Low-dimensional compartment models for biological systems can be fitted to time series data using Monte Carlo particle filter methods. As dimension increases, for example when analyzing a collection of spatially coupled populations, particle filter methods rapidly degenerate. We show that many independent Monte Carlo calculations, each of which does not attempt to solve the filtering problem, can be combined to give a global filtering solution with favorable theoretical scaling properties under a weak coupling condition. The independent Monte Carlo calculations are called islands, and the operation carried out on each island is called adapted simulation, so the complete algorithm is called an adapted simulation island filter. We demonstrate this methodology and some related algorithms on a model for measles transmission within and between cities.[-]

In recent years, new pandemic threats have become more and more frequent (SARS, bird flu, swine flu, Ebola, MERS, nCoV...) and analyses of data from the early spread more and more common and rapid. Particular interest is usually focused on the estimation of $ R_{0}$ and various methods, essentially based estimates of exponential growth rate and generation time distribution, have been proposed. Other parameters, such as fatality rate, are also of interest. In this talk, various sources of bias arising because observations are made in the early phase of spread will be discussed and also possible remedies proposed.[-]

Inferring causal effects of a treatment or policy from observational data is central to many applications. However, state-of-the-art methods for causal inference suffer when covariates have missing values, which is ubiquitous in application.
Missing data greatly complicate causal analyses as they either require strong assumptions about the missing data generating mechanism or an adapted unconfoundedness hypothesis. In this talk, I will first provide a classification of existing methods according to the main underlying assumptions, which are based either on variants of the classical unconfoundedness assumption or relying on assumptions about the mechanism that generates the missing values. Then, I will present two recent contributions on this topic: (1) an extension of doubly robust estimators that allows handling of missing attributes, and (2) an approach to causal inference based on variational autoencoders adapted to incomplete data.
I will illustrate the topic an an observational medical database which has heterogeneous data and a multilevel structure to assess the impact of the administration of a treatment on survival.[-]

Living systems often attempt to calculate and predict the future state of the environment. Given the stochastic nature of many biological systems how is that possible ? Does host-pathogen co-evolution constrain the space viral trajectories? I will show that co-evolution between immune systems and viruses in a finite-dimensional antigenic space can be described by an antigenic wave pushed forward and canalized by host-pathogen interactions. This leads to a new emergent timescale, the persistence time of the wave's direction in antigenic space, which can be much longer than the coalescence time of the viral population.
Since predicting the future state of a viral environment requires weighing the trust in new observations against prior experiences, I will present a view of the host immune system as a dynamic Bayesian machinery that updates its memory repertoire by balancing evidence from new pathogen encounters against past experience of infection to predict and prepare for future threats[-]

In the scenario where multiple instances of networks with same nodes are available and nodes are attached to spatial features, it is worth combining both information in order to explain the role of the nodes. The explainability of node role in complex networks is very difficult, however crucial in different application scenarios such as social science, neuroscience, computer science... Many efforts have been made on the quantification of hubs revealing particular nodes in a network using a given structural property. Yet, for spatio-temporal networks, the identification of node role remains largely unexplored. In this talk, I will show limitations of classical methods on a real datasets coming from brain connectivity comparing healthy subjects to coma patients. Then, I will present recent work using equivalence relation of the nodal structural properties. Comparisons of graphs with same nodes set is evaluated with a new similarity score based on graph structural patterns. This score provides a nodal index to determine node role distinctiveness in a graph family. Finally, illustrations on different datasets concerning human brain functional connectivity will be described.[-]

Faced with data containing a large number of inter-related explanatory variables, finding ways to investigate complex multi-factorial effects is an important statistical task. This is particularly relevant for epidemiological study designs where large numbers of covariates are typically collected in an attempt to capture complex interactions between host characteristics and risk factors. A related task, which is of great interest in stratified medicine, is to use multi-omics data to discover subgroups of patients with distinct molecular phenotypes and clinical outcomes, thus providing the potential to target treatments more precisely. Flexible clustering is a natural way to tackle such problems. It can be used in an unsupervised or a semi-supervised manner by adding a link between the clustering structure and outcomes and performing joint modelling. In this case, the clustering structure is used to help predict the outcome. This latter approach, known as profile regression, has been implemented recently using a Bayesian non parametric DP modelling framework, which specifies a joint clustering model for covariates and outcome, with an additional variable selection step to uncover the variables driving the clustering (Papathomas et al, 2012). In this talk, two related issues will be discussed. Firstly, we will focus on categorical covariates, a common situation in epidemiological studies, and examine the relation between: (i) dependence structures highlighted by Bayesian partitioning of the covariate space incorporating variable selection; and (ii) log linear modelling with interaction terms, a traditional approach to model dependence. We will show how the clustering approach can be employed to assist log-linear model determination, a challenging task as the model space becomes quickly very large (Papathomas and Richardson, 2015). Secondly, we will discuss clustering as a tool for integrating information from multiple datasets, with a view to discover useful structure for prediction. In this context several related issues arise. It is clear that each dataset may carry a different amount of information for the predictive task. Methods for learning how to reweight each data type for this task will therefore be presented. In the context of multi-omics datasets, the efficiency of different methods for performing integrative clustering will also be discussed, contrasting joint modelling and stepwise approaches. This will be illustrated by analysis of genomics cancer datasets.
Joint work with Michael Papathomas and Paul Kirk.[-]

Dans une première partie, je présenterai différentes problématiques liées à des statistiques d'occurrences de mots dans des génomes et décortiquerai plus en détail la question de savoir comment détecter si un mot a une fréquence d'apparition significativement anormale dans une séquence. Dans une deuxième partie, je présenterai différentes extensions pour tenir compte du fait qu'un motif d'ADN fonctionnel n'est pas toujours un « mot », mais qu'il peut avoir une structure plus complexe qui nécessite le développement de nouvelles méthodes statistiques.[-]

Many data can be represented as rankings or permutations, raising the question of developing machine learning models on the symmetric group. When the number of items in the permutations gets large, manipulating permutations can quickly become computationally intractable. I will discuss two computationally efficient embeddings of the symmetric groups in Euclidean spaces leading to fast machine learning algorithms, and illustrate their relevance on biological applications and image classification.[-]