ABC likelihood-freee methods for model choice in Gibbs random fields

Gibbs random fields (GRF) are polymorphous statistical models that can be used to analyse different types of dependence, in particular for spatially correlated data. However, when those models are faced with the challenge of selecting a dependence structure from many, the use of standard model choice methods is hampered by the unavailability of the normalising constant in the Gibbs likelihood. In particular, from a Bayesian perspective, the computation of the posterior probabilities of the models under competition requires special likelihood-free simulation techniques like the Approximate Bayesian Computation (ABC) algorithm that is intensively used in population genetics. We show in this paper how to implement an ABC algorithm geared towards model choice in the general setting of Gibbs random fields, demonstrating in particular that there exists a sufficient statistic across models. The accuracy of the approximation to the posterior probabilities can be further improved by importance sampling on the distribution of the models. The practical aspects of the method are detailed through two applications, the test of an iid Bernoulli model versus a first-order Markov chain, and the choice of a folding structure for two proteins.Comment: 19 pages, 5 figures, to appear in Bayesian Analysi

Collective motion, sensor networks, and ocean sampling

Author Posting. © IEEE, 2007. This article is posted here by permission of IEEE for personal use, not for redistribution. The definitive version was published in Proceedings of the IEEE 95 (2007): 48-74, doi:10.1109/jproc.2006.887295.This paper addresses the design of mobile sensor networks for optimal data collection. The development is strongly motivated by the application to adaptive ocean sampling for an autonomous ocean observing and prediction system. A performance metric, used to derive optimal paths for the network of mobile sensors, defines the optimal data set as one which minimizes error in a model estimate of the sampled field. Feedback control laws are presented that stably coordinate sensors on structured tracks that have been optimized over a minimal set of parameters. Optimal, closed-loop solutions are computed in a number of low-dimensional cases to illustrate the methodology. Robustness of the performance to the influence of a steady flow field on relatively slow-moving mobile sensors is also explored

Nonlinear Refraction and Absorption of Ag 29 Nanoclusters: Evidence for Two-Photon Absorption Saturation

International audienc

Choix de modèle pour les champs de Gibbs par un algorithme ABC.

International audienceLes champs de Gibbs sont des modèles souvent utilisés pour l'analyse de données présentant des corrélations spatiales. La définition du modèle est alors liée à un système de voisinage ; dans certains cas, plusieurs peuvent être proposés. Pour chaque système de voisinage, un modèle de champ de Gibbs peut être construit et sélectionner le système de voisinage est finalement un problème de choix de modèle. Nous travaillons dans un cadre Bayésien. Nous définissons un nouveau paramètre incluant les paramètres de chacun des modèles et l'indice du modèle. Le choix de modèle repose alors sur l'évaluation des probabilités a posteriori des modèles ou des facteurs de Bayes. Les méthodes utilisées habituellement ne peuvent être appliquées ici car la vraisemblance des champs de Gibbs est disponible à un facteur de normalisation près. Nous proposons donc une approche “ sans vraisemblance”, basée sur un algorithme ABC (Approximate Bayesian Computation). L'algorithme ABC-MC (MC signifiant Model Choice) génère un échantillon dont la distribution est approximativement la distribution a posteriori de l'ensemble des paramètres, échantillon que nous utilisons pour évaluer les probabilités a posteriori des modèles. Nous étudions les performances de cette méthode sur deux modèles qui sont des cas particuliers de champs de Gibbs pour lesquels la vraisemblance est entièrement disponible. Nous utilisons ensuite l'algorithme ABC-MC pour choisir la structure 3D d'une protéine parmi un ensemble de candidats proposés par une méthode de threading. Nous montrons les résultats obtenus pour une protéine de la bactérie Thermotaga maritima

Codage temps-espace en blocs combiné avec un système multiporteuse à étalement de spectre de type MC-CDMA

Ce papier présente les performances de systèmes MIMO MC-CDMA à Nt antennes d'émission et Nr antennes de réception offrant une efficacité spectrale de 1 ou 2 bit/s/Hz. Les résultats sont obtenus pour différents schémas de codage temps-espace en blocs (STBC) dans le cas de la liaison descendante synchrone sur des canaux de Rayleigh sélectifs en fréquence pour les deux techniques de détection Zéro-Forcing (ZF) et Minimum Mean Square Error (MMSE). En outre, une méthode générale pour décoder les codes STBC orthogonaux associés aux signaux MC-CDMA est décrite. Par ailleurs, ces résultats démontrent l'intérêt d'un système STBC MC-CDMA reposant sur l'utilisation de codes temps-espace de rendement 1, et qu'il est en conséquence préférable d'utiliser la redondance au niveau du codage de canal et non au niveau du codage temps-espace

