Analysis of Reaction Network Systems Using Tropical Geometry

We discuss a novel analysis method for reaction network systems with polynomial or rational rate functions. This method is based on computing tropical equilibrations defined by the equality of at least two dominant monomials of opposite signs in the differential equations of each dynamic variable. In algebraic geometry, the tropical equilibration problem is tantamount to finding tropical prevarieties, that are finite intersections of tropical hypersurfaces. Tropical equilibrations with the same set of dominant monomials define a branch or equivalence class. Minimal branches are particularly interesting as they describe the simplest states of the reaction network. We provide a method to compute the number of minimal branches and to find representative tropical equilibrations for each branch.Comment: Proceedings Computer Algebra in Scientific Computing CASC 201

Making and breaking power laws in evolutionary algorithm population dynamics

Deepening our understanding of the characteristics and behaviors of population-based search algorithms remains an important ongoing challenge in Evolutionary Computation. To date however, most studies of Evolutionary Algorithms have only been able to take place within tightly restricted experimental conditions. For instance, many analytical methods can only be applied to canonical algorithmic forms or can only evaluate evolution over simple test functions. Analysis of EA behavior under more complex conditions is needed to broaden our understanding of this population-based search process. This paper presents an approach to analyzing EA behavior that can be applied to a diverse range of algorithm designs and environmental conditions. The approach is based on evaluating an individual’s impact on population dynamics using metrics derived from genealogical graphs.\ud From experiments conducted over a broad range of conditions, some important conclusions are drawn in this study. First, it is determined that very few individuals in an EA population have a significant influence on future population dynamics with the impact size fitting a power law distribution. The power law distribution indicates there is a non-negligible probability that single individuals will dominate the entire population, irrespective of population size. Two EA design features are however found to cause strong changes to this aspect of EA behavior: i) the population topology and ii) the introduction of completely new individuals. If the EA population topology has a long path length or if new (i.e. historically uncoupled) individuals are continually inserted into the population, then power law deviations are observed for large impact sizes. It is concluded that such EA designs can not be dominated by a small number of individuals and hence should theoretically be capable of exhibiting higher degrees of parallel search behavior

Hybridizing Non-dominated Sorting Algorithms: Divide-and-Conquer Meets Best Order Sort

Many production-grade algorithms benefit from combining an asymptotically efficient algorithm for solving big problem instances, by splitting them into smaller ones, and an asymptotically inefficient algorithm with a very small implementation constant for solving small subproblems. A well-known example is stable sorting, where mergesort is often combined with insertion sort to achieve a constant but noticeable speed-up. We apply this idea to non-dominated sorting. Namely, we combine the divide-and-conquer algorithm, which has the currently best known asymptotic runtime of $O(N (\log N)^{M - 1})$, with the Best Order Sort algorithm, which has the runtime of $O(N^2 M)$ but demonstrates the best practical performance out of quadratic algorithms. Empirical evaluation shows that the hybrid's running time is typically not worse than of both original algorithms, while for large numbers of points it outperforms them by at least 20%. For smaller numbers of objectives, the speedup can be as large as four times.Comment: A two-page abstract of this paper will appear in the proceedings companion of the 2017 Genetic and Evolutionary Computation Conference (GECCO 2017

Multi-Person Brain Activity Recognition via Comprehensive EEG Signal Analysis

An electroencephalography (EEG) based brain activity recognition is a fundamental field of study for a number of significant applications such as intention prediction, appliance control, and neurological disease diagnosis in smart home and smart healthcare domains. Existing techniques mostly focus on binary brain activity recognition for a single person, which limits their deployment in wider and complex practical scenarios. Therefore, multi-person and multi-class brain activity recognition has obtained popularity recently. Another challenge faced by brain activity recognition is the low recognition accuracy due to the massive noises and the low signal-to-noise ratio in EEG signals. Moreover, the feature engineering in EEG processing is time-consuming and highly re- lies on the expert experience. In this paper, we attempt to solve the above challenges by proposing an approach which has better EEG interpretation ability via raw Electroencephalography (EEG) signal analysis for multi-person and multi-class brain activity recognition. Specifically, we analyze inter-class and inter-person EEG signal characteristics, based on which to capture the discrepancy of inter-class EEG data. Then, we adopt an Autoencoder layer to automatically refine the raw EEG signals by eliminating various artifacts. We evaluate our approach on both a public and a local EEG datasets and conduct extensive experiments to explore the effect of several factors (such as normalization methods, training data size, and Autoencoder hidden neuron size) on the recognition results. The experimental results show that our approach achieves a high accuracy comparing to competitive state-of-the-art methods, indicating its potential in promoting future research on multi-person EEG recognition.Comment: 10 page

