arXiv subjects

Paul Bastide

Publications and source records attributed to Paul Bastide.

22 records · Page 2Linked to original sources

arXiv2021

On Extending Brandt's Speedup Theorem from LOCAL to Round-Based Full-Information Models

Given any task $Π$, Brandt's speedup theorem (PODC 2019) provides a mechanical way to design another task~$Π'$ on the same input-set as $Π$ such that, for any $t\geq 1$, $Π$ is solvable in $t$ rounds if and only if $Π'$ is solvable in $t-1$ rounds. The theorem applies to the anonymous variant of the LOCAL model, in graphs with sufficiently large girth, and to locally checkable labeling (LCL) tasks. In this paper, using combinatorial topology applied to distributed computing, we dissect the construction in Brandt's speedup theorem for expressing it in the broader framework of round-based models supporting full information protocols, which includes models as different as wait-free shared-memory computing with iterated immediate snapshots, and synchronous failure-free network computing. In particular, we provide general definitions for notions such as local checkability and local independence, in our broader framework. In this way, we are able to identify the hypotheses on the computing model, and on the tasks, that are sufficient for Brandt's speedup theorem to apply. More precisely, we identify which hypotheses are sufficient for the each direction of the if-and-only-if condition. Interestingly, these hypotheses are of different natures. Our general approach enables to extend Brandt's speedup theorem from LOCAL to directed networks, to hypergraphs, to dynamic networks, and even to graphs including short cyclic dependencies between processes (i.e., the large girth condition is, to some extend, not necessary). The theorem can even be extended to shared-memory wait-free computing. In particular, we provide new impossibility proofs for consensus and perfect renaming in 2-process systems.

cs.DC↗

arXiv2020

Efficient Bayesian Inference of General Gaussian Models on Large Phylogenetic Trees

Phylogenetic comparative methods correct for shared evolutionary history among a set of non-independent organisms by modeling sample traits as arising from a diffusion process along on the branches of a possibly unknown history. To incorporate such uncertainty, we present a scalable Bayesian inference framework under a general Gaussian trait evolution model that exploits Hamiltonian Monte Carlo (HMC). HMC enables efficient sampling of the constrained model parameters and takes advantage of the tree structure for fast likelihood and gradient computations, yielding algorithmic complexity linear in the number of observations. This approach encompasses a wide family of stochastic processes, including the general Ornstein-Uhlenbeck (OU) process, with possible missing data and measurement errors. We implement inference tools for a biologically relevant subset of all these models into the BEAST phylogenetic software package and develop model comparison through marginal likelihood estimation. We apply our approach to study the morphological evolution in the superfamilly of Musteloidea (including weasels and allies) as well as the heritability of HIV virulence. This second problem furnishes a new measure of evolutionary heritability that demonstrates its utility through a targeted simulation study.

stat.AP↗

arXiv2020

Large-scale inference of correlation among mixed-type biological traits with phylogenetic multivariate probit models

Inferring concerted changes among biological traits along an evolutionary history remains an important yet challenging problem. Besides adjusting for spurious correlation induced from the shared history, the task also requires sufficient flexibility and computational efficiency to incorporate multiple continuous and discrete traits as data size increases. To accomplish this, we jointly model mixed-type traits by assuming latent parameters for binary outcome dimensions at the tips of an unknown tree informed by molecular sequences. This gives rise to a phylogenetic multivariate probit model. With large sample sizes, posterior computation under this model is problematic, as it requires repeated sampling from a high-dimensional truncated normal distribution. Current best practices employ multiple-try rejection sampling that suffers from slow-mixing and a computational cost that scales quadratically in sample size. We develop a new inference approach that exploits 1) the bouncy particle sampler (BPS) based on piecewise deterministic Markov processes to simultaneously sample all truncated normal dimensions, and 2) novel dynamic programming that reduces the cost of likelihood and gradient evaluations for BPS to linear in sample size. In an application with 535 HIV viruses and 24 traits that necessitates sampling from a 12,840-dimensional truncated normal, our method makes it possible to estimate the across-trait correlation and detect factors that affect the pathogen's capacity to cause disease. This inference framework is also applicable to a broader class of covariance structures beyond comparative biology.

stat.ME↗

arXiv2016

Detection of adaptive shifts on phylogenies using shifted stochastic processes on a tree

Comparative and evolutive ecologists are interested in the distribution of quantitative traits among related species. The classical framework for these distributions consists of a random process running along the branches of a phylogenetic tree relating the species. We consider shifts in the process parameters, which reveal fast adaptation to changes of ecological niches. We show that models with shifts are not identifiable in general. Constraining the models to be parsimonious in the number of shifts partially alleviates the problem but several evolutionary scenarios can still provide the same joint distribution for the extant species. We provide a recursive algorithm to enumerate all the equivalent scenarios and to count the effectively different scenarios. We introduce an incomplete-data framework and develop a maximum likelihood estimation procedure based on the EM algorithm. Finally, we propose a model selection procedure, based on the cardinal of effective scenarios, to estimate the number of shifts and prove an oracle inequality.

stat.AP↗