Br J Haematol

Immune thrombocytopenia (ITP) is defined by a low platelet count that can trigger potentially life-threatening haemorrhages. Three-quarters of adult patients exhibit persistent or chronic disease and require second-line treatments. Among these, rituximab, an anti-CD20 antibody, has yielded valuable results, with global responses in 60% of patients at 6 months and complete responses in 30% at 5 years. Factors predictive of response to ITP therapy would help physicians choose optimal treatments. We retrospectively analysed clinical courses, biological markers and blood lymphocyte subset numbers of 72 patients on rituximab to treat persistent/chronic ITP followed-up in our department between 2007 and 2021, divided into three groups according to the platelet count at 6 months: complete, partial or no response. Among all studied parameters, a low number of CD3 CD16 CD56 circulating NK cells was associated with the complete response to rituximab. We also found that, after rituximab therapy, complete responders exhibited increased NK and decreased activated CD8 T cell percentages. These results emphasize that the role played by NK cells in ITP remains incompletely known but that factors predictive of response to rituximab can be easily derived using blood lymphocyte subset data

Reproducibility of Brain Responses: High for Speech Perception, Low for Reading Difficulties

Neuroscience findings have recently received critique on the lack of replications. To examine the reproducibility of brain indices of speech sound discrimination and their role in dyslexia, a specific reading difficulty, brain event-related potentials using EEG were measured using the same cross-linguistic passive oddball paradigm in about 200 dyslexics and 200 typically reading 8-12-year-old children from four countries with different native languages. Brain responses indexing speech and non-speech sound discrimination were extremely reproducible, supporting the validity and reliability of cognitive neuroscience methods. Significant differences between typical and dyslexic readers were found when examined separately in different country and language samples. However, reading group differences occurred at different time windows and for different stimulus types between the four countries. This finding draws attention to the limited generalizability of atypical brain response findings in children with dyslexia across language environments and raises questions about a common neurobiological factor for dyslexia. Our results thus show the robustness of neuroscience methods in general while highlighting the need for multi-sample studies in the brain research of language disorders

: PLoS One

International audienceIn 31 participants who started first-line antiretroviral therapy in the NEAT 001/ANRS 143 clinical trial, we found after 96 weeks a statistically significant increase in blood telomere length (TL) of 0.04 (T/S Ratio) (p = 0.03). This increase was positively correlated with both the change in the percentage of CD4+ T-cells and with the decrease of CD38+ molecules on Central Memory CD8+ and negatively correlated with the change in the percentage of CD4+ Effector Memory cells. Increase in TL could be an expression of immune reconstitution and the associated decrease in immune activation. We acknowledge for the low statistical power due to the small sample size and the potential for false positive results due to multiple testing. Hence, further studies are needed to confirm these observations

Temporal trends of population viral suppression in the context of Universal Test and Treat: the ANRS 12249 TasP trial in rural South Africa

Introduction: The universal test-and-treat (UTT) strategy aims to maximize population viral suppression (PVS), that is, the proportion of all people living with HIV (PLHIV) on antiretroviral treatment (ART) and virally suppressed, with the goal of reducing HIV transmission at the population level. This article explores the extent to which temporal changes in PVS explain the observed lack of association between universal treatment and cumulative HIV incidence seen in the ANRS 12249 TasP trial conducted in rural South Africa. Methods: The TasP cluster-randomized trial (2012 to 2016) implemented six-monthly repeat home-based HIV counselling and testing (RHBCT) and referral of PLHIV to local HIV clinics in 2 9 11 clusters opened sequentially. ART was initiated according to national guidelines in control clusters and regardless of CD4 count in intervention clusters. We measured residency status, HIV status, and HIV care status for each participant on a daily basis. PVS was computed per cluster among all resident PLHIV (≥16, including those not in care) at cluster opening and daily thereafter. We used a mixed linear model to explore time patterns in PVS, adjusting for sociodemographic changes at the cluster level. Results: 8563 PLHIV were followed. During the course of the trial, PVS increased significantly in both arms (23.5% to 46.2% in intervention, +22.8, p < 0.001; 26.0% to 44.6% in control, +18.6, p < 0.001). That increase was similar in both arms (p = 0.514). In the final adjusted model, PVS increase was most associated with increased RHBCT and the implementation of local trial clinics (measured by time since cluster opening). Contextual changes (measured by calendar time) also contributed slightly. The effect of universal ART (trial arm) was positive but limited. Conclusions: PVS was improved significantly but similarly in both trial arms, explaining partly the null effect observed in terms of cumulative HIV incidence between arms. The PVS gains due to changes in ART-initiation guidelines alone are relatively small compared to gains obtained by strategies to maximize testing and linkage to care. The achievement of the 90-90-90 targets will not be met if the operational and implementational challenges limiting access to care and treatment, often context-specific, are not properly addressed. Clinical trial number: NCT01509508 (clinicalTrials.gov)/DOH-27-0512-3974 (South African National Clinical Trials Register)