Saeedi, Ardavan, Bouchard-côté, Alexandre

We introduce the Gamma-Exponential Process (GEP), a prior over a large family ofcontinuous time stochastic processes. A hierarchical version of this prior (HGEP; the Hierarchical GEP) yields a useful model for analyzing complex time series. Models based on HGEPs display many attractive properties: conjugacy, exchangeability and closed-form predictive distribution for the waiting times, and exact Gibbs updates for the time scale parameters. After establishing these properties, weshow how posterior inference can be carried efficiently using Particle MCMC methods [1]. This yields a MCMC algorithm that can resample entire sequences atomicallywhile avoiding the complications of introducing slice and stick auxiliary variables of the beam sampler [2]. We applied our model to the problem of estimating the disease progression in multiple sclerosis [3], and to RNA evolutionary modeling[4]. In both domains, we found that our model outperformed the standard rate matrix estimation approach.

Volant, Stevenn, Magniette, Marie-Laure Martin, Robin, Stéphane

We consider a binary unsupervised classification problem where each observation is associated with an unobserved label that we want to retrieve. More precisely, we assume that there are two groups of observation: normal and abnormal. The `normal' observations are coming from a known distribution whereas the distribution of the `abnormal' observations is unknown. Several models have been developed to fit this unknown distribution. In this paper, we propose an alternative based on a mixture of Gaussian distributions. The inference is done within a variational Bayesian framework and our aim is to infer the posterior probability of belonging to the class of interest. To this end, it makes no sense to estimate the mixture component number since each mixture model provides more or less relevant information to the posterior probability estimation. By computing a weighted average (named aggregated estimator) over the model collection, Bayesian Model Averaging (BMA) is one way of combining models in order to account for information provided by each model. The aim is then the estimation of the weights and the posterior probability for one specific model. In this work, we derive optimal approximations of these quantities from the variational theory and propose other approximations of the weights. To perform our method, we consider that the data are dependent (Markovian dependency) and hence we consider a Hidden Markov Model. A simulation study is carried out to evaluate the accuracy of the estimates in terms of classification. We also present an application to the analysis of public health surveillance systems.

Mckeigue, Paul, Krohn, Jon, Storkey, Amos J., Agakov, Felix V.

This paper describes a probabilistic framework for studying associations between multiple genotypes, biomarkers, and phenotypic traits in the presence of noise and unobserved confounders for large genetic studies. The framework builds on sparse linear methods developed for regression and modified here for inferring causal structures of richer networks with latent variables. The method is motivated by the use of genotypes as ``instruments'' to infer causal associations between phenotypic biomarkers and outcomes, without making the common restrictive assumptions of instrumental variable methods. The method may be used for an effective screening of potentially interesting genotype phenotype and biomarker-phenotype associations in genome-wide studies, which may have important implications for validating biomarkers as possible proxy endpoints for early stage clinical trials. Where the biomarkers are gene transcripts, the method can be used for fine mapping of quantitative trait loci (QTLs) detected in genetic linkage studies. The method is applied for examining effects of gene transcript levels in the liver on plasma HDL cholesterol levels for a sample of sequenced mice from a heterogeneous stock, with $\sim 10^5$ genetic instruments and $\sim 47 \times 10^3$ gene transcripts.

Diabetes is one of deadliest diseases in the world. It is not only a disease but also a creator of different kinds of diseases like heart attack, blindness, kidney diseases, etc. The normal identifying process is that patients need to visit a diagnostic center, consult their doctor, and sit tight for a day or more to get their reports. Moreover, every time they want to get their diagnosis report, they have to waste their money in vain. But with the rise of Machine Learning approaches we have the ability to find a solution to this issue, we have developed a system using data mining which has the ability to predict whether the patient has diabetes or not.

Rahmadi, Ridho, Groot, Perry, Heskes, Tom

In our previous study, we introduced stable specification search for cross-sectional data (S3C). It is an exploratory causal method that combines stability selection concept and multi-objective optimization to search for stable and parsimonious causal structures across the entire range of model complexities. In this study, we extended S3C to S3C-Latent, to model causal relations between latent variables. We evaluated S3C-Latent on simulated data and compared the results to those of PC-MIMBuild, an extension of the PC algorithm, the state-of-the-art causal discovery method. The comparison showed that S3C-Latent achieved better performance. We also applied S3C-Latent to real-world data of children with attention deficit/hyperactivity disorder and data about measuring mental abilities among pupils. The results are consistent with those of previous studies.