Secondary structure prediction with support vector machines

Motivation: A new method that uses support vector machines (SVMs) to predict protein secondary structure is described and evaluated. The study is designed to develop a reliable prediction method using an alternative technique and to investigate the applicability of SVMs to this type of bioinformatics problem. Methods: Binary SVMs are trained to discriminate between two structural classes. The binary classifiers are combined in several ways to predict multi-class secondary structure. Results: The average three-state prediction accuracy per protein (Q3) is estimated by cross-validation to be 77.07 ± 0.26% with a segment overlap (Sov) score of 73.32 ± 0.39%. The SVM performs similarly to the 'state-of-the-art' PSIPRED prediction method on a non-homologous test set of 121 proteins despite being trained on substantially fewer examples. A simple consensus of the SVM, PSIPRED and PROFsec achieves significantly higher prediction accuracy than the individual methods. Availability: The SVM classifier is available from the authors. Work is in progress to make the method available on-line and to integrate the SVM predictions into the PSIPRED server.

Parkinson’s Disease tremor classification – a comparison between Support Vector Machines and neural networks

Deep Brain Stimulation has been used in the study of and for treating Parkinson’s Disease (PD) tremor symptoms since the 1980s. In the research reported here we have carried out a comparative analysis to classify tremor onset based on intraoperative microelectrode recordings of a PD patient’s brain Local Field Potential (LFP) signals. In particular, we compared the performance of a Support Vector Machine (SVM) with two well known artificial neural network classifiers, namely a Multiple Layer Perceptron (MLP) and a Radial Basis Function Network (RBN). The results show that in this study, using specifically PD data, the SVM provided an overall better classification rate achieving an accuracy of 81% recognition.

People or machines? Assessing the impacts of smart meters and load controllers in Italian office spaces

Government initiatives in several developed and developing countries to roll-out smart meters call for research on the sustainability impacts of these devices. In principle smart meters bring about higher control over energy theft and lower consumption, but require a high level of engagement by end-users. An alternative consists of load controllers, which control the load according to pre-set parameters. To date, research has focused on the impacts of these two alternatives separately. This study compares the sustainability impacts of smart meters and load controllers in an occupied office building in Italy. The assessment is carried out on three different floors of the same building. Findings show that demand reductions associated with a smart meter device are 5.2% higher than demand reductions associated with the load controller.

The new localism, anti-political development machines, and the role of planning consultants: lessons from London's South Bank

This paper draws on a study of the politics of development planning in London’s South Bank to examine wider trends in the governance of contemporary cities. It assesses the impacts and outcomes of so-called new localist reforms and argues that we are witnessing two principal trends. First, governance processes are increasingly dominated by anti-democratic development machines, characterized by new assemblages of public- and private-sector experts. These machines reflect and reproduce a type of development politics in which there is a greater emphasis on a pragmatic realism and a politics of delivery. Second, the presence of these machines is having a significant impact on the politics of planning. Democratic engagement is not seen as the basis for new forms of localism and community control. Instead, it is presented as a potentially disruptive force that needs to be managed by a new breed of skilled private-sector consultant. The paper examines these wider shifts in urban politics before focusing on the connections between emerging development machines and local residential and business communities. It ends by highlighting some of the wider implications of change for democratic modes of engagement and nodes of resistance in urban politics.

Transmathematical basis of infinitely scalable pipeline machines

We describe infinitely scalable pipeline machines with perfect parallelism, in the sense that every instruction of an inline program is executed, on successive data, on every clock tick. Programs with shared data effectively execute in less than a clock tick. We show that pipeline machines are faster than single or multi-core, von Neumann machines for sufficiently many program runs of a sufficiently time consuming program. Our pipeline machines exploit the totality of transreal arithmetic and the known waiting time of statically compiled programs to deliver the interesting property that they need no hardware or software exception handling.

NATO and the environment: the committee on the challenges of modern society

Launched with considerable fanfare in 1969, the Committee on the Challenges of Modern Society (CCMS) was supposed to bring new life to NATO by both re-energising public support and engaging with a variety of themes, issues and partners well beyond the alliance’s traditional scope. The first aim of this article is to go beyond the careful media operation that surrounded the launch of the CCMS and to examine the scepticism and resistance of some European partners, particularly the British. The second aim is to demonstrate that NATO started to think in terms of crisis management, disaster relief and environmental disasters well before 1989. The sheer military strength of the alliance and of its partners did remain central – and notably came back to the forefront in 1979 – but the alliance did start to see itself as a geopolitical player and to consider engagement beyond its strictly defined geographical area as early as 1969.

Checking Completeness of Tests for Finite State Machines

In testing from a Finite State Machine