phylogenetic inference with ant colony optimization

... tio n 3.1 The Ant Algorithms 20 20 3.1.1 3.1.2 Ant S y s te m 22 3.1.3 Ant Colony S y s te m 24 3.1.4 3.2 Double bridge experim ents 20 Max-Min Ant S ystem ... criteria in phylogenetic tree reconstruction problem C h a p te r P hylogenetic Inference w ith A nt Colony O ptim ization In this chapter, we propose a general framework to apply Ant Colony Optimiza­ ... widely used in phylogenetic analysis :t Both types of molecular sequences (nucleotides and amino acids) play an im portant role in molecular phy­ logenetics especially in phylogenetic inferences...

Ngày tải lên: 25/03/2015, 09:38

... Stützle, T (2004) Ant colony optimization Cambridge: MIT Press Graỗa, A., Marques-silva, J., Lynce, I., & Oliveira, A L (2007) Efficient haplotype inference with pseudoBoolean optimization In H ... of G 3.2.1 Pheromone trail update Pheromone trail update is a crucial step in ant colony optimization as it guides ants to find good solutions The heterozygous step uses pheromone trail τivs as ... ACO for haplotype inference under pure parsimony In M Dorigo, M Birattari, C Blum, M Clerc, T Stützle, & A Winfield (Eds.), Lecture notes in computer science: Vol 5217 Ant colony optimization and...

Ngày tải lên: 14/12/2017, 16:57

... ACO and CP 1.1.2 Ant colony optimization The second part of this book describes ant colony optimization As for other heuristic approaches described in Chapters and 6, ant colony optimization only ... 1.1.3 Constraint programming with ant colony optimization Algorithms based on ant colony optimization have proven to be very effective for solving many combinatorial optimization problems In this ... 1.1.1 Constraint programming 1.1.2 Ant colony optimization 1.1.3 Constraint programming with ant colony optimization Chapter Computational Complexity 4 ...

Ngày tải lên: 24/04/2014, 14:36

... between the nest and the food source 2 14 Ant Colony Optimization Ant Colony Optimization - Methods and Applications Some ant colony techniques aimed at dynamic optimization have been described in ... ant approximately Artificial ant colony system is made from the principle of ant colony system for solving kinds of optimization problems Pheromone is the key of the decision-making of ants Ant ... components 6 18 Ant Colony Optimization Ant Colony Optimization - Methods and Applications Fig Every ant constructs a complete solution which includes n dimensions CANDO: charged ants for continuous...

Ngày tải lên: 29/06/2014, 13:20

... return path: end if end return paths; end proc Ant Colony Optimization Dưới mã Maple Ant Colony Optimization Ant Colony Optimization 2.4.Thủ tục thuật tốn Ant System Khi ta có thủ tục tìm đường cho ... Maple Giảng viên hướng dẫn PGS.TS Đỗ Văn Nhơn Ant Colony Optimization Học viên: Huỳnh Lê Quốc Vương 02 – 2013 MỤC LỤC MHV: CH1101158 Ant Colony Optimization MỞ ĐẦU Bài toán tối ưu hóa tổ hợp ... thành tốt thu hoạch Ant Colony Optimization I PHƯƠNG PHÁP ANT COLONY OPTIMIZATION Giới thiệu Phương pháp tối ưu hóa đàn kiến (Ant Colony Optimization - ACO) mơ hình để thiết kế thuật toán metaheuristic...

Ngày tải lên: 10/04/2015, 01:31

... classification scheme ACO ant colony optimization ACS ant colony system AC2 ant colony control Ai accessible operation list ANTS approximate non-deterministic tree search AS ant system AS rank the ... their nest and a food source This optimization mechanism is realized through simple interaction rules among ants and modeled as an algorithm titled Ant Colony Optimization (ACO), which is promising ... be guided by those agents with global views Recent research on the foraging behaviour of a natural MAS, namely an ant colony, has found that autonomous agents like ants can find the shortest...

Ngày tải lên: 13/09/2015, 20:40

... letters assigned to the nodes (presented by circles) and dummy nodes are indicated by squares B Ant Colony Optimization method To assess the quality of an alignment, we use the scoring function for ... scoring function for alignment quality Define 3(Scoring function) In each iteration, each ant in the m ant colony will build the solution on the Construction graph from a starting set C0 and randomly ... (denoted as a1), ants will randomly walk across the layers to Gn as follows If ants have built vectors (a1,…,ai) where aq is the vertex j of Gi then selected node k in Gi +1 with probability...

