A new iterative algorithm for computing a quality approximate median of strings based on edit operations

This paper presents a new algorithm that can be used to compute an approximation to the median of a set of strings. The approximate median is obtained through the successive improvements of a partial solution. The edit distance from the partial solution to all the strings in the set is computed in each iteration, thus accounting for the frequency of each of the edit operations in all the positions of the approximate median. A goodness index for edit operations is later computed by multiplying their frequency by the cost. Each operation is tested, starting from that with the highest index, in order to verify whether applying it to the partial solution leads to an improvement. If successful, a new iteration begins from the new approximate median. The algorithm finishes when all the operations have been examined without a better solution being found. Comparative experiments involving Freeman chain codes encoding 2D shapes and the Copenhagen chromosome database show that the quality of the approximate median string is similar to benchmark approaches but achieves a much faster convergence.This work is partially supported by the Spanish CICYT under project DPI2006-15542-C04-01, the Spanish MICINN through project TIN2009-14205-CO4-01 and by the Spanish research program Consolider Ingenio 2010: MIPRCV (CSD2007-00018)

Boosting Perturbation-Based Iterative Algorithms to Compute the Median String

[Abstract] The most competitive heuristics for calculating the median string are those that use perturbation-based iterative algorithms. Given the complexity of this problem, which under many formulations is NP-hard, the computational cost involved in the exact solution is not affordable. In this work, the heuristic algorithms that solve this problem are addressed, emphasizing its initialization and the policy to order possible editing operations. Both factors have a significant weight in the solution of this problem. Initial string selection influences the algorithm’s speed of convergence, as does the criterion chosen to select the modification to be made in each iteration of the algorithm. To obtain the initial string, we use the median of a subset of the original dataset; to obtain this subset, we employ the Half Space Proximal (HSP) test to the median of the dataset. This test provides sufficient diversity within the members of the subset while at the same time fulfilling the centrality criterion. Similarly, we provide an analysis of the stop condition of the algorithm, improving its performance without substantially damaging the quality of the solution. To analyze the results of our experiments, we computed the execution time of each proposed modification of the algorithms, the number of computed editing distances, and the quality of the solution obtained. With these experiments, we empirically validated our proposal.This work was supported in part by the Comisión Nacional de Investigación Científica y Tecnológica - Programa de Formación de Capital Humano Avanzado (CONICYT-PCHA)/Doctorado Nacional/2014-63140074 through the Ph.D. Scholarship, in part by the European Union's Horizon 2020 under the Marie Sklodowska-Curie under Grant 690941, in part by the Millennium Institute for Foundational Research on Data (IMFD), and in part by the FONDECYT-CONICYT under Grant 1170497. The work of ÓSCAR PEDREIRA was supported in part by the Xunta de Galicia/FEDER-UE refs under Grant CSI ED431G/01 and Grant GRC: ED431C 2017/58, in part by the Office of the Vice President for Research and Postgraduate Studies of the Universidad Católica de Temuco, VIPUCT Project 2020EM-PS-08, and in part by the FEQUIP 2019-INRN-03 of the Universidad Católica de TemucoXunta de Galicia; ED431G/01Xunta de Galicia; ED431C 2017/58Chile. Comisión Nacional de Investigación Científica y Tecnológica; 2014-63140074Chile. Comisión Nacional de Investigación Científica y Tecnológica; 1170497Universidad Católica de Temuco (Chile); 2020EM-PS-08Universidad Católica de Temuco (Chile); 2019-INRN-0

