BSML: A Binding Schema Markup Language for Data Interchange in Problem Solving Environments (PSEs)

We describe a binding schema markup language (BSML) for describing data interchange between scientific codes. Such a facility is an important constituent of scientific problem solving environments (PSEs). BSML is designed to integrate with a PSE or application composition system that views model specification and execution as a problem of managing semistructured data. The data interchange problem is addressed by three techniques for processing semistructured data: validation, binding, and conversion. We present BSML and describe its application to a PSE for wireless communications system design

Status and Future Perspectives for Lattice Gauge Theory Calculations to the Exascale and Beyond

In this and a set of companion whitepapers, the USQCD Collaboration lays out a program of science and computing for lattice gauge theory. These whitepapers describe how calculation using lattice QCD (and other gauge theories) can aid the interpretation of ongoing and upcoming experiments in particle and nuclear physics, as well as inspire new ones.Comment: 44 pages. 1 of USQCD whitepapers

Categorical Ontology of Complex Systems, Meta-Systems and Theory of Levels: The Emergence of Life, Human Consciousness and Society

Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quantum states emerging from complex quantum dynamics of interacting networks of biomolecules, such as proteins and nucleic acids that are now collectively defined as quantum interactomics. On the other hand, the time dependent evolution over several generations of cancer cells --that are generally known to undergo frequent and extensive genetic mutations and, indeed, suffer genomic transformations at the chromosome level (such as extensive chromosomal aberrations found in many colon cancers)-- cannot be correctly represented in the ‘standard’ terms of quantum automaton modules, as the normal somatic cells can. This significant difference at the cancer cell genomic level is therefore reflected in major changes in cancer cell interactomics often from one cancer cell ‘cycle’ to the next, and thus it requires substantial changes in the modeling strategies, mathematical tools and experimental designs aimed at understanding cancer mechanisms. Novel solutions to this important problem in carcinogenesis are proposed and experimental validation procedures are suggested. From a medical research and clinical standpoint, this approach has important consequences for addressing and preventing the development of cancer resistance to medical therapy in ongoing clinical trials involving stage III cancer patients, as well as improving the designs of future clinical trials for cancer treatments.\ud \ud \ud KEYWORDS: Emergence of Life and Human Consciousness;\ud Proteomics; Artificial Intelligence; Complex Systems Dynamics; Quantum Automata models and Quantum Interactomics; quantum-weave dynamic patterns underlying human consciousness; specific molecular processes underlying extensive memory, learning, anticipation mechanisms and human consciousness; emergence of human consciousness during the early brain development in children; Cancer cell ‘cycling’; interacting networks of proteins and nucleic acids; genetic mutations and chromosomal aberrations in cancers, such as colon cancer; development of cancer resistance to therapy; ongoing clinical trials involving stage III cancer patients’ possible improvements of the designs for future clinical trials and cancer treatments. \ud \u

Building a binary outranking relation in uncertain, imprecise and multi-experts contexts: The application of evidence theory

AbstractWe consider multicriteria decision problems where the actions are evaluated on a set of ordinal criteria. The evaluation of each alternative with respect to each criterion may be uncertain and/or imprecise and is provided by one or several experts. We model this evaluation as a basic belief assignment (BBA). In order to compare the different pairs of alternatives according to each criterion, the concept of first belief dominance is proposed. Additionally, criteria weights are also expressed by means of a BBA. A model inspired by ELECTRE I is developed and illustrated by a pedagogical example

A reverse engineering approach to the suppression of citation biases reveals universal properties of citation distributions

The large amount of information contained in bibliographic databases has recently boosted the use of citations, and other indicators based on citation numbers, as tools for the quantitative assessment of scientific research. Citations counts are often interpreted as proxies for the scientific influence of papers, journals, scholars, and institutions. However, a rigorous and scientifically grounded methodology for a correct use of citation counts is still missing. In particular, cross-disciplinary comparisons in terms of raw citation counts systematically favors scientific disciplines with higher citation and publication rates. Here we perform an exhaustive study of the citation patterns of millions of papers, and derive a simple transformation of citation counts able to suppress the disproportionate citation counts among scientific domains. We find that the transformation is well described by a power-law function, and that the parameter values of the transformation are typical features of each scientific discipline. Universal properties of citation patterns descend therefore from the fact that citation distributions for papers in a specific field are all part of the same family of univariate distributions.Comment: 9 pages, 6 figures. Supporting information files available at http://filrad.homelinux.or

A Constructivist View of Newton’s Mechanics

In the present essay we attempt to reconstruct Newtonian mechanics under the guidance of logical principles and of a constructive approach related to the genetic epistemology of Piaget and García (Psychogenesis and the history of science, Columbia University Press, New York, 1989). Instead of addressing Newton’s equations as a set of axioms, ultimately given by the revelation of a prodigious mind, we search for the fundamental knowledge, beliefs and provisional assumptions that can produce classical mechanics. We start by developing our main tool: the no arbitrariness principle, that we present in a form that is apt for a mathematical theory as classical mechanics. Subsequently, we introduce the presence of the observer, analysing then the relation objective–subjective and seeking objectivity going across subjectivity. We take special care of establishing the precedence among all contributions to mechanics, something that can be better appreciated by considering the consequences of removing them: (a) the consequence of renouncing logic and the laws of understanding is not being able to understand the world, (b) renouncing the early elaborations of primary concepts such as time and space leads to a dissociation between everyday life and physics, the latter becoming entirely pragmatic and justified a-posteriori (because it is convenient), (c) changing our temporary beliefs has no real cost other than effort. Finally, we exemplify the present approach by reconsidering the constancy of the velocity of light. It is shown that it is a result of Newtonian mechanics, rather than being in contradiction with it. We also indicate the hidden assumption that leads to the (apparent) contradiction.Fil: Solari, Hernan Gustavo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; ArgentinaFil: Natiello, Mario Alberto. Lund University; Sueci