arXiv subjects

V. C. Barbosa

Publications and source records attributed to V. C. Barbosa.

18 recordsLinked to original sources

arXiv2011

Experimental analysis of lateral impact on planar brittle material: spatial properties of the cracks

The breakup of glass and alumina plates due to planar impacts on one of their lateral sides is studied. Particular attention is given to investigating the spatial location of the cracks within the plates. Analysis based on a phenomenological model suggests that bifurcations along the cracks' paths are more likely to take place closer to the impact region than far away from it, i. e., the bifurcation probability seems to lower as the perpendicular distance from the impacted lateral in- creases. It is also found that many observables are not sensitive to the plate material used in this work, as long as the fragment multiplicities corresponding to the fragmentation of the plates are similar. This gives support to the universal properties of the fragmentation process reported in for- mer experiments. However, even under the just mentioned circumstances, some spatial observables are capable of distinguishing the material of which the plates are made and, therefore, it suggests that this universality should be carefully investigated.

cond-mat.mtrl-sci↗

arXiv2009

Experimental analysis of lateral impact on planar brittle material

The fragmentation of alumina and glass plates due to lateral impact is studied. A few hundred plates have been fragmented at different impact velocities and the produced fragments are analyzed. The method employed in this work allows one to investigate some geometrical properties of the fragments, besides the traditional size distribution usually studied in former experiments. We found that, although both materials exhibit qualitative similar fragment size distribution function, their geometrical properties appear to be quite different. A schematic model for two-dimensional fragmentation is also presented and its predictions are compared to our experimental results. The comparison suggests that the analysis of the fragments' geometrical properties constitutes a more stringent test of the theoretical models' assumptions than the size distribution.

cond-mat.stat-mech↗

arXiv2005

A methodology for determining amino-acid substitution matrices from set covers

We introduce a new methodology for the determination of amino-acid substitution matrices for use in the alignment of proteins. The new methodology is based on a pre-existing set cover on the set of residues and on the undirected graph that describes residue exchangeability given the set cover. For fixed functional forms indicating how to obtain edge weights from the set cover and, after that, substitution-matrix elements from weighted distances on the graph, the resulting substitution matrix can be checked for performance against some known set of reference alignments and for given gap costs. Finding the appropriate functional forms and gap costs can then be formulated as an optimization problem that seeks to maximize the performance of the substitution matrix on the reference alignment set. We give computational results on the BAliBASE suite using a genetic algorithm for optimization. Our results indicate that it is possible to obtain substitution matrices whose performance is either comparable to or surpasses that of several others, depending on the particular scenario under consideration.

q-bio.QM↗

arXiv2005

Minimal chordal sense of direction and circulant graphs

A sense of direction is an edge labeling on graphs that follows a globally consistent scheme and is known to considerably reduce the complexity of several distributed problems. In this paper, we study a particular instance of sense of direction, called a chordal sense of direction (CSD). In special, we identify the class of k-regular graphs that admit a CSD with exactly k labels (a minimal CSD). We prove that connected graphs in this class are Hamiltonian and that the class is equivalent to that of circulant graphs, presenting an efficient (polynomial-time) way of recognizing it when the graphs' degree k is fixed.

cs.DM↗

arXiv2004

Multiple sequence alignment based on set covers

We introduce a new heuristic for the multiple alignment of a set of sequences. The heuristic is based on a set cover of the residue alphabet of the sequences, and also on the determination of a significant set of blocks comprising subsequences of the sequences to be aligned. These blocks are obtained with the aid of a new data structure, called a suffix-set tree, which is constructed from the input sequences with the guidance of the residue-alphabet set cover and generalizes the well-known suffix tree of the sequence set. We provide performance results on selected BAliBASE amino-acid sequences and compare them with those yielded by some prominent approaches.

q-bio.QM↗

arXiv2004

Local heuristics and the emergence of spanning subgraphs in complex networks

We study the use of local heuristics to determine spanning subgraphs for use in the dissemination of information in complex networks. We introduce two different heuristics and analyze their behavior in giving rise to spanning subgraphs that perform well in terms of allowing every node of the network to be reached, of requiring relatively few messages and small node bandwidth for information dissemination, and also of stretching paths with respect to the underlying network only modestly. We contribute a detailed mathematical analysis of one of the heuristics and provide extensive simulation results on random graphs for both of them. These results indicate that, within certain limits, spanning subgraphs are indeed expected to emerge that perform well in respect to all requirements. We also discuss the spanning subgraphs' inherent resilience to failures and adaptability to topological changes.

