A new emerging paradigm of Uncertain Risk of Suspicion, Threat and Danger, observed across the field of information security, is described. Based on this paradigm a novel approach to anomaly detection is presented. Our approach is based on a simple yet powerful analogy from the innate part of the human immune system, the Toll-Like Receptors. We argue that such receptors incorporated as part of an anomaly detector enhance the detector's ability to distinguish normal and anomalous behaviour. In addition we propose that Toll-Like Receptors enable the classification of detected anomalies based on the types of attacks that perpetrate the anomalous behaviour. Classification of such type is either missing in existing literature or is not fit for the purpose of reducing the burden of an administrator of an intrusion detection system. For our model to work, we propose the creation of a taxonomy of the digital Acytota, based on which our receptors are created.

The Dendritic Cell Algorithm is an immune-inspired algorithm orig- inally based on the function of natural dendritic cells. The original instantiation of the algorithm is a highly stochastic algorithm. While the performance of the algorithm is good when applied to large real-time datasets, it is difficult to anal- yse due to the number of random-based elements. In this paper a deterministic version of the algorithm is proposed, implemented and tested using a port scan dataset to provide a controllable system. This version consists of a controllable amount of parameters, which are experimented with in this paper. In addition the effects are examined of the use of time windows and variation on the number of cells, both which are shown to influence the algorithm. Finally a novel metric for the assessment of the algorithms output is introduced and proves to be a more sensitive metric than the metric used with the original Dendritic Cell Algorithm.

Interval temporal logics (ITLs) are logics for reasoning about temporal statements expressed over intervals, i.e., periods of time. The most famous ITL studied so far is Halpern and Shoham's HS, which is the logic of the thirteen Allen's interval relations. Unfortunately, HS and most of its fragments have an undecidable satisfiability problem. This discouraged the research in this area until recently, when a number non-trivial decidable ITLs have been discovered. This paper is a contribution towards the complete classification of all different fragments of HS. We consider different combinations of the interval relations Begins, After, Later and their inverses Abar, Bbar, and Lbar. We know from previous works that the combination ABBbarAbar is decidable only when finite domains are considered (and undecidable elsewhere), and that ABBbar is decidable over the natural numbers. We extend these results by showing that decidability of ABBar can be further extended to capture the language ABBbarLbar, which lays in between ABBar and ABBbarAbar, and that turns out to be maximal w.r.t decidability over strongly discrete linear orders (e.g. finite orders, the naturals, the integers). We also prove that the proposed decision procedure is optimal with respect to the complexity class.

Objectives: Text categorization has been used in biomedical informatics for identifying documents containing relevant topics of interest. We developed a simple method that uses a chi-square-based scoring function to determine the likelihood of MEDLINE citations containing genetic relevant topic. Methods: Our procedure requires construction of a genetic and a nongenetic domain document corpus. We used MeSH descriptors assigned to MEDLINE citations for this categorization task. We compared frequencies of MeSH descriptors between two corpora applying chi-square test. A MeSH descriptor was considered to be a positive indicator if its relative observed frequency in the genetic domain corpus was greater than its relative observed frequency in the nongenetic domain corpus. The output of the proposed method is a list of scores for all the citations, with the highest score given to those citations containing MeSH descriptors typical for the genetic domain. Results: Validation was done on a set of 734 manually annotated MEDLINE citations. It achieved predictive accuracy of 0.87 with 0.69 recall and 0.64 precision. We evaluated the method by comparing it to three machine learning algorithms (support vector machines, decision trees, na\"ive Bayes). Although the differences were not statistically significantly different, results showed that our chi-square scoring performs as good as compared machine learning algorithms. Conclusions: We suggest that the chi-square scoring is an effective solution to help categorize MEDLINE citations. The algorithm is implemented in the BITOLA literature-based discovery support system as a preprocessor for gene symbol disambiguation process.

