis.kuleuven.ac.be/stat/robust.html.

Algorithms↗
PubMed2006

Accessing bioscience images from abstract sentences.

Images (e.g., figures) are important experimental results that are typically reported in bioscience full-text articles. Biologists need to access images to validate research facts and to formulate or to test novel research hypotheses. On the other hand, biologists live in an age of information explosion. As thousands of biomedical articles are published every day, systems that help biologists efficiently access images in literature would greatly facilitate biomedical research. We hypothesize that much of image content reported in a full-text article can be summarized by the sentences in the abstract of the article. In our study, more than one hundred biologists had tested this hypothesis and more than 40 biologists had evaluated a novel user-interface BioEx that allows biologists to access images directly from abstract sentences. Our results show that 87.8% biologists were in favor of BioEx over two other baseline user-interfaces. We further developed systems that explored hierarchical clustering algorithms to automatically identify abstract sentences that summarize the images. One of the systems achieves a precision of 100% that corresponds to a recall of 4.6%.

Abstracting and Indexing↗
PubMed2003

Molecular diagnostics of injury and repair responses in critical illness: what is the future of "monitoring" in the intensive care unit?

OBJECTIVE: To identify potential future means of monitoring injury and repair in critical illness. DESIGN: Review of the literature. RESULTS: Critically ill patients are monitored extensively and intensively by such means as hemodynamics, laboratory values, and radiologic studies. In general, however, the goal of monitoring has been to measure the degree of injury and to prevent further injury, rather than to measure repair. Measures of repair have been limited to phenotypic end points such as return of organ function, as measured by blood chemistry. In this article, I examine how it may be possible in the future to monitor the progress of repair using genomic and proteomic biomarkers. These types of monitors would enable clinicians to control the healing environment using real time, rapid biomarkers, and sophisticated techniques to target therapy to the patient's current inflammatory state, taking into account the genetic makeup of the patient and his or her likely response to a given drug. CONCLUSIONS: The rapidly evolving sciences of genomics, proteomics, computational biology, and complex system theory can be used a) to model critical illness; b) to model adaptive and maladaptive responses to critical illness; c) to tailor treatments to create an ideal inflammatory environment for repair and regeneration, taking into account the individual genetic contribution; and d) to monitor the progress of repair. The major obstacles to reaching these goals are technological, and experience suggests that they will be overcome.

Adaptation, Physiological↗
PubMed2002

Adaptation and survivors in a random Boolean network.

We introduce the competitive agent with imitation strategy in a random Boolean network, in which the agent plays a competitive game that rewards those in minority. After a long time interval, the worst performer changes its strategy to the one of the best and the process is repeated. The network, initially in a chaotic state, evolves to an intermittent state and finally reaches a frozen state. Time series of survived species (whose strategies are imitated by other agents) in the system depend on the connectivity of each agent. In a system with various connectivity groups, the low connectivity groups win the minority game over the high connectivity groups. We also compared the result with mutation strategy system.

Adaptation, Psychological↗
PubMed2004

Algorithmic mechanism design for load balancing in distributed systems.

Computational grids are promising next-generation computing platforms for large-scale problems in science and engineering. Grids are large-scale computing systems composed of geographically distributed resources (computers, storage etc.) owned by self interested agents or organizations. These agents may manipulate the resource allocation algorithm in their own benefit, and their selfish behavior may lead to severe performance degradation and poor efficiency. In this paper, we investigate the problem of designing protocols for resource allocation involving selfish agents. Solving this kind of problems is the object of mechanism design theory. Using this theory, we design a truthful mechanism for solving the static load balancing problem in heterogeneous distributed systems. We prove that using the optimal allocation algorithm the output function admits a truthful payment scheme satisfying voluntary participation. We derive a protocol that implements our mechanism and present experiments to show its effectiveness.

Journal Article↗
PubMed2004

Uses and abuses of mathematics in biology.

In the physical sciences, mathematical theory and experimental investigation have always marched together. Mathematics has been less intrusive in the life sciences, possibly because they have until recently been largely descriptive, lacking the invariance principles and fundamental natural constants of physics. Increasingly in recent decades, however, mathematics has become pervasive in biology, taking many different forms: statistics in experimental design; pattern seeking in bioinformatics; models in evolution, ecology, and epidemiology; and much else. I offer an opinionated overview of such uses--and abuses.

Allergy and Immunology↗
PubMed2005

A life science Semantic Web: are we there yet?

