Data-driven modelling of biological multi-scale processes

Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript we review mathematical modelling approaches used to describe the individual spatial scales and how they are integrated into holistic models. We discuss the relation between spatial and temporal scales and the implication of that on multi-scale modelling. Based upon this overview over state-of-the-art modelling approaches, we formulate key challenges in mathematical and computational modelling of biological multi-scale and multi-physics processes. In particular, we considered the availability of analysis tools for multi-scale models and model-based multi-scale data integration. We provide a compact review of methods for model-based data integration and model-based hypothesis testing. Furthermore, novel approaches and recent trends are discussed, including computation time reduction using reduced order and surrogate models, which contribute to the solution of inference problems. We conclude the manuscript by providing a few ideas for the development of tailored multi-scale inference methods.Comment: This manuscript will appear in the Journal of Coupled Systems and Multiscale Dynamics (American Scientific Publishers

Distributed Hybrid Simulation of the Internet of Things and Smart Territories

This paper deals with the use of hybrid simulation to build and compose heterogeneous simulation scenarios that can be proficiently exploited to model and represent the Internet of Things (IoT). Hybrid simulation is a methodology that combines multiple modalities of modeling/simulation. Complex scenarios are decomposed into simpler ones, each one being simulated through a specific simulation strategy. All these simulation building blocks are then synchronized and coordinated. This simulation methodology is an ideal one to represent IoT setups, which are usually very demanding, due to the heterogeneity of possible scenarios arising from the massive deployment of an enormous amount of sensors and devices. We present a use case concerned with the distributed simulation of smart territories, a novel view of decentralized geographical spaces that, thanks to the use of IoT, builds ICT services to manage resources in a way that is sustainable and not harmful to the environment. Three different simulation models are combined together, namely, an adaptive agent-based parallel and distributed simulator, an OMNeT++ based discrete event simulator and a script-language simulator based on MATLAB. Results from a performance analysis confirm the viability of using hybrid simulation to model complex IoT scenarios.Comment: arXiv admin note: substantial text overlap with arXiv:1605.0487

Accelerating Eulerian Fluid Simulation With Convolutional Networks

Efficient simulation of the Navier-Stokes equations for fluid flow is a long standing problem in applied mathematics, for which state-of-the-art methods require large compute resources. In this work, we propose a data-driven approach that leverages the approximation power of deep-learning with the precision of standard solvers to obtain fast and highly realistic simulations. Our method solves the incompressible Euler equations using the standard operator splitting method, in which a large sparse linear system with many free parameters must be solved. We use a Convolutional Network with a highly tailored architecture, trained using a novel unsupervised learning framework to solve the linear system. We present real-time 2D and 3D simulations that outperform recently proposed data-driven methods; the obtained results are realistic and show good generalization properties.Comment: Significant revisio

An agent-driven semantical identifier using radial basis neural networks and reinforcement learning

Due to the huge availability of documents in digital form, and the deception possibility raise bound to the essence of digital documents and the way they are spread, the authorship attribution problem has constantly increased its relevance. Nowadays, authorship attribution,for both information retrieval and analysis, has gained great importance in the context of security, trust and copyright preservation. This work proposes an innovative multi-agent driven machine learning technique that has been developed for authorship attribution. By means of a preprocessing for word-grouping and time-period related analysis of the common lexicon, we determine a bias reference level for the recurrence frequency of the words within analysed texts, and then train a Radial Basis Neural Networks (RBPNN)-based classifier to identify the correct author. The main advantage of the proposed approach lies in the generality of the semantic analysis, which can be applied to different contexts and lexical domains, without requiring any modification. Moreover, the proposed system is able to incorporate an external input, meant to tune the classifier, and then self-adjust by means of continuous learning reinforcement.Comment: Published on: Proceedings of the XV Workshop "Dagli Oggetti agli Agenti" (WOA 2014), Catania, Italy, Sepember. 25-26, 201

Combining Physical Simulators and Object-Based Networks for Control

Physics engines play an important role in robot planning and control; however, many real-world control problems involve complex contact dynamics that cannot be characterized analytically. Most physics engines therefore employ . approximations that lead to a loss in precision. In this paper, we propose a hybrid dynamics model, simulator-augmented interaction networks (SAIN), combining a physics engine with an object-based neural network for dynamics modeling. Compared with existing models that are purely analytical or purely data-driven, our hybrid model captures the dynamics of interacting objects in a more accurate and data-efficient manner.Experiments both in simulation and on a real robot suggest that it also leads to better performance when used in complex control tasks. Finally, we show that our model generalizes to novel environments with varying object shapes and materials.Comment: ICRA 2019; Project page: http://sain.csail.mit.ed