http://hdl.handle.net/2117/3487 Wed, 22 May 2013 17:47:55 GMT 2013-05-22T17:47:55Z webmaster.bupc@upc.edu Universitat Politècnica de Catalunya. Servei de Biblioteques i Documentació no http://hdl.handle.net/2117/19025 Title: The parameters of Menzerath-Altmann law in genomes Authors: Baixeries i Juvillà, Jaume; Hernández Fernández, Antonio; Forns, Núria; Ferrer Cancho, Ramon Abstract: The relationship between the size of the whole and the size of the parts in language and music is known to follow the Menzerath-Altmann law at many levels of description (morphemes, words, sentences, …). Qualitatively, the law states that the larger the whole, the smaller its parts, e.g. the longer a word (in syllables) the shorter its syllables (in letters or phonemes). This patterning has also been found in genomes: the longer a genome (in chromosomes), the shorter its chromosomes (in base pairs). However, it has been argued recently that mean chromosome length is trivially a pure power function of chromosome number with an exponent of -1. The functional dependency between mean chromosome size and chromosome number in groups of organisms from three different kingdoms is studied. The fit of a pure power function yields exponents between -1.6 and 0.1. It is shown that an exponent of -1 is unlikely for fungi, gymnosperm plants, insects, reptiles, ray-finned fishes and amphibians. Even when the exponent is very close to -1, adding an exponential component is able to yield a better fit with regard to a pure power-law in plants, mammals, ray-finned fishes and amphibians. The parameters of the Menzerath-Altmann law in genomes deviate significantly from a power law with a -1 exponent with the exception of birds and cartilaginous fishes. Fri, 26 Apr 2013 18:45:28 GMT http://hdl.handle.net/2117/19025 2013-04-26T18:45:28Z Baixeries i Juvillà, Jaume; Hernández Fernández, Antonio; Forns, Núria; Ferrer Cancho, Ramon no The relationship between the size of the whole and the size of the parts in language and music is known to follow the Menzerath-Altmann law at many levels of description (morphemes, words, sentences, …). Qualitatively, the law states that the larger the whole, the smaller its parts, e.g. the longer a word (in syllables) the shorter its syllables (in letters or phonemes). This patterning has also been found in genomes: the longer a genome (in chromosomes), the shorter its chromosomes (in base pairs). However, it has been argued recently that mean chromosome length is trivially a pure power function of chromosome number with an exponent of -1. The functional dependency between mean chromosome size and chromosome number in groups of organisms from three different kingdoms is studied. The fit of a pure power function yields exponents between -1.6 and 0.1. It is shown that an exponent of -1 is unlikely for fungi, gymnosperm plants, insects, reptiles, ray-finned fishes and amphibians. Even when the exponent is very close to -1, adding an exponential component is able to yield a better fit with regard to a pure power-law in plants, mammals, ray-finned fishes and amphibians. The parameters of the Menzerath-Altmann law in genomes deviate significantly from a power law with a -1 exponent with the exception of birds and cartilaginous fishes. http://hdl.handle.net/2117/18260 Title: Learning probabilistic automata : a study in state distinguishability Authors: Balle Pigem, Borja de; Castro Rabal, Jorge; Gavaldà Mestre, Ricard Abstract: Known algorithms for learning PDFA can only be shown to run in time polynomial in the so-called distinguishability μ of the target machine, besides the number of states and the usual accuracy and confidence parameters. We show that the dependence on μ is necessary in the worst case for every algorithm whose structure resembles existing ones. As a technical tool, a new variant of Statistical Queries termed View the MathML source-queries is defined. We show how to simulate View the MathML source-queries using classical Statistical Queries and show that known PAC algorithms for learning PDFA are in fact statistical query algorithms. Our results include a lower bound: every algorithm to learn PDFA with queries using a reasonable tolerance must make Ω(1/μ1−c) queries for every c>0. Finally, an adaptive algorithm that PAC-learns w.r.t. another measure of complexity is described. This yields better efficiency in many cases, while retaining the same inevitable worst-case behavior. Our algorithm requires fewer input parameters than previously existing ones, and has a better sample bound. Wed, 13 Mar 2013 13:49:57 GMT http://hdl.handle.net/2117/18260 2013-03-13T13:49:57Z Balle Pigem, Borja de; Castro Rabal, Jorge; Gavaldà Mestre, Ricard no Known algorithms for learning PDFA can only be shown to run in time polynomial in the so-called distinguishability μ of the target machine, besides the number of states and the usual accuracy and confidence parameters. We show that the dependence on μ is necessary in the worst case for every algorithm whose structure