The growth of filamentous microorganisms is contributed by tip extension and branching. In order to describe the microscopic process, many models have been considered in the literature. Motivated by these models, we introduce a model of a Parallel Communicating (PC) Grammar System, discuss the branching structures and developmental sequences of microorganisms using this system. Further we compare this PC Grammar System with Apical Growth Pure Context free grammars and subapical deterministic bracketed L-systems.
{"title":"Apical Growth Filamentous and Branching PC Grammar Systems","authors":"J. D. Emerald","doi":"10.1109/BIC-TA.2011.66","DOIUrl":"https://doi.org/10.1109/BIC-TA.2011.66","url":null,"abstract":"The growth of filamentous microorganisms is contributed by tip extension and branching. In order to describe the microscopic process, many models have been considered in the literature. Motivated by these models, we introduce a model of a Parallel Communicating (PC) Grammar System, discuss the branching structures and developmental sequences of microorganisms using this system. Further we compare this PC Grammar System with Apical Growth Pure Context free grammars and subapical deterministic bracketed L-systems.","PeriodicalId":211822,"journal":{"name":"2011 Sixth International Conference on Bio-Inspired Computing: Theories and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132413517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Auto-Disturbance Rejection Controller (ADRC) has been proved to be a capable replacement of PID with unmistakable advantage in performance and practicality. But it is difficult to obtain a set of optimal parameters, for ADRC controller has too many parameters and has no deterministic rules to compute the parameters. In this paper, Objective function is constructed based on the control system performance indexes. Combined with experienced parameters of ADRC, an invasive weed optimization algorithm (IWO) is employed to obtain a set of key parameters. The simulation results show the validity of the IWO algorithm.
{"title":"Tuning of Auto-Disturbance Rejection Controller Based on the Invasive Weed Optimization","authors":"Zhihua Chen, Shuo Wang, Zhonghua Deng, Xuncai Zhang","doi":"10.1109/BIC-TA.2011.45","DOIUrl":"https://doi.org/10.1109/BIC-TA.2011.45","url":null,"abstract":"Auto-Disturbance Rejection Controller (ADRC) has been proved to be a capable replacement of PID with unmistakable advantage in performance and practicality. But it is difficult to obtain a set of optimal parameters, for ADRC controller has too many parameters and has no deterministic rules to compute the parameters. In this paper, Objective function is constructed based on the control system performance indexes. Combined with experienced parameters of ADRC, an invasive weed optimization algorithm (IWO) is employed to obtain a set of key parameters. The simulation results show the validity of the IWO algorithm.","PeriodicalId":211822,"journal":{"name":"2011 Sixth International Conference on Bio-Inspired Computing: Theories and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128221694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Common algorithmic problem is an optimization problem, which has the nice property that several other NP-complete problems can be reduced to it in linear time. A tissue P system with cell division is a computing model which has two basic characters: intercellular communication and the ability of cell division. The ability of cell division allows us to obtain an exponential amount of cells in linear time and to design cellular solutions to computationally hard problems in polynomial time. We here present an effective solution to the common algorithmic decision problem using a family of recognizer tissue P systems with cell division.
{"title":"A Uniform Solution to Common Algorithmic Problem by Tissue P Systems with Cell Division","authors":"Yunyun Niu, L. Pan, M. Pérez-Jiménez","doi":"10.1109/BIC-TA.2011.43","DOIUrl":"https://doi.org/10.1109/BIC-TA.2011.43","url":null,"abstract":"Common algorithmic problem is an optimization problem, which has the nice property that several other NP-complete problems can be reduced to it in linear time. A tissue P system with cell division is a computing model which has two basic characters: intercellular communication and the ability of cell division. The ability of cell division allows us to obtain an exponential amount of cells in linear time and to design cellular solutions to computationally hard problems in polynomial time. We here present an effective solution to the common algorithmic decision problem using a family of recognizer tissue P systems with cell division.","PeriodicalId":211822,"journal":{"name":"2011 Sixth International Conference on Bio-Inspired Computing: Theories and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132973403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In this paper we introduce a new graph generative device called hyper edge replacement graph P system. We consider the application of the hyper edge replacement graph rewriting rules in the regions of a parallel rewriting P system with a feature of conditional communication. We examine the generative power of this hyper edge replacement graph P system and obtain some fruitful results.
