Network Intrusion Detection Systems (NIDS) are computer systems which monitor a network with the aim of discerning malicious from benign activity on that network. While a wide range of approaches have met varying levels of success, most IDSs rely on having access to a database of known attack signatures which are written by security experts. Nowadays, in order to solve problems with false positive alerts, correlation algorithms are used to add additional structure to sequences of IDS alerts. However, such techniques are of no help in discovering novel attacks or variations of known attacks, something the human immune system (HIS) is capable of doing in its own specialised domain. This paper presents a novel immune algorithm for application to the IDS problem. The goal is to discover packets containing novel variations of attacks covered by an existing signature base.

We discuss here the mean-field theory for a cellular automata model of meta-learning. The meta-learning is the process of combining outcomes of individual learning procedures in order to determine the final decision with higher accuracy than any single learning method. Our method is constructed from an ensemble of interacting, learning agents, that acquire and process incoming information using various types, or different versions of machine learning algorithms. The abstract learning space, where all agents are located, is constructed here using a fully connected model that couples all agents with random strength values. The cellular automata network simulates the higher level integration of information acquired from the independent learning trials. The final classification of incoming input data is therefore defined as the stationary state of the meta-learning system using simple majority rule, yet the minority clusters that share opposite classification outcome can be observed in the system. Therefore, the probability of selecting proper class for a given input data, can be estimated even without the prior knowledge of its affiliation. The fuzzy logic can be easily introduced into the system, even if learning agents are build from simple binary classification machine learning algorithms by calculating the percentage of agreeing agents.

Mass spectrometry (MS) is an important technique for chemical profiling which calculates for a sample a high dimensional histogram-like spectrum. A crucial step of MS data processing is the peak picking which selects peaks containing information about molecules with high concentrations which are of interest in an MS investigation. We present a new procedure of the peak picking based on a sparse coding algorithm. Given a set of spectra of different classes, i.e. with different positions and heights of the peaks, this procedure can extract peaks by means of unsupervised learning. Instead of an $l_1$-regularization penalty term used in the original sparse coding algorithm we propose using an elastic-net penalty term for better regularization. The evaluation is done by means of simulation. We show that for a large region of parameters the proposed peak picking method based on the sparse coding features outperforms a mean spectrum-based method. Moreover, we demonstrate the procedure applying it to two real-life datasets.

LiveJournal is a social network journal service with focus on user interactions. As for many other online social networks, predicting potential friendships in the LiveJournal network is a problem of great practical interest. Previous work has shown that graph features extracted from the graph associated with the network are good predictors for friendship links. However, contrary to the intuition, user data (e.g., interests shared by two users) does not always improve the predictions obtained with graph features alone. This could be due to the fact that features constructed from a large number of user declared interests cannot capture the implicit semantic of the interests. To test this hypothesis, we use a clustering approach to build an interest ontology, and explore the ability of the ontology to improve the performance of learning algorithms at predicting friendship links, when interest-based features are used alone or in combination with graph-based features. The results show that ontology-based features can help improve the performance of several machine learning classifiers (in particular, random forest classifiers) at the task of predicting links in the LiveJournal social network.

This paper explores the following question: what kind of statistical guarantees can be given when doing variable selection in high-dimensional models? In particular, we look at the error rates and power of some multi-stage regression methods. In the first stage we fit a set of candidate models. In the second stage we select one model by cross-validation. In the third stage we use hypothesis testing to eliminate some variables. We refer to the first two stages as "screening" and the last stage as "cleaning." We consider three screening methods: the lasso, marginal regression, and forward stepwise regression. Our method gives consistent variable selection under certain conditions.

Motivation: Prediction of ligands for proteins of known 3D structure is important to understand structure-function relationship, predict molecular function, or design new drugs. Results: We explore a new approach for ligand prediction in which binding pockets are represented by atom clouds. Each target pocket is compared to an ensemble of pockets of known ligands. Pockets are aligned in 3D space with further use of convolution kernels between clouds of points. Performance of the new method for ligand prediction is compared to those of other available measures and to docking programs. We discuss two criteria to compare the quality of similarity measures: area under ROC curve (AUC) and classification based scores. We show that the latter is better suited to evaluate the methods with respect to ligand prediction. Our results on existing and new benchmarks indicate that the new method outperforms other approaches, including docking. Availability: The new method is available at http://cbio.ensmp.fr/paris/ Contact: mikhail.zaslavskiy@mines-paristech.fr

The problem of multiple hypothesis testing arises when there are more than one hypothesis to be tested simultaneously for statistical significance. This is a very common situation in many data mining applications. For instance, assessing simultaneously the significance of all frequent itemsets of a single dataset entails a host of hypothesis, one for each itemset. A multiple hypothesis testing method is needed to control the number of false positives (Type I error). Our contribution in this paper is to extend the multiple hypothesis framework to be used with a generic data mining algorithm. We provide a method that provably controls the family-wise error rate (FWER, the probability of at least one false positive) in the strong sense. We evaluate the performance of our solution on both real and generated data. The results show that our method controls the FWER while maintaining the power of the test.

We introduce a symmetry reduction technique for model checking temporal-epistemic properties of multi-agent systems defined in the mainstream interpreted systems framework. The technique, based on counterpart semantics, aims to reduce the set of initial states that need to be considered in a model. We present theoretical results establishing that there are neither false positives nor false negatives in the reduced model. We evaluate the technique by presenting the results of an implementation tested against two well known applications of epistemic logic, the muddy children and the dining cryptographers. The experimental results obtained confirm that the reduction in model checking time can be dramatic, thereby allowing for the verification of hitherto intractable systems.

Mechanical design tools would be considerably more useful if we could interact with them in the way that human designers communicate design ideas to one another, i.e., using crude sketches and informal speech. Those crude sketches frequently contain pen strokes of two different sorts, one type portraying device structure, the other denoting gestures, such as arrows used to indicate motion. We report here on techniques we developed that use information from both sketch and speech to distinguish gesture strokes from non-gestures -- a critical first step in understanding a sketch of a device. We collected and analyzed unconstrained device descriptions, which revealed six common types of gestures. Guided by this knowledge, we developed a classifier that uses both sketch and speech features to distinguish gesture strokes from non-gestures. Experiments with our techniques indicate that the sketch and speech modalities alone produce equivalent classification accuracy, but combining them produces higher accuracy.

Building and using agent-based models is often impractical, in part due to the cost of including expensive subject matter experts (SMEs) in the development process. In this paper, we describe a method for "bootstrapping" model building to lower the cost of overall model development. The models we are interested in here capture dynamic phenomena related to international and subnational conflict. The method of acquiring these models begins with event data drawn from news reports about a conflict region, and infers model characteristics particular to a conflict modeling framework called the Power Structure Toolkit (PSTK). We describe the toolkit and how it has been used prior to this work. We then describe the current problem of modeling conflict and the empirical data available to learn models, and extensions to the PSTK for model generation from this data. We also describe a formative evaluation of the system that compares the performance and costs of models built entirely by an SME against models built with an SME aided by the automated model generation process. Early results indicate at least equivalent prediction rates with significant savings in model generation costs.