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Bio-Inspired Metaheuristic Optimization Algorithms for Biomarker Identification in Mass Spectrometry Analysis 质谱分析中生物标志物鉴定的启发式优化算法
Int. J. Nat. Comput. Res. Pub Date : 2012-04-01 DOI: 10.4018/jncr.2012040104
Syarifah Adilah Mohamed Yusoff, Ibrahim Venkat, U. K. Yusof, R. Abdullah
{"title":"Bio-Inspired Metaheuristic Optimization Algorithms for Biomarker Identification in Mass Spectrometry Analysis","authors":"Syarifah Adilah Mohamed Yusoff, Ibrahim Venkat, U. K. Yusof, R. Abdullah","doi":"10.4018/jncr.2012040104","DOIUrl":"https://doi.org/10.4018/jncr.2012040104","url":null,"abstract":"Mass spectrometry is an emerging technique that is continuously gaining momentum among bioinformatics researchers who intend to study biological or chemical properties of complex structures such as protein sequences. This advancement also embarks in the discovery of proteomic biomarkers through accessible body fluids such as serum, saliva, and urine. Recently, literature reveals that sophisticated computational techniques mimetic survival and natural processes adapted from biological life for reasoning voluminous mass spectrometry data yields promising results. Such advanced approaches can provide efficient ways to mine mass spectrometry data in order to extract parsimonious features that represent vital information, specifically in discovering disease-related protein patterns in complex proteins sequences. This article intends to provide a systematic survey on bio-inspired approaches for feature subset selection via mass spectrometry data for biomarker analysis.","PeriodicalId":369881,"journal":{"name":"Int. J. Nat. Comput. Res.","volume":"2016 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126004347","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}
引用次数: 7
Artificial Bee Colony Algorithm for Solving Educational Timetabling Problems 求解教学排课问题的人工蜂群算法
Int. J. Nat. Comput. Res. Pub Date : 2012-04-01 DOI: 10.4018/jncr.2012040101
Asaju La'aro Bolaji, A. Khader, M. Al-Betar, M. Awadallah
{"title":"Artificial Bee Colony Algorithm for Solving Educational Timetabling Problems","authors":"Asaju La'aro Bolaji, A. Khader, M. Al-Betar, M. Awadallah","doi":"10.4018/jncr.2012040101","DOIUrl":"https://doi.org/10.4018/jncr.2012040101","url":null,"abstract":"This paper presents an artificial bee colony algorithm (ABC) for Education Timetabling Problem (ETP). It is aimed at developing a good-quality solution for the problem. The initial population of solutions was generated using Saturation Degree (SD) and Backtracking Algorithm (BA) to ensure the feasibility of the solutions. At the improvement stage in the solution method, ABC uses neighbourhood structures iteratively within the employed and onlooker bee operators, in order to rigorously navigate the UTP search space. The technique was evaluated using curriculum-based course timetabling (CB-CTT) and Uncapacitated Examination Timetabling Problem (UETP) problem instances. The experimental results on UETP showed that the technique is comparable with other state-of-the-art techniques and provides encouraging results on CB-CTT.","PeriodicalId":369881,"journal":{"name":"Int. J. Nat. Comput. Res.","volume":"39 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127664227","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}
引用次数: 11
Harmony Search with Greedy Shuffle for Nurse Rostering 和谐搜索贪心洗牌护士名册
Int. J. Nat. Comput. Res. Pub Date : 2012-04-01 DOI: 10.4018/jncr.2012040102
M. Awadallah, A. Khader, M. Al-Betar, Asaju La'aro Bolaji
{"title":"Harmony Search with Greedy Shuffle for Nurse Rostering","authors":"M. Awadallah, A. Khader, M. Al-Betar, Asaju La'aro Bolaji","doi":"10.4018/jncr.2012040102","DOIUrl":"https://doi.org/10.4018/jncr.2012040102","url":null,"abstract":"In this paper, a hybridization of Harmony Search Algorithm (HSA) with a greedy shuffle move is proposed for Nurse Rostering Problem (NRP). NRP is a combinatorial optimization problem that is tackled by assigning a set of nurses with different skills and contracts to different types of shifts, over a pre-determined scheduling period. HSA is a population-based method which mimics the improvisation process that has been successfully applied for a wide range of optimization problems. The performance of HSA is enhanced by hybridizing it with a greedy shuffle move. The proposed method is evaluated using a dataset defined in first International Nurse Rostering Competition (INRC2010). The hybrid HSA obtained the best results of the comparative methods in four datasets.","PeriodicalId":369881,"journal":{"name":"Int. J. Nat. Comput. Res.","volume":"79 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131463906","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}
引用次数: 19
