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[from wnpxrz] ScienceDirect - Cell : A Brief History of the Hypothesis
"Two terms used as frameworks for scientific experimentation—the “hypothesis” and the “model”—carry distinct philosophical assumptions, with important consequences for the practicing scientist."
[from wnpxrz] BioBayes: A software package for Bayesian inference in systems biology -- Vyshemirsky and Girolami 24 (17): 1933 -- Bioinformatics
"provides a framework for Bayesian parameter estimation and evidential model ranking over models of biochemical systems defined using ordinary differential equations"
[from wnpxrz] BMC Bioinformatics
Proceedings of the 10th Bio-Ontologies Special Interest Group Workshop 2007. Ten years past and looking to the future
[from wnpxrz] [0801.0849] Towards understanding the immune system
"e propose that fractional order differential equations are more suitable than the familiar integer order differential equations. A fractional order example of two immune effectors attacking an antigen is given."
[from wnpxrz] [0801.0847] On Modelling The Immune System as a Complex system
"Modelling complex systems is discussed. Cellular automata (CA) type models are successful but there are much less analytic results about CA than about other less successful models e.g. partial differential equations (PDE). A compromise is proposed"
[from wnpxrz] [q-bio/0504013] PCA and K-Means decipher genome
"In this paper, we aim to give a tutorial for undergraduate students studying statistical methods and/or bioinformatics."
[from wnpxrz] [0709.1167] Using RDF to Model the Structure and Process of Systems
"This article will provide an introduction to RDF/RDFS/OWL and an examination of its suitability to model discrete element complex systems."
[from wnpxrz] [0712.4290] Updating Probabilities: A Complex Agent Based Example
"In this paper we show a complex agent based example of inference with two different forms of information
[from wnpxrz] [0712.3900] Integrating heterogeneous knowledges for understanding biological behaviors: a probabilistic approach
Although current investigations successfully focus on qualitative behaviors of macromolecular networks, others approaches show partial quantitative informations like protein concentration variations over times. We consider that both informations, qualitat
Independently Extensible Solutions to the Expression Problem
Suppose we have a datatype which is defined by a set of cases and we have processors which operate on this datatype. • Extend datatype with variants, • Add new processors. How support both?
[from wnpxrz] Bayesian Ranking of Biochemical System Models.
"We investigate the variance of Bayes factor estimates, and highlight the stability of the Annealed Importance Sampling and the Annealing-Melting Integration methods for the purposes of comparing nonlinear models."
[from wnpxrz] Extracting protein regulatory networks with graphical models.
"postgenomic data. Along with the increasing amount of available data, a lot of novel statistical methods have been developed and proposed in the literature. This article gives a non-mathematical overview of three widely used reverse engineering methods,
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