Artificial Immune Systems

Name: Artificial Immune Systems | 10th International Conference, ICARIS 2011, Cambridge, UK, July 18-21, 2011. Proceedings
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10th International Conference, ICARIS 2011, Cambridge, UK, July 18-21, 2011. Proceedings

Pietro Lio Giuseppe Nicosia Thomas Stibor(Editor)

Springer (Publisher)

Published on 6. July 2011

XVI, 468 pages

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978-3-642-22371-6 (ISBN)

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Content

Title
Preface
Organization
Table of Contents
Part I: Immunoinformatics and Computational Immunology
The Value of Inflammatory Signals in Adaptive Immune Responses
Introduction
A Review of the Relevant Immunology
Goals and Hypotheses
Ordinary Differential Equation Model
ODE Model 1: CTL Search without an Inflammation Signal
ODE Model 2: CTL Search with an Inflammatory Signal
Agent Based Model
ABM Model 1: Dynamics without Inflammation
ABM Model 2: Dynamics with Inflammation and CTL Recirculation
Discussion
Summary of Results
Caveats and Limitations
Conclusions
References
Large Scale Agent-Based Modeling of the Humoral and Cellular Immune Response
Introduction
Agent-Based Modeling
Immuno Responses
Cross-Reactivity and Epithelial Cell Signaling
Modeling and Simulation by Stochastic $\pi$-Calculus
SPiM
Modeling HBV Infection with SPiM
Conclusions
References
Logic-Based Representation of Connectivity Routes in the Immune System
Approach
Ontology
Structural Primer
Processual Primer
Topological Primer
Knowledge - Integration - Application
Conclusion
References
Refitting Harel Statecharts for Systemic Mathematical Models in Computational Immunology
Introduction
Background and Related Work
Cellular Processes: A Motivating Example
The Complexity of Systemic Models Grows Multiplicatively
Using Statecharts to Factor Model Complexity
Beyond Model Representation
Conclusion
References
In Silico Investigation into CD8Treg Mediated Recovery in Murine Experimental Autoimmune Encephalomyelitis
References
Classification of MHC I Proteins According to Their Ligand-Type Specificity
Introduction
Materials and Methods
Sequence Collection and Processing
Sequence Similarity Reduction and Similarity Analyses
Model Building and Evaluation
Classification of MHC I Sequences Using BLAST
Results and Discussion
Dataset of MHC I Molecules of Known Ligand-Type Specificity
ML-Based Classifiers Predicting the Ligand-Type Specificity of MHC I Molecules
Comparison of the Generalization Power of ML-Based Classifiers and BLAST
Conclusions and Limitations
References
Towards Argument-Driven Validation of an $in silico$ Model of Immune Tissue Organogenesis
Introduction
Model and Simulation
Domain Model
Platform Model
Analysis of Initial Results
Explaining the Differences Between the $in vivo$ and $in silico$ Results
Conclusion
References
Simulating the Dynamics of T Cell Subsets throughout the Lifetime
Introduction to System Dynamics Modelling of Immunity
The Need for Balance: T_$h$17s and T_$reg$s throughout the Lifetime
Method: Simulation of T_$reg$ Dynamics
Discussion and Concluding Remarks
References
Modelling Containment Mechanisms in theImmune System for Applications in Engineering
References
Systems Dynamics or Agent-Based Modelling for Immune Simulation?
Introduction
Related Work
From SDS to ABS
The Mathematical Model
The SDS Model
The ABS Model
Results Comparison
From ABS to SDS
Simulation Problem Description and Conceptual Modelling
ABS for Model 1
SDS for Model 1
Results for Model 1
ABS for Model 2
SDS for Model 2
Results for Model 2
Conclusions
References
Implementation of a Computational Model of the Innate Immune System
Introduction
Biological Background
Mathematical Model
Implementation
Numerical Results
Conclusions and Future Works
References
Relevance of Pattern Recognition in a Non-deterministic Model of Immune Responses
Introduction
Methods
Results
Discussion
Conclusions
References
Part II: Theory of Immunological Computation
On the Analysis of the Immune-Inspired B-Cell Algorithm for the Vertex Cover Problem
Introduction
Preliminaries
The BCA Outperforms Mutation-Based EAs
