Revealing differences in gene network inference algorithms on the network level by ensemble methods

Motivation: The inference of regulatory networks from large-scale expression data holds great promise because of the potentially causal interpretation of these networks. However, due to the difficulty to establish reliable methods based on observational data there is so far only incomplete knowledge about possibilities and limitations of such inference methods in this context.

Results: In this article, we conduct a statistical analysis investigating differences and similarities of four network inference algorithms, ARACNE, CLR, MRNET and RN, with respect to local network-based measures. We employ ensemble methods allowing to assess the inferability down to the level of individual edges. Our analysis reveals the bias of these inference methods with respect to the inference of various network components and, hence, provides guidance in the interpretation of inferred regulatory networks from expression data. Further, as application we predict the total number of regulatory interactions in human B cells and hypothesize about the role of Myc and its targets regarding molecular information processing.

Cognitive biases and addiction: an evolution in theory and method

An evolution in theoretical models and methodological paradigms for investigating cognitive biases in the addictions is discussed. Anomalies in traditional cognitive perspectives, and problems with the self-report methods which underpin them, are highlighted. An emergent body of cognitive research, contextualized within the principles and paradigms of cognitive neuropsychology rather than social learning theory, is presented which, it is argued, addresses these anomalies and problems. Evidence is presented that biases in the processing of addiction-related stimuli, and in the network of propositions which motivate addictive behaviours, occur at automatic, implicit and pre-conscious levels of awareness. It is suggested that methods which assess such implicit cognitive biases (e.g. Stroop, memory, priming and reaction-time paradigms) yield findings which have better predictive utility for ongoing behaviour than those biases determined by self-report methods of introspection. The potential utility of these findings for understanding "loss of control" phenomena, and the desynchrony between reported beliefs and intentions and ongoing addictive behaviours, is discussed. Applications to the practice of cognitive therapy are considered.

Network Topology, Higher Orders of Stability and Efficiency

Stable networks of order r where r is a natural number refer to those networks that are immune to coalitional deviation of size r or less. In this paper, we introduce stability of a finite order and examine its relation with efficient networks under anonymous and component additive value functions and the component-wise egalitarian allocation rule. In particular, we examine shapes of networks or network architectures that would resolve the conflict between stability and efficiency in the sense that if stable networks assume those shapes they would be efficient and if efficient networks assume those shapes, they would be stable with minimal further restrictions on value functions.

Network Usage Determination for Transmission Cost Allocation using a Transformer Analogy

This study presents a new method for determining the transmission network usage by loads and generators, which can then be used for transmission cost/loss allocation in an explainable and justifiable manner. The proposed method is based on solid physical grounds and circuit theory. It relies on dividing the currents through the network into two components; the first one is attributed to power flows from generators to loads, whereas the second one is because of the generators only. Unlike almost all the available methods, the proposed method is assumption free and hence it is more accurate than similar methods even those having some physical basis. The proposed method is validated through a transformer analogy, and theoretical derivations. The method is verified through application to the IEEE 30 bus system and the IEEE 118 test system. The results obtained verified many desirable features of the proposed method. Being more accurate in determining the network usage, in an explainable transparent manner, and in giving accurate cost signals, indicating the best locations to add loads and generation, are among the many desirable features.

Video Event Recognition by Dempster-Shafer Theory

This paper presents an event recognition framework, based on Dempster-Shafer theory, that combines evidence of events from low-level computer vision analytics. The proposed method employing evidential network modelling of composite events, is able to represent uncertainty of event output from low level video analysis and infer high level events with semantic meaning along with degrees of belief. The method has been evaluated on videos taken of subjects entering and leaving a seated area. This has relevance to a number of transport scenarios, such as onboard buses and trains, and also in train stations and airports. Recognition results of 78% and 100% for four composite events are encouraging.

