Departament de Ciències de la Computació
http://hdl.handle.net/2117/3971
2016-02-12T09:55:58ZThe extracellular N-terminal domain suffices to discriminate class C G Protein-Coupled Receptor subtypes from n-grams of their sequences
http://hdl.handle.net/2117/82851
The extracellular N-terminal domain suffices to discriminate class C G Protein-Coupled Receptor subtypes from n-grams of their sequences
König, Caroline; Alquézar Mancho, René; Vellido Alcacena, Alfredo; Giraldo Arjonilla, Jesús
The investigation of protein functionality often relies on the knowledge of crystal 3-D structure. This structure is not always known or easily unravelled, which is the case of eukaryotic cell membrane proteins such as G Protein-Coupled Receptors (GPCRs) and specially of those of class C, which are the target of the current study. In the absence of information about tertiary or quaternary structures, functionality can be investigated from the primary structure, that is, from the amino acid sequence. In previous research, we found that the different subtypes of class C GPCRs could be discriminated with a high level of accuracy from the n-gram transformation of their complete primary sequences, using a method that combined two-stage feature selection with kernel classifiers. This study aims at discovering whether subunits of the complete sequence retain such discrimination capabilities. We report experiments that show that the extracellular N-terminal domain of the receptor suffices to retain the classification accuracy of the complete sequence and that it does so using a reduced selection of n-grams whose length of up to five amino acids opens up an avenue for class C GPCR signature motif discovery.
2016-02-11T12:53:37ZKönig, CarolineAlquézar Mancho, RenéVellido Alcacena, AlfredoGiraldo Arjonilla, JesúsThe investigation of protein functionality often relies on the knowledge of crystal 3-D structure. This structure is not always known or easily unravelled, which is the case of eukaryotic cell membrane proteins such as G Protein-Coupled Receptors (GPCRs) and specially of those of class C, which are the target of the current study. In the absence of information about tertiary or quaternary structures, functionality can be investigated from the primary structure, that is, from the amino acid sequence. In previous research, we found that the different subtypes of class C GPCRs could be discriminated with a high level of accuracy from the n-gram transformation of their complete primary sequences, using a method that combined two-stage feature selection with kernel classifiers. This study aims at discovering whether subunits of the complete sequence retain such discrimination capabilities. We report experiments that show that the extracellular N-terminal domain of the receptor suffices to retain the classification accuracy of the complete sequence and that it does so using a reduced selection of n-grams whose length of up to five amino acids opens up an avenue for class C GPCR signature motif discovery.Rewriting in categories of spans
http://hdl.handle.net/2117/82838
Rewriting in categories of spans
Monserrat, Miquel; Rosselló, Francesc; Torrens, Joan; Valiente Feruglio, Gabriel Alejandro
Single-pushout transformation in a category of spans, in some sense a
generalization of the usual notion of partial morphism,
is studied in this paper. Contrary to the usual notion of partial
morphism, spans are single objects instead of equivalence
classes. A necessary condition for the existence of the pushout of two spans is
established which involves properties of the base category, from which the
category of spans is derived, as well as properties of the spans themselves.
Several interesting categories of partial morphisms of hypergraphs
are proved to satisfy the necessary condition.
2016-02-11T11:24:40ZMonserrat, MiquelRosselló, FrancescTorrens, JoanValiente Feruglio, Gabriel AlejandroSingle-pushout transformation in a category of spans, in some sense a
generalization of the usual notion of partial morphism,
is studied in this paper. Contrary to the usual notion of partial
morphism, spans are single objects instead of equivalence
classes. A necessary condition for the existence of the pushout of two spans is
established which involves properties of the base category, from which the
category of spans is derived, as well as properties of the spans themselves.
Several interesting categories of partial morphisms of hypergraphs
are proved to satisfy the necessary condition.Algebraic transformation of unary partial algebras I: double-pushout approach
http://hdl.handle.net/2117/82835
Algebraic transformation of unary partial algebras I: double-pushout approach
Burmeister, P.; Rossello, F.; Torrens, J.; Valiente Feruglio, Gabriel Alejandro
The transformation of total graph structures has been studied from the
algebraic point of view over more than two decades now, and it has
motivated the development of the so-called double-pushout and
single-pushout approaches to graph transformation. In this
article we extend the double-pushout approach to the algebraic
transformation of partial many-sorted unary algebras.
