scholarly journals Rule-based modeling using wildcards

2017 ◽  
Author(s):  
Steven S. Andrews
Keyword(s):  
Reaction Network ◽  
Distinct Species ◽  
Unintended Consequences ◽  
Biological Molecules ◽  
Post Translational Modifications ◽  
Rule Based ◽  
New Approach ◽  
Signaling Systems ◽  
Formal Rule ◽  
Chain Lengths

SummaryMany biological molecules exist in multiple variants, such as proteins with different post-translational modifications, DNAs with different sequences, and phospholipids with different chain lengths. Representing these variants as distinct species, as most biochemical simulators do, leads to the problem that the number of species, and chemical reactions that interconvert them, typically increase combinatorially with the number of ways that the molecules can vary. This can be alleviated by “rule-based modeling methods,” in which software generates the chemical reaction network from relatively simple “rules.” This article presents a new approach to rule-based modeling. It is based on wildcards that match to species names, much as wildcards can match to file names in computer operating systems. It is much simpler to use than the formal rule-based modeling approaches developed previously but can also lead to unintended consequences if not used carefully. This article demonstrates rule-based modeling with wildcards through examples for: signaling systems, protein complexation, polymerization, nucleic acid sequence copying and mutation, the “SMILES” chemical notation, and others. The method is implemented in Smoldyn, a spatial and stochastic biochemical simulator, for both the generate-first and on-the-fly expansion, meaning whether the reaction network is generated before or during the simulation.

ACRIPPER: A New Associative Classification Based on RIPPER Algorithm

2021 ◽  
Vol 20 (01) ◽  
pp. 2150013
Author(s):  
Mohammed Abu-Arqoub ◽  
Wael Hadi ◽  
Abdelraouf Ishtaiwi
Keyword(s):  
Decision Making ◽  
Class Imbalance ◽  
The Other ◽  
Associative Classification ◽  
Rule Based ◽  
New Approach ◽  
New Novel ◽  
Accuracy Measure ◽  
High Level ◽  
Substantial Interest

Associative Classification (AC) classifiers are of substantial interest due to their ability to be utilised for mining vast sets of rules. However, researchers over the decades have shown that a large number of these mined rules are trivial, irrelevant, redundant, and sometimes harmful, as they can cause decision-making bias. Accordingly, in our paper, we address these challenges and propose a new novel AC approach based on the RIPPER algorithm, which we refer to as ACRIPPER. Our new approach combines the strength of the RIPPER algorithm with the classical AC method, in order to achieve: (1) a reduction in the number of rules being mined, especially those rules that are largely insignificant; (2) a high level of integration among the confidence and support of the rules on one hand and the class imbalance level in the prediction phase on the other hand. Our experimental results, using 20 different well-known datasets, reveal that the proposed ACRIPPER significantly outperforms the well-known rule-based algorithms RIPPER and J48. Moreover, ACRIPPER significantly outperforms the current AC-based algorithms CBA, CMAR, ECBA, FACA, and ACPRISM. Finally, ACRIPPER is found to achieve the best average and ranking on the accuracy measure.

scholarly journals A New Approach to Multiple Fault Diagnosis: A Combination of Diagnostic Matrices, Graphs, Algebraic and Rule-Based Models. The Case of Two-Layer Models

2008 ◽  
Vol 18 (4) ◽  
pp. 465-476 ◽  
Author(s):  
Antoni Ligęza ◽  
Jan Kościelny
Keyword(s):  
Fault Diagnosis ◽  
Simultaneous Occurrence ◽  
Diagnostic Model ◽  
Rule Based ◽  
New Approach ◽  
Multiple Fault ◽  
Multiple Faults ◽  
Model Based ◽  
Multiple Fault Diagnosis ◽  
System Variables

A New Approach to Multiple Fault Diagnosis: A Combination of Diagnostic Matrices, Graphs, Algebraic and Rule-Based Models. The Case of Two-Layer ModelsThe diagnosis of multiple faults is significantly more difficult than singular fault diagnosis. However, in realistic industrial systems the possibility of simultaneous occurrence of multiple faults must be taken into account. This paper investigates some of the limitations of the diagnostic model based on the simple binary diagnostic matrix in the case of multiple faults. Several possible interpretations of the diagnostic matrix with rule-based systems are provided and analyzed. A proposal of an extension of the basic, single-level model based on diagnostic matrices to a two-level one, founded on causal analysis and incorporating an OR and an AND matrix is put forward. An approach to the diagnosis of multiple faults based on inconsistency analysis is outlined, and a refinement procedure using a qualitative model of dependencies among system variables is sketched out.