resembles existing ones. As a technical tool, a new variant of Statistical Queries termed View the MathML source-queries is defined. We show how to simulate View the MathML source-queries using classical Statistical Queries and show that known PAC algorithms for learning PDFA are in fact statistical query algorithms. Our results include a lower bound: every algorithm to learn PDFA with queries using a reasonable tolerance must make Ω(1/μ1−c) queries for every c>0. Finally, an adaptive algorithm that PAC-learns w.r.t. another measure of complexity is described. This yields better efficiency in many cases, while retaining the same inevitable worst-case behavior. Our algorithm requires fewer input parameters than previously existing ones, and has a better sample bound. http://hdl.handle.net/2117/18232 Title: A graphical tool for describing the temporal evolution of clusters in financial stock markets Authors: Arratia Quesada, Argimiro Alejandro; Cabaña, Ana Alejandra Tue, 12 Mar 2013 16:27:48 GMT http://hdl.handle.net/2117/18232 2013-03-12T16:27:48Z Arratia Quesada, Argimiro Alejandro; Cabaña, Ana Alejandra no http://hdl.handle.net/2117/16067 Title: Energy-efficient and multifaceted resource management for profit-driven virtualized data centers Authors: Goiri Presa, Íñigo; Berral García, Josep Lluís; Fitó, Josep Oriol; Julià Massó, Ferran; Nou Castell, Ramon; Guitart Fernández, Jordi; Gavaldà Mestre, Ricard; Torres Viñals, Jordi Abstract: As long as virtualization has been introduced in data centers, it has been opening new chances for resource management. Nowadays, it is not just used as a tool for consolidating underused nodes and save power; it also allows new solutions to well-known challenges, such as heterogeneity management. Virtualization helps to encapsulate Web-based applications or HPC jobs in virtual machines (VMs) and see them as a single entity which can be managed in an easier and more efficient way. We propose a new scheduling policy that models and manages a virtualized data center. It focuses on the allocation of VMs in data center nodes according to multiple facets to optimize the provider’s profit. In particular, it considers energy efficiency, virtualization overheads, and SLA violation penalties, and supports the outsourcing to external providers. The proposed approach is compared to other common scheduling policies, demonstrating that a provider can improve its benefit by 30% and save power while handling other challenges, such as resource outsourcing, in a better and more intuitive way than other typical approaches do. Sat, 16 Jun 2012 10:58:35 GMT http://hdl.handle.net/2117/16067 2012-06-16T10:58:35Z Goiri Presa, Íñigo; Berral García, Josep Lluís; Fitó, Josep Oriol; Julià Massó, Ferran; Nou Castell, Ramon; Guitart Fernández, Jordi; Gavaldà Mestre, Ricard; Torres Viñals, Jordi no As long as virtualization has been introduced in data centers, it has been opening new chances for resource management. Nowadays, it is not just used as a tool for consolidating underused nodes and save power; it also allows new solutions to well-known challenges, such as heterogeneity management. Virtualization helps to encapsulate Web-based applications or HPC jobs in virtual machines (VMs) and see them as a single entity which can be managed in an easier and more efficient way. We propose a new scheduling policy that models and manages a virtualized data center. It focuses on the allocation of VMs in data center nodes according to multiple facets to optimize the provider’s profit. In particular, it considers energy efficiency, virtualization overheads, and SLA violation penalties, and supports the outsourcing to external providers. The proposed approach is compared to other common scheduling policies, demonstrating that a provider can improve its benefit by 30% and save power while handling other challenges, such as resource outsourcing, in a better and more intuitive way than other typical approaches do. http://hdl.handle.net/2117/14563 Title: Random models of Menzerath-Altmann law in genomes Authors: Baixeries i Juvillà, Jaume; Hernández Fernández, Antonio; Ferrer Cancho, Ramon Abstract: Recently, a random breakage model has been proposed to explain the negative correlation between mean chromosome length and chromosome number that is found in many groups of species and is consistent with Menzerath–Altmann law, a statistical law that defines the dependency between the mean size of the whole and the number of parts in quantitative linguistics. Here, the central assumption of the model, namely that genome size is independent from chromosome number is reviewed. This assumption is shown to be unrealistic from the perspective of chromosome structure and the statistical analysis of real genomes. A general class of random models, including that random breakage model, is analyzed. For any model within this class, a power law with an exponent of −1 is predicted for the expectation of the mean chromosome size as a function of chromosome length, a