Guillermo M. Mallén Fullerton | Universidad Iberoamericana - Mexico (original) (raw)

Uploads

Papers by Guillermo M. Mallén Fullerton

Dynamical Systems - Analytical and Computational Techniques, 2017

Preservation is related to local asymptotic stability in nonlinear systems by using dynamical sys... more Preservation is related to local asymptotic stability in nonlinear systems by using dynamical systems tools. It is known that a system, which is stable, asymptotically stable, or unstable at origin, through a transformation can remain stable, asymptotically stable, or unstable. Some systems permit partition of its nonlinear equation in a linear and nonlinear part. Some authors have stated that such systems preserve their local asymptotic stability through the transformations on their linear part. The preservation of synchronization is a typical application of these types of tools and it is considered an interesting topic by scientific community. This chapter is devoted to extend the methodology of the dynamical systems through a partition in the linear part and the nonlinear part, transforming the linear part using the Tracy-Singh product in the Jacobian matrix. This methodology preserves the structure of signs through the real part of eigenvalues of the Jacobian matrix of the dynamical systems in their equilibrium points. The principal part of this methodology is that it permits to extend the fundamental theorems of the dynamical systems, given a linear transformation. The results allow us to infer the hyperbolicity, the stability and the synchronization of transformed systems of higher dimension.

The Astrophysical Journal, 2003

Planet transit searches promise to be the next breakthrough for planet detection, and will bring ... more Planet transit searches promise to be the next breakthrough for planet detection, and will bring extrasolar planet characterization into a new era. Every transiting planet discovered will have a measured radius, which will provide constraints on planet composition, evolution, and migration history. Together with radial velocity measurements, the absolute mass of every transiting planet will be determined. In this paper we discuss the design considerations of the EXPLORE (EXtra-solar PLanet Occultation REsearch) project, a series of transiting planet searches using 4-m-class telescopes to continuously monitor a single field of stars in the Galactic Plane in each ∼ 2 week observing campaign. We discuss the general factors which determine the efficiency and the number of planets found by a transit search, including time sampling strategy and field selection. The primary goal is to select the most promising planet candidates for radial velocity follow-up observations. We show that with very high photometric precision light curves that have frequent time sampling and at least two detected transits, it is possible to uniquely solve for the main parameters of the eclipsing system (including planet radius) based on several important assumptions about the central star. Together with a measured spectral type for the star, this unique solution for orbital parameters provides a powerful method for ruling out most contaminants to transiting planet candidates. For the EXPLORE project, radial velocity follow-up observations for companion mass determination of the best candidates are done on 8-m-class telescopes within two or three months of the photometric campaigns. This same-season follow-up is made possible by the use of efficient pipelines to produce high quality light curves within weeks of the observations. We conclude by presenting early results from our first search, EXPLORE I, in which we reached < 1% rms photometric precision (measured over a full night) on ∼37,000 stars to I ≤ 18.2.

… in Research on …, 2003

The EXPLORE Project is a series of searches for transiting extrasolar planets using large-format ... more The EXPLORE Project is a series of searches for transiting extrasolar planets using large-format mosaic CCD cameras on 4-m class telescopes. Radial velocity follow-up is done on transiting planet candidates with 8-10m class telescopes. We present a summary of transit candidates from the EXPLORE Project for which we have radial velocity data.

The DNA fragment assembly is an important phase required to obtain complete genomes. Optimization... more The DNA fragment assembly is an important phase required to obtain complete genomes. Optimization using nature inspired algorithms has been proposed by several authors. We present another nature inspired algorithm based on Particle Swarm Optimization and Differential Evolution. These algorithms are compared using a set of common benchmarks and show that our proposed algorithm has some advantages. We also applied the Traveling Salesman Problem (TSP) with better results than the nature inspired algorithms as we could obtain the true optima for 16 commonly used benchmarks for the first time to the best of our knowledge. The benchmarks are much smaller than the real organism assembly problems and scaling up from the benchmarks to real organisms presents important challenges. We propose a way to solve the scale up problems and test them using the Staphylococcus aureus COL Main Chromosome with the TSP approach. Keywords— DNA, Fragment Assembly, Particle Swarm Optimization, Traveling Sales...

2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 2014

The Fragment Assembly Problem is a major component of the DNA sequencing process that is identifi... more The Fragment Assembly Problem is a major component of the DNA sequencing process that is identified as being NP-Hard. A variety of approaches to this problem have been used, including overlap-layout-consensus, de Bruijn graphs, and greedy graph based algorithms. The overlap-layout-consensus approach is one of the more popular strategies which has been studied on a collection of heuristics and metaheuristics. In this study heuristics and Genetic Algorithm variations are combined to exploit their respective benefits. These algorithms were able to produce results that surpassed the best results obtained by a collection of state-of-the-art metaheuristics on ten of sixteen popular benchmark data sets.

