Regular and Estimable Inverse Demand Systems: A Distance Function Approach

To be useful for realistic policy simulation in an environment of rapid structural change, inverse demand systems must remain regular over substantial variations in quantities. The distance function is a convenient vehicle for generating such systems. While it directly yields Hicksian inverse demand functions, those functions will not usually have an explicit representation in terms of the observable variables. Note however that this problem need not hinder estimation and could be solved by using the numerical inversion estimation approach. This paper develops the formal theory for using distance functions in this context, and demonstrates the operational feasibility of the method.Inverse Demands; Distance Functions; Numerical Inversion Estimation Method; Separability.

Group-theoretic models of the inversion process in bacterial genomes

The variation in genome arrangements among bacterial taxa is largely due to the process of inversion. Recent studies indicate that not all inversions are equally probable, suggesting, for instance, that shorter inversions are more frequent than longer, and those that move the terminus of replication are less probable than those that do not. Current methods for establishing the inversion distance between two bacterial genomes are unable to incorporate such information. In this paper we suggest a group-theoretic framework that in principle can take these constraints into account. In particular, we show that by lifting the problem from circular permutations to the affine symmetric group, the inversion distance can be found in polynomial time for a model in which inversions are restricted to acting on two regions. This requires the proof of new results in group theory, and suggests a vein of new combinatorial problems concerning permutation groups on which group theorists will be needed to collaborate with biologists. We apply the new method to inferring distances and phylogenies for published Yersinia pestis data.Comment: 19 pages, 7 figures, in Press, Journal of Mathematical Biolog

Using phonetic constraints in acoustic-to-articulatory inversion

The goal of this work is to recover articulatory information from the speech signal by acoustic-to-articulatory inversion. One of the main difficulties with inversion is that the problem is underdetermined and inversion methods generally offer no guarantee on the phonetical realism of the inverse solutions. A way to adress this issue is to use additional phonetic constraints. Knowledge of the phonetic caracteristics of French vowels enable the derivation of reasonable articulatory domains in the space of Maeda parameters: given the formants frequencies (F1,F2,F3) of a speech sample, and thus the vowel identity, an "ideal" articulatory domain can be derived. The space of formants frequencies is partitioned into vowels, using either speaker-specific data or generic information on formants. Then, to each articulatory vector can be associated a phonetic score varying with the distance to the "ideal domain" associated with the corresponding vowel. Inversion experiments were conducted on isolated vowels and vowel-to-vowel transitions. Articulatory parameters were compared with those obtained without using these constraints and those measured from X-ray data

On the Inversion-Indel Distance

Willing E, Zaccaria S, Dias Vieira Braga M, Stoye J. On the Inversion-Indel Distance. BMC Bioinformatics. 2013;14(Suppl 15: Proc. of RECOMB-CG 2013): S3.Background The inversion distance, that is the distance between two unichromosomal genomes with the same content allowing only inversions of DNA segments, can be computed thanks to a pioneering approach of Hannenhalli and Pevzner in 1995. In 2000, El-Mabrouk extended the inversion model to allow the comparison of unichromosomal genomes with unequal contents, thus insertions and deletions of DNA segments besides inversions. However, an exact algorithm was presented only for the case in which we have insertions alone and no deletion (or vice versa), while a heuristic was provided for the symmetric case, that allows both insertions and deletions and is called the inversion-indel distance. In 2005, Yancopoulos, Attie and Friedberg started a new branch of research by introducing the generic double cut and join (DCJ) operation, that can represent several genome rearrangements (including inversions). Among others, the DCJ model gave rise to two important results. First, it has been shown that the inversion distance can be computed in a simpler way with the help of the DCJ operation. Second, the DCJ operation originated the DCJ-indel distance, that allows the comparison of genomes with unequal contents, considering DCJ, insertions and deletions, and can be computed in linear time. Results In the present work we put these two results together to solve an open problem, showing that, when the graph that represents the relation between the two compared genomes has no bad components, the inversion-indel distance is equal to the DCJ-indel distance. We also give a lower and an upper bound for the inversion-indel distance in the presence of bad components

Bayes and maximum likelihood for L1L^1-Wasserstein deconvolution of Laplace mixtures

We consider the problem of recovering a distribution function on the real line from observations additively contaminated with errors following the standard Laplace distribution. Assuming that the latent distribution is completely unknown leads to a nonparametric deconvolution problem. We begin by studying the rates of convergence relative to the $L^2$-norm and the Hellinger metric for the direct problem of estimating the sampling density, which is a mixture of Laplace densities with a possibly unbounded set of locations: the rate of convergence for the Bayes' density estimator corresponding to a Dirichlet process prior over the space of all mixing distributions on the real line matches, up to a logarithmic factor, with the $n^{-3/8}\log^{1/8}n$ rate for the maximum likelihood estimator. Then, appealing to an inversion inequality translating the $L^2$-norm and the Hellinger distance between general kernel mixtures, with a kernel density having polynomially decaying Fourier transform, into any $L^p$-Wasserstein distance, $p\geq1$, between the corresponding mixing distributions, provided their Laplace transforms are finite in some neighborhood of zero, we derive the rates of convergence in the $L^1$-Wasserstein metric for the Bayes' and maximum likelihood estimators of the mixing distribution. Merging in the $L^1$-Wasserstein distance between Bayes and maximum likelihood follows as a by-product, along with an assessment on the stochastic order of the discrepancy between the two estimation procedures

The closest elastic tensor of arbitrary symmetry to an elasticity tensor of lower symmetry

The closest tensors of higher symmetry classes are derived in explicit form for a given elasticity tensor of arbitrary symmetry. The mathematical problem is to minimize the elastic length or distance between the given tensor and the closest elasticity tensor of the specified symmetry. Solutions are presented for three distance functions, with particular attention to the Riemannian and log-Euclidean distances. These yield solutions that are invariant under inversion, i.e., the same whether elastic stiffness or compliance are considered. The Frobenius distance function, which corresponds to common notions of Euclidean length, is not invariant although it is simple to apply using projection operators. A complete description of the Euclidean projection method is presented. The three metrics are considered at a level of detail far greater than heretofore, as we develop the general framework to best fit a given set of moduli onto higher elastic symmetries. The procedures for finding the closest elasticity tensor are illustrated by application to a set of 21 moduli with no underlying symmetry.Comment: 48 pages, 1 figur

Velocity estimation via registration-guided least-squares inversion

This paper introduces an iterative scheme for acoustic model inversion where the notion of proximity of two traces is not the usual least-squares distance, but instead involves registration as in image processing. Observed data are matched to predicted waveforms via piecewise-polynomial warpings, obtained by solving a nonconvex optimization problem in a multiscale fashion from low to high frequencies. This multiscale process requires defining low-frequency augmented signals in order to seed the frequency sweep at zero frequency. Custom adjoint sources are then defined from the warped waveforms. The proposed velocity updates are obtained as the migration of these adjoint sources, and cannot be interpreted as the negative gradient of any given objective function. The new method, referred to as RGLS, is successfully applied to a few scenarios of model velocity estimation in the transmission setting. We show that the new method can converge to the correct model in situations where conventional least-squares inversion suffers from cycle-skipping and converges to a spurious model.Comment: 20 pages, 13 figures, 1 tabl