An evolutionary computing model for the study of within-host evolution

Evolution of an individual within another individual is known as within-host dynamics (WHD). The most common modeling technique to study WHD involves ordinary differential equations (ODEs). In the field of biology, models of this kind assume, for example, that both the number of viruses and the number of mouse cells susceptible to being infected change according to their interaction as stated in the ODE model. However, viruses can undergo mutations and, consequently, evolve inside the mouse, whereas the mouse, in turn, displays evolutionary mechanisms through its immune system (e.g., clonal selection), defending against the invading virus. In this work, as the main novelty, we propose an evolutionary WHD model simulating the coexistence of an evolving invader within a host. In addition, instead of using ODEs we developed an alternative methodology consisting of the hybridization of a genetic algorithm with an artificial immune system. Aside from the model, interest in biology, and its potential clinical use, the proposed WHD model may be useful in those cases where the invader exhibits evolutionary changes, for instance, in the design of anti-virus software, intrusion detection algorithms in a corporation’s computer systems, etc. The model successfully simulates two intruder detection paradigms (i.e., humoral detection, danger detection) in which the intruder represents an evolving invader or guest (e.g., virus, computer program,) that infects a host (e.g., mouse, computer memory). The obtained results open up the possibility of simulating environments in which two entities (guest versus host) compete evolutionarily with each other when occupying the same space (e.g., organ cells, computer memory, network

Empirical Study of a Hybrid Algorithm Based on Clonal Selection and Small Population Based PSO.

In this paper, a hybrid algorithm, based on clonal selection algorithm (CSA) and small population based particle swarm optimization (SPPSO) is introduced. The performance of this new algorithm (CS2P2SO) is observed for four well known benchmark functions. The SPPSO is a variant of conventional PSO (CPSO), introduced by the second author of this paper, where a very small number of initial particles are used and after a few iterations, the best particle is kept and the rest are replaced by the same number of regenerated particles. On the other hand, CSA belongs to the family of artificial immune system (AIS). It is an evolutionary algorithm, where, during evolution, the antibodies which can recognize the antigens proliferate by cloning. With the hybridization of these two algorithms, the strength of CPSO is enhanced to a great extent. The concept of SPPSO helps to find the optimum solution with less memory requirement and the concept of CSA increases the exploration capability and reduces the chances of convergence to local minima. The test results show that CS2P2SO performs better than CPSO and SPPSO for the Sphere, Rosenbrockpsilas, Rastriginpsilas and Griewankpsilas functions

Hybrid nature-inspired computation methods for optimization

The focus of this work is on the exploration of the hybrid Nature-Inspired Computation (NIC) methods with application in optimization. In the dissertation, we first study various types of the NIC algorithms including the Clonal Selection Algorithm (CSA), Particle Swarm Optimization (PSO), Ant Colony Optimization (ACO), Simulated Annealing (SA), Harmony Search (HS), Differential Evolution (DE), and Mind Evolution Computing (MEC), and propose several new fusions of the NIC techniques, such as CSA-DE, HS-DE, and CSA-SA. Their working principles, structures, and algorithms are analyzed and discussed in details. We next investigate the performances of our hybrid NIC methods in handling nonlinear, multi-modal, and dynamical optimization problems, e.g., nonlinear function optimization, optimal LC passive power filter design, and optimization of neural networks and fuzzy classification systems. The hybridization of these NIC methods can overcome the shortcomings of standalone algorithms while still retaining all the advantages. It has been demonstrated using computer simulations that the proposed hybrid NIC approaches are capable of yielding superior optimization performances over the individual NIC methods as well as conventional methodologies with regard to the search efficiency, convergence speed, and quantity and quality of the optimal solutions achieved

A Comprehensive Review of Bio-Inspired Optimization Algorithms Including Applications in Microelectronics and Nanophotonics

