In the light of regularized dynamic time warping kernels, this paper re-considers the concept of time elastic centroid for a setof time series. We derive a new algorithm based on a probabilistic interpretation of kernel alignment matrices. This algorithm expressesthe averaging process in terms of a stochastic alignment automata. It uses an iterative agglomerative heuristic method for averagingthe aligned samples, while also averaging the times of occurrence of the aligned samples. By comparing classification accuracies for45 heterogeneous time series datasets obtained by first nearest centroid medoid classifiers we show that: i) centroid-basedapproaches significantly outperform medoid-based approaches, ii) for the considered datasets, our algorithm that combines averagingin the sample space and along the time axes, emerges as the most significantly robust model for time-elastic averaging with apromising noise reduction capability. We also demonstrate its benefit in an isolated gesture recognition experiment and its ability tosignificantly reduce the size of training instance sets. Finally we highlight its denoising capability using demonstrative synthetic data:we show that it is possible to retrieve, from few noisy instances, a signal whose components are scattered in a wide spectral band.
It is shown that the multiple alignment problem with SP-score is NP-hard for each scoring matrix in a broad class M that includes most scoring matrices actually used in biological applications. The problem remains NP-hard even if sequences can only be shifted relative to each other and no internal gaps are allowed. It is also shown that there is a scoring matrix M0 such that the multiple alignment problem for M0 is MAX-SNP-hard, regardless of whether or not internal gaps are allowed.  The study and comparison of sequences of characters from a finite alphabet is relevant to various areas of science, notably molecular biology. The measurement of sequence similarity involves the consideration of the different possible sequence alignments in order to find an optimal one for which the “distance” between sequences is minimum. By associating a path in a lattice to each alignment, a geometric insight can be brought into the problem of finding an optimal alignment. This problem can then be solved by applying a dynamic programming algorithm. However, the computational effort grows rapidly with the number N of sequences to be compared @math , where l is the mean length of the sequences to be compared).It is proved here that knowledge of the measure of an arbitrarily chosen alignment can be used in combination with information from the pairwise alignments to considerably restrict the size of the region of the lattice in consideration. This reduction implies fewer computations and less memory ... ABSTRACT We study the computational complexity of two popular problems in multiple sequence alignment: multiple alignment with SP-score and multiple tree alignment. It is shown that the first problem is NP-complete and the second is MAX SNP-hard. The complexity of tree alignment with a given phylogeny is also considered.