2013 IEEE Congress on Evolutionary Computation, 2013

ABSTRACT The DNA fragment assembly is an important phase required to obtain complete genomes. Opt... more ABSTRACT The DNA fragment assembly is an important phase required to obtain complete genomes. Optimization using nature inspired algorithms has been proposed by several authors. We present another nature inspired algorithm based on Particle Swarm Optimization and Differential Evolution. These algorithms are compared using a set of common benchmarks and showing some advantages in our proposed algorithm. We also applied the Traveling Salesman Problem (TSP) with better results than the nature inspired algorithms as we could obtain the true optima for 16 commonly used benchmarks for the first time to the best of our knowledge. The benchmarks are much smaller than the real organism assembly problems and scaling up from the benchmarks to real organisms presents important challenges. We propose a way to solve the scale up problems and test them using the Staphylococcus aureus COL Main Chromosome with the TSP approach.

DNA fragment assembly requirements have generated an important computational problem created by t... more DNA fragment assembly requirements have generated an important computational problem created by their structure and the volume of data. Therefore, it is important to develop algorithms able to produce high-quality information that use computer resources efficiently. Such an algorithm, using graph theory, is introduced in the present article. We first determine the overlaps between DNA fragments, obtaining the edges of a directed graph; with this information, the next step is to construct an adjacency list with some particularities. Using the adjacency list, it is possible to obtain the DNA contigs (group of assembled fragments building a contiguous element) using graph theory. We performed a set of experiments on real DNA data and compared our results to those obtained with common assemblers (Edena and Velvet). Finally, we searched the contigs in the original genome, in our results and in those of Edena and Velvet.

DNA fragment assembly represents an important challenge to the development of efficient and pract... more DNA fragment assembly represents an important challenge to the development of efficient and practical algorithms due to the large number of elements to be assembled. In this study, we present some graph theoretical linear time algorithms to solve the problem. To achieve linear time complexity, a heap with constant time operations was developed, for the special case where the edge weights are integers and do not depend on the problem size. The experiments presented show that modified classical graph theoretical algorithms can solve the DNA fragment assembly problem efficiently.

International Journal of Bio-Inspired Computation, 2013

Many computational intelligence approaches have been used for the fragment assembly problem. Howe... more Many computational intelligence approaches have been used for the fragment assembly problem. However, the comparison and analysis of these approaches is difficult due to the lack of availability of standard benchmarks. Although similar datasets may be used as a starting point, there is not enough information to reproduce the exact overlaps matrix for the fragments used by the various approaches, creating a problem for consistency. This paper presents a collection of benchmark datasets for a wide range of fragment lengths, number of fragments, and sequence lengths, along with a description of the method used to produce them. A website has been created to maintain the datasets and the tables of results at http://chac.sis.uia.mx/fragbench/. Researchers are invited to add to the datasets by following the method described, as well as to submit results obtained by their algorithms on the benchmarks.

International Journal of Bio-Inspired Computation, 2013

Dynamical Systems - Analytical and Computational Techniques, 2017

Preservation is related to local asymptotic stability in nonlinear systems by using dynamical sys... more Preservation is related to local asymptotic stability in nonlinear systems by using dynamical systems tools. It is known that a system, which is stable, asymptotically stable, or unstable at origin, through a transformation can remain stable, asymptotically stable, or unstable. Some systems permit partition of its nonlinear equation in a linear and nonlinear part. Some authors have stated that such systems preserve their local asymptotic stability through the transformations on their linear part. The preservation of synchronization is a typical application of these types of tools and it is considered an interesting topic by scientific community. This chapter is devoted to extend the methodology of the dynamical systems through a partition in the linear part and the nonlinear part, transforming the linear part using the Tracy-Singh product in the Jacobian matrix. This methodology preserves the structure of signs through the real part of eigenvalues of the Jacobian matrix of the dynamical systems in their equilibrium points. The principal part of this methodology is that it permits to extend the fundamental theorems of the dynamical systems, given a linear transformation. The results allow us to infer the hyperbolicity, the stability and the synchronization of transformed systems of higher dimension.

The Astrophysical Journal, 2003

Planet transit searches promise to be the next breakthrough for planet detection, and will bring ... more Planet transit searches promise to be the next breakthrough for planet detection, and will bring extrasolar planet characterization into a new era. Every transiting planet discovered will have a measured radius, which will provide constraints on planet composition, evolution, and migration history. Together with radial velocity measurements, the absolute mass of every transiting planet will be determined. In this paper we discuss the design considerations of the EXPLORE (EXtra-solar PLanet Occultation REsearch) project, a series of transiting planet searches using 4-m-class telescopes to continuously monitor a single field of stars in the Galactic Plane in each ∼ 2 week observing campaign. We discuss the general factors which determine the efficiency and the number of planets found by a transit search, including time sampling strategy and field selection. The primary goal is to select the most promising planet candidates for radial velocity follow-up observations. We show that with very high photometric precision light curves that have frequent time sampling and at least two detected transits, it is possible to uniquely solve for the main parameters of the eclipsing system (including planet radius) based on several important assumptions about the central star. Together with a measured spectral type for the star, this unique solution for orbital parameters provides a powerful method for ruling out most contaminants to transiting planet candidates. For the EXPLORE project, radial velocity follow-up observations for companion mass determination of the best candidates are done on 8-m-class telescopes within two or three months of the photometric campaigns. This same-season follow-up is made possible by the use of efficient pipelines to produce high quality light curves within weeks of the observations. We conclude by presenting early results from our first search, EXPLORE I, in which we reached < 1% rms photometric precision (measured over a full night) on ∼37,000 stars to I ≤ 18.2.