Such a generalization has been motivated by the need to model the
transformation of structures which are richer and more complex than
acyclic graphs and hypergraphs. The main result presented in this
article is an algebraic characterization of the double-pushout
transformation in the categories of all homomorphisms and all closed
homomorphisms of unary partial algebras over a given signature,
together with a corresponding operational characterization which may
serve as a basis for implementation.
Moreover, both categories are shown to satisfy the strongest of the
HLR (High Level Replacement) conditions with respect to closed
monomorphisms. HLR conditions are
fundamental to rewriting because they guarantee the satisfaction of many
rewriting theorems concerning confluence, parallelism and
concurrency.
2016-02-11T11:17:38ZBurmeister, P.Rossello, F.Torrens, J.Valiente Feruglio, Gabriel AlejandroThe transformation of total graph structures has been studied from the
algebraic point of view over more than two decades now, and it has
motivated the development of the so-called double-pushout and
single-pushout approaches to graph transformation. In this
article we extend the double-pushout approach to the algebraic
transformation of partial many-sorted unary algebras.
Such a generalization has been motivated by the need to model the
transformation of structures which are richer and more complex than
acyclic graphs and hypergraphs. The main result presented in this
article is an algebraic characterization of the double-pushout
transformation in the categories of all homomorphisms and all closed
homomorphisms of unary partial algebras over a given signature,
together with a corresponding operational characterization which may
serve as a basis for implementation.
Moreover, both categories are shown to satisfy the strongest of the
HLR (High Level Replacement) conditions with respect to closed
monomorphisms. HLR conditions are
fundamental to rewriting because they guarantee the satisfaction of many
rewriting theorems concerning confluence, parallelism and
concurrency.Logic as general rationality: a survey
http://hdl.handle.net/2117/82830
Logic as general rationality: a survey
Sales Porta, Ton
Logic and probability, which happen to share historical origins,
are asked nowadays to solve new problems such as reasoning under
uncertainty, or with incomplete information or imprecisely
formulated statements. The paper surveys how both fields have striven
to solve them and how a common formalism, already suggested by
Kolmogorov and Popper, may be what both disciplines lack to become
a general theory of rationality.
2016-02-11T10:59:05ZSales Porta, TonLogic and probability, which happen to share historical origins,
are asked nowadays to solve new problems such as reasoning under
uncertainty, or with incomplete information or imprecisely
formulated statements. The paper surveys how both fields have striven
to solve them and how a common formalism, already suggested by
Kolmogorov and Popper, may be what both disciplines lack to become
a general theory of rationality.Computational coverage of TLG: displacement
http://hdl.handle.net/2117/82818
Computational coverage of TLG: displacement
Morrill, Glyn; Valentín Fernández Gallart, José Oriol
This paper reports on the coverage of TLG of Morrill (1994) and Moortgat (1997), and on how it has been computer implemented. We computer-analyse examples of displacement: discontinuous idioms, quantification, (medial) relativisation, VP ellipsis, (medial) pied piping, appositive relativisation, parentheticals, gapping, comparative
subdeletion, and reflexivisation, and, in the appendix, Dutch verb raising and crossserial dependency.
2016-02-11T09:25:44ZMorrill, GlynValentín Fernández Gallart, José OriolThis paper reports on the coverage of TLG of Morrill (1994) and Moortgat (1997), and on how it has been computer implemented. We computer-analyse examples of displacement: discontinuous idioms, quantification, (medial) relativisation, VP ellipsis, (medial) pied piping, appositive relativisation, parentheticals, gapping, comparative
subdeletion, and reflexivisation, and, in the appendix, Dutch verb raising and crossserial dependency.Computational coverage of TLG: nonlinearity
http://hdl.handle.net/2117/82813
Computational coverage of TLG: nonlinearity
Morrill, Glyn; Valentín Fernández Gallart, José Oriol
We study nonlinear connectives (exponentials) in the context of Type Logical Grammar (TLG). We devise four conservative extensions of the displacement calculus with brackets, Db!, Db!?, Db!b and Db!b?r which contain the universal and existential exponential modalities of linear logic (LL). These modalities do not exhibit the same structural properties as in LL, which in TLG are especially adapted for linguistic purposes. The universal modality ! for TLG allows only the commutative and contraction rules, but not weakening, whereas the existential modality ? allows the so-called (intuitionistic) Mingle rule, which derives a restricted version of weakening. We provide a Curry-Howard labelling for both exponential connectives. As it turns out, controlled contraction by ! gives a way to account for the so-called parasitic gaps, and controlled Mingle ? iteration, in particular iterated coordination.