{"title":"Hyperedge Replacement Graph P System","authors":"M. Sankar, N. David, D. G. Thomas","doi":"10.1109/BIC-TA.2011.39","DOIUrl":"https://doi.org/10.1109/BIC-TA.2011.39","url":null,"abstract":"In this paper we introduce a new graph generative device called hyper edge replacement graph P system. We consider the application of the hyper edge replacement graph rewriting rules in the regions of a parallel rewriting P system with a feature of conditional communication. We examine the generative power of this hyper edge replacement graph P system and obtain some fruitful results.","PeriodicalId":211822,"journal":{"name":"2011 Sixth International Conference on Bio-Inspired Computing: Theories and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130452165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Asaju La'aro Bolaji, A. Khader, M. Al-Betar, M. Awadallah
The Artificial Bee Colony Algorithm (ABC) is an emerging nature-inspired, metaheuristic optimisation algorithm. In this paper, an improved ABC algorithm is proposed for tackling Curriculum-Based Course Timetabling Problem (CBCTT). The ABC as a population-based algorithm, the initial population is generated using Saturation Degree (SD) followed by Backtracking Algorithm (BA) to ensure that all the solutions in the population are feasible. The improvement loop in ABC used neighbourhood structures severally within the employed and onlooker bees operators in order to navigate the CB-CTT search space tightly. The performance of ABC is tested using dataset prepared by second international timetabling competition (ITC-2007), the ABC is able to achieved good quality results, yet these are not comparable with the best results obtained by other methods. Future work can be directed further improve the ABC operators to achieve a better results.
{"title":"An Improved Artificial Bee Colony for Course Timetabling","authors":"Asaju La'aro Bolaji, A. Khader, M. Al-Betar, M. Awadallah","doi":"10.1109/BIC-TA.2011.74","DOIUrl":"https://doi.org/10.1109/BIC-TA.2011.74","url":null,"abstract":"The Artificial Bee Colony Algorithm (ABC) is an emerging nature-inspired, metaheuristic optimisation algorithm. In this paper, an improved ABC algorithm is proposed for tackling Curriculum-Based Course Timetabling Problem (CBCTT). The ABC as a population-based algorithm, the initial population is generated using Saturation Degree (SD) followed by Backtracking Algorithm (BA) to ensure that all the solutions in the population are feasible. The improvement loop in ABC used neighbourhood structures severally within the employed and onlooker bees operators in order to navigate the CB-CTT search space tightly. The performance of ABC is tested using dataset prepared by second international timetabling competition (ITC-2007), the ABC is able to achieved good quality results, yet these are not comparable with the best results obtained by other methods. Future work can be directed further improve the ABC operators to achieve a better results.","PeriodicalId":211822,"journal":{"name":"2011 Sixth International Conference on Bio-Inspired Computing: Theories and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115956189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Binding-Blocking Automata is an automaton model that is inspired by peptide computing. This is a finite state automaton together with the facility to postpone the reading of some symbols to a later part of time by blocking of symbols. In this paper, we study some of the properties of binding-blocking automaton using a measure called blocking quotient and show that any Binding-Blocking Automata can accept only languages where the length grows in a linear fashion. This is the first attempt to study the properties of binding-blocking automata and we feel that this will lead us to investigate further into the properties of this automaton model.
{"title":"Properties of Binding-Blocking Automata: A Study","authors":"M. Balan","doi":"10.1109/BIC-TA.2011.73","DOIUrl":"https://doi.org/10.1109/BIC-TA.2011.73","url":null,"abstract":"Binding-Blocking Automata is an automaton model that is inspired by peptide computing. This is a finite state automaton together with the facility to postpone the reading of some symbols to a later part of time by blocking of symbols. In this paper, we study some of the properties of binding-blocking automaton using a measure called blocking quotient and show that any Binding-Blocking Automata can accept only languages where the length grows in a linear fashion. This is the first attempt to study the properties of binding-blocking automata and we feel that this will lead us to investigate further into the properties of this automaton model.","PeriodicalId":211822,"journal":{"name":"2011 Sixth International Conference on Bio-Inspired Computing: Theories and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131112980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jinbang Xu, A. Shen, Cheng Yang, Wenpei Rao, Xuan Yang
In photovoltaic (PV) generation systems, to get the maximum of the solar output power is the essential part to raise the efficiency of the whole system. A new Artificial Neural Network (ANN) based algorithm for Maximum Power Point Tracking (MPPT) has been proposed in this work. By using the duty ratio data generated from the finest results of the traditional Incremental Conductance (IncCond) method as the neural network training data, and building the DC-DC boost tracker to test it in Saber simulation software, the simulation results are shown to clarity the effectiveness of the proposed method.