cs.NI↗

arXiv2004

Modeling the input history of programs for improved instruction-memory performance

When a program is loaded into memory for execution, the relative position of its basic blocks is crucial, since loading basic blocks that are unlikely to be executed first places them high in the instruction-memory hierarchy only to be dislodged as the execution goes on. In this paper we study the use of Bayesian networks as models of the input history of a program. The main point is the creation of a probabilistic model that persists as the program is run on different inputs and at each new input refines its own parameters in order to reflect the program's input history more accurately. As the model is thus tuned, it causes basic blocks to be reordered so that, upon arrival of the next input for execution, loading the basic blocks into memory automatically takes into account the input history of the program. We report on extensive experiments, whose results demonstrate the efficacy of the overall approach in progressively lowering the execution times of a program on identical inputs placed randomly in a sequence of varied inputs. We provide results on selected SPEC CINT2000 programs and also evaluate our approach as compared to the gcc level-3 optimization and to Pettis-Hansen reordering.

cs.OS↗

arXiv2004

Probabilistic heuristics for disseminating information in networks

We study the problem of disseminating a piece of information through all the nodes of a network, given that it is known originally only to a single node. In the absence of any structural knowledge on the network other than the nodes' neighborhoods, this problem is traditionally solved by flooding all the network's edges. We analyze a recently introduced probabilistic algorithm for flooding and give an alternative probabilistic heuristic that can lead to some cost-effective improvements, like better trade-offs between the message and time complexities involved. We analyze the two algorithms both mathematically and by means of simulations, always within a random-graph framework and considering relevant node-degree distributions.

cs.NI↗

arXiv2004

Cell-centric heuristics for the classification of cellular automata

We study the classification of cellular-automaton update rules into Wolfram's four classes. We start with the notion of the input entropy of a spatiotemporal block in the evolution of a cellular automaton, and build on it by introducing two novel entropy measures, one that is also based on inputs to the cells, the other based on state transitions by the cells. Our two new entropies are both targeted at the classification of update rules by parallel machines, being therefore mindful of the necessary communications requirements; we call them cell-centric input entropy and cell-centric transition entropy to reflect this fact. We report on extensive computational experiments on both one- and two-dimensional cellular automata. These experiments allow us to conclude that the two new entropies possess strong discriminatory capabilities, therefore providing valuable aid in the classification process.

nlin.CG↗

arXiv2003

A graph model for the evolution of specificity in humoral immunity

The immune system protects the body against health-threatening entities, known as antigens, through very complex interactions involving the antigens and the system's own entities. One remarkable feature resulting from such interactions is the immune system's ability to improve its capability to fight antigens commonly found in the individual's environment. This adaptation process is called the evolution of specificity. In this paper, we introduce a new mathematical model for the evolution of specificity in humoral immunity, based on Jerne's functional, or idiotypic, network. The evolution of specificity is modeled as the dynamic updating of connection weights in a graph whose nodes are related to the network's idiotypes. At the core of this weight-updating mechanism are the increase in specificity caused by clonal selection and the decrease in specificity due to the insertion of uncorrelated idiotypes by the bone marrow. As we demonstrate through numerous computer experiments, for appropriate choices of parameters the new model correctly reproduces, in qualitative terms, several immune functions.

q-bio.CB↗

arXiv2003

The combinatorics of resource sharing

We discuss general models of resource-sharing computations, with emphasis on the combinatorial structures and concepts that underlie the various deadlock models that have been proposed, the design of algorithms and deadlock-handling policies, and concurrency issues. These structures are mostly graph-theoretic in nature, or partially ordered sets for the establishment of priorities among processes and acquisition orders on resources. We also discuss graph-coloring concepts as they relate to resource sharing.

cs.OS↗

arXiv2003

The interleaved multichromatic number of a graph

For $k\ge 1$, we consider interleaved $k$-tuple colorings of the nodes of a graph, that is, assignments of $k$ distinct natural numbers to each node in such a way that nodes that are connected by an edge receive numbers that are strictly alternating between them with respect to the relation $<$. If it takes at least $χ_{int}^k(G)$ distinct numbers to provide graph $G$ with such a coloring, then the interleaved multichromatic number of $G$ is $χ_{int}^*(G)=\inf_{k\ge 1}χ_{int}^k(G)/k$ and is known to be given by a function of the simple cycles of $G$ under acyclic orientations if $G$ is connected [1]. This paper contains a new proof of this result. Unlike the original proof, the new proof makes no assumptions on the connectedness of $G$, nor does it resort to the possible applications of interleaved $k$-tuple colorings and their properties.