Pivot Selection for Median String Problem

The Median String Problem is W[1]-Hard under the Levenshtein distance, thus, approximation heuristics are used. Perturbation-based heuristics have been proved to be very competitive as regards the ratio approximation accuracy/convergence speed. However, the computational burden increase with the size of the set. In this paper, we explore the idea of reducing the size of the problem by selecting a subset of representative elements, i.e. pivots, that are used to compute the approximate median instead of the whole set. We aim to reduce the computation time through a reduction of the problem size while achieving similar approximation accuracy. We explain how we find those pivots and how to compute the median string from them. Results on commonly used test data suggest that our approach can reduce the computational requirements (measured in computed edit distances) by $8$\% with approximation accuracy as good as the state of the art heuristic. This work has been supported in part by CONICYT-PCHA/Doctorado Nacional/$2014-63140074$ through a Ph.D. Scholarship; Universidad Cat\'{o}lica de la Sant\'{i}sima Concepci\'{o}n through the research project DIN-01/2016; European Union's Horizon 2020 under the Marie Sk\l odowska-Curie grant agreement $690941$; Millennium Institute for Foundational Research on Data (IMFD); FONDECYT-CONICYT grant number $1170497$; and for O. Pedreira, Xunta de Galicia/FEDER-UE refs. CSI ED431G/01 and GRC: ED431C 2017/58

Learning the Consensus of Multiple Correspondences between Data Structures

En aquesta tesi presentem un marc de treball per aprendre el consens donades múltiples correspondències. S'assumeix que les diferents parts involucrades han generat aquestes correspondències per separat, i el nostre sistema actua com un mecanisme que calibra diferents característiques i considera diferents paràmetres per aprendre les millors assignacions i així, conformar una correspondència amb la major precisió possible a costa d'un cost computacional raonable. Aquest marc de treball de consens és presentat en una forma gradual, començant pels desenvolupaments més bàsics que utilitzaven exclusivament conceptes ben definits o únicament un parell de correspondències, fins al model final que és capaç de considerar múltiples correspondències, amb la capacitat d'aprendre automàticament alguns paràmetres de ponderació. Cada pas d'aquest marc de treball és avaluat fent servir bases de dades de naturalesa variada per demostrar efectivament que és possible tractar diferents escenaris de matching. Addicionalment, dos avanços suplementaris relacionats amb correspondències es presenten en aquest treball. En primer lloc, una nova mètrica de distància per correspondències s'ha desenvolupat, la qual va derivar en una nova estratègia per a la cerca de mitjanes ponderades. En segon lloc, un marc de treball específicament dissenyat per a generar correspondències al camp del registre d'imatges s'ha modelat, on es considera que una de les imatges és una imatge completa, i l'altra és una mostra petita d'aquesta. La conclusió presenta noves percepcions de com el nostre marc de treball de consens pot ser millorada, i com els dos desenvolupaments paral·lels poden convergir amb el marc de treball de consens.En esta tesis presentamos un marco de trabajo para aprender el consenso dadas múltiples correspondencias. Se asume que las distintas partes involucradas han generado dichas correspondencias por separado, y nuestro sistema actúa como un mecanismo que calibra distintas características y considera diferentes parámetros para aprender las mejores asignaciones y así, conformar una correspondencia con la mayor precisión posible a expensas de un costo computacional razonable. El marco de trabajo de consenso es presentado en una forma gradual, comenzando por los acercamientos más básicos que utilizaban exclusivamente conceptos bien definidos o únicamente un par de correspondencias, hasta el modelo final que es capaz de considerar múltiples correspondencias, con la capacidad de aprender automáticamente algunos parámetros de ponderación. Cada paso de este marco de trabajo es evaluado usando bases de datos de naturaleza variada para demostrar efectivamente que es posible tratar diferentes escenarios de matching. Adicionalmente, dos avances suplementarios relacionados con correspondencias son presentados en este trabajo. En primer lugar, una nueva métrica de distancia para correspondencias ha sido desarrollada, la cual derivó en una nueva estrategia para la búsqueda de medias ponderadas. En segundo lugar, un marco de trabajo específicamente diseñado para generar correspondencias en el campo del registro de imágenes ha sido establecida, donde se considera que una de las imágenes es una imagen completa, y la otra es una muestra pequeña de ésta. La conclusión presenta nuevas percepciones de cómo nuestro marco de trabajo de consenso puede ser mejorada, y cómo los dos desarrollos paralelos pueden converger con éste.In this work, we present a framework to learn the consensus given multiple correspondences. It is assumed that the several parties involved have generated separately these correspondences, and our system acts as a mechanism that gauges several characteristics and considers different parameters to learn the best mappings and thus, conform a correspondence with the highest possible accuracy at the expense of a reasonable computational cost. The consensus framework is presented in a gradual form, starting from the most basic approaches that used exclusively well-known concepts or only two correspondences, until the final model which is able to consider multiple correspondences, with the capability of automatically learning some weighting parameters. Each step of the framework is evaluated using databases of varied nature to effectively demonstrate that it is capable to address different matching scenarios. In addition, two supplementary advances related on correspondences are presented in this work. Firstly, a new distance metric for correspondences has been developed, which lead to a new strategy for the weighted mean correspondence search. Secondly, a framework specifically designed for correspondence generation in the image registration field has been established, where it is considered that one of the images is a full image, and the other one is a small sample of it. The conclusion presents insights of how our consensus framework can be enhanced, and how these two parallel developments can converge with it

