On evaluating how well a biomarker can predict treatment response with survival data

One of the objectives of personalized medicine is to take treatment decisions based on a biomarker measurement. Therefore, it is often interesting to evaluate how well a biomarker can predict the response to a treatment. To do so, a popular methodology consists of using a regression model and testing for an interaction between treatment assignment and biomarker. However, the existence of an interaction is not sufficient for a biomarker to be predictive. It is only necessary. Hence, the use of the marker‐by‐treatment predictiveness curve has been recommended. In addition to evaluate how well a single continuous biomarker predicts treatment response, it can further help to define an optimal threshold. This curve displays the risk of a binary outcome as a function of the quantiles of the biomarker, for each treatment group. Methods that assume a binary outcome or rely on a proportional hazard model for a time‐to‐event outcome have been proposed to estimate this curve. In this work, we propose some extensions for censored data. They rely on a time‐dependent logistic model, and we propose to estimate this model via inverse probability of censoring weighting. We present simulations results and three applications to prostate cancer, liver cirrhosis, and lung cancer data. They suggest that a large number of events need to be observed to define a threshold with sufficient accuracy for clinical usefulness. They also illustrate that when the treatment effect varies with the time horizon which defines the outcome, then the optimal threshold also depends on this time horizon.     

Slowing time: Markov-modulated Brownian motions with a sticky boundary

We define a new family of stochastic processes called Markov modulated Brownian motions with a sticky boundary at zero. Intuitively, each process is a regulated Markov-modulated Brownian motion whose boundary behavior is modified to slow down at level zero.

To determine the stationary distribution of a sticky MMBM, we follow a Markov-regenerative approach similar to the one developed with great success in the context of quasi-birth-and-death processes and fluid queues. Our analysis also relies on recent work showing that Markov-modulated Brownian motions arise as limits of a parametrized family of fluid queues.     

The dynamic stochastic topic block model for dynamic networks with textual edges

Statistics and Computing - The present paper develops a probabilistic model to cluster the nodes of a dynamic graph, accounting for the content of textual edges as well as their frequency. Vertices...     

Variational Bayes model averaging for graphon functions and motif frequencies inference in <Emphasis Type="Italic">W</Emphasis>-graph models

W-graph refers to a general class of random graph models that can be seen as a random graph limit. It is characterized by both its graphon function and its motif frequencies. In this paper, relying on an existing variational Bayes algorithm for the stochastic block models (SBMs) along with the corresponding weights for model averaging, we derive an estimate of the graphon function as an average of SBMs with increasing number of blocks. In the same framework, we derive the variational posterior frequency of any motif. A simulation study and an illustration on a social network complete our work.     

Multiple change points detection and clustering in dynamic networks

The increasing amount of data stored in the form of dynamic interactions between actors necessitates the use of methodologies to automatically extract relevant information. The interactions can be represented by dynamic networks in which most existing methods look for clusters of vertices to summarize the data. In this paper, a new framework is proposed in order to cluster the vertices while detecting change points in the intensities of the interactions. These change points are key in the understanding of the temporal interactions. The model used involves non-homogeneous Poisson point processes with cluster-dependent piecewise constant intensity functions and common discontinuity points. A variational expectation maximization algorithm is derived for inference. We show that the pruned exact linear time method, originally developed for change points detection in univariate time series, can be considered for the maximization step. This allows the detection of both the number of change points and their location. Experiments on artificial and real datasets are carried out, and the proposed approach is compared with related methods.     

A competing risks approach for nonparametric estimation of transition probabilities in a non-Markov illness-death model

Competing risks model time to first event and type of first event. An example from hospital epidemiology is the incidence of hospital-acquired infection, which has to account for hospital discharge of non-infected patients as a competing risk. An illness-death model would allow to further study hospital outcomes of infected patients. Such a model typically relies on a Markov assumption. However, it is conceivable that the future course of an infected patient does not only depend on the time since hospital admission and current infection status but also on the time since infection. We demonstrate how a modified competing risks model can be used for nonparametric estimation of transition probabilities when the Markov assumption is violated.     

Degree-based goodness-of-fit tests for heterogeneous random graph models: Independent and exchangeable cases

The degrees are a classical and relevant way to study the topology of a network. They can be used to assess the goodness of fit for a given random graph model. In this paper, we introduce goodness-of-fit tests for two classes of models. First, we consider the case of independent graph models such as the heterogeneous Erdös-Rényi model in which the edges have different connection probabilities. Second, we consider a generic model for exchangeable random graphs called the W-graph. The stochastic block model and the expected degree distribution model fall within this framework. We prove the asymptotic normality of the degree mean square under these independent and exchangeable models and derive formal tests. We study the power of the proposed tests and we prove the asymptotic normality under specific sparsity regimes. The tests are illustrated on real networks from social sciences and ecology, and their performances are assessed via a simulation study.     

Perturbation analysis of Markov modulated fluid models

ABSTRACT

We consider perturbations of positive recurrent Markov modulated fluid models. In addition to the infinitesimal generator of the phases, we also perturb the rate matrix, and analyze the effect of those perturbations on the matrix of first return probabilities to the initial level. Our main contribution is the construction of a substitute for the matrix of first return probabilities, which enables us to analyze the effect of the perturbation under consideration.     

The stochastic topic block model for the clustering of vertices in networks with textual edges

Due to the significant increase of communications between individuals via social media (Facebook, Twitter, Linkedin) or electronic formats (email, web, e-publication) in the past two decades, network analysis has become an unavoidable discipline. Many random graph models have been proposed to extract information from networks based on person-to-person links only, without taking into account information on the contents. This paper introduces the stochastic topic block model, a probabilistic model for networks with textual edges. We address here the problem of discovering meaningful clusters of vertices that are coherent from both the network interactions and the text contents. A classification variational expectation-maximization algorithm is proposed to perform inference. Simulated datasets are considered in order to assess the proposed approach and to highlight its main features. Finally, we demonstrate the effectiveness of our methodology on two real-word datasets: a directed communication network and an undirected co-authorship network.     

Exact dimensionality selection for Bayesian PCA

We present a Bayesian model selection approach to estimate the intrinsic dimensionality of a high-dimensional dataset. To this end, we introduce a novel formulation of the probabilisitic principal component analysis model based on a normal-gamma prior distribution. In this context, we exhibit a closed-form expression of the marginal likelihood which allows to infer an optimal number of components. We also propose a heuristic based on the expected shape of the marginal likelihood curve in order to choose the hyperparameters. In nonasymptotic frameworks, we show on simulated data that this exact dimensionality selection approach is competitive with both Bayesian and frequentist state-of-the-art methods.