Most definitions of ontology, viewed as a "specification of a conceptualization", agree on the fact that if an ontology can take different forms, it necessarily includes a vocabulary of terms and some specification of their meaning in relation to the domain's conceptualization. And as domain knowledge is mainly conveyed through scientific and technical texts, we can hope to extract some useful information from them for building ontology. But is it as simple as this? In this article we shall see that the lexical structure, i.e. the network of words linked by linguistic relationships, does not necessarily match the domain conceptualization. We have to bear in mind that writing documents is the concern of textual linguistics, of which one of the principles is the incompleteness of text, whereas building ontology - viewed as task-independent knowledge - is concerned with conceptualization based on formal and not natural languages. Nevertheless, the famous Sapir and Whorf hypothesis, concerning the interdependence of thought and language, is also applicable to formal languages. This means that the way an ontology is built and a concept is defined depends directly on the formal language which is used; and the results will not be the same. The introduction of the notion of ontoterminology allows to take into account epistemological principles for formal ontology building.

Large graphs are natural mathematical models for describing the structure of the data in a wide variety of fields, such as web mining, social networks, information retrieval, biological networks, etc. For all these applications, automatic tools are required to get a synthetic view of the graph and to reach a good understanding of the underlying problem. In particular, discovering groups of tightly connected vertices and understanding the relations between those groups is very important in practice. This paper shows how a kernel version of the batch Self Organizing Map can be used to achieve these goals via kernels derived from the Laplacian matrix of the graph, especially when it is used in conjunction with more classical methods based on the spectral analysis of the graph. The proposed method is used to explore the structure of a medieval social network modeled through a weighted graph that has been directly built from a large corpus of agrarian contracts.

Multiagent systems is an expanding field that blends classical fields like game theory and decentralized control with modern fields like computer science and machine learning. This monograph provides a concise introduction to the subject, covering the theoretical foundations as well as more recent developments in a coherent and readable manner. The text is centered on the concept of an agent as decision maker. Chapter 1 is a short introduction to the field of multiagent systems. Chapter 2 covers the basic theory of singleagent decision making under uncertainty.

We consider the scenario where training and test data are drawn from different distributions, commonly referred to as sample selection bias. Most algorithms for this setting try to first recover sampling distributions and then make appropriate corrections based on the distribution estimate. We present a nonparametric method which directly produces resampling weights without distribution estimation. Our method works by matching distributions between training and testing sets in feature space. Experimental results demonstrate that our method works well in practice.

Modelling the dynamics of transcriptional processes in the cell requires the knowledge of a number of key biological quantities. While some of them are relatively easy to measure, such as mRNA decay rates and mRNA abundance levels, it is still very hard to measure the active concentration levels of the transcription factor proteins that drive the process and the sensitivity of target genes to these concentrations. In this paper we show how these quantities for a given transcription factor can be inferred from gene expression levels of a set of known target genes. We treat the protein concentration as a latent function with a Gaussian process prior, and include the sensitivities, mRNA decay rates and baseline expression levels as hyperparameters. We apply this procedure to a human leukemia dataset, focusing on the tumour repressor p53 and obtaining results in good accordance with recent biological studies.

We describe Hidden Semi-Markov Support Vector Machines (SHM SVMs), an extension of HM SVMs to semi-Markov chains. This allows us to predict segmentations of sequences based on segment-based features measuring properties such as the length of the segment. We propose a novel technique to partition the problem into sub-problems. The independently obtained partial solutions can then be recombined in an efficient way, which allows us to solve label sequence learning problems with several thousands of labeled sequences. We have tested our algorithm for predicting gene structures, an important problem in computational biology. Results on a well-known model organism illustrate the great potential of SHM SVMs in computational biology.

This paper develops a multi-frame image super-resolution approach from a Bayesian viewpoint by marginalizing over the unknown registration parameters relating the set of input low-resolution views. In Tipping and Bishop's Bayesian image super-resolution approach [16], the marginalization was over the superresolution image, necessitating the use of an unfavorable image prior. By integrating over the registration parameters rather than the high-resolution image, our method allows for more realistic prior distributions, and also reduces the dimension of the integral considerably, removing the main computational bottleneck of the other algorithm. In addition to the motion model used by Tipping and Bishop, illumination components are introduced into the generative model, allowing us to handle changes in lighting as well as motion. We show results on real and synthetic datasets to illustrate the efficacy of this approach.

We present a method for binary online classification of triggered but temporally blurred events that are embedded in noisy time series in the context of online discrimination between left and right imaginary hand-movement. In particular the goal of the binary classification problem is to obtain the decision, as fast and as reliably as possible from the recorded EEG single trials. To provide a probabilistic decision at every time-point t the presented method gathers information from two distinct sequences of features across time. In order to incorporate decisions from prior time-points we suggest an appropriate weighting scheme, that emphasizes time instances, providing a higher discriminatory power between the instantaneous class distributions of each feature, where the discriminatory power is quantified in terms of the Bayes error of misclassification. The effectiveness of this procedure is verified by its successful application in the 3rd BCI competition. Disclosure of the data after the competition revealed this approach to be superior with single trial error rates as low as 10.7, 11.5 and 16.7% for the three different subjects under study.

We present a method for binary online classification of triggered but temporally blurredevents that are embedded in noisy time series in the context of online discrimination between left and right imaginary hand-movement. In particular the goal of the binary classification problem is to obtain the decision, as fast and as reliably as possible from the recorded EEG single trials. To provide a probabilistic decision at every time-point t the presented methodgathers information from two distinct sequences of features across time. In order to incorporate decisions from prior time-points we suggest an appropriate weighting scheme, that emphasizes time instances, providing a higher discriminatory power between the instantaneous class distributions of each feature, where the discriminatory power is quantified in terms of the Bayes error of misclassification. The effectiveness of this procedure is verified by its successful application in the 3rd BCI competition. Disclosure of the data after the competition revealed this approach to be superior with single trial error rates as low as 10.7, 11.5 and 16.7% for the three different subjects under study.

Multinomial logistic regression provides the standard penalised maximum-likelihood solution to multi-Class pattern recognition problems.