Genetic Expression Level Prediction Based on Extended Fuzzy Petri Nets

2017 ◽  
Vol 31 (10) ◽  
pp. 1750036 ◽  
Author(s):  
Xiaozhong Li ◽  
Yong Li ◽  
Ying Liu ◽  
Long Wang
Keyword(s):  
Petri Nets ◽  
Dna Sequence ◽  
Petri Net ◽  
Expression Level ◽  
Biological Research ◽  
Colored Petri Net ◽  
Typical Experiment ◽  
Fuzzy Petri Net ◽  
Fuzzy Petri Nets ◽  
Gene Regulatory

With the advances in technique for high throughput data gathering such as microarrays, DNA sequencing machines and continuous development of human genome project, the traditional physical and chemical methods have been more difficult to meet the requests of time consuming and results accuracy. Exploring and understanding the causal relationship of complex gene regulatory networks and transforming the massive data of large-scale biological research to useful biological knowledge are the present challenge. As a result, there are two typical applications both the confidence value prediction of DNA sequence and influence degree prediction of gene expression which have become the hot issues in our daily life. In this paper, two extended fuzzy Petri nets approaches are proposed, based on the existing fuzzy Petri net model, to model and analyze for the hot issues respectively. One is the fuzzy colored Petri net, which combines fuzzy Petri net with colored Petri net to model fuzzy rule-based reasoning and determine confidence values for bases called in DNA sequence. The other is extended fuzzy Petri net, which integrates reverse reasoning into fuzzy Petri net and is proposed to model gene regulatory network. It can predict the change in expression level of target based on the input expression level of activator/repressor. Compared with the method of fuzzy Petri net, the two extended fuzzy Petri nets models perform more accurately in the following typical experiment reasoning outcomes and show that the proposed methods are feasible and available.

scholarly journals An Intelligent Algorithm for Decision Making System and Control of the GEMMA Guide Paradigm Using the Fuzzy Petri Nets Approach

Electronics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 489
Author(s):  
Oz Yakrangi ◽  
Roque J. Saltarén Pazmiño ◽  
Juan S. Cely ◽  
Alejandro Rodríguez ◽  
Cecilia E. García Cena ◽  
...  
Keyword(s):  
Petri Nets ◽  
Petri Net ◽  
Production Systems ◽  
Proper Solution ◽  
Fuzzy Petri Net ◽  
Decision Making System ◽  
Fuzzy Petri Nets ◽  
Fuzzy Logic Approach ◽  
Logic Approach ◽  
And Control

The aim of this article is to present the fuzzy Petri net algorithm and its implementation on the Guide d’etude des modes de marche et d’arrêt (GEMMA) guide paradigm. Additionally, this article presents a brief description of the GEMMA guide paradigm, the fuzzy logic approach, the Petri nets theory, and fuzzy Petri nets. Each algorithm is intended for a specific set of transitions, depending on their essential conditions. All these algorithms generate intelligent and safe control of the GEMMA guide paradigm in order to have the best control system for the machine. Moreover, the algorithms are able to make the best decision automatically depending on the machine’s situation and condition, something that allows the machine to be placed in the appropriate mode for each situation. The results show that the different fuzzy Petri net algorithms were working properly for the GEMMA guide paradigm and provided a proper solution for the automation of production systems.

Some Possibilities of Modeling Colored Petri Nets

2021 ◽  
pp. 77-91
Author(s):  
Goharik Petrosyan ◽  
Armen Gaboutchian ◽  
Vladimir Knyaz
Keyword(s):  
Petri Nets ◽  
Petri Net ◽  
Optimal Allocation ◽  
Production Systems ◽  
Oriented Graph ◽  
Discrete Systems ◽  
Colored Petri Nets ◽  
Venn Diagram ◽  
Colored Petri Net ◽  
Language Class

