AND-NOT logic framework for steady state analysis of Boolean network models

Finite dynamical systems (e.g. Boolean networks and logical models) have been used in modeling biological systems to focus attention on the qualitative features of the system, such as the wiring diagram. Since the analysis of such systems is hard, it is necessary to focus on subclasses that have the properties of being general enough for modeling and simple enough for theoretical analysis. In this paper we propose the class of AND-NOT networks for modeling biological systems and show that it provides several advantages. Some of the advantages include: Any finite dynamical system can be written as an AND-NOT network with similar dynamical properties. There is a one-to-one correspondence between AND-NOT networks, their wiring diagrams, and their dynamics. Results about AND-NOT networks can be stated at the wiring diagram level without losing any information. Results about AND-NOT networks are applicable to any Boolean network. We apply our results to a Boolean model of Th-cell differentiation

Modeling structural change in spatial system dynamics: A Daisyworld example

System dynamics (SD) is an effective approach for helping reveal the temporal behavior of complex systems. Although there have been recent developments in expanding SD to include systems' spatial dependencies, most applications have been restricted to the simulation of diffusion processes; this is especially true for models on structural change (e.g. LULC modeling). To address this shortcoming, a Python program is proposed to tightly couple SD software to a Geographic Information System (GIS). The approach provides the required capacities for handling bidirectional and synchronized interactions of operations between SD and GIS. In order to illustrate the concept and the techniques proposed for simulating structural changes, a fictitious environment called Daisyworld has been recreated in a spatial system dynamics (SSD) environment. The comparison of spatial and non-spatial simulations emphasizes the importance of considering spatio-temporal feedbacks. Finally, practical applications of structural change models in agriculture and disaster management are proposed

Incremental Semiparametric Inverse Dynamics Learning

This paper presents a novel approach for incremental semiparametric inverse dynamics learning. In particular, we consider the mixture of two approaches: Parametric modeling based on rigid body dynamics equations and nonparametric modeling based on incremental kernel methods, with no prior information on the mechanical properties of the system. This yields to an incremental semiparametric approach, leveraging the advantages of both the parametric and nonparametric models. We validate the proposed technique learning the dynamics of one arm of the iCub humanoid robot

Dynamic facial expressions of emotion transmit an evolving hierarchy of signals over time

Designed by biological and social evolutionary pressures, facial expressions of emotion comprise specific facial movements to support a near-optimal system of signaling and decoding. Although highly dynamical, little is known about the form and function of facial expression temporal dynamics. Do facial expressions transmit diagnostic signals simultaneously to optimize categorization of the six classic emotions, or sequentially to support a more complex communication system of successive categorizations over time? Our data support the latter. Using a combination of perceptual expectation modeling, information theory, and Bayesian classifiers, we show that dynamic facial expressions of emotion transmit an evolving hierarchy of “biologically basic to socially specific” information over time. Early in the signaling dynamics, facial expressions systematically transmit few, biologically rooted face signals supporting the categorization of fewer elementary categories (e.g., approach/avoidance). Later transmissions comprise more complex signals that support categorization of a larger number of socially specific categories (i.e., the six classic emotions). Here, we show that dynamic facial expressions of emotion provide a sophisticated signaling system, questioning the widely accepted notion that emotion communication is comprised of six basic (i.e., psychologically irreducible) categories, and instead suggesting four

Neural-Attention-Based Deep Learning Architectures for Modeling Traffic Dynamics on Lane Graphs

Deep neural networks can be powerful tools, but require careful application-specific design to ensure that the most informative relationships in the data are learnable. In this paper, we apply deep neural networks to the nonlinear spatiotemporal physics problem of vehicle traffic dynamics. We consider problems of estimating macroscopic quantities (e.g., the queue at an intersection) at a lane level. First-principles modeling at the lane scale has been a challenge due to complexities in modeling social behaviors like lane changes, and those behaviors' resultant macro-scale effects. Following domain knowledge that upstream/downstream lanes and neighboring lanes affect each others' traffic flows in distinct ways, we apply a form of neural attention that allows the neural network layers to aggregate information from different lanes in different manners. Using a microscopic traffic simulator as a testbed, we obtain results showing that an attentional neural network model can use information from nearby lanes to improve predictions, and, that explicitly encoding the lane-to-lane relationship types significantly improves performance. We also demonstrate the transfer of our learned neural network to a more complex road network, discuss how its performance degradation may be attributable to new traffic behaviors induced by increased topological complexity, and motivate learning dynamics models from many road network topologies.Comment: To appear at 2019 IEEE Conference on Intelligent Transportation System

A Business Application of the System Dynamics Approach: Word-of-Mouth and Its Effect in an Online Environment

In this article, we illustrate the use of system dynamics modeling approach to study a complex system: word-of-mouth. Word-of-mouth plays an important role in reducing risk and uncertainty in purchase and consumption. Most of the prior research on word-of-mouth focused on studying either the factors that trigger consumers’ participation (sending or receiving) in word-of-mouth activities or the impact word-of-mouth information has on consumers’ buying decisions. The relationship between the two decision processes, however, is recursive and dynamic. Most prior studies have not focused on a recursive relationship. Our objective is to present a system dynamics model for the study of the relationship between the buying decision and the decision to participate in word-of-mouth communication. We also discuss how system dynamics modeling can be used in other complex problems in business such as the creation of a global business

INTEGRATING HAWKES PROCESS- ND BIOMASS MODELS TO CAPTURE IMPULSIVE POPULATION DYNAMICS

This paper presents a modeling framework that captures the impulsive biomass dynamics (bust-boom) of a fish stock. The framework is based on coupling a Hawkes-process model to a discrete-time, ages-structured population dynamics model. Simulation results are presented to demonstrate the efficacy of the framework in capturing impulsive events in the population trajectory. The results presented in this paper are significant in three ways: • A framework has been presented that demonstrates how premonitory information may be extracted from exogenous observations from complex environmental systems • We have demonstrated how exogenous information may be parameterized and incorporated into the modeling process for better understanding of the link between environmental drivers and the population dynamical system • The framework has been successfully applied in modeling and short-term prediction of the population dynamics of an empirical fish stock.publishedVersio