functional dependency that is not supported by real genomes. The random breakage and variants keeping genome size and chromosome number independent raise no serious objection to the relevance of correlations consistent with Menzerath–Altmann law across taxonomic groups and the possibility of a connection between human language and genomes through that law. Mon, 16 Jan 2012 11:48:19 GMT http://hdl.handle.net/2117/14563 2012-01-16T11:48:19Z Baixeries i Juvillà, Jaume; Hernández Fernández, Antonio; Ferrer Cancho, Ramon no Recently, a random breakage model has been proposed to explain the negative correlation between mean chromosome length and chromosome number that is found in many groups of species and is consistent with Menzerath–Altmann law, a statistical law that defines the dependency between the mean size of the whole and the number of parts in quantitative linguistics. Here, the central assumption of the model, namely that genome size is independent from chromosome number is reviewed. This assumption is shown to be unrealistic from the perspective of chromosome structure and the statistical analysis of real genomes. A general class of random models, including that random breakage model, is analyzed. For any model within this class, a power law with an exponent of −1 is predicted for the expectation of the mean chromosome size as a function of chromosome length, a functional dependency that is not supported by real genomes. The random breakage and variants keeping genome size and chromosome number independent raise no serious objection to the relevance of correlations consistent with Menzerath–Altmann law across taxonomic groups and the possibility of a connection between human language and genomes through that law. http://hdl.handle.net/2117/13368 Title: Size of the whole versus number of parts in genomes Authors: Hernández Fernández, Antonio; Baixeries i Juvillà, Jaume; Forns, Núria; Ferrer Cancho, Ramon Abstract: It is known that chromosome number tends to decrease as genome size increases in angiosperm plants. Here the relationship between number of parts (the chromosomes) and size of the whole (the genome) is studied for other groups of organisms from different kingdoms. Two major results are obtained. First, the finding of relationships of the kind "the more parts the smaller the whole" as in angiosperms, but also relationships of the kind "the more parts the larger the whole". Second, these dependencies are not linear in general. The implications of the dependencies between genome size and chromosome number are two-fold. First, they indicate that arguments against the relevance of the finding of negative correlations consistent with Menzerath-Altmann law (a linguistic law that relates the size of the parts with the size of the whole) in genomes are seriously flawed. Second, they unravel the weakness of a recent model of chromosome lengths based upon random breakage that assumes that chromosome number and genome size are independent. Wed, 28 Sep 2011 08:53:18 GMT http://hdl.handle.net/2117/13368 2011-09-28T08:53:18Z Hernández Fernández, Antonio; Baixeries i Juvillà, Jaume; Forns, Núria; Ferrer Cancho, Ramon no It is known that chromosome number tends to decrease as genome size increases in angiosperm plants. Here the relationship between number of parts (the chromosomes) and size of the whole (the genome) is studied for other groups of organisms from different kingdoms. Two major results are obtained. First, the finding of relationships of the kind "the more parts the smaller the whole" as in angiosperms, but also relationships of the kind "the more parts the larger the whole". Second, these dependencies are not linear in general. The implications of the dependencies between genome size and chromosome number are two-fold. First, they indicate that arguments against the relevance of the finding of negative correlations consistent with Menzerath-Altmann law (a linguistic law that relates the size of the parts with the size of the whole) in genomes are seriously flawed. Second, they unravel the weakness of a recent model of chromosome lengths based upon random breakage that assumes that chromosome number and genome size are independent. http://hdl.handle.net/2117/12055 Title: Estimating the horizon of predictability in time-series predictions using inductive modelling tools Authors: López Herrera, Josefina; Cellier, François E.; Cembrano Gennari, Gabriela Abstract: This paper deals with the assessment of how far into the future a time series can be safely predicted using inductive modelling and extrapolation techniques. Three different time series representing the water demand of the city of Barcelona, another characterizing the water demand of a section of the city of Rotterdam, and a third describing weather data for the city of Tucson. Fuzzy inductive reasoning (FIR) is used to predict future values of these time series on the basis of their own past. FIR predictions come with two different built-in measures of confidence that can be used