{"title":"ANN Based on IncCond Algorithm for MPP Tracker","authors":"Jinbang Xu, A. Shen, Cheng Yang, Wenpei Rao, Xuan Yang","doi":"10.1109/BIC-TA.2011.16","DOIUrl":"https://doi.org/10.1109/BIC-TA.2011.16","url":null,"abstract":"In photovoltaic (PV) generation systems, to get the maximum of the solar output power is the essential part to raise the efficiency of the whole system. A new Artificial Neural Network (ANN) based algorithm for Maximum Power Point Tracking (MPPT) has been proposed in this work. By using the duty ratio data generated from the finest results of the traditional Incremental Conductance (IncCond) method as the neural network training data, and building the DC-DC boost tracker to test it in Saber simulation software, the simulation results are shown to clarity the effectiveness of the proposed method.","PeriodicalId":211822,"journal":{"name":"2011 Sixth International Conference on Bio-Inspired Computing: Theories and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126932709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Hirabayashi, A. Nishikawa, Fumiaki Tanaka, M. Hagiya, H. Kojima, K. Oiwa
Unbreakable encryption is theoretically possible but perfect operation is difficult. It is expected that DNA-based cryptography provides new solutions to realize a perfect secrecy system. For example, the self-assembly process in DNA logical computation can generate physical random numbers for encryption keys. Furthermore DNA-based steganography offers a unique method to keep the key and the cipher in safe. In this paper we describe a theoretical background on perfect secrecy based on Shannon entropy and present an empirical analysis on effectiveness of a DNA-based cryptosystem using a DNA motif called "triple crossover tile." In DNA computation, troublesome procedures to read out the calculation results prevent the realization of practical applications. To solve this problem, we already presented the idea of a direct readout method called "tile sequencing" with atomic force microscopy image analysis. "Tile sequencing" makes it possible to extract random calculation results, which is difficult to read out by existing methods. Here we discuss the appropriate application of the DNA cryptosystem taking advantage of "tile sequencing." Although there are still problems to be solved, the separation storage of specific information, such as medical records, and personal data using personal identifiers encrypted by DNA cryptography will be one of promising applications.
{"title":"Analysis on Secure and Effective Applications of a DNA-Based Cryptosystem","authors":"M. Hirabayashi, A. Nishikawa, Fumiaki Tanaka, M. Hagiya, H. Kojima, K. Oiwa","doi":"10.1109/BIC-TA.2011.29","DOIUrl":"https://doi.org/10.1109/BIC-TA.2011.29","url":null,"abstract":"Unbreakable encryption is theoretically possible but perfect operation is difficult. It is expected that DNA-based cryptography provides new solutions to realize a perfect secrecy system. For example, the self-assembly process in DNA logical computation can generate physical random numbers for encryption keys. Furthermore DNA-based steganography offers a unique method to keep the key and the cipher in safe. In this paper we describe a theoretical background on perfect secrecy based on Shannon entropy and present an empirical analysis on effectiveness of a DNA-based cryptosystem using a DNA motif called \"triple crossover tile.\" In DNA computation, troublesome procedures to read out the calculation results prevent the realization of practical applications. To solve this problem, we already presented the idea of a direct readout method called \"tile sequencing\" with atomic force microscopy image analysis. \"Tile sequencing\" makes it possible to extract random calculation results, which is difficult to read out by existing methods. Here we discuss the appropriate application of the DNA cryptosystem taking advantage of \"tile sequencing.\" Although there are still problems to be solved, the separation storage of specific information, such as medical records, and personal data using personal identifiers encrypted by DNA cryptography will be one of promising applications.","PeriodicalId":211822,"journal":{"name":"2011 Sixth International Conference on Bio-Inspired Computing: Theories and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121586082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In this paper, we define $theta$-bordered factor of a word, the concept of $theta$-valence of a bordered factor and $theta$-sub word complexity of a word. We study some properties of involutively $theta$-bordered factors of a word. This study can be applied in DNA computation as it gives information on the number of sites in a DNA strand that can bind with each other affecting subsequent computations.