Petri nets are a mathematical apparatus for modelling dynamic discrete systems. Their feature is the ability to display parallelism, asynchrony and hierarchy. First was described by Karl Petri in 1962 [1,2,8]. The Petri net is a bipartite oriented graph consisting of two types of vertices - positions and transitions connected by arcs between each other; vertices of the same type cannot be directly connected. Positions can be placed by tags (markers) that can move around the network. [2] Petri Nets (PN) used for modelling real systems is sometimes referred to as Condition/Events nets. Places identify the conditions of the parts of the system (working, idling, queuing, and failing), and transitions describe the passage from one state to another (end of a task, failure, repair...). An event occurs (a transition fire) when all the conditions are satisfied (input places are marked) and give concession to the event. The occurrence of the event entirely or partially modifies the status of the conditions (marking). The number of tokens in a place can be used to identify the number of resources lying in the condition denoted by that place [1,2,8]. Coloured Petri nets (CPN) is a graphical oriented language for design, specification, simulation and verification of systems [3-6,9,15]. It is in particular well-suited for systems that consist of several processes which communicate and synchronize. Typical examples of application areas are communication protocols, distributed systems, automated production systems, workflow analysis and VLSI chips. In the Classical Petri Net, tokens do not differ; we can say that they are colourless. Unlike standard Petri nets in Colored Petri Net of a position can contain tokens of arbitrary complexity, such as lists, etc., that enables modelling to be more reliable. The article is devoted to the study of the possibilities of modelling Colored Petri nets. The article discusses the interrelation of languages of the Colored Petri nets and traditional formal languages. The Venn diagram, which the author has modified, shows the relationship between the languages of the Colored Petri nets and some traditional languages. The language class of the Colored Petri nets includes a whole class of Context-free languages and some other classes. The paper shows modelling the task synchronization Patil using Colored Petri net, which can't be modeled using well- known operations P and V or by classical Petri network, since the operations P and V and classical Petri networks have limited mathematical properties which do not allow to model the mechanisms in which the process should be synchronized with the optimal allocation of resources.

scholarly journals Modeling of critical systems implementing negative events using dual Petri nets

2018 ◽  
Vol 226 ◽  
pp. 04001 ◽  
Author(s):  
Marina A. Ganzhur ◽  
Aleksei P. Ganzhur ◽  
Olga V. Smirnova
Keyword(s):  
Fuzzy Logic ◽  
Data Analysis ◽  
Expert Systems ◽  
Petri Nets ◽  
Petri Net ◽  
Negative Events ◽  
Linguistic Variables ◽  
Critical Systems ◽  
Fuzzy Petri Net ◽  
Fuzzy Nets

This work is devoted to solving the problem of modeling critical systems based on the use of modified Petri nets. The dual (binary) Petri net one of the modifications, which allows us to view inversing events at the same time, solving the problem with the possibility of deadlocks. Construction of schemes using fuzzy logic makes it possible to calculate the values of linguistic variables obtained knowledge. Petri dual network allows you to organize the exclusion of negative events by introducing additional links. In accordance with the rules, it is possible to construct a dual fuzzy Petri net, which involves the use of maximum and minimum transitions or appropriate logical calculations of conjunctions and disjunctions. Transition from classical Petri nets to dual fuzzy nets, realizes fuzzy knowledge of logical deriving that gives the chance in construction of expert systems with fuzzy logic solving a problem of data analysis.

scholarly journals A New Approach for Modelling Gene Regulatory Networks Using Fuzzy Petri Nets

2010 ◽  
Vol 7 (1) ◽  
pp. 1-16 ◽  
Author(s):  
Raed I. Hamed ◽  
S. I. Ahson ◽  
R. Parveen
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Fuzzy Model ◽  
Fuzzy Reasoning ◽  
Search Space ◽  
Expression Level ◽  
Regulatory Relationship ◽  
Computer Scientists ◽  
Fuzzy Petri Nets ◽  
Gene Regulatory

SummaryGene Regulatory Networks are models of genes and gene interactions at the expression level. The advent of microarray technology has challenged computer scientists to develop better algorithms for modeling the underlying regulatory relationship in between the genes. Fuzzy system has an ability to search microarray datasets for activator/repressor regulatory relationship. In this paper, we present a fuzzy reasoning model based on the Fuzzy Petri Net. The model considers the regulatory triplets by means of predicting changes in expression level of the target based on input expression level. This method eliminates possible false predictions from the classical fuzzy model thereby allowing a wider search space for inferring regulatory relationship. Through formalization of fuzzy reasoning, we propose an approach to construct a rule-based reasoning system. The experimental results show the proposed approach is feasible and acceptable to predict changes in expression level of the target gene.

Protocol Design of Inkjet Printing System Based on Petri Nets

2011 ◽  
Vol 268-270 ◽  
pp. 1968-1973
Author(s):  
Ye Li Li ◽  
Biao Guo ◽  
Li Kun Lu
Keyword(s):  
Petri Nets ◽  
Petri Net ◽  
Inkjet Printing ◽  
Communication Protocol ◽  
Protocol Design ◽  
Colored Petri Net ◽  
Cpn Tools ◽  
Printing System ◽  
Data Bus

This paper defined a kind of communication protocol between the RIP card and the printhead circuit for the inkjet printing system. Protocol project was chosen in the protocol design, for which Petri net was used. After defining the message, the protocol model was established based on colored Petri net with inhibitor arcs. The model has priority and allow different message to transmit on the same data bus subsequently. Though analyzing and simulating in CPN Tools, the model was proved to be able to realize the function.