math.CO↗

arXiv2003

On the phase transitions of graph coloring and independent sets

We study combinatorial indicators related to the characteristic phase transitions associated with coloring a graph optimally and finding a maximum independent set. In particular, we investigate the role of the acyclic orientations of the graph in the hardness of finding the graph's chromatic number and independence number. We provide empirical evidence that, along a sequence of increasingly denser random graphs, the fraction of acyclic orientations that are `shortest' peaks when the chromatic number increases, and that such maxima tend to coincide with locally easiest instances of the problem. Similar evidence is provided concerning the `widest' acyclic orientations and the independence number.

cond-mat.stat-mech↗

arXiv2003

Finding approximate palindromes in strings

We introduce a novel definition of approximate palindromes in strings, and provide an algorithm to find all maximal approximate palindromes in a string with up to $k$ errors. Our definition is based on the usual edit operations of approximate pattern matching, and the algorithm we give, for a string of size $n$ on a fixed alphabet, runs in $O(k^2 n)$ time. We also discuss two implementation-related improvements to the algorithm, and demonstrate their efficacy in practice by means of both experiments and an average-case analysis.

cs.DS↗

arXiv2003

A distributed algorithm to find k-dominating sets

We consider a connected undirected graph $G(n,m)$ with $n$ nodes and $m$ edges. A $k$-dominating set $D$ in $G$ is a set of nodes having the property that every node in $G$ is at most $k$ edges away from at least one node in $D$. Finding a $k$-dominating set of minimum size is NP-hard. We give a new synchronous distributed algorithm to find a $k$-dominating set in $G$ of size no greater than $\lfloor n/(k+1)\rfloor$. Our algorithm requires $O(k\log^*n)$ time and $O(m\log k+n\log k\log^*n)$ messages to run. It has the same time complexity as the best currently known algorithm, but improves on that algorithm's message complexity and is, in addition, conceptually simpler.

cs.DC↗

arXiv2003

On reducing the complexity of matrix clocks

Matrix clocks are a generalization of the notion of vector clocks that allows the local representation of causal precedence to reach into an asynchronous distributed computation's past with depth $x$, where $x\ge 1$ is an integer. Maintaining matrix clocks correctly in a system of $n$ nodes requires that everymessage be accompanied by $O(n^x)$ numbers, which reflects an exponential dependency of the complexity of matrix clocks upon the desired depth $x$. We introduce a novel type of matrix clock, one that requires only $nx$ numbers to be attached to each message while maintaining what for many applications may be the most significant portion of the information that the original matrix clock carries. In order to illustrate the new clock's applicability, we demonstrate its use in the monitoring of certain resource-sharing computations.

cs.DC↗

arXiv2003

Two novel evolutionary formulations of the graph coloring problem

We introduce two novel evolutionary formulations of the problem of coloring the nodes of a graph. The first formulation is based on the relationship that exists between a graph's chromatic number and its acyclic orientations. It views such orientations as individuals and evolves them with the aid of evolutionary operators that are very heavily based on the structure of the graph and its acyclic orientations. The second formulation, unlike the first one, does not tackle one graph at a time, but rather aims at evolving a `program' to color all graphs belonging to a class whose members all have the same number of nodes and other common attributes. The heuristics that result from these formulations have been tested on some of the Second DIMACS Implementation Challenge benchmark graphs, and have been found to be competitive when compared to the several other heuristics that have also been tested on those graphs.

cs.NE↗

arXiv2003

A novel evolutionary formulation of the maximum independent set problem

We introduce a novel evolutionary formulation of the problem of finding a maximum independent set of a graph. The new formulation is based on the relationship that exists between a graph's independence number and its acyclic orientations. It views such orientations as individuals and evolves them with the aid of evolutionary operators that are very heavily based on the structure of the graph and its acyclic orientations. The resulting heuristic has been tested on some of the Second DIMACS Implementation Challenge benchmark graphs, and has been found to be competitive when compared to several of the other heuristics that have also been tested on those graphs.

cs.NE↗