Study on Different Topology Manipulation Algorithms in Wireless Sensor Network

Wireless sensor network (WSN) comprises of spatially distributed autonomous sensors to screen physical or environmental conditions and to agreeably go their information through the network to a principle area. One of the critical necessities of a WSN is the efficiency of vitality, which expands the life time of the network. At the same time there are some different variables like Load Balancing, congestion control, coverage, Energy Efficiency, mobility and so on. A few methods have been proposed via scientists to accomplish these objectives that can help in giving a decent topology control. In the piece, a few systems which are accessible by utilizing improvement and transformative strategies that give a multi target arrangement are examined. In this paper, we compare different algorithms' execution in view of a few parameters intended for every target and the outcomes are analyzed. DOI: 10.17762/ijritcc2321-8169.15029

Stochastic analysis of nonlinear dynamics and feedback control for gene regulatory networks with applications to synthetic biology

The focus of the thesis is the investigation of the generalized repressilator model (repressing genes ordered in a ring structure). Using nonlinear bifurcation analysis stable and quasi-stable periodic orbits in this genetic network are characterized and a design for a switchable and controllable genetic oscillator is proposed. The oscillator operates around a quasi-stable periodic orbit using the classical engineering idea of read-out based control. Previous genetic oscillators have been designed around stable periodic orbits, however we explore the possibility of quasi-stable periodic orbit expecting better controllability. The ring topology of the generalized repressilator model has spatio-temporal symmetries that can be understood as propagating perturbations in discrete lattices. Network topology is a universal cross-discipline transferable concept and based on it analytical conditions for the emergence of stable and quasi-stable periodic orbits are derived. Also the length and distribution of quasi-stable oscillations are obtained. The findings suggest that long-lived transient dynamics due to feedback loops can dominate gene network dynamics. Taking the stochastic nature of gene expression into account a master equation for the generalized repressilator is derived. The stochasticity is shown to influence the onset of bifurcations and quality of oscillations. Internal noise is shown to have an overall stabilizing effect on the oscillating transients emerging from the quasi-stable periodic orbits. The insights from the read-out based control scheme for the genetic oscillator lead us to the idea to implement an algorithmic controller, which would direct any genetic circuit to a desired state. The algorithm operates model-free, i.e. in principle it is applicable to any genetic network and the input information is a data matrix of measured time series from the network dynamics. The application areas for readout-based control in genetic networks range from classical tissue engineering to stem cells specification, whenever a quantitatively and temporarily targeted intervention is required

Data Driven Modelling and Optimization of MEA Absorption Process for CO2 Capture

Global warming is a rising issue and there are many research studies aiming to reduce greenhouse gas emissions. Carbon capture and storage technologies improved throughout the years to contribute as a solution to this problem. In this work the post-combustion carbon capture unit is used to develop surrogated models for operation optimization. Previous work included mechanistic and detailed modeling of steady-state and dynamic systems. Furthermore, control structures and optimization approaches have been studied. Moreover, various solutions such as MEA, DEA, and MDEA have been tested and simulated to determine the efficiency and the behavior of the system. In this work a dynamic model with MEA solution developed by (Nittaya, 2014) and (Harun, 2012) is used to generate operational data. The system is simulated using gProms v.5.1 with six PI controllers. The model illustrated that the regeneration of the solvent is the most energy-consuming part of the process. Due to the changes in electricity supply and demand, also, the importance of achieving a specific %CC and purity of carbon dioxide as outputs of this process, surrogated models are developed and used to predict the outputs and to optimize the operating conditions of the process. Multiple machine learning and data-driven models has been developed using simulation data generated after a proper choice of the operating variables and the important outputs. Steady-state and transient state models have been developed and evaluated. The models were used to predict the outputs of the process and used later to optimize the operating conditions of the process. The flue gas flow rate, temperature, pressure, reboiler pressure, reboiler, and condenser duties were selected as the operating variables of the system (inputs). The system energy requirements, %CC, and the purity of carbon dioxide were selected to be the outputs of the process. For steady-state modeling, artificial neural network (ANN) model with backpropagation and momentum was developed to predict the process outputs. The ANN model efficiency was compared to other machine learning models such as Gaussian Process Regression (GPR), rational quadratic GPR, squared exponential GPR, tree regression and matern GPR. The ANN excelled all other models in terms of prediction and accuracy, however, the other model’s regression coefficient (R2) was never below 0.95. For dynamic modelling, recurrent neural networks (RNN) have been used to predict the outputs of the system. Two training algorithms have been used to create the neural network: Levenberg-Marquardt (LM) and Broyden-Fletcher-Goldfrab-Shanno (BFGS). The RNN was able to predict the outputs of the system accurately. Sequential quadratic programming (SQP) and genetic algorithm (GA) were used to optimize the surrogated models and determine the optimum operating conditions following an objective of maximizing the purity of CO2 and %CC and minimizing the system energy requirements