Class prediction is an important application of microarray gene expression data analysis. The high-dimensionality of microarray data, where number of genes (variables) is very large compared to the number of samples (obser- vations), makes the application of many prediction techniques (e.g., logistic regression, discriminant analysis) difficult. An efficient way to solve this prob- lem is by using dimension reduction statistical techniques. Increasingly used in psychology-related applications, Rasch model (RM) provides an appealing framework for handling high-dimensional microarray data. In this paper, we study the potential of RM-based modeling in dimensionality reduction with binarized microarray gene expression data and investigate its prediction ac- curacy in the context of class prediction using linear discriminant analysis. Two different publicly available microarray data sets are used to illustrate a general framework of the approach. Performance of the proposed method is assessed by re-randomization scheme using principal component analysis (PCA) as a benchmark method. Our results show that RM-based dimension reduction is as effective as PCA-based dimension reduction. The method is general and can be applied to the other high-dimensional data problems.

We present a method for the reconstruction of networks, based on the order of nodes visited by a stochastic branching process. Our algorithm reconstructs a network of minimal size that ensures consistency with the data. Crucially, we show that global consistency with the data can be achieved through purely local considerations, inferring the neighbourhood of each node in turn. The optimisation problem solved for each individual node can be reduced to a Set Covering Problem, which is known to be NP-hard but can be approximated well in practice. We then extend our approach to account for noisy data, based on the Minimum Description Length principle. We demonstrate our algorithms on synthetic data, generated by an SIR-like epidemiological model.

We consider the empirical risk minimization problem for linear supervised learning, with regularization by structured sparsity-inducing norms. These are defined as sums of Euclidean norms on certain subsets of variables, extending the usual $\ell_1$-norm and the group $\ell_1$-norm by allowing the subsets to overlap. This leads to a specific set of allowed nonzero patterns for the solutions of such problems. We first explore the relationship between the groups defining the norm and the resulting nonzero patterns, providing both forward and backward algorithms to go back and forth from groups to patterns. This allows the design of norms adapted to specific prior knowledge expressed in terms of nonzero patterns. We also present an efficient active set algorithm, and analyze the consistency of variable selection for least-squares linear regression in low and high-dimensional settings.

Paraphrasing methods recognize, generate, or extract phrases, sentences, or longer natural language expressions that convey almost the same information. Textual entailment methods, on the other hand, recognize, generate, or extract pairs of natural language expressions, such that a human who reads (and trusts) the first element of a pair would most likely infer that the other element is also true. Paraphrasing can be seen as bidirectional textual entailment and methods from the two areas are often similar. Both kinds of methods are useful, at least in principle, in a wide range of natural language processing applications, including question answering, summarization, text generation, and machine translation. We summarize key ideas from the two areas by considering in turn recognition, generation, and extraction methods, also pointing to prominent articles and resources.

Grounding is the task of reducing a first-order theory and finite domain to an equivalent propositional theory. It is used as preprocessing phase in many logic-based reasoning systems. Such systems provide a rich first-order input language to a user and can rely on efficient propositional solvers to perform the actual reasoning. Besides a first-order theory and finite domain, the input for grounders contains in many applications also additional data. By exploiting this data, the size of the grounder's output can often be reduced significantly. A common practice to improve the efficiency of a grounder in this context is by manually adding semantically redundant information to the input theory, indicating where and when the grounder should exploit the data. In this paper we present a method to compute and add such redundant information automatically. Our method therefore simplifies the task of writing input theories that can be grounded efficiently by current systems. We first present our method for classical first-order logic (FO) theories. Then we extend it to FO(ID), the extension of FO with inductive definitions, which allows for more concise and comprehensive input theories. We discuss implementation issues and experimentally validate the practical applicability of our method.

Paraphrasing methods recognize, generate, or extract phrases, sentences, or longer natural language expressions that convey almost the same information. Textual entailment methods, on the other hand, recognize, generate, or extract pairs of natural language expressions, such that a human who reads (and trusts) the first element of a pair would most likely infer that the other element is also true. Paraphrasing can be seen as bidirectional textual entailment and methods from the two areas are often similar. Both kinds of methods are useful, at least in principle, in a wide range of natural language processing applications, including question answering, summarization, text generation, and machine translation. We summarize key ideas from the two areas by considering in turn recognition, generation, and extraction methods, also pointing to prominent articles and resources.