Accurate immunological models offer the possibility of performing highthroughput experiments in silico that can predict, or at least suggest, in vivo phenomena. In this chapter, we compare various models of immunological memory. We first validate an experimental immunological simulator, developed by the authors, by simulating several theories of immunological memory with known results. We then use the same system to evaluate the predicted effects of a theory of immunological memory. The resulting model has not been explored before in artificial immune systems research, and we compare the simulated in silico output with in vivo measurements. Although the theory appears valid, we suggest that there are a common set of reasons why immunological memory models are a useful support tool; not conclusive in themselves.

Inter-subject parcellation of functional Magnetic Resonance Imaging (fMRI) data based on a standard General Linear Model (GLM)and spectral clustering was recently proposed as a means to alleviate the issues associated with spatial normalization in fMRI. However, for all its appeal, a GLM-based parcellation approach introduces its own biases, in the form of a priori knowledge about the shape of Hemodynamic Response Function (HRF) and task-related signal changes, or about the subject behaviour during the task. In this paper, we introduce a data-driven version of the spectral clustering parcellation, based on Independent Component Analysis (ICA) and Partial Least Squares (PLS) instead of the GLM. First, a number of independent components are automatically selected. Seed voxels are then obtained from the associated ICA maps and we compute the PLS latent variables between the fMRI signal of the seed voxels (which covers regional variations of the HRF) and the principal components of the signal across all voxels. Finally, we parcellate all subjects data with a spectral clustering of the PLS latent variables. We present results of the application of the proposed method on both single-subject and multi-subject fMRI datasets. Preliminary experimental results, evaluated with intra-parcel variance of GLM t-values and PLS derived t-values, indicate that this data-driven approach offers improvement in terms of parcellation accuracy over GLM based techniques.

We mark up a corpus of LaTeX lecture notes semantically and expose them as Linked Data in XHTML+MathML+RDFa. Our application makes the resulting documents interactively browsable for students. Our ontology helps to answer queries from students and lecturers, and paves the path towards an integration of our corpus with external sites.

As one of the newest members in the field of artificial immune systems (AIS), the Dendritic Cell Algorithm (DCA) is based on behavioural models of natural dendritic cells (DCs). Unlike other AIS, the DCA does not rely on training data, instead domain or expert knowledge is required to predetermine the mapping between input signals from a particular instance to the three categories used by the DCA. This data preprocessing phase has received the criticism of having manually over-fitted the data to the algorithm, which is undesirable. Therefore, in this paper we have attempted to ascertain if it is possible to use principal component analysis (PCA) techniques to automatically categorise input data while still generating useful and accurate classification results. The integrated system is tested with a biometrics dataset for the stress recognition of automobile drivers. The experimental results have shown the application of PCA to the DCA for the purpose of automated data preprocessing is successful.

Dendritic cells are antigen presenting cells that provide a vital link between the innate and adaptive immune system. Research into this family of cells has revealed that they perform the role of coordinating T-cell based immune responses, both reactive and for generating tolerance. We have derived an algorithm based on the functionality of these cells, and have used the signals and differentiation pathways to build a control mechanism for an artificial immune system. We present our algorithmic details in addition to some preliminary results, where the algorithm was applied for the purpose of anomaly detection. We hope that this algorithm will eventually become the key component within a large, distributed immune system, based on sound immunological concepts.

This thesis investigates the use of problem-specific knowledge to enhance a genetic algorithm approach to multiple-choice optimisation problems.It shows that such information can significantly enhance performance, but that the choice of information and the way it is included are important factors for success.Two multiple-choice problems are considered.The first is constructing a feasible nurse roster that considers as many requests as possible.In the second problem, shops are allocated to locations in a mall subject to constraints and maximising the overall income.Genetic algorithms are chosen for their well-known robustness and ability to solve large and complex discrete optimisation problems.However, a survey of the literature reveals room for further research into generic ways to include constraints into a genetic algorithm framework.Hence, the main theme of this work is to balance feasibility and cost of solutions.In particular, co-operative co-evolution with hierarchical sub-populations, problem structure exploiting repair schemes and indirect genetic algorithms with self-adjusting decoder functions are identified as promising approaches.The research starts by applying standard genetic algorithms to the problems and explaining the failure of such approaches due to epistasis.To overcome this, problem-specific information is added in a variety of ways, some of which are designed to increase the number of feasible solutions found whilst others are intended to improve the quality of such solutions.As well as a theoretical discussion as to the underlying reasons for using each operator,extensive computational experiments are carried out on a variety of data.These show that the indirect approach relies less on problem structure and hence is easier to implement and superior in solution quality.