{"title":"Bordered Factors of a Finite Word","authors":"V. Dare, C. Darshini","doi":"10.1109/BIC-TA.2011.22","DOIUrl":"https://doi.org/10.1109/BIC-TA.2011.22","url":null,"abstract":"In this paper, we define $theta$-bordered factor of a word, the concept of $theta$-valence of a bordered factor and $theta$-sub word complexity of a word. We study some properties of involutively $theta$-bordered factors of a word. This study can be applied in DNA computation as it gives information on the number of sites in a DNA strand that can bind with each other affecting subsequent computations.","PeriodicalId":211822,"journal":{"name":"2011 Sixth International Conference on Bio-Inspired Computing: Theories and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116634144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Protein-protein interactions (PPIs) play a key role in many cellular processes. These interactions form the basis of phenomena such as DNA replication and transcription, metabolic pathway, signaling pathway, and cell cycle control. Knowing how proteins interact with each other can help the biological scientist understand the molecular mechanism of the cell. Unfortunately, the experimental methods of identifying PPIs are both time-consuming and expensive. Therefore, developing computational approaches for predicting PPIs would be of significant value. Here, we propose a novel method for predicting the PPI using distance frequency of amino acids grouped with their physicochemical properties (hydrophobicity, normalized van der Waals volume, polarity and polarizability) and PCA. First, the 20 basic amino acids were divided into three groups according to the four kinds of physicochemical property values. Second, the distance frequency feature extraction method was introduced to represent the protein pairs, and also fused the feature vectors extracted with four physicochemical properties to form different feature vector sets. Third, the PCA method was used to reduce the vector dimension, and support vector machine was adopted as the classifier. The overall success rate of our method for hydrophobicity, normalized van der Waals volume, polarity and polarizability are 89.88%, 89.72%, 89.28% and 89.24% in 10CV test, which are 6.65%, 8.05%, 9.72% and 8.09% higher than that of Guo's auto-covariance function feature extraction method respectively. The total predicting accuracy of fusing the four physicochemical properties arrives at 91.79%. The results show that the current approach is very promising for predicting PPI, and may become a useful tool in the relevant areas.
{"title":"Prediction of Protein-Protein Interaction Using Distance Frequency of Amino Acids Grouped with their Physicochemical Properties","authors":"Shaowu Zhang, Yong-mei Cheng, Li Luo, Q. Pan","doi":"10.1109/BIC-TA.2011.53","DOIUrl":"https://doi.org/10.1109/BIC-TA.2011.53","url":null,"abstract":"Protein-protein interactions (PPIs) play a key role in many cellular processes. These interactions form the basis of phenomena such as DNA replication and transcription, metabolic pathway, signaling pathway, and cell cycle control. Knowing how proteins interact with each other can help the biological scientist understand the molecular mechanism of the cell. Unfortunately, the experimental methods of identifying PPIs are both time-consuming and expensive. Therefore, developing computational approaches for predicting PPIs would be of significant value. Here, we propose a novel method for predicting the PPI using distance frequency of amino acids grouped with their physicochemical properties (hydrophobicity, normalized van der Waals volume, polarity and polarizability) and PCA. First, the 20 basic amino acids were divided into three groups according to the four kinds of physicochemical property values. Second, the distance frequency feature extraction method was introduced to represent the protein pairs, and also fused the feature vectors extracted with four physicochemical properties to form different feature vector sets. Third, the PCA method was used to reduce the vector dimension, and support vector machine was adopted as the classifier. The overall success rate of our method for hydrophobicity, normalized van der Waals volume, polarity and polarizability are 89.88%, 89.72%, 89.28% and 89.24% in 10CV test, which are 6.65%, 8.05%, 9.72% and 8.09% higher than that of Guo's auto-covariance function feature extraction method respectively. The total predicting accuracy of fusing the four physicochemical properties arrives at 91.79%. The results show that the current approach is very promising for predicting PPI, and may become a useful tool in the relevant areas.","PeriodicalId":211822,"journal":{"name":"2011 Sixth International Conference on Bio-Inspired Computing: Theories and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114940787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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