… in Research on …, 2003

The EXPLORE Project is a series of searches for transiting extrasolar planets using large-format ... more The EXPLORE Project is a series of searches for transiting extrasolar planets using large-format mosaic CCD cameras on 4-m class telescopes. Radial velocity follow-up is done on transiting planet candidates with 8-10m class telescopes. We present a summary of transit candidates from the EXPLORE Project for which we have radial velocity data.

The DNA fragment assembly is an important phase required to obtain complete genomes. Optimization... more The DNA fragment assembly is an important phase required to obtain complete genomes. Optimization using nature inspired algorithms has been proposed by several authors. We present another nature inspired algorithm based on Particle Swarm Optimization and Differential Evolution. These algorithms are compared using a set of common benchmarks and show that our proposed algorithm has some advantages. We also applied the Traveling Salesman Problem (TSP) with better results than the nature inspired algorithms as we could obtain the true optima for 16 commonly used benchmarks for the first time to the best of our knowledge. The benchmarks are much smaller than the real organism assembly problems and scaling up from the benchmarks to real organisms presents important challenges. We propose a way to solve the scale up problems and test them using the Staphylococcus aureus COL Main Chromosome with the TSP approach. Keywords— DNA, Fragment Assembly, Particle Swarm Optimization, Traveling Sales...

2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 2014

The Fragment Assembly Problem is a major component of the DNA sequencing process that is identifi... more The Fragment Assembly Problem is a major component of the DNA sequencing process that is identified as being NP-Hard. A variety of approaches to this problem have been used, including overlap-layout-consensus, de Bruijn graphs, and greedy graph based algorithms. The overlap-layout-consensus approach is one of the more popular strategies which has been studied on a collection of heuristics and metaheuristics. In this study heuristics and Genetic Algorithm variations are combined to exploit their respective benefits. These algorithms were able to produce results that surpassed the best results obtained by a collection of state-of-the-art metaheuristics on ten of sixteen popular benchmark data sets.

2013 IEEE Congress on Evolutionary Computation, 2013

ABSTRACT The DNA fragment assembly is an important phase required to obtain complete genomes. Opt... more ABSTRACT The DNA fragment assembly is an important phase required to obtain complete genomes. Optimization using nature inspired algorithms has been proposed by several authors. We present another nature inspired algorithm based on Particle Swarm Optimization and Differential Evolution. These algorithms are compared using a set of common benchmarks and showing some advantages in our proposed algorithm. We also applied the Traveling Salesman Problem (TSP) with better results than the nature inspired algorithms as we could obtain the true optima for 16 commonly used benchmarks for the first time to the best of our knowledge. The benchmarks are much smaller than the real organism assembly problems and scaling up from the benchmarks to real organisms presents important challenges. We propose a way to solve the scale up problems and test them using the Staphylococcus aureus COL Main Chromosome with the TSP approach.

DNA fragment assembly requirements have generated an important computational problem created by t... more DNA fragment assembly requirements have generated an important computational problem created by their structure and the volume of data. Therefore, it is important to develop algorithms able to produce high-quality information that use computer resources efficiently. Such an algorithm, using graph theory, is introduced in the present article. We first determine the overlaps between DNA fragments, obtaining the edges of a directed graph; with this information, the next step is to construct an adjacency list with some particularities. Using the adjacency list, it is possible to obtain the DNA contigs (group of assembled fragments building a contiguous element) using graph theory. We performed a set of experiments on real DNA data and compared our results to those obtained with common assemblers (Edena and Velvet). Finally, we searched the contigs in the original genome, in our results and in those of Edena and Velvet.

DNA fragment assembly represents an important challenge to the development of efficient and pract... more DNA fragment assembly represents an important challenge to the development of efficient and practical algorithms due to the large number of elements to be assembled. In this study, we present some graph theoretical linear time algorithms to solve the problem. To achieve linear time complexity, a heap with constant time operations was developed, for the special case where the edge weights are integers and do not depend on the problem size. The experiments presented show that modified classical graph theoretical algorithms can solve the DNA fragment assembly problem efficiently.

International Journal of Bio-Inspired Computation, 2013

Many computational intelligence approaches have been used for the fragment assembly problem. Howe... more Many computational intelligence approaches have been used for the fragment assembly problem. However, the comparison and analysis of these approaches is difficult due to the lack of availability of standard benchmarks. Although similar datasets may be used as a starting point, there is not enough information to reproduce the exact overlaps matrix for the fragments used by the various approaches, creating a problem for consistency. This paper presents a collection of benchmark datasets for a wide range of fragment lengths, number of fragments, and sequence lengths, along with a description of the method used to produce them. A website has been created to maintain the datasets and the tables of results at http://chac.sis.uia.mx/fragbench/. Researchers are invited to add to the datasets by following the method described, as well as to submit results obtained by their algorithms on the benchmarks.

International Journal of Bio-Inspired Computation, 2013