Likelihood-based inference of B-cell clonal families

The human immune system depends on a highly diverse collection of antibody-making B cells. B cell receptor sequence diversity is generated by a random recombination process called "rearrangement" forming progenitor B cells, then a Darwinian process of lineage diversification and selection called "affinity maturation." The resulting receptors can be sequenced in high throughput for research and diagnostics. Such a collection of sequences contains a mixture of various lineages, each of which may be quite numerous, or may consist of only a single member. As a step to understanding the process and result of this diversification, one may wish to reconstruct lineage membership, i.e. to cluster sampled sequences according to which came from the same rearrangement events. We call this clustering problem "clonal family inference." In this paper we describe and validate a likelihood-based framework for clonal family inference based on a multi-hidden Markov Model (multi-HMM) framework for B cell receptor sequences. We describe an agglomerative algorithm to find a maximum likelihood clustering, two approximate algorithms with various trade-offs of speed versus accuracy, and a third, fast algorithm for finding specific lineages. We show that under simulation these algorithms greatly improve upon existing clonal family inference methods, and that they also give significantly different clusters than previous methods when applied to two real data sets

A novel energy-efficient resource allocation algorithm based on immune clonal optimization for green cloud computing

Cloud computing is a style of computing in which dynamically scalable and other virtualized resources are provided as a service over the Internet. The energy consumption and makespan associated with the resources allocated should be taken into account. This paper proposes an improved clonal selection algorithm based on time cost and energy consumption models in cloud computing environment. We have analyzed the performance of our approach using the CloudSim toolkit. The experimental results show that our approach has immense potential as it offers significant improvement in the aspects of response time and makespan, demonstrates high potential for the improvement in energy efficiency of the data center, and can effectively meet the service level agreement requested by the users.Comment: arXiv admin note: text overlap with arXiv:1006.0308 by other author

Artificial Immune System for Solving Global Optimization Problems

In this paper, we present a novel model of an artificial immune system (AIS), based on the process that suffers the T-Cell. The proposed model is used for global optimization problems. The model operates on four populations: Virgins, Effectors (CD4 and CD8) and Memory. Each of them has a different role, representation and procedures. We validate our proposed approach with a set of test functions taken from the specialized literature, we also compare our results with the results obtained by different bio-inspired approaches and we statistically analyze the results gotten by our approach.Fil: Aragon, Victoria Soledad. Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Departamento de Informática. Laboratorio Investigación y Desarrollo En Inteligencia Computacional; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis; ArgentinaFil: Esquivel, Susana C.. Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Departamento de Informática. Laboratorio Investigación y Desarrollo en Inteligencia Computacional; ArgentinaFil: Coello Coello, Carlos A.. CINVESTAV-IPN; Méxic

Monitoring and Control Framework for Advanced Power Plant Systems Using Artificial Intelligence Techniques

This dissertation presents the design, development, and simulation testing of a monitoring and control framework for dynamic systems using artificial intelligence techniques. A comprehensive monitoring and control system capable of detecting, identifying, evaluating, and accommodating various subsystem failures and upset conditions is presented. The system is developed by synergistically merging concepts inspired from the biological immune system with evolutionary optimization algorithms and adaptive control techniques.;The proposed methodology provides the tools for addressing the complexity and multi-dimensionality of the modern power plants in a comprehensive and integrated manner that classical approaches cannot achieve. Current approaches typically address abnormal condition (AC) detection of isolated subsystems of low complexity, affected by specific AC involving few features with limited identification capability. They do not attempt AC evaluation and mostly rely on control system robustness for accommodation. Addressing the problem of power plant monitoring and control under AC at this level of completeness has not yet been attempted.;Within the proposed framework, a novel algorithm, namely the partition of the universe, was developed for building the artificial immune system self. As compared to the clustering approach, the proposed approach is less computationally intensive and facilitates the use of full-dimensional self for system AC detection, identification, and evaluation. The approach is implemented in conjunction with a modified and improved dendritic cell algorithm. It allows for identifying the failed subsystems without previous training and is extended to address the AC evaluation using a novel approach.;The adaptive control laws are designed to augment the performance and robustness of baseline control laws under normal and abnormal operating conditions. Artificial neural network-based and artificial immune system-based approaches are developed and investigated for an advanced power plant through numerical simulation.;This dissertation also presents the development of an interactive computational environment for the optimization of power plant control system using evolutionary techniques with immunity-inspired enhancements. Several algorithms mimicking mechanisms of the immune system of superior organisms, such as cloning, affinity-based selection, seeding, and vaccination are used. These algorithms are expected to enhance the computational effectiveness, improve convergence, and be more efficient in handling multiple local extrema, through an adequate balance between exploration and exploitation.;The monitoring and control framework formulated in this dissertation applies to a wide range of technical problems. The proposed methodology is demonstrated with promising results using a high validity DynsimRTM model of the acid gas removal unit that is part of the integrated gasification combined cycle power plant available at West Virginia University AVESTAR Center. The obtained results show that the proposed system is an efficient and valuable technique to be applied to a real world application. The implementation of this methodology can potentially have significant impacts on the operational safety of many complex systems