Finally, the four calculi are proved to be Cut-Free, and decidability is proved for a linguistically suffcient special case of Db!b?r (and hence
Db!b).
2016-02-11T09:02:19ZMorrill, GlynValentín Fernández Gallart, José OriolWe study nonlinear connectives (exponentials) in the context of Type Logical Grammar (TLG). We devise four conservative extensions of the displacement calculus with brackets, Db!, Db!?, Db!b and Db!b?r which contain the universal and existential exponential modalities of linear logic (LL). These modalities do not exhibit the same structural properties as in LL, which in TLG are especially adapted for linguistic purposes. The universal modality ! for TLG allows only the commutative and contraction rules, but not weakening, whereas the existential modality ? allows the so-called (intuitionistic) Mingle rule, which derives a restricted version of weakening. We provide a Curry-Howard labelling for both exponential connectives. As it turns out, controlled contraction by ! gives a way to account for the so-called parasitic gaps, and controlled Mingle ? iteration, in particular iterated coordination.
Finally, the four calculi are proved to be Cut-Free, and decidability is proved for a linguistically suffcient special case of Db!b?r (and hence
Db!b).Hybrid methodologies for electricity load forecasting: Entropy-based feature selection with machine learning and soft computing techniques
http://hdl.handle.net/2117/82810
Hybrid methodologies for electricity load forecasting: Entropy-based feature selection with machine learning and soft computing techniques
Jurado Gómez, Sergio; Nebot Castells, M. Àngela; Múgica Álvarez, Francisco; Avellana, Narcís
Scientific community is currently doing a great effort of research in the area of Smart Grids because energy production, distribution, and consumption play a critical role in the sustainability of the planet. The main challenge lies in intelligently integrating the actions of all users connected to the grid. In this context, electricity load forecasting methodologies is a key component for demand-side management. This research compares the accuracy of different Machine Learning methodologies for the hourly energy forecasting in buildings. The main goal of this work is to demonstrate the performance of these models and their scalability for different consumption profiles. We propose a hybrid methodology that combines feature selection based on entropies with soft computing and machine learning approaches, he. Fuzzy Inductive Reasoning, Random Forest and Neural Networks. They are also compared with a traditional statistical technique ARIMA (Auto Regressive Integrated Moving Average). In addition, in contrast to the general approaches where offline modelling takes considerable time, the approaches discussed in this work generate fast and reliable models, with low computational costs. These approaches could be embedded, for instance, in a second generation of smart meters, where they could generate on-site electricity forecasting of the next hours, or even trade the excess of energy.
2016-02-11T08:26:50ZJurado Gómez, SergioNebot Castells, M. ÀngelaMúgica Álvarez, FranciscoAvellana, NarcísScientific community is currently doing a great effort of research in the area of Smart Grids because energy production, distribution, and consumption play a critical role in the sustainability of the planet. The main challenge lies in intelligently integrating the actions of all users connected to the grid. In this context, electricity load forecasting methodologies is a key component for demand-side management. This research compares the accuracy of different Machine Learning methodologies for the hourly energy forecasting in buildings. The main goal of this work is to demonstrate the performance of these models and their scalability for different consumption profiles. We propose a hybrid methodology that combines feature selection based on entropies with soft computing and machine learning approaches, he. Fuzzy Inductive Reasoning, Random Forest and Neural Networks. They are also compared with a traditional statistical technique ARIMA (Auto Regressive Integrated Moving Average). In addition, in contrast to the general approaches where offline modelling takes considerable time, the approaches discussed in this work generate fast and reliable models, with low computational costs. These approaches could be embedded, for instance, in a second generation of smart meters, where they could generate on-site electricity forecasting of the next hours, or even trade the excess of energy.Visual characterization of misclassified Class C GPCRs through Manifold-based machine learning methods
http://hdl.handle.net/2117/82781
Visual characterization of misclassified Class C GPCRs through Manifold-based machine learning methods
Cárdenas Domínguez, Martha Ivón; Vellido Alcacena, Alfredo; König, Caroline; Alquézar Mancho, René; Giraldo Arjonilla, Jesús
G-protein-coupled receptors are cell membrane proteins of great interest in biology and pharmacology. Previous analysis of Class C of these receptors has revealed the existence of an upper boundary on the accuracy that can be achieved in the classification of their standard subtypes from the unaligned transformation of their primary sequences. To further investigate this apparent boundary, the focus of the analysis in this paper is placed on receptor sequences that were previously misclassified using supervised learning methods. In our experiments, these sequences are visualized using a nonlinear dimensionality reduction technique and phylogenetic trees. They are subsequently characterized against the rest of the data and, particularly, against the rest of cases of their own subtype. This exploratory visualization should help us to discriminate between different types of misclassification and to build hypotheses about database quality problems and the extent to which GPCR sequence transformations limit subtype discriminability. The reported experiments provide a proof of concept for the proposed method.