In a previous paper the authors argued the case for incorporating ideas from innate immunity into artificial immune systems (AISs) and presented an outline for a conceptual framework for such systems. A number of key general properties observed in the biological innate and adaptive immune systems were highlighted, and how such properties might be instantiated in artificial systems was discussed in detail. The next logical step is to take these ideas and build a software system with which AISs with these properties can be implemented and experimentally evaluated. This paper reports on the results of that step - the libtissue system.

This paper treats the problem of learning the interaction structure of a spatiotemporal graphical model for a discrete state and discrete time stochastic process known as the susceptible, infected, recovered (SIR) model. The presence of spatial interactions cause adjacent nodes in the graph to affect each others states over time. Learning the topology of this graph is known as model selection. We cast this graphical model selection problem as a penalized likelihood problem, resulting in a convex program for which convex optimization solvers can be applied. SIR spatiotemporal graphical models are commonly used in modeling the random propagation of information between nodes in large networks in bioinformatics, signal processing, public health, and national security (4; 9; 21). Knowing the network link structure allows accurate prediction of individual node states and can aid the development of control and intervention strategies for such networks. This paper develops a tractable method to estimate the topology of the network for the SIR spatiotemporal graphical model from empirical data. Exact solutions of the graphical model selection problem is NP hard due to the combinatorial nature of enumeration through the discrete space of possible graph topologies.

Terrorism has led to many problems in Thai societies, not only property damage but also civilian casualties. Predicting terrorism activities in advance can help prepare and manage risk from sabotage by these activities. This paper proposes a framework focusing on event classification in terrorism domain using fuzzy inference systems (FISs). Each FIS is a decision-making model combining fuzzy logic and approximate reasoning. It is generated in five main parts: the input interface, the fuzzification interface, knowledge base unit, decision making unit and output defuzzification interface. Adaptive neuro-fuzzy inference system (ANFIS) is a FIS model adapted by combining the fuzzy logic and neural network. The ANFIS utilizes automatic identification of fuzzy logic rules and adjustment of membership function (MF). Moreover, neural network can directly learn from data set to construct fuzzy logic rules and MF implemented in various applications. FIS settings are evaluated based on two comparisons. The first evaluation is the comparison between unstructured and structured events using the same FIS setting. The second comparison is the model settings between FIS and ANFIS for classifying structured events. The data set consists of news articles related to terrorism events in three southern provinces of Thailand. The experimental results show that the classification performance of the FIS resulting from structured events achieves satisfactory accuracy and is better than the unstructured events. In addition, the classification of structured events using ANFIS gives higher performance than the events using only FIS in the prediction of terrorism events.

This paper proposes a method to construct an adaptive agent that is universal with respect to a given class of experts, where each expert is an agent that has been designed specifically for a particular environment. This adaptive control problem is formalized as the problem of minimizing the relative entropy of the adaptive agent from the expert that is most suitable for the unknown environment. If the agent is a passive observer, then the optimal solution is the well-known Bayesian predictor. However, if the agent is active, then its past actions need to be treated as causal interventions on the I/O stream rather than normal probability conditions. Here it is shown that the solution to this new variational problem is given by a stochastic controller called the Bayesian control rule, which implements adaptive behavior as a mixture of experts. Furthermore, it is shown that under mild assumptions, the Bayesian control rule converges to the control law of the most suitable expert.