An Energy Aware Resource Utilization Framework to Control Traffic in Cloud Network and Overloads

Energy consumption in cloud computing occur due to the unreasonable way in which tasks are scheduled. So energy aware task scheduling is a major concern in cloud computing as energy consumption results into significant waste of energy, reduce the profit margin and also high carbon emissions which is not environmentally sustainable. Hence, energy efficient task scheduling solutions are required to attain variable resource management, live migration, minimal virtual machine design, overall system efficiency, reduction in operating costs, increasing system reliability, and prompting environmental protection with minimal performance overhead. This paper provides a comprehensive overview of the energy efficient techniques and approaches and proposes the energy aware resource utilization framework to control traffic in cloud networks and overloads

DATA DRIVEN INTELLIGENT AGENT NETWORKS FOR ADAPTIVE MONITORING AND CONTROL

To analyze the characteristics and predict the dynamic behaviors of complex systems over time, comprehensive research to enable the development of systems that can intelligently adapt to the evolving conditions and infer new knowledge with algorithms that are not predesigned is crucially needed. This dissertation research studies the integration of the techniques and methodologies resulted from the fields of pattern recognition, intelligent agents, artificial immune systems, and distributed computing platforms, to create technologies that can more accurately describe and control the dynamics of real-world complex systems. The need for such technologies is emerging in manufacturing, transportation, hazard mitigation, weather and climate prediction, homeland security, and emergency response. Motivated by the ability of mobile agents to dynamically incorporate additional computational and control algorithms into executing applications, mobile agent technology is employed in this research for the adaptive sensing and monitoring in a wireless sensor network. Mobile agents are software components that can travel from one computing platform to another in a network and carry programs and data states that are needed for performing the assigned tasks. To support the generation, migration, communication, and management of mobile monitoring agents, an embeddable mobile agent system (Mobile-C) is integrated with sensor nodes. Mobile monitoring agents visit distributed sensor nodes, read real-time sensor data, and perform anomaly detection using the equipped pattern recognition algorithms. The optimal control of agents is achieved by mimicking the adaptive immune response and the application of multi-objective optimization algorithms. The mobile agent approach provides potential to reduce the communication load and energy consumption in monitoring networks. The major research work of this dissertation project includes: (1) studying effective feature extraction methods for time series measurement data; (2) investigating the impact of the feature extraction methods and dissimilarity measures on the performance of pattern recognition; (3) researching the effects of environmental factors on the performance of pattern recognition; (4) integrating an embeddable mobile agent system with wireless sensor nodes; (5) optimizing agent generation and distribution using artificial immune system concept and multi-objective algorithms; (6) applying mobile agent technology and pattern recognition algorithms for adaptive structural health monitoring and driving cycle pattern recognition; (7) developing a web-based monitoring network to enable the visualization and analysis of real-time sensor data remotely. Techniques and algorithms developed in this dissertation project will contribute to research advances in networked distributed systems operating under changing environments