A Memetic Algorithm for Phylogenetic Reconstruction with Maximum Parsimony

The Maximum Parsimony problem aims at reconstructing a phylogenetic tree from DNA, RNA or protein sequences while minimizing the number of evolutionary changes. Much work has been devoted by the research community to solve this NP-complete problem and many algorithms and techniques have been devised in order to find high quality solutions with reasonable computational resources. In this paper we present a memetic algorithm (implemented in the software Hydra) which is based on an integration of an effective local search operator with a specific topological tree crossover operator. We report computational results of Hydra on a set of 12 benchmark instances from the literature and demonstrate its effectiveness with respect to one of the most powerful software (TNT). We also study the behavior of the algorithm with respect to some fundamental ingredients

Innovation as Evolution

Cellular phone is one of the most developing technological artifacts today. The evolution occurs through random innovation. Our effort is trying to view the evolution of this artifact from memetic’s point of view. By constructing a phylomemetic tree based on cellular phone memes to infer or estimate the evolutionary history and relationship among cellular phone. We adopt several methods, which are commonly used in constructing phylogenetic tree, they are UPGMA algorithm and Parsimony Maximum algorithm to construct cellphone phylomemetic tree. Therefore we compare with the innovation tree, which is based on serial number and their appearance time. From phylomemetic tree, we then analyze the process of a cellular phone innovation through looking out on the cellular phone type lies in the same cluster. The comparison of the simulation tree result shows a generally different branching pattern, giving a presumption that innovation in cellular phone is not really relating with their serial number, but occurs merely because of random mutation of allomeme design and competes with its technological development

Innovation as Evolution

Cellular phone is one of the most developing technological artifacts today. The evolution occurs through random innovation. Our effort is trying to view the evolution of this artifact from memetics. By constructing a phylomemetic tree based on cellular phone memes to infer or estimate the evolutionary history and relationship among cellular phone. We adopt several methods, which are commonly used in constructing phylogenetic tree, they are UPGMA algorithm and Parsimony Maximum algorithm to construct cellphone phylomemetic tree. Therefore we compare with the innovation tree, which is based on serial number and their appearance time. From phylomemetic tree, we then analyze the process of a cellular phone innovation through looking out on the cellular phone type lies in the same cluster. The comparison of the simulation tree result shows a generally different branching pattern, giving a presumption that innovation in cellular phone is not really relating with their serial number, but occurs merely because of random mutation of allomeme design and competes with its technological development.artifact, innovation, evolution, memetics, phylomemetic tree, cellular phone.

On the role of metaheuristic optimization in bioinformatics

Metaheuristic algorithms are employed to solve complex and large-scale optimization problems in many different fields, from transportation and smart cities to finance. This paper discusses how metaheuristic algorithms are being applied to solve different optimization problems in the area of bioinformatics. While the text provides references to many optimization problems in the area, it focuses on those that have attracted more interest from the optimization community. Among the problems analyzed, the paper discusses in more detail the molecular docking problem, the protein structure prediction, phylogenetic inference, and different string problems. In addition, references to other relevant optimization problems are also given, including those related to medical imaging or gene selection for classification. From the previous analysis, the paper generates insights on research opportunities for the Operations Research and Computer Science communities in the field of bioinformatics

FPGAを用いた最節約法による進化系統樹構築アルゴリズムの高速化

筑波大学 (University of Tsukuba)201

FPGA Hardware Acceleration of a Phylogenetic Tree Reconstruction with Maximum Parsimony Algorithm

In this paper, we present an FPGA hardware implementation for a phylogenetic tree reconstruction with a maximum parsimony algorithm. We base our approach on a particular stochastic local search algorithm that uses the Progressive Neighborhood and the Indirect Calculation of Tree Lengths method. This method is widely used for the acceleration of the phylogenetic tree reconstruction algorithm in software. In our implementation, we define a tree structure and accelerate the search by parallel and pipeline processing. We show results for eight real-world biological datasets. We compare execution times against our previous hardware approach, and TNT, the fastest available parsimony program, which is also accelerated by the Indirect Calculation of Tree Lengths method. Acceleration rates between 34 to 45 per rearrangement, and 2 to 6 for the whole search, are obtained against our previous hardware approach. Acceleration rates between 2 to 36 per rearrangement, and 18 to 112 for the whole search, are obtained against TNT

Reconstructing weighted phylogenetic trees and phylogenetic networks using answer set programming

Evolutionary relationships between species can be modeled as a tree (called a phylogeny) whose nodes represent the species, internal vertices represent their ancestors and edges represent genetic relationships. If there are borrowings between species, then a small number of edges that denote such borrowings can be added to phylogenies turning them into (phylogenetic) networks. However, there are too many such trees/networks for a given family of species but no phylogenetic system to automatically analyze them. This thesis fulfills this need in phylogenetics, by introducing novel computational methods and tools for computing weighted phylogenies/networks, using Answer Set Programming (ASP). The main idea is to define a weight function for phylogenies/networks that characterizes their plausibility, and to reconstruct phylogenies/networks whose weights are over a given threshold using ASP solvers. We have studied computational problems related to reconstructing weighted phylogenies/networks based on the compatibility criterion, analyzed their computational complexity, and introduced two sorts of ASP-based methods (representation-based and search-based) for computing weighted phylogenies/networks. Utilizing these methods, we have introduced a novel divide-and-conquer algorithm for computing large weighted phylogenies, and implemented a phylogenetic system (Phylo-ASP) based on it. We have also implemented a phylogenetic system (PhyloNet-ASP) for reconstructing weighted networks. We have shown the applicability and the effectiveness of our methods by performing experiments on two real datasets: Indo European languages, and Quercus species in Turkey. Moreover, we have extended our methods to computing weighted solutions in ASP and modified an ASP solver accordingly, providing a useful tool (CLASP-W) for various ASP applications

Kielen muutos evolutiivisena prosessina

In the thesis it is discussed in what ways concepts and methodology developed in evolutionary biology can be applied to the explanation and research of language change. The parallel nature of the mechanisms of biological evolution and language change is explored along with the history of the exchange of ideas between these two disciplines. Against this background computational methods developed in evolutionary biology are taken into consideration in terms of their applicability to the study of historical relationships between languages. Different phylogenetic methods are explained in common terminology, avoiding the technical language of statistics. The thesis is on one hand a synthesis of earlier scientific discussion, and on the other an attempt to map out the problems of earlier approaches in addition to finding new guidelines in the study of language change on their basis. Primarily literature about the connections between evolutionary biology and language change, along with research articles describing applications of phylogenetic methods into language change have been used as source material. The thesis starts out by describing the initial development of the disciplines of evolutionary biology and historical linguistics, a process which right from the beginning can be seen to have involved an exchange of ideas concerning the mechanisms of language change and biological evolution. The historical discussion lays the foundation for the handling of the generalised account of selection developed during the recent few decades. This account is aimed for creating a theoretical framework capable of explaining both biological evolution and cultural change as selection processes acting on self-replicating entities. This thesis focusses on the capacity of the generalised account of selection to describe language change as a process of this kind. In biology, the mechanisms of evolution are seen to form populations of genetically related organisms through time. One of the central questions explored in this thesis is whether selection theory makes it possible to picture languages are forming populations of a similar kind, and what a perspective like this can offer to the understanding of language in general. In historical linguistics, the comparative method and other, complementing methods have been traditionally used to study the development of languages from a common ancestral language. Computational, quantitative methods have not become widely used as part of the central methodology of historical linguistics. After the fading of a limited popularity enjoyed by the lexicostatistical method since the 1950s, only in the recent years have also the computational methods of phylogenetic inference used in evolutionary biology been applied to the study of early language history. In this thesis the possibilities offered by the traditional methodology of historical linguistics and the new phylogenetic methods are compared. The methods are approached through the ways in which they have been applied to the Indo-European languages, which is the most thoroughly investigated language family using both the traditional and the phylogenetic methods. The problems of these applications along with the optimal form of the linguistic data used in these methods are explored in the thesis. The mechanisms of biological evolution are seen in the thesis as parallel in a limited sense to the mechanisms of language change, however sufficiently so that the development of a generalised account of selection is deemed as possibly fruiful for understanding language change. These similarities are also seen to support the validity of using phylogenetic methods in the study of language history, although the use of linguistic data and the models of language change employed by these models are seen to await further development.Tutkielma käsittelee evoluutiobiologiassa kehitetyn käsitteistön ja metodologian soveltamista kielenmuutoksen selittämiseen ja tutkimukseen. Tutkielmassa taustoitetaan biologisen evoluution ja kielenmuutoksen mekanismien rinnasteisuutta sekä näiden kahden eri alan teoreettisen tutkimuksen välisen vuoropuhelun historiaa. Tämän taustan pohjalta käsitellään evoluutiobiologiassa käytettyjen laskennallisten menetelmien soveltuvuutta kielihistorian selvittämiseen. Erilaiset menetelmät pyritään myös esittelemään yleistajuisesti jättäen tilastotieteen teknisen terminologian taustalle. Tutkielma on toisaalta synteesi aihepiirin aiemmasta tieteellisestä keskustelusta, ja toisaalta pyrkimys kartoittaa tähänastisten lähestymistapojen ongelmakohtia sekä löytää uusia suuntaviivoja kielen muutoksen tutkimuksessa niiden pohjalta. Lähdeaineistona on käytetty ensi sijassa evoluutiobiologian ja kielenmuutoksen välisiä yhteyksiä käsittelevää kirjallisuutta sekä fylogeneettisiä menetelmiä kielenmuutokseen soveltavia tutkimusartikkeleita. Tutkielma lähtee liikkeelle kuvaamalla evoluutiobiologian ja historiallisen kielitieteen tutkimusalojen kehitystä, johon nähdään kuuluneen alusta alkaen vuoropuhelu kielenmuutoksen ja biologisen evoluution mekanismeista. Historiallinen käsittely luo pohjaa viime vuosikymmeninä kehitetyn nk. yleisen valintateorian lähestymiselle. Yleinen valintateoria pyrkii muodostamaan viitekehyksen, joka pystyisi selittämään sekä biologista että kulttuurista evoluutiota replikaatioon perustuvana valintaprosessina. Tutkielmassa keskitytään tarkastelemaan yleisen valintateorian kykyä kuvata kielenmuutosta tällaisena prosessina. Biologiassa evoluution mekanismien nähdään muodostavan eliöiden populaatioita ajan kuluessa. Yksi keskeisistä tutkielmassa käsiteltävistä kysymyksistä on se, mahdollistaako valintateoria nähdä kielten muodostavan populaatioita, ja mitä tällaisesta näkökulmasta seuraa kielen ymmärtämiselle. Historiallisessa kielitieteessä kielten kehittymistä yhteisestä kantamuodosta on tutkittu perinteisesti vertailumenetelmällä ja muilla, sitä täydentävillä, menetelmillä joilla käsitellään suurta määrää kielellisiä muotoja koskevia muutoksia. Laskennalliset menetelmät eivät ole toistaiseksi tulleet osaksi historiallisen kielitieteen vakiometodologiaa. 1950-luvulta lähtien rajallisesti käytetyn leksikostatistisen merkityksen vähennyttyä entisestään kielihistorian tutkimukseen on aivan viime vuosina sovellettu myös evoluutiobiologiassa käytettyjä tilastollisia fylogeneettisen päättelyn laskennallisia malleja. Tutkielma vertaa historiallisen kielitieteen perinteistä metodologiaa ja uusien fylogeneettisten menetelmien tarjoamia mahdollisuuksia. Menetelmiä lähestytään sen kautta, miten niitä on sovellettu indoeurooppalaisiin kieliin, joka on eniten tutkittu kielikunta sekä perinteisillä että fylogeneettisillä menetelmillä. Tutkielmassa käydään läpi fylogeneettisten menetelmien sovellusten tähänastisia ongelmia sekä käytettävän kieliaineiston optimaalista muotoa. Biologisen evoluution mekanismit nähdään tutkielmassa rajallisessa määrin rinnasteisina kielenmuutoksen mekanismeihin, kuitenkin siinä määrin että yleisen valintateorian kehittäminen todetaan mahdollisesti hedelmälliseksi kielenmuutoksen ymmärtämiseksi. Yhtäläisyyksien ansiosta myös biologisesta tutkimuksesta peräisin olevien fylogeneettisten menetelmien nähdään olevan päteviä apuvälineitä kielenmuutoksen tutkimukseen, joskin kieliaineiston käytön ja menetelmien käyttämien kielenmuutoksen mallien todetaan odottavan lisäkehitystä