Global parameter identification of stochastic reaction networks from single trajectories

We consider the problem of inferring the unknown parameters of a stochastic biochemical network model from a single measured time-course of the concentration of some of the involved species. Such measurements are available, e.g., from live-cell fluorescence microscopy in image-based systems biology. In addition, fluctuation time-courses from, e.g., fluorescence correlation spectroscopy provide additional information about the system dynamics that can be used to more robustly infer parameters than when considering only mean concentrations. Estimating model parameters from a single experimental trajectory enables single-cell measurements and quantification of cell--cell variability. We propose a novel combination of an adaptive Monte Carlo sampler, called Gaussian Adaptation, and efficient exact stochastic simulation algorithms that allows parameter identification from single stochastic trajectories. We benchmark the proposed method on a linear and a non-linear reaction network at steady state and during transient phases. In addition, we demonstrate that the present method also provides an ellipsoidal volume estimate of the viable part of parameter space and is able to estimate the physical volume of the compartment in which the observed reactions take place.Comment: Article in print as a book chapter in Springer's "Advances in Systems Biology

Autonomous search and rescue rotorcraft mission stochastic planning with generic DBNs

This paper proposes an original generic hierarchical framework in order to facilitate the modeling stage of complex autonomous robotics mission planning problems with action uncertainties. Such stochastic planning problems can be modeled as Markov Decision Processes [5]. This work is motivated by a real application to autonomous search and rescue rotorcraft within the ReSSAC1 project at ONERA. As shown in Figure 1.a, an autonomous rotorcraft must y and explore over regions, using waypoints, and in order to nd one (roughly localized) person per region (dark small areas). Uncertainties can come from the unpredictability of the environment (wind, visibility) or from a partial knowledge of it: map of obstacles, or elevation map etc. After a short presentation of the framework of structured Markov Decision Processes (MDPs), we present a new original hierarchical MDP model based on generic Dynamic Bayesian Network templates. We illustrate the bene ts of our approach on the basis of search and rescue missions of the ReSSAC project.IFIP International Conference on Artificial Intelligence in Theory and Practice - Planning and SchedulingRed de Universidades con Carreras en Informática (RedUNCI

Influence-Optimistic Local Values for Multiagent Planning --- Extended Version

Recent years have seen the development of methods for multiagent planning under uncertainty that scale to tens or even hundreds of agents. However, most of these methods either make restrictive assumptions on the problem domain, or provide approximate solutions without any guarantees on quality. Methods in the former category typically build on heuristic search using upper bounds on the value function. Unfortunately, no techniques exist to compute such upper bounds for problems with non-factored value functions. To allow for meaningful benchmarking through measurable quality guarantees on a very general class of problems, this paper introduces a family of influence-optimistic upper bounds for factored decentralized partially observable Markov decision processes (Dec-POMDPs) that do not have factored value functions. Intuitively, we derive bounds on very large multiagent planning problems by subdividing them in sub-problems, and at each of these sub-problems making optimistic assumptions with respect to the influence that will be exerted by the rest of the system. We numerically compare the different upper bounds and demonstrate how we can achieve a non-trivial guarantee that a heuristic solution for problems with hundreds of agents is close to optimal. Furthermore, we provide evidence that the upper bounds may improve the effectiveness of heuristic influence search, and discuss further potential applications to multiagent planning.Comment: Long version of IJCAI 2015 paper (and extended abstract at AAMAS 2015

An Auction-based Coordination Strategy for Task-Constrained Multi-Agent Stochastic Planning with Submodular Rewards

In many domains such as transportation and logistics, search and rescue, or cooperative surveillance, tasks are pending to be allocated with the consideration of possible execution uncertainties. Existing task coordination algorithms either ignore the stochastic process or suffer from the computational intensity. Taking advantage of the weakly coupled feature of the problem and the opportunity for coordination in advance, we propose a decentralized auction-based coordination strategy using a newly formulated score function which is generated by forming the problem into task-constrained Markov decision processes (MDPs). The proposed method guarantees convergence and at least 50% optimality in the premise of a submodular reward function. Furthermore, for the implementation on large-scale applications, an approximate variant of the proposed method, namely Deep Auction, is also suggested with the use of neural networks, which is evasive of the troublesome for constructing MDPs. Inspired by the well-known actor-critic architecture, two Transformers are used to map observations to action probabilities and cumulative rewards respectively. Finally, we demonstrate the performance of the two proposed approaches in the context of drone deliveries, where the stochastic planning for the drone league is cast into a stochastic price-collecting Vehicle Routing Problem (VRP) with time windows. Simulation results are compared with state-of-the-art methods in terms of solution quality, planning efficiency and scalability.Comment: 17 pages, 5 figure

Collaborative sparse regression using spatially correlated supports - Application to hyperspectral unmixing

This paper presents a new Bayesian collaborative sparse regression method for linear unmixing of hyperspectral images. Our contribution is twofold; first, we propose a new Bayesian model for structured sparse regression in which the supports of the sparse abundance vectors are a priori spatially correlated across pixels (i.e., materials are spatially organised rather than randomly distributed at a pixel level). This prior information is encoded in the model through a truncated multivariate Ising Markov random field, which also takes into consideration the facts that pixels cannot be empty (i.e, there is at least one material present in each pixel), and that different materials may exhibit different degrees of spatial regularity. Secondly, we propose an advanced Markov chain Monte Carlo algorithm to estimate the posterior probabilities that materials are present or absent in each pixel, and, conditionally to the maximum marginal a posteriori configuration of the support, compute the MMSE estimates of the abundance vectors. A remarkable property of this algorithm is that it self-adjusts the values of the parameters of the Markov random field, thus relieving practitioners from setting regularisation parameters by cross-validation. The performance of the proposed methodology is finally demonstrated through a series of experiments with synthetic and real data and comparisons with other algorithms from the literature