2016-02-10T13:39:14ZCárdenas Domínguez, Martha IvónVellido Alcacena, AlfredoKönig, CarolineAlquézar Mancho, RenéGiraldo Arjonilla, JesúsG-protein-coupled receptors are cell membrane proteins of great interest in biology and pharmacology. Previous analysis of Class C of these receptors has revealed the existence of an upper boundary on the accuracy that can be achieved in the classification of their standard subtypes from the unaligned transformation of their primary sequences. To further investigate this apparent boundary, the focus of the analysis in this paper is placed on receptor sequences that were previously misclassified using supervised learning methods. In our experiments, these sequences are visualized using a nonlinear dimensionality reduction technique and phylogenetic trees. They are subsequently characterized against the rest of the data and, particularly, against the rest of cases of their own subtype. This exploratory visualization should help us to discriminate between different types of misclassification and to build hypotheses about database quality problems and the extent to which GPCR sequence transformations limit subtype discriminability. The reported experiments provide a proof of concept for the proposed method.El escritor crítico de artículos
http://hdl.handle.net/2117/82780
El escritor crítico de artículos
Pérez Poch, Antoni
Se introducen una serie de reflexiones sobre la escritura eficiente de artículos científicos, y los factores que intervienen en el proceso.
2016-02-10T13:27:58ZPérez Poch, AntoniSe introducen una serie de reflexiones sobre la escritura eficiente de artículos científicos, y los factores que intervienen en el proceso.Characterizing chronic disease and polymedication prescription patterns from electronic health records
http://hdl.handle.net/2117/82778
Characterizing chronic disease and polymedication prescription patterns from electronic health records
Zamora, Martí; Baradad, Manel; Amado, Ester; Cordomí, Sílvia; Limón, Esther; Ribera, Juliana; Arias Vicente, Marta; Gavaldà Mestre, Ricard
Population aging in developed countries brings an increased prevalence of chronic disease and of polymedication-patients with several prescribed types of medication. Attention to chronic, polymedicated patients is a priority for its high cost and the associated risks, and tools for analyzing, understanding, and managing this reality are becoming necessary. We describe a prototype of a system for discovering, analyzing, and visualizing the co-occurrence of diagnostics, interventions, and medication prescriptions in a large patient database. The final tool is intended to be used both by health managers and planners and for primary care clinicians in direct contact with patients (for example for detecting unusual disease patterns and incorrect or missing medication). At the core of the analysis module there is a representation of diagnostics and medications as a hypergraph, and the most crucial functionalities rely on hypergraph transversal/variants of association rule discovery methods, with particular emphasis on discovering surprising or alarming combinations. The test database comes from the primary care system in the area of Barcelona for 2013, with over 1.6 million potential patients and almost 20 million diagnostics and prescriptions.
2016-02-10T13:17:39ZZamora, MartíBaradad, ManelAmado, EsterCordomí, SílviaLimón, EstherRibera, JulianaArias Vicente, MartaGavaldà Mestre, RicardPopulation aging in developed countries brings an increased prevalence of chronic disease and of polymedication-patients with several prescribed types of medication. Attention to chronic, polymedicated patients is a priority for its high cost and the associated risks, and tools for analyzing, understanding, and managing this reality are becoming necessary. We describe a prototype of a system for discovering, analyzing, and visualizing the co-occurrence of diagnostics, interventions, and medication prescriptions in a large patient database. The final tool is intended to be used both by health managers and planners and for primary care clinicians in direct contact with patients (for example for detecting unusual disease patterns and incorrect or missing medication). At the core of the analysis module there is a representation of diagnostics and medications as a hypergraph, and the most crucial functionalities rely on hypergraph transversal/variants of association rule discovery methods, with particular emphasis on discovering surprising or alarming combinations. The test database comes from the primary care system in the area of Barcelona for 2013, with over 1.6 million potential patients and almost 20 million diagnostics and prescriptions.