Principles for Managing Information Security in the New Millennium

2011 ◽  
pp. 173-177 ◽  
Author(s):  
Gurpreet Dhillon
Keyword(s):  
Information Security ◽  
Rule Based ◽  
Formal Rule ◽  
Technical Systems ◽  
Pragmatic Aspects ◽  
New Millennium

This chapter sketches out three classes of principles. Following a brief description of the class, each principle is elaborated and suggestions made thereof as to its applicability. The three classes of principles are: Principles for managing the pragmatic aspects of an organization; Principles for managing the formal rule-based aspects of an organization; Principles for managing the technical systems

scholarly journals Chemical models of interstellar cyanomethanimine isomers

2020 ◽  
Vol 497 (1) ◽  
pp. 609-625
Author(s):  
Xia Zhang ◽  
Donghui Quan ◽  
Qiang Chang ◽  
Eric Herbst ◽  
Jarken Esimbek ◽  
...  
Keyword(s):  
Physical Environment ◽  
Reasonable Agreement ◽  
Reaction Network ◽  
Biological Molecules ◽  
Rotational Spectra ◽  
Chemical Models ◽  
Shock Models ◽  
Synthetic Routes ◽  
The Impact ◽  
Green Bank Telescope

ABSTRACT The E-isomer of cyanomethanimine (HNCHCN) was first identified in Sagittarius B2(N) (Sgr B2(N)) by a comparison of the publicly available Green Bank Telescope (GBT) PRIMOS survey with laboratory rotational spectra. Recently, Z-cyanomethanimine was detected in the quiescent molecular cloud G+0.693−0.027 with the IRAM 30-m telescope. Cyanomethanimine is a chemical intermediate in the proposed synthetic routes of adenine, and may play an important role in forming biological molecules in the interstellar medium. Here we present a new modelling study of cyanomethanimine, using the nautilus gas–grain reaction network and code with the addition of over 400 chemical reactions of the three cyanomethanimine isomers and related species. We apply cold isothermal core, hot core, and C-type shock models to simulate the complicated and heterogeneous physical environment in and in front of Sgr B2(N), and in G+0.693−0.027. We identify the major formation and destruction routes of cyanomethanimine, and find that the calculated abundances of the cyanomethanimine isomers and the ratio of Z-isomer to E-isomer are both in reasonable agreement with observations for selected environments. In particular, we conclude that these isomers are most likely formed within or near the hot core without the impact of shocks, or in the cold regions with shocks.

scholarly journals Analysis of the Networks Controlling the Antimicrobial-Peptide-Dependent Induction of Klebsiella pneumoniae Virulence Factors

2011 ◽  
Vol 79 (9) ◽  
pp. 3718-3732 ◽  
Author(s):  
Enrique Llobet ◽  
Miguel A. Campos ◽  
Paloma Giménez ◽  
David Moranta ◽  
José A. Bengoechea
Keyword(s):  
Klebsiella Pneumoniae ◽  
Defense Mechanisms ◽  
Lipid A ◽  
Multidrug Resistant ◽  
Cross Resistance ◽  
New Approach ◽  
Content Type ◽  
Signaling Systems ◽  
Transcriptional Changes ◽  
Initial Target

ABSTRACTAntimicrobial peptides (APs) impose a threat to the survival of pathogens, and it is reasonable to postulate that bacteria have developed strategies to counteract them. Polymyxins are becoming the last resort to treat infections caused by multidrug-resistant Gram-negative bacteria and, similar to APs, they interact with the anionic lipopolysaccharide. Given that polymyxins and APs share the initial target, it is possible that bacterial defense mechanisms against polymyxins will be also effective against host APs. We sought to determine whether exposure to polymyxin will increaseKlebsiella pneumoniaeresistance to host APs. Indeed, exposure ofK. pneumoniaeto polymyxin induces cross-resistance not only to polymyxin itself but also to APs present in the airways. Polymyxin treatment upregulates the expression of the capsule polysaccharide operon and the loci required to modify the lipid A with aminoarabinose and palmitate with a concomitant increase in capsule and lipid A species containing such modifications. Moreover, these surface changes contribute to APs resistance and also to polymyxin-induced cross-resistance to APs. Bacterial loads of lipid A mutants in trachea and lungs of intranasally infected mice were lower than those of wild-type strain. PhoPQ, PmrAB, and the Rcs system govern polymyxin-induced transcriptional changes, and there is a cross talk between PhoPQ and the Rcs system. Our findings support the notion thatKlebsiellaactivates a defense program against APs that is controlled by three signaling systems. Therapeutic strategies directed to prevent the activation of this program could be a new approach worth exploring to facilitate the clearance of the pathogen from the airways.