Ngày tải lên: 16/12/2017, 09:02

... on, onto, outside, over, through, to, toward, towards, under, underneath, until, up, upon, with, within, without), which we adopt from previous work Every prepositional phrase (PP) that is governed ... multi-class classification problem with m classes can be cast as m binary classification problems in a one-vs-rest arrangement The prediction of the classifier is the class with the ˆ highest score Y = ... Alternating Structure Optimization This section describes the ASO algorithm and shows how it can be used for grammatical error correction 5.1 The ASO algorithm Alternating Structure Optimization (Ando...

Ngày tải lên: 17/03/2014, 00:20

... terms are used within the DP formulation When taking an inference step to prove theorem i, the value fm (x, i ) M is combined into the calculation m=1 λm of that theorem’s value, along with the values ... Importantly, this permits us to calculate the exact gradient of the approximate summation with respect to axiom values, following Eisner et al (2005) This is desirable when carrying out the optimization ... summing problem, which marginalizes the proof probabilities (without normalization): y (x) = argmaxy∈Y ˆ s(x) = 2.4 Features and Inference Let X be the space of inputs to our logic program, i.e.,...

Ngày tải lên: 17/03/2014, 22:20

... truncation m Analytic results (with W64 ) m Simulated results (with W64 ) m Analytic results (with W512 ) m Simulated results (with W512 ) Figure 7: Analytic and simulated quantization mean squared ... operating frequency with reduced complexity Finite Precision Effect and Word-Length Optimization To design a proper word-length searching procedure, we need to realize the mean squared quantization error ... necessary In Figure 5, the circle with “Q” denotes the introduction of the probable quantization effect due to truncation In the following, the mean squared quantization errors resulted from these...

Ngày tải lên: 21/06/2014, 08:20

... measurements were performed with a quantitative sandwich enzyme immunoassay (R&D Systems, British Biotechnology, Abingdon, UK) Supernatants were assayed for TNFα, IL-1β, IL-6 and IL-10 with enzyme immunoassays ... significantly higher baseline levels than control individuals (except for IL-1) There was a significant increase in all cytokines in response to LPS – reaching levels that were significantly higher ... compared with monocytes from non-neutropenic septic ARDS patients and healthy control individuals These results correlate with our previous study suggesting that neutropenic patients with septic...

Ngày tải lên: 13/08/2014, 10:20

... Notes Ant 1.0 Really Ant 0.9; with Tomcat 3.1 July 2000 Ant 1.1 First stand-alone Ant release October 2000 Ant 1.2 March 2001 Ant 1.3 September 2001 Ant 1.4 July 2002 14 Ant version March 2000 Ant ... Learning Ant 1 Introducing Ant 1.1 What is Ant? What is a build process and why you need one? Why we think Ant makes a great build tool? 1.2 The core concepts of Ant An example project 1.3 Why use Ant? ... with Ant 1.5 as it took shape—and indeed helped shape this version of Ant while considering it for this book They hope that you will find Ant 1.5 to be useful—and that Java Development with Ant...

Ngày tải lên: 13/08/2014, 22:21

... combinations: ant ant init ant clean 36 CHAPTER GETTING STARTED WITH ANT Simpo PDF Merge and Split Unregistered Version - http://www.simpopdf.com ant compile ant archive ant clean archive Calling Ant with ... lib\jtidy-04aug2000r7-dev\build\Tidy.jar; C:\AntBook\jakarta -ant- 1.5\lib \ant. jar; -sourcepath src -g src\org\example\antbook \ant\ lucene\*.java The following Java compilation with Ant, utilizing Ant s datatypes and properties, ... [echo] [echo] [echo] 66 ant. file = C:\AntBook\Sections\Learning\datatypes\properties.xml ant. home = c:\AntBook\jakarta -ant- 1.5Beta1 ant. java.version = 1.3 ant. version = Apache Ant version 1.5Beta1...