Compositional colored Petri net approach to multiscale modeling for systems biology

2014 ◽  
Vol 05 (04) ◽  
pp. 1450017 ◽  
Author(s):  
Fei Liu ◽  
Ming Yang
Keyword(s):  
Systems Biology ◽  
Petri Nets ◽  
Multiscale Modeling ◽  
Petri Net ◽  
Multiscale Model ◽  
Hierarchical Organization ◽  
Colored Petri Nets ◽  
Colored Petri Net ◽  
Multiscale Models ◽  
Multiscale Systems

Colored Petri nets have been demonstrated as a powerful tool for modeling multiscale systems biology. However, the construction of colored Petri nets for biological systems requires prior knowledge about colored Petri nets and is often error-prone and cumbersome for biologists, especially when the communication between components and hierarchical organization of components in a multiscale model are an issue. To address this problem, an established way is to develop small components and then compose them into bigger models. In this paper, we present a compositional colored Petri net approach to aid automatic modeling of systems biology, and demonstrate it with two case studies. We focus on the modeling of communication between components and hierarchical organization of components as they are key to build multiscale models.

Research of Power Communication Network System’s Reliability Based on Cloud Model and Fuzzy Petri Nets

2014 ◽  
Vol 635-637 ◽  
pp. 1140-1146
Author(s):  
Hong Zhang Zhao ◽  
Zhan Jun Hao ◽  
Fen Fang Li
Keyword(s):  
Petri Net ◽  
System Reliability ◽  
Communication Systems ◽  
Evaluation Method ◽  
Cloud Model ◽  
The Other ◽  
Fuzzy Petri Net ◽  
Complex Power ◽  
Fuzzy Petri Nets ◽  
Simulation Results

For the varied circumstances in the evaluation of complex power communication systems, this paper proposes a reliable evaluation method based on normal cloud model and fuzzy Petri net. The simulation results show that the model in this paper can effectively evaluate the system reliability when compared with the other models for the same factor.

scholarly journals Representing Conversations for Scalable Overhearing

2006 ◽  
Vol 25 ◽  
pp. 349-387 ◽  
Author(s):  
G. Gutnik ◽  
G. A. Kaminka
Keyword(s):  
Petri Nets ◽  
Petri Net ◽  
Academic Community ◽  
Important Task ◽  
Colored Petri Nets ◽  
Colored Petri Net ◽  
Multi Agent Systems ◽  
Agent Systems ◽  
Interesting Approach ◽  
Multi Agent

Open distributed multi-agent systems are gaining interest in the academic community and in industry. In such open settings, agents are often coordinated using standardized agent conversation protocols. The representation of such protocols (for analysis, validation, monitoring, etc) is an important aspect of multi-agent applications. Recently, Petri nets have been shown to be an interesting approach to such representation, and radically different approaches using Petri nets have been proposed. However, their relative strengths and weaknesses have not been examined. Moreover, their scalability and suitability for different tasks have not been addressed. This paper addresses both these challenges. First, we analyze existing Petri net representations in terms of their scalability and appropriateness for overhearing, an important task in monitoring open multi-agent systems. Then, building on the insights gained, we introduce a novel representation using Colored Petri nets that explicitly represent legal joint conversation states and messages. This representation approach offers significant improvements in scalability and is particularly suitable for overhearing. Furthermore, we show that this new representation offers a comprehensive coverage of all conversation features of FIPA conversation standards. We also present a procedure for transforming AUML conversation protocol diagrams (a standard human-readable representation), to our Colored Petri net representation.

scholarly journals Robustness Optimization of FMS Under Production Plan Variations: Preliminary Results

1998 ◽  
Author(s):  
Kazuhiro Saitou ◽  
Helge Qvam
Keyword(s):  
Petri Nets ◽  
Petri Net ◽  
Flexible Manufacturing ◽  
Manufacturing Systems ◽  
Production Costs ◽  
Production Plan ◽  
Colored Petri Net ◽  
Multiple Production ◽  
Optimal Resource ◽  
Robustness Optimization

Abstract A method for robustness optimization of flexible manufacturing systems is presented which undergoes forecasted product plan variations. A configuration of an FMS is modeled by a colored Petri net and the associated transition firing sequence. The robustness optimization of the colored Petri net model is formulated as an multi-objective optimization problem which minimizes production costs under multiple production plans, and reconfiguration cost due to production plan changes. As a first attempt, machines with limited flexibility are considered, and a genetic algorithm, coupled with a simple FIFO dispatching rule, is used to simultaneously find an semi-optimal resource allocation and event-driven schedule of a colored Petri net. The resulting Petri nets are then compared with the Petri nets optimized for a particular production plan in order to address the effectiveness of the robustness optimization for simultaneous production of products with different similarities. The simulation results suggest that the robustness optimization should be considered when the products are moderately different in their manufacturing processes.

Sign in / Sign up

Export Citation Format

Share Document