Unorganized Machines: From Turing's Ideas to Modern Connectionist Approaches 无组织机器:从图灵的思想到现代连接主义方法
Int. J. Nat. Comput. Res. Pub Date : 2011-10-01 DOI: 10.4018/jncr.2011100101
L. Boccato, Everton S. Soares, Marcos M. L. P. Fernandes, D. Soriano, R. Attux
{"title":"Unorganized Machines: From Turing's Ideas to Modern Connectionist Approaches","authors":"L. Boccato, Everton S. Soares, Marcos M. L. P. Fernandes, D. Soriano, R. Attux","doi":"10.4018/jncr.2011100101","DOIUrl":"https://doi.org/10.4018/jncr.2011100101","url":null,"abstract":"This work presents a discussion about the relationship between the contributions of Alan Turing – the centenary of whose birth is celebrated in 2012 – to the field of artificial neural networks and modern unorganized machines: reservoir computing (RC) approaches and extreme learning machines (ELMs). Firstly, the authors review Turing’s connectionist proposals and also expose the fundamentals of the main RC paradigms – echo state networks and liquid state machines, - as well as of the design and training of ELMs. Throughout this exposition, the main points of contact between Turing’s ideas and these modern perspectives are outlined, being, then, duly summarized in the second and final part of the work. This paper is useful in offering a distinct appreciation of Turing’s pioneering contributions to the field of neural networks and also in indicating some perspectives for the future development of the field that may arise from the synergy between these views.","PeriodicalId":369881,"journal":{"name":"Int. J. Nat. Comput. Res.","volume":"6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125599071","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}
引用次数: 15
Ecosystems Computing: Introduction to Biogeographic Computation 生态系统计算:生物地理计算导论
Int. J. Nat. Comput. Res. Pub Date : 2011-10-01 DOI: 10.4018/jncr.2011100104
Rodrigo Pasti, F. V. Zuben, L. Castro
{"title":"Ecosystems Computing: Introduction to Biogeographic Computation","authors":"Rodrigo Pasti, F. V. Zuben, L. Castro","doi":"10.4018/jncr.2011100104","DOIUrl":"https://doi.org/10.4018/jncr.2011100104","url":null,"abstract":"The main issue to be presented in this paper is based on the premise that Nature computes, that is, processes information. This is the fundamental of Natural Computing. Biogeographic Computation will be presented as a Natural Computing approach aimed at investigating ecosystems computing. The first step towards formalizing Biogeographic Computation will be given by defining a metamodel, a framework capable of generating models that compute through the elements of an ecosystem. It will also be discussed how this computing can be realized in current computers.","PeriodicalId":369881,"journal":{"name":"Int. J. Nat. Comput. Res.","volume":"18 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128803769","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}
引用次数: 13
The Grand Challenges in Natural Computing Research: The Quest for a New Science 自然计算研究中的重大挑战:对新科学的探索
Int. J. Nat. Comput. Res. Pub Date : 2011-10-01 DOI: 10.4018/jncr.2011100102
L. Castro, R. Xavier, Rodrigo Pasti, R. D. Maia, Alexandre Szabo, D. Ferrari
{"title":"The Grand Challenges in Natural Computing Research: The Quest for a New Science","authors":"L. Castro, R. Xavier, Rodrigo Pasti, R. D. Maia, Alexandre Szabo, D. Ferrari","doi":"10.4018/jncr.2011100102","DOIUrl":"https://doi.org/10.4018/jncr.2011100102","url":null,"abstract":"An important premise of Natural Computing is that some form of computation goes on in Nature, and that computing capability has to be understood, modeled, abstracted, and used for different objectives and in different contexts. Therefore, it is necessary to propose a new language capable of describing and allowing the comprehension of natural systems as a union of computing phenomena, bringing an information processing perspective to Nature. To develop this new language and convert Natural Computing into a new science it is imperative to overcome three specific Grand Challenges in Natural Computing Research: Transforming Natural Computing into a Transdisciplinary Discipline, Unveiling and Harnessing Information Processing in Natural Systems, Engineering Natural Computing Systems.","PeriodicalId":369881,"journal":{"name":"Int. J. Nat. Comput. Res.","volume":"38 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124635969","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}
引用次数: 18
Towards Automated Verification of P Systems Using Spin 利用自旋实现P系统的自动验证
Int. J. Nat. Comput. Res. Pub Date : 2011-07-01 DOI: 10.4018/jncr.2011070101
R. Lefticaru, C. Tudose, F. Ipate