The BCA Outperforms Crossover-Based EAs
Limitations of the BCA and Bounds on Approximation
Conclusions
References
Variation in Artificial Immune Systems: Hypermutations with Mutation Potential
Introduction
Definitions, Algorithms and Notations
Hypermutations with Mutation Potential
Adding `Stop at the First Constructive Mutation Step'
Improving Hypermutations with Mutation Potential
Conclusions
References
Stochastic Search with Locally Clustered Targets: Learning from T Cells
Introduction
Model Definition and Contributions
Background: Modelling T Cell Immune Surveillance
Formal Statement of the Special Case
Optimizing a Single Searcher
The Expected Hitting Time
Asymptotics of the Expected Hitting Time
The Optimal Residence Time
Asymptotics of the Optimal Residence Time
Implications for Robustness and Parameter Estimation
Parallel Search
Conclusions and Future Work
References
An AIS-Based Mathematical Programming Method
Introduction
Multi-agent Coordination Problems
A Mathematical Network Model
Lagrangian Relaxation for Decomposition
Immunity-Inspired Cooperative Interaction Scheme
The Integrated Algorithm
Migration and Maturation of Dendritic Cells
Conclusion
References
Quiet in Class: Classification, Noise and the Dendritic Cell Algorithm
Introduction
Related Work
The Dendritic Cell Algorithm
Machine Learning Concepts
Signal Processing Concepts
Research Aims
Algorithmic Details
Static Moving Window Function
Dynamic Moving Window Function
Experimental Design
Synthetic Datasets
Algorithm Setup
Statistical Tests
Results and Analysis
Discussion and Future Work
References
A Lymphocyte-Cytokine Network Inspired Algorithm for Data Analysis
Introduction
Related Work
Immune Inspiration
Algorithm
Experiments
Test Bench
Results
Conclusion and Future Work
References
Part III: Applied Immunological Computation
Inferring Systems of Ordinary Differential Equations via Grammar-Based Immune Programming
Introduction
Inference of System of Ordinary Differential Equations
Grammar-Based Immune Programming
Grammatical Evolution
The Repair Method
Computational Experiments
Experiment 1: Artificial Model
Experiment 2: Chemical Reaction Model
Experiment 3: Fertility Equation
Experiment 4: Three-Species Lotka-Volterra Model
Experiment 5: Identifying a Gene Regulatory Network
Concluding Remarks and Future Works
References
Applying Antigen-Receptor Degeneracy Behavior for Misbehavior Response Selection in Wireless Sensor Networks
Introduction
Wireless Ad Hoc and Sensor Networks
Problem Formulation
Cognitive Immune System
Pathogen Recognition Model
Towards an Active Response Selection Mechanism
Antigen Receptor Response Selection Mechanism
The Algorithm
Experimental Setup
Misbehavior
Responses
Results
Conclusion
References
Parameter Optimisation in the Receptor Density Algorithm
Introduction
The Receptor Density and Signature Matching Algorithms
The Receptor Density Algorithm
The RDA for Anomaly Detection in Spectra
Signature Matching and Libraries
Genetic Algorithm for Optimising Parameters
Algorithm Description
Mass Spectrometry Benchmark
Results
Acceleration of Genetic Algorithm Using CUDA
Conclusion
References
An Engineering-Informed Modelling Approach to AIS
Introduction
On Immunology, Engineering and Modelling
The Application Domain: SpeckNets
Scoping the Model by Consideration of Engineering
An Engineering Constrained Immunological Model
Validation of the Model
Model Implementation
Assumptions and Simplifications from an Engineering Perspective
Analysis of the Model from an Engineering Perspective
Dendritic Cell Generation
Trafficking of Immature Dendritic Cells
Routing via Gradients
Conclusion
References
Collective Self-detection Scheme for Adaptive Error Detection in a Foraging Swarm of Robots
Introduction
Background and Related Work
Error Detection in Swarm Robotics
Receptor Density Algorithm
Experimental Setting
Simulation Setting
Modes of Failure
Dynamic Environment
Performance Metrics
Results and Discussion
Performance
Parameter Tuning
On Robustness
Conclusions
References
Principles and Methods of Artificial Immune System Vaccination of Learning Systems
Introduction