The application of artificial intelligence in everyday life is becoming all-pervasive and unavoidable. Within that vast field, a special place belongs to biomimetic/bio-inspired algorithms for multiparameter optimization, which find their use in a large number of areas. Novel methods and advances are being published at an accelerated pace. Because of that, in spite of the fact that there are a lot of surveys and reviews in the field, they quickly become dated. Thus, it is of importance to keep pace with the current developments. In this review, we first consider a possible classification of bio-inspired multiparameter optimization methods because papers dedicated to that area are relatively scarce and often contradictory. We proceed by describing in some detail some more prominent approaches, as well as those most recently published. Finally, we consider the use of biomimetic algorithms in two related wide fields, namely microelectronics (including circuit design optimization) and nanophotonics (including inverse design of structures such as photonic crystals, nanoplasmonic configurations and metamaterials). We attempted to keep this broad survey self-contained so it can be of use not only to scholars in the related fields, but also to all those interested in the latest developments in this attractive area

免疫学的および進化的アルゴリズムに基づく改良された群知能最適化に関する研究

富山大学・富理工博甲第175号・楊玉・2020/3/24富山大学202

Inspection and Monitoring of Structural Damage Using Vibration Signatures and Smart Techniques

The structural damage detection plays an important role in the evaluation of structural systems and to ensure their safety. Structures like large bridges should be continuously monitored for detection of damage. The cracks usually change the physical parameters like stiffness and flexibility which in turn changes the dynamic properties such as natural frequencies and mode shapes. Crack detection of a beam element comprises of two aspects: the first one is the forward problem which is achieved from the Eigen parameters and the second one is the process to locate and quantify the effect of damage and is termed as ‘inverse process of damage detection’. In the present investigation the analytical and numerical methods are known as the forward problem includes determination of natural frequencies from the knowledge of beam geometry and crack dimension. The vibration signals are derived from the forward problem is exploited in the inverse problem. The natural frequency changes occur due to the various reasons such as boundary condition changes, temperature variations etc. Among all the changes boundary condition changes are the most important factors in structural elements. Many major structures like bridges are made up of uniform beams of unknown boundary conditions. So in the present investigation two of the boundary conditions i.e. fixed -free and fixed- fixed are considered. Using the forward solution method, the natural frequencies are determined. In the inverse solution method various Artificial Intelligence (AI) techniques with their hybrid methods are proposed and implemented. Damage detection problems using Artificial Intelligence techniques require a number of training data sets that represent the uncracked and cracked scenarios of practical structural elements. In the second part of the work different AI techniques like Fuzzy Logic, Genetic Algorithm, Clonal Selection Algorithm, Differential Evolution Algorithm and their hybrid methods are designed and developed. In summary this investigation is a step towards to forecast the position of the damage using the Artificial Intelligence techniques and compare their results. Finally, the results from the Artificial Intelligence techniques and their hybridized algorithms are validated by doing experimental analysis

Every which way? On predicting tumor evolution using cancer progression models

Successful prediction of the likely paths of tumor progression is valuable for diagnostic, prognostic, and treatment purposes. Cancer progression models (CPMs) use cross-sectional samples to identify restrictions in the order of accumulation of driver mutations and thus CPMs encode the paths of tumor progression. Here we analyze the performance of four CPMs to examine whether they can be used to predict the true distribution of paths of tumor progression and to estimate evolutionary unpredictability. Employing simulations we show that if fitness landscapes are single peaked (have a single fitness maximum) there is good agreement between true and predicted distributions of paths of tumor progression when sample sizes are large, but performance is poor with the currently common much smaller sample sizes. Under multi-peaked fitness landscapes (i.e., those with multiple fitness maxima), performance is poor and improves only slightly with sample size. In all cases, detection regime (when tumors are sampled) is a key determinant of performance. Estimates of evolutionary unpredictability from the best performing CPM, among the four examined, tend to overestimate the true unpredictability and the bias is affected by detection regime; CPMs could be useful for estimating upper bounds to the true evolutionary unpredictability. Analysis of twenty-two cancer data sets shows low evolutionary unpredictability for several of the data sets. But most of the predictions of paths of tumor progression are very unreliable, and unreliability increases with the number of features analyzed. Our results indicate that CPMs could be valuable tools for predicting cancer progression but that, currently, obtaining useful predictions of paths of tumor progression from CPMs is dubious, and emphasize the need for methodological work that can account for the probably multi-peaked fitness landscapes in cancerWork partially supported by BFU2015- 67302-R (MINECO/FEDER, EU) to RDU. CV supported by PEJD-2016-BMD-2116 from Comunidad de Madrid to RD