Ngày tải lên: 13/08/2014, 22:21

... C:\jakarta -ant\ docs\manual\OptionalTasks\jspc.html [java] 6: C:\jakarta -ant\ docs\manual\CoreTasks\overview.html [java] 7: C:\jakarta -ant\ docs \ant_ in_anger.html [java] 8: C:\jakarta -ant\ docs\external.html ... Setting the classpath The task runs with Ant s classpath, in the absence of any specified classpath; that of ant. jar and any other libraries in the ANT_ HOME/lib directory, plus anything in ... C:\jakarta -ant\ docs\manual\coretasklist.html 3: C:\jakarta -ant\ docs\manual\CoreTasks\unzip.html 4: C:\jakarta -ant\ docs\manual\CoreTasks\ear.html 5: C:\jakarta -ant\ docs\manual\OptionalTasks\jspc.html 6: C:\jakarta -ant\ docs\manual\CoreTasks\overview.html...

Ngày tải lên: 13/08/2014, 22:21

...

Ngày tải lên: 13/08/2014, 22:21

... very special set of Ant tasks: XDoclet Ant s web site provides links to additional third-party tasks If Ant doesn’t provide what you need, check with the Ant web site or with the vendor of the ... this: = The ... these with caution and with knowledge of the alternatives THE ANT- CONTRIB TASKS 253 Simpo PDF Merge and Split Unregistered Version - http://www.simpopdf.com Installing the ant- contrib tasks The ant- contrib...

Ngày tải lên: 13/08/2014, 22:21

... T E R Working with web services 15.1 What are web services and what is SOAP? 356 15.2 Creating a SOAP client application with Ant 357 15.3 Creating a SOAP service with Axis and Ant 363 15.4 Adding ... XSLT engines; complications that programs like Ant have to address What this all boils down to is that a normal Ant 1.5 installation of Ant comes with the Xerces XML parser, which can be used ... can download it from http://xml.apache.org/ Prior to Ant 1.5, Ant shipped with Crimson and JAXP libraries The xalan.jar library must go into ANT_ HOME/lib Although some tasks, such as , have...

Ngày tải lên: 13/08/2014, 22:21

... to start with A value of 1.1.1 is a reasonable start This file needs to be committed to your source code repository Getting Anthill to work with Ant 1.5 Anthill comes with Ant 1.3 and Ant 1.4, ... look at NAnt, a NET version of Ant, found at SourceForge (http:// nant.sourceforge.net), and maybe , the NAnt build from our Ant task Alternatively, we might write an task for Ant Finally, ... in Ant 1.5 We copied our Ant 1.5 installation into an ant1 .5 directory under our installation’s lib directory, and in the Anthill Properties settings of the web administration, we set anthill .ant. home...

Ngày tải lên: 13/08/2014, 22:21

... methods that you will work with most frequently Ant ships with complete Javadoc references and is well documented With Ant s source code being open, it is easy to learn Ant task development tricks ... org.apache.tools .ant. BuildException; org.apache.tools .ant. DirectoryScanner; org.apache.tools .ant. Project; org.apache.tools .ant. Task; org.apache.tools .ant. taskdefs.Execute; org.apache.tools .ant. taskdefs.LogStreamHandler; ... follows represents a single Ant class, with the important methods of the class noted 19.2.1 470 Task The org.apache.tools .ant. Task abstract class is the typical base class for Ant tasks It is the main...

Ngày tải lên: 13/08/2014, 22:21

... external integration with Ant, and custom-writing them is easy Ant comes with several listeners and loggers already, which are detailed in Ant s documentation Familiarize yourself with these before ... Ant [Apps]$ pwd /home/slo/Java/Apps [Apps]$ ls jakarta -ant- 1.5-bin.tar.gz [Apps]$ ls jakarta -ant- 1.5-bin.tar.gz [Apps]$ tar xzf jakarta -ant- 1.5-bin.tar.gz [Apps]$ ls jakarta -ant- 1.5 jakarta -ant- 1.5-bin.tar ... installed) setenv ANT_ HOME= (wherever Ant is installed) setenv PATH=$PATH\: $ANT_ HOME/bin\:$JAVA_HOME/bin There is a place where Ant options (such as ANT_ OPTS) can be set in Unix, the antrc file in...

Ngày tải lên: 13/08/2014, 22:21