{"title":"Towards Automated Verification of P Systems Using Spin","authors":"R. Lefticaru, C. Tudose, F. Ipate","doi":"10.4018/jncr.2011070101","DOIUrl":"https://doi.org/10.4018/jncr.2011070101","url":null,"abstract":"This paper presents an approach to P systems verification using the Spin model checker. The authors have developed a tool which implements the proposed approach and can automatically transform P system specifications from P-Lingua into Promela, the language accepted by the well known model checker Spin. The properties expected for the P system are specified using some patterns, representing high level descriptions of frequently asked questions, formulated in natural language. These properties are automatically translated into LTL specifications for the Promela model and the Spin model checker is run against them. In case a counterexample is received, the Spin trace is decoded and expressed as a P system computation. The tool has been tested on a number of examples and the results obtained are presented in the paper.","PeriodicalId":369881,"journal":{"name":"Int. J. Nat. Comput. Res.","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128347093","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}
引用次数: 12
Linear Time Solution to Prime Factorization by Tissue P Systems with Cell Division 带细胞分裂的组织P系统质因数分解的线性时间解
Int. J. Nat. Comput. Res. Pub Date : 2011-07-01 DOI: 10.4018/jncr.2011070105
Xingyi Zhang, Yunyun Niu, L. Pan, M. Pérez-Jiménez
{"title":"Linear Time Solution to Prime Factorization by Tissue P Systems with Cell Division","authors":"Xingyi Zhang, Yunyun Niu, L. Pan, M. Pérez-Jiménez","doi":"10.4018/jncr.2011070105","DOIUrl":"https://doi.org/10.4018/jncr.2011070105","url":null,"abstract":"Prime factorization is useful and crucial for public-key cryptography, and its application in public-key cryptography is possible only because prime factorization has been presumed to be difficult. A polynomial-time algorithm for prime factorization on a quantum computer was given by P. W. Shor in 1997. In this work, it is considered as a function problem, and in the framework of tissue P systems with cell division, a linear-time solution to prime factorization problem is given on biochemical computational devices – tissue P systems with cell division, instead of computational devices based on the laws of quantum physical.","PeriodicalId":369881,"journal":{"name":"Int. J. Nat. Comput. Res.","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125078546","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}
引用次数: 11
Implementation on CUDA of the Smoothing Problem with Tissue-Like P Systems 类组织P系统平滑问题的CUDA实现
Int. J. Nat. Comput. Res. Pub Date : 2011-07-01 DOI: 10.4018/jncr.2011070103
Francisco Peña-Cantillana, D. Díaz-Pernil, H. Christinal, M. A. Gutiérrez-Naranjo
{"title":"Implementation on CUDA of the Smoothing Problem with Tissue-Like P Systems","authors":"Francisco Peña-Cantillana, D. Díaz-Pernil, H. Christinal, M. A. Gutiérrez-Naranjo","doi":"10.4018/jncr.2011070103","DOIUrl":"https://doi.org/10.4018/jncr.2011070103","url":null,"abstract":"Smoothing is often used in Digital Imagery for improving the quality of an image by reducing its level of noise. This paper presents a parallel implementation of an algorithm for smoothing 2D images in the framework of Membrane Computing. The chosen formal framework has been tissue-like P systems. The algorithm has been implemented by using a novel device architecture called CUDA (Compute Unified Device Architecture) which allows the parallel NVIDIA Graphics Processors Units (GPUs) to solve many complex computational problems. Some examples are presented and compared; research lines for the future are also discussed.","PeriodicalId":369881,"journal":{"name":"Int. J. Nat. Comput. Res.","volume":"16 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133384668","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}
引用次数: 28
Elementary Active Membranes Have the Power of Counting 基本活性膜具有计数能力
Int. J. Nat. Comput. Res. Pub Date : 2011-07-01 DOI: 10.4018/jncr.2011070104
A. Porreca, A. Leporati, G. Mauri, C. Zandron
{"title":"Elementary Active Membranes Have the Power of Counting","authors":"A. Porreca, A. Leporati, G. Mauri, C. Zandron","doi":"10.4018/jncr.2011070104","DOIUrl":"https://doi.org/10.4018/jncr.2011070104","url":null,"abstract":"P systems with active membranes have the ability of solving computationally hard problems. In this paper, the authors prove that uniform families of P systems with active membranes operating in polynomial time can solve the whole class of PP decision problems, without using nonelementary membrane division or dissolution rules. This result also holds for families having a stricter uniformity condition than the usual one.","PeriodicalId":369881,"journal":{"name":"Int. J. Nat. Comput. Res.","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122359346","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}
引用次数: 20
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