Towards an inclusion driven learning of Bayesian Networks

Two or more Bayesian Networks are Markov equivalent when their corresponding acyclic digraphs encode the same set of conditional independence (= CI) restrictions. Therefore, the search space of Bayesian Networks may be organized in classes of equivalence, where each of them consists of a particular set of CI restrictions. The collection of sets of CI restrictions obeys a partial order, the graphical Markov model inclusion partial order, or inclusion order for short. This paper discusses in depth the role that inclusion order plays in learning the structure of Bayesian networks. We prove that under very special conditions the traditional hill-climber always recovers the right structure. Moreover, we extend the recent experimental results presented in (Kocka and Castelo, 2001). We show how learning algorithms for Bayesian Networks, that take the inclusion order into account, perform better than those that do not, and we introduce two new ones in the context of heuristic search and the MCMC method

Evolutionary approaches for the reverse-engineering of gene regulatory networks: A study on a biologically realistic dataset

<p>Abstract</p> <p>Background</p> <p>Inferring gene regulatory networks from data requires the development of algorithms devoted to structure extraction. When only static data are available, gene interactions may be modelled by a Bayesian Network (BN) that represents the presence of direct interactions from regulators to regulees by conditional probability distributions. We used enhanced evolutionary algorithms to stochastically evolve a set of candidate BN structures and found the model that best fits data without prior knowledge.</p> <p>Results</p> <p>We proposed various evolutionary strategies suitable for the task and tested our choices using simulated data drawn from a given bio-realistic network of 35 nodes, the so-called insulin network, which has been used in the literature for benchmarking. We assessed the inferred models against this reference to obtain statistical performance results. We then compared performances of evolutionary algorithms using two kinds of recombination operators that operate at different scales in the graphs. We introduced a niching strategy that reinforces diversity through the population and avoided trapping of the algorithm in one local minimum in the early steps of learning. We show the limited effect of the mutation operator when niching is applied. Finally, we compared our best evolutionary approach with various well known learning algorithms (MCMC, K2, greedy search, TPDA, MMHC) devoted to BN structure learning.</p> <p>Conclusion</p> <p>We studied the behaviour of an evolutionary approach enhanced by niching for the learning of gene regulatory networks with BN. We show that this approach outperforms classical structure learning methods in elucidating the original model. These results were obtained for the learning of a bio-realistic network and, more importantly, on various small datasets. This is a suitable approach for learning transcriptional regulatory networks from real datasets without prior knowledge.</p

Transcendental-Phenomenological Proof and Descriptive Metaphysics

Following P.F. Strawson's reading of Kant, the majority of the literature on transcendental arguments seeks to divorce such arguments from their original Kantian context. This thesis is concerned with Mark Sacks's recent defence of transcendental arguments, which takes a different approach. A critique is given of Sacks's work and extensions and modifications of his approach are recommended. It is proposed that certain difficulties encountered by Kant's transcendentally-ideal approach can be overcome with Hegelian solutions

The Rise and Fall of "Respectable" Spanish Liberalism, 1808-1923: An Explanatory Framework

The article focuses on the reasons behind both the consolidation of what I have termed “respectable” liberalism between the 1830s and the 1840s and its subsequent decline and fall between 1900 and 1923. In understanding both processes I study the links established between “respectable” liberals and propertied elites, the monarchy, and the Church. In the first phase these links served to consolidate the liberal polity. However, they also meant that many tenets of liberal ideology were compromised. Free elections were undermined by the operation of caciquismo, monarchs established a powerful position, and despite the Church hierarchy working with liberalism, the doctrine espoused by much of the Church was still shaped by the Counter-Reformation. Hence, “respectable” liberalism failed to achieve a popular social base. And the liberal order was increasingly denigrated as part of the corrupt “oligarchy” that ruled Spain. Worse still, between 1916 and 1923 the Church, monarch, and the propertied elite increasingly abandoned the liberal Monarchist Restoration. Hence when General Primo de Rivera launched his coup the rug was pulled from under the liberals’ feet and there was no one to cushion the fall

Guilds in the transition to modernity: the cases of Germany, United Kingdom, and the Netherlands

One important aspect of the transition to modernity is the survival of elements of the Old Regime beyond the French Revolution. It has been claimed that this can explain why in the late 19th and early 20th centuries some Western countries adopted national corporatist structures while others transformed into liberal market economies. One of those elements is the persistence or absence of guild traditions. This is usually analyzed in a national context. This paper aims to contribute to the debate by investigating the development of separate trades in Germany, the United Kingdom and the Netherlands throughout the 19th century. We distinguish six scenarios of what might have happened to crafts and investigate how the prevalence of each of these scenarios in the three countries impacted on the emerging national political economies. By focusing on trades, rather than on the national political economy, our analysis demonstrates that in each country the formation of national political economies and citizenship rights was not the result of a national pattern of guild survival. Rather, the pattern that emerged by the end of the 19th century was determined by the balance between old and new industries, and between national and regional or local government

Understanding management gurus and historical narratives: The benefits of a historic turn in management and organization studies

A historic turn in organization studies requires a basic theoretical understanding of ‘doing history’ and an appreciation of the centrality of narrative in history. Following the cultural turn in history, narrativist historians and philosophers of history such as Hayden White, Frank Ankersmit and Paul Ricoeur have made the case that narrative is an essential and unavoidable component in history. We demonstrate the persuasive capacity of narrative through a narrativist critique of three best-selling ‘management gurus’. This analysis illustrates the following: (1) the narrative features of popular organizational theories; (2) the basis of the success of guru literature; and (3) why gurus and organizational scientists themselves do not understand the narratological mechanisms behind their success. Finally, we maintain that historical narrativism offers the possibility for positioning organizational history as a highly relevant field for management academics, gurus and even managers, providing support for a historic turn