A new approach to modularity in rule-based programming

2002 ◽  
Author(s):  
J.C. Browne ◽  
A. Emerson ◽  
M.G. Gouda ◽  
D.P. Miranker ◽  
A. Mok ◽  
...  
Keyword(s):  
Rule Based ◽  
New Approach

Incorporation of a hydration layer in the `dummy atom'ab initiostructural modelling of biological macromolecules

2013 ◽  
Vol 46 (6) ◽  
pp. 1884-1888 ◽  
Author(s):  
Alexandros Koutsioubas ◽  
Javier Pérez
Keyword(s):  
Small Angle ◽  
Biological Molecules ◽  
Scattering Data ◽  
Biological Macromolecules ◽  
Hydration Layer ◽  
New Approach ◽  
The Past ◽  
Dummy Atom ◽  
Angle Scattering ◽  
Minimal Information

Ab initioalgorithms for the restoration of biomacromolecular structure from small-angle scattering data have gained popularity in the past 15 years. In particular, `dummy atom' models that require minimal information about the system under study have been proven capable of recovering the low-resolution shape of proteins and nucleic acids in many published works. However, consideration of solvated biological molecules as particles of uniform electron density contrast relative to the solvent neglects the presence of a hydration layer around their surface, leading to an overall apparent swelling of the obtained models and to a large overestimation of the volume of the particle. Here this problem is addressed by the introduction of an additional type of `dummy atom', representing the hydration layer. Successful applications of this new approach are illustrated for several proteins, and related results are compared with those from the programDAMMIN[Svergun (1999).Biophys. J.76, 2879–2886].

scholarly journals Stationary Equations for Non-Markovian Biochemical Systems

2018 ◽  
Author(s):  
Jiajun Zhang ◽  
Tianshou Zhou
Keyword(s):  
Master Equation ◽  
Stochastic Analysis ◽  
Waiting Times ◽  
Reaction Network ◽  
State Variables ◽  
New Approach ◽  
Reaction Systems ◽  
Linear Noise Approximation ◽  
Biochemical Systems ◽  
Markovian System

AbstractWe develop a new approach for stochastic analysis of biochemical reaction systems with arbitrary distributions of waiting times between reaction events. Specifically, we derive a stationary generalized chemical master equation for a non-Markovian reaction network. Importantly, this equation allows to transform the original non-Markovian problem into a Markovian one by introducing a mean reaction propensity function for every reaction in the network. Furthermore, we derive a stationary generalized linear noise approximation for the non-Markovian system, which is convenient to the direct estimation of the stationary noise in state variables. These derived equations can have broad applications, and exemplars of two representative non-Markovian models provide evidence of their applicability.

scholarly journals Graph-Based Generation of Referring Expressions

2003 ◽  
Vol 29 (1) ◽  
pp. 53-72 ◽  
Author(s):  
Emiel Krahmer ◽  
Sebastiaan van Erk ◽  
André Verleg
Keyword(s):  
Current Approach ◽  
Direct Access ◽  
Cost Functions ◽  
Search Process ◽  
Referring Expressions ◽  
Rule Based ◽  
New Approach ◽  
Content Selection ◽  
Combined Use ◽  
The Many

This article describes a new approach to the generation of referring expressions. We propose to formalize a scene (consisting of a set of objects with various properties and relations) as a labeled directed graph and describe content selection (which properties to include in a referring expression) as a subgraph construction problem. Cost functions are used to guide the search process and to give preference to some solutions over others. The current approach has four main advantages: (1) Graph structures have been studied extensively, and by moving to a graph perspective we get direct access to the many theories and algorithms for dealing with graphs; (2) many existing generation algorithms can be reformulated in terms of graphs, and this enhances comparison and integration of the various approaches; (3) the graph perspective allows us to solve a number of problems that have plagued earlier algorithms for the generation of referring expressions; and (4) the combined use of graphs and cost functions paves the way for an integration of rule-based generation techniques with more recent stochastic approaches.

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