Background to Artificial Immune System
HAIS Supervised Learning Algorithm
Proposed Hybrid Method
Experimental Results
Simulated Data
Iris Data
Breast Cancer Data
Conclusion
References
Immune System Inspired Reliable Query Dissemination in Wireless Sensor Networks
Introduction
Related Work
Inspirations from Immune Systems
Problem Formulation
Artificial Immune Systems
Insights from Immune Systems
Local Discovery and Recovery of Query Losses
Local Query Loss Detection
Localized Query-Address Resolution
Localized Query Loss Recovery
Analytical Evaluation
Successful Query Delivery Probability
Scalability of Loss Discovery
The Route Length of Recovery (RLR)
Conclusion
References
Fault Detection in Analog Circuits Using a Fuzzy Dendritic Cell Algorithm
Introduction
Challenges in Analog Circuit Fault Detection
AIS Applied to Fault Detection
Negative Selection
Dendritic Cell Algorithm
Proposed Method
Case Study
Conclusions
References
A Memetic Immunological Algorithm for Resource Allocation Problem
Introduction
The Problem
The Memetic Immunological Algorithm
Results
Conclusion
References
Artificial Immune System Based on Clonal Selection and Game Theory Principles for Multiobjective Optimization
Introduction
Multi-criteria Decision Making and Multiobjective Optimization
Multiobjective Optimization
Evaluation of the Results
Evolutionary Algorithms
Artificial Immune Systems
Game Theory
Description of the IMmune GAme Theory MultiObective (IMGAMO) Algorithm
Numerical Tests
The DTLZ1 Problem
The DTLZ2 Problem
The DTLZ4 Problem
Conclusions
References
Tunable Immune Detectors for Behaviour-Based Network Intrusion Detection
Introduction
TAT Model
TAT-AIS Framework
Data Format and Representation
Run Parameters Set Discovery and Choice
APC Processing Algorithm
Experimental Evaluation and Results
Methodology for Experiments
Data Sets Analysis
Data Set Preprocessing
Parameters Set Optimisation
Results
Conclusions
References
Population-Based Artificial Immune System Clustering Algorithm
Introduction
Background to Artificial Immune System
Humoral-Mediated Clustering Algorithm (HAIS)
Population-Based HAIS Algorithm and its Explanation
Experimental Results
Conclusion
References
Clonal Selection Algorithm for Classification
Introduction
Immune Network Theory
Negative Selection Mechanism
Clonal Selection Principle
Review of Artificial Immune System and Classification
CLONALG for Classification
Proposed Classification Algorithm CLONAX
Training Phase
Testing Phase
Experiment
Discussion
Conclusion
References
Towards a Mapping of Modern AIS and LCS
Introduction
YCSC: Clustering with LCS Gives a Type of AIS
A Simple Model of YCSC
Performance
Rule Compaction
Conclusions
References
Towards an Artificial Immune System for Online Fraud Detection
Introduction
Related Work
An Immune Inspired System for Online Fraud Detection
Innate Layer
Adaptive Layer
Experimental Setup and Results Analysis
Experimental Setup
Results Analysis
Conclusions
References
Immune Approach for Neuro-Fuzzy Systems Learning Using Multiantibody Model
Introduction
ANFIS Structure
Immune Approach for ANFIS Learning
Parametrical Identification of ANFIS
Parametrical and Structural Identification
Experimental Results
Conclusions
References
The Danger Theory Applied to Vegetal Image Pattern Classification
Introduction
The Danger Theory
The Dendritic Cell Algorithm
Aggregation phase
Image Classification
The Application of the DCA to Image Classification
Immune Representation Using the DCA
Outline of the Proposed Approach
Results and Discussion
Conclusion and Future Work
References
Further Exploration of the Fuzzy Dendritic Cell Method
Introduction
Fuzzy Set Theory
Fuzzy C-Means Clustering
The Dendritic Cell Algorithm
Introducing Dendritic Cells
Abstract View of the Dendritic Cell Algorithm
The Modified Fuzzy Dendritic Cell Method
Fuzzy System Inputs-Output Variables
Linguistic Variables
Fuzzy and Membership Functions Construction
The Fuzzy Rule Sets Description
The Fuzzy Context Assessment
Experiments
Experimental Setup
Results and Discussion
Conclusion and Future Works
References
Author Index

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