Collaborative Scholarship on the Margins: An Epistolary Network

This article explores collaborative scholarship on the margins of intellectual life in eighteenth-century England via a close examination of George Ballard's collected correspondence from women letter-writers. Ballard was both a man of trade and an antiquary, and his modest social status inhibited his freedom to move in scholarly circles. Ballard's only published book documented the lives and works of "learned ladies" of Britain from the fifteenth to the eighteenth centuries, and his female correspondents included the Anglo-Saxon scholar Elizabeth Elstob. His collected correspondence provides an insight into a network that operated outside of the major institutions of scholarship and far from the coffee houses of metropolitan life, but which supported its participants in their intellectual endeavours. By examining the collection materially, and by plotting the correspondents geographically, a more precise picture can be drawn of how women and lower-status men could engage in intellectual life from the peripheries of scholarly society. 

Activity and coke formation of nickel and nickel carbide in dry reforming: A deactivation scheme from density functional theory

Dry reforming is a promising reaction to utilise the greenhouse gases CO2 and CH4. Nickel-based catalysts are the most popular catalysts for the reaction, and the coke formation on the catalysts is the main obstacle to the commercialisation of dry reforming. In this study, the whole reaction network of dry reformation on both flat and stepped nickel catalysts (Ni(111) and Ni(211)) as well as nickel carbide (flat: Ni3C(001); stepped: Ni3C(111)) is investigated using density functional theory calculations. The overall reaction energy profiles in the free energy landscape are obtained, and kinetic analyses are utilised to evaluate the activity of the four surfaces. By careful examination of our results, we find the following regarding the activity: (i) flat surfaces are more active than stepped surfaces for the dry reforming and (ii) metallic nickel catalysts are more active than those of nickel carbide, and therefore, the phase transformation from nickel to nickel carbide will reduce the activity. With respect to the coke formation, the following is found: (i) the coke formation probability can be measured by the rate ratio of CH oxidation pathway to C oxidation pathway (r(CH)/r(C)) and the barrier of CO dissociation, (ii) on Ni(111), the coke is unlikely to form, and (iii) the coke formations on the stepped surfaces of both nickel and nickel carbide can readily occur. A deactivation scheme, using which experimental results can be rationalised, is proposed. 

Improvisation, Indeterminacy and Game-Mediated Participation in Network Music Performance

This chapter focuses on the relationship between improvisation and indeterminacy. We discuss the two practices by referring to play theory and game studies and situate it in recent network music performance. We will develop a parallel with game theory in which indeterminacy is seen as a way of articulating situations where structural decisions are left to the discernment of the performers and discuss improvisation as a method of play. The improvisation-indeterminacy relationship is discussed in the context of network music performance, which employs digital networks in the exchange of data between performers and hence relies on topological structures with varying degrees of openness and flexibility. Artists such as Max Neuhaus and The League of Automatic Music Composers initiated the development of a multitude of practices and technologies exploring the network as an environment for music making. Even though the technologies behind “the network” have shifted dramatically since Neuhaus’ use of radio in the 1960’s, a preoccupation with distribution and sharing of artistic agency has remained at the centre of networked practices. Gollo Föllmer, after undertaking an extensive review of network music initiatives, produced a typology that comprises categories as diverse as remix lists, sound toys, real/virtual space installations and network performances. For Föllmer, “the term ‘Net music’ comprises all formal and stylistic kinds of music upon which the specifics of electronic networks leave considerable traces, whereby the electronic networks strongly influence the process of musical production, the musical aesthetic, or the way music is received” (2005: 185).

“Paths for Action”: Leadership Theory and Practice in Complex Public Sector Systems

The nature and challenges of public sector leadership and management are examined in four case studies of project management in complex metropolitan environments. The cases selected by the authors as representative of contextual factors affecting decision-making processes and project outcomes. Drawing on recent theoretical work on complex leadership approaches (Uhl-Bein et al 2007, Hazy 2008, Lichtenstein & Plowman 2009), the authors assess leadership practices enacted and the circumstances that influence these practices. Leadership types theorized by Uhl-Bein et al (2007) are identified operating at different levels and across networks, with contextual factors outlined. The article concludes with a framework for leadership practice and management identifying network facilitation and complexity friendly tools as a practice within complex public sector systems.