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Trends in modeling Biomedical Complex Systems.
In this paper we provide an introduction to the techniques for multi-scale complex biological systems, from the single bio-molecule to the cell, combining theoretical modeling, experiments, informatics tools and technologies suitable for biological and biomedical research, which are becoming increasingly multidisciplinary, multidimensional and information-driven. The most important concepts on mathematical modeling methodologies and statistical inference, bioinformatics and standards tools to investigate complex biomedical systems are discussed and the prominent literature useful to both the practitioner and the theoretician are presented.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are
Trends in modeling Biomedical Complex Systems
In this paper we provide an introduction to the techniques for multi-scale complex biological systems, from the single bio-molecule to the cell, combining theoretical modeling, experiments, informatics tools and technologies suitable for biological and biomedical research, which are becoming increasingly multidisciplinary, multidimensional and information-driven. The most important concepts on mathematical modeling methodologies and statistical inference, bioinformatics and standards tools to investigate complex biomedical systems are discussed and the prominent literature useful to both the practitioner and the theoretician are presented
From time-series to complex networks: Application to the cerebrovascular flow patterns in atrial fibrillation
A network-based approach is presented to investigate the cerebrovascular flow
patterns during atrial fibrillation (AF) with respect to normal sinus rhythm
(NSR). AF, the most common cardiac arrhythmia with faster and irregular
beating, has been recently and independently associated with the increased risk
of dementia. However, the underlying hemodynamic mechanisms relating the two
pathologies remain mainly undetermined so far; thus the contribution of
modeling and refined statistical tools is valuable. Pressure and flow rate
temporal series in NSR and AF are here evaluated along representative cerebral
sites (from carotid arteries to capillary brain circulation), exploiting
reliable artificially built signals recently obtained from an in silico
approach. The complex network analysis evidences, in a synthetic and original
way, a dramatic signal variation towards the distal/capillary cerebral regions
during AF, which has no counterpart in NSR conditions. At the large artery
level, networks obtained from both AF and NSR hemodynamic signals exhibit
elongated and chained features, which are typical of pseudo-periodic series.
These aspects are almost completely lost towards the microcirculation during
AF, where the networks are topologically more circular and present random-like
characteristics. As a consequence, all the physiological phenomena at
microcerebral level ruled by periodicity - such as regular perfusion, mean
pressure per beat, and average nutrient supply at cellular level - can be
strongly compromised, since the AF hemodynamic signals assume irregular
behaviour and random-like features. Through a powerful approach which is
complementary to the classical statistical tools, the present findings further
strengthen the potential link between AF hemodynamic and cognitive decline.Comment: 12 pages, 10 figure
User-centered visual analysis using a hybrid reasoning architecture for intensive care units
One problem pertaining to Intensive Care Unit information systems is that, in some cases, a very dense display of data can result. To ensure the overview and readability of the increasing volumes of data, some special features are required (e.g., data prioritization, clustering, and selection mechanisms) with the application of analytical methods (e.g., temporal data abstraction, principal component analysis, and detection of events). This paper addresses the problem of improving the integration of the visual and analytical methods applied to medical monitoring systems. We present a knowledge- and machine learning-based approach to support the knowledge discovery process with appropriate analytical and visual methods. Its potential benefit to the development of user interfaces for intelligent monitors that can assist with the detection and explanation of new, potentially threatening medical events. The proposed hybrid reasoning architecture provides an interactive graphical user interface to adjust the parameters of the analytical methods based on the users' task at hand. The action sequences performed on the graphical user interface by the user are consolidated in a dynamic knowledge base with specific hybrid reasoning that integrates symbolic and connectionist approaches. These sequences of expert knowledge acquisition can be very efficient for making easier knowledge emergence during a similar experience and positively impact the monitoring of critical situations. The provided graphical user interface incorporating a user-centered visual analysis is exploited to facilitate the natural and effective representation of clinical information for patient care
Mapping the complexity of higher education in the developing world
This repository item contains a single issue of Issues in Brief, a series of policy briefs that began publishing in 2008 by the Boston University Frederick S. Pardee Center for the Study of the Longer-Range Future.On October 27 and 28, 2009, a workshop of experts on higher education in developing countries was convened by the Boston University Frederick S. Pardee Center for the Study of the Longer-Range Future. The meeting was supported by a grant from the National Academies Keck Futures Initiative with additional support from the Pardee Center and the Office of the Boston University Provost. The meeting brought together experts in economics, public policy, education, development, university management, and quantitative modeling who had rich experiences across the developing world. These experts offered a variety of conceptual tools with which to look at the particular complexities associated with higher education in developing countries. The meeting was convened by the authors of this paper. This policy brief builds upon and reflects on the discussion at this meeting, but is not a meeting report, per se
What's unusual in online disease outbreak news?
Background: Accurate and timely detection of public health events of
international concern is necessary to help support risk assessment and response
and save lives. Novel event-based methods that use the World Wide Web as a
signal source offer potential to extend health surveillance into areas where
traditional indicator networks are lacking. In this paper we address the issue
of systematically evaluating online health news to support automatic alerting
using daily disease-country counts text mined from real world data using
BioCaster. For 18 data sets produced by BioCaster, we compare 5 aberration
detection algorithms (EARS C2, C3, W2, F-statistic and EWMA) for performance
against expert moderated ProMED-mail postings. Results: We report sensitivity,
specificity, positive predictive value (PPV), negative predictive value (NPV),
mean alerts/100 days and F1, at 95% confidence interval (CI) for 287
ProMED-mail postings on 18 outbreaks across 14 countries over a 366 day period.
Results indicate that W2 had the best F1 with a slight benefit for day of week
effect over C2. In drill down analysis we indicate issues arising from the
granular choice of country-level modeling, sudden drops in reporting due to day
of week effects and reporting bias. Automatic alerting has been implemented in
BioCaster available from http://born.nii.ac.jp. Conclusions: Online health news
alerts have the potential to enhance manual analytical methods by increasing
throughput, timeliness and detection rates. Systematic evaluation of health
news aberrations is necessary to push forward our understanding of the complex
relationship between news report volumes and case numbers and to select the
best performing features and algorithms
SAFS: A Deep Feature Selection Approach for Precision Medicine
In this paper, we propose a new deep feature selection method based on deep
architecture. Our method uses stacked auto-encoders for feature representation
in higher-level abstraction. We developed and applied a novel feature learning
approach to a specific precision medicine problem, which focuses on assessing
and prioritizing risk factors for hypertension (HTN) in a vulnerable
demographic subgroup (African-American). Our approach is to use deep learning
to identify significant risk factors affecting left ventricular mass indexed to
body surface area (LVMI) as an indicator of heart damage risk. The results show
that our feature learning and representation approach leads to better results
in comparison with others
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