More than ever, life science researchers depend on information from multiple sources. The Semantic Web offers a powerful new strategy for consolidating both text and structured data into a comprehensive collections and views. In addition, these aggregates are readable by both humans and machines and could be the basis of information management and knowledge exchange.

Biological Science Disciplines↗
PubMed2007

Participatory design in health sciences: Using cooperative experimental methods in developing health services and computer technology.

Participatory design (PD) is a research approach to the development of technological solutions to real-world problems, an approach that shares many concerns and some of its roots with action research. In this article, the authors discuss their experience in conducting a PD research project intended to develop a technological and a related organizational intervention to support the treatment of foot ulcers for people with diabetes at home. They provide a historical overview of the PD approach and a description of how they used it in their research study. They describe their experience in conducting the research, including the participants' responses, the outcomes of the research, and the challenges confronted in bridging the practical and disciplinary issues that arose. In the conclusion, they propose that PD holds potential as a research approach that might effectively merge computer technology and health-related interventional research.

Biomedical Research↗
PubMed2006

Pilot using World Wide Web to prevent diabetes in adolescents.

This pilot study tested the effects of an interactive nutrition education Web site on fruit, vegetable, and fat consumption in minority adolescents genetically at risk for Type 2 diabetes. A one-group nonexperimental pretest, posttest focus group design was used. Twenty-one sixth-grade to eighth-grade junior high adolescents who were minorities volunteered to participate. Participants received 5 hours of Web-based nutrition education over 3 weeks. A significant difference in fat consumption was supported from the computerized dietary assessment. No difference was found in fruit or vegetable consumption. Comparative data indicated a rise in body mass index (BMI) percentile from 88.03 (1999) to 88.40 (2002; boys) and 88.25 (1999) to 91.2 (2002; girls). Focus group responses supported the satisfaction of adolescents in the study with the use of the Web-based intervention for nutrition education. Healthy eating interventions using Web-based nutrition education should be further investigated with adolescents.

Adolescent↗
PubMed2025

Algorithms and tools for data-driven omics integration to achieve multilayer biological insights: a narrative review.

Systems biology is a holistic approach to biological sciences that combines experimental and computational strategies, aimed at integrating information from different scales of biological processes to unravel pathophysiological mechanisms and behaviours. In this scenario, high-throughput technologies have been playing a major role in providing huge amounts of omics data, whose integration would offer unprecedented possibilities in gaining insights on diseases and identifying potential biomarkers. In the present review, we focus on strategies that have been applied in literature to integrate genomics, transcriptomics, proteomics, and metabolomics in the year range 2018-2024. Integration approaches were divided into three main categories: statistical-based approaches, multivariate methods, and machine learning/artificial intelligence techniques. Among them, statistical approaches (mainly based on correlation) were the ones with a slightly higher prevalence, followed by multivariate approaches, and machine learning techniques. Integrating multiple biological layers has shown great potential in uncovering molecular mechanisms, identifying putative biomarkers, and aid classification, most of the time resulting in better performances when compared to single omics analyses. However, significant challenges remain. The high-throughput nature of omics platforms introduces issues such as variable data quality, missing values, collinearity, and dimensionality. These challenges further increase when combining multiple omics datasets, as the complexity and heterogeneity of the data increase with integration. We report different strategies that have been found in literature to cope with these challenges, but some open issues still remain and should be addressed to disclose the full potential of omics integration.

Algorithms↗
PubMed1999

Visual simulations, artificial animals and virtual ecosystems.

This review is about a field that does not traditionally belong to biological sciences. A branch of computer animation has its mission to create active self-powered objects living artificial lives in the theoretical biology zone. Selected work, of particular interest to biologists, is presented here. These works include animated simulations of legged locomotion, flexible-bodied animals swimming and crawling, artificial fish in virtual ecosystems, automated learning of swimming and the evolution of virtual creatures with respect to morphology, locomotion and behaviour. The corresponding animations are available for downloading via the Internet. I hope that watching these intriguing pieces of visual simulation will stimulate digitally oriented biologists to seize the interactive methods made possible by ever-increasing computing power.

Animals↗
PubMed2003

Light tunneling in clouds.

Solar radiation, traveling outside cloud water droplets, excites sharp resonances and surface waves by tunneling into the droplets. This effect contributes substantially to the total absorption (typically, of the order of 20%) and yields the major contribution to backscattering, producing the meteorological glory. Usual computational practices in atmospheric science misrepresent resonance contributions and cannot be relied on in the assessment of possible anomalies in cloud absorption.

Journal Article↗