Summarizing Diverging String Sequences, with Applications to Chain-Letter Petitions

Algorithms to find optimal alignments among strings, or to find a parsimonious summary of a collection of strings, are well studied in a variety of contexts, addressing a wide range of interesting applications. In this paper, we consider chain letters, which contain a growing sequence of signatories added as the letter propagates. The unusual constellation of features exhibited by chain letters (one-ended growth, divergence, and mutation) make their propagation, and thus the corresponding reconstruction problem, both distinctive and rich. Here, inspired by these chain letters, we formally define the problem of computing an optimal summary of a set of diverging string sequences. From a collection of these sequences of names, with each sequence noisily corresponding to a branch of the unknown tree $T$ representing the letter's true dissemination, can we efficiently and accurately reconstruct a tree $T' \approx T$? In this paper, we give efficient exact algorithms for this summarization problem when the number of sequences is small; for larger sets of sequences, we prove hardness and provide an efficient heuristic algorithm. We evaluate this heuristic on synthetic data sets chosen to emulate real chain letters, showing that our algorithm is competitive with or better than previous approaches, and that it also comes close to finding the true trees in these synthetic datasets.Comment: 18 pages, 6 figures. Accepted to Combinatorial Pattern Matching (CPM) 202

Generalised median of a set of correspondences based on the hamming distance.

A correspondence is a set of mappings that establishes a relation between the elements of two data structures (i.e. sets of points, strings, trees or graphs). If we consider several correspondences between the same two structures, one option to define a representative of them is through the generalised median correspondence. In general, the computation of the generalised median is an NP-complete task. In this paper, we present two methods to calculate the generalised median correspondence of multiple correspondences. The first one obtains the optimal solution in cubic time, but it is restricted to the Hamming distance. The second one obtains a sub-optimal solution through an iterative approach, but does not have any restrictions with respect to the used distance. We compare both proposals in terms of the distance to the true generalised median and runtime

Data Reduction in the String Space for Efficient kNN Classification through Space Partitioning

Within the Pattern Recognition field, two representations are generally considered for encoding the data: statistical codifications, which describe elements as feature vectors, and structural representations, which encode elements as high-level symbolic data structures such as strings, trees or graphs. While the vast majority of classifiers are capable of addressing statistical spaces, only some particular methods are suitable for structural representations. The kNN classifier constitutes one of the scarce examples of algorithms capable of tackling both statistical and structural spaces. This method is based on the computation of the dissimilarity between all the samples of the set, which is the main reason for its high versatility, but in turn, for its low efficiency as well. Prototype Generation is one of the possibilities for palliating this issue. These mechanisms generate a reduced version of the initial dataset by performing data transformation and aggregation processes on the initial collection. Nevertheless, these generation processes are quite dependent on the data representation considered, being not generally well defined for structural data. In this work we present the adaptation of the generation-based reduction algorithm Reduction through Homogeneous Clusters to the case of string data. This algorithm performs the reduction by partitioning the space into class-homogeneous clusters for then generating a representative prototype as the median value of each group. Thus, the main issue to tackle is the retrieval of the median element of a set of strings. Our comprehensive experimentation comparatively assesses the performance of this algorithm in both the statistical and the string-based spaces. Results prove the relevance of our approach by showing a competitive compromise between classification rate and data reduction.This research work was partially funded by “Programa I+D+i de la Generalitat Valenciana” through grant ACIF/2019/ 042 and the Spanish Ministry through HISPAMUS project TIN2017-86576-R, partially funded by the EU