to obtain a quantitative estimate of how far into the future a time series can be predicted. Thu, 24 Mar 2011 18:15:27 GMT http://hdl.handle.net/2117/12055 2011-03-24T18:15:27Z López Herrera, Josefina; Cellier, François E.; Cembrano Gennari, Gabriela no This paper deals with the assessment of how far into the future a time series can be safely predicted using inductive modelling and extrapolation techniques. Three different time series representing the water demand of the city of Barcelona, another characterizing the water demand of a section of the city of Rotterdam, and a third describing weather data for the city of Tucson. Fuzzy inductive reasoning (FIR) is used to predict future values of these time series on the basis of their own past. FIR predictions come with two different built-in measures of confidence that can be used to obtain a quantitative estimate of how far into the future a time series can be predicted. http://hdl.handle.net/2117/10845 Title: Horn query learning with multiple refinement Authors: Sierra Santibáñez, Josefina; Santibáñez Velilla, Josefina Abstract: In this paper we try to understand the heuristics that underlie the decisions made by the Horn query learning algorithm proposed in [1]. We take advantage of our explicit representation of such heuristics in order to present an alternative termination proof for the algorithm, as well as to justify its decisions by showing that they always guarantee that the negative examples in the sequence maintained by the algorithm violate different clauses in the target formula. Finally, we propose a new algorithm that allows multiple refinement when we can prove that such a refinement does not affect the independence of the negative examples in the sequence maintained by the algorithm. Thu, 30 Dec 2010 09:01:50 GMT http://hdl.handle.net/2117/10845 2010-12-30T09:01:50Z Sierra Santibáñez, Josefina; Santibáñez Velilla, Josefina no Horn clauses, Learning (artificial intelligence), Query processing In this paper we try to understand the heuristics that underlie the decisions made by the Horn query learning algorithm proposed in [1]. We take advantage of our explicit representation of such heuristics in order to present an alternative termination proof for the algorithm, as well as to justify its decisions by showing that they always guarantee that the negative examples in the sequence maintained by the algorithm violate different clauses in the target formula. Finally, we propose a new algorithm that allows multiple refinement when we can prove that such a refinement does not affect the independence of the negative examples in the sequence maintained by the algorithm. http://hdl.handle.net/2117/6835 Title: Mining frequent closed rooted trees Authors: Balcázar Navarro, José Luis; Bifet Figuerol, Albert Carles; Lozano Bojados, Antoni Abstract: Many knowledge representation mechanisms are based on tree-like structures, thus symbolizing the fact that certain pieces of information are related in one sense or another. There exists a well-studied process of closure-based data mining in the itemset framework: we consider the extension of this process into trees. We focus mostly on the case where labels on the nodes are nonexistent or unreliable, and discuss algorithms for closurebased mining that only rely on the root of the tree and the link structure. We provide a notion of intersection that leads to a deeper understanding of the notion of support-based closure, in terms of an actual closure operator. We describe combinatorial characterizations and some properties of ordered trees, discuss their applicability to unordered trees, and rely on them to design efficient algorithms for mining frequent closed subtrees both in the ordered and the unordered settings. Empirical validations and comparisons with alternative algorithms are provided. Tue, 30 Mar 2010 09:00:52 GMT http://hdl.handle.net/2117/6835 2010-03-30T09:00:52Z Balcázar Navarro, José Luis; Bifet Figuerol, Albert Carles; Lozano Bojados, Antoni no Many knowledge representation mechanisms are based on tree-like structures, thus symbolizing the fact that certain pieces of information are related in one sense or another. There exists a well-studied process of closure-based data mining in the itemset framework: we consider the extension of this process into trees. We focus mostly on the case where labels on the nodes are nonexistent or unreliable, and discuss algorithms for closurebased mining that only rely on the root of the tree and the link structure. We provide a notion of intersection that leads to a deeper understanding of the notion of support-based closure, in terms of an actual closure operator. We describe combinatorial characterizations and some properties of ordered trees, discuss their applicability to unordered trees, and rely on them to design efficient algorithms for mining frequent closed subtrees both in the ordered and the unordered settings. Empirical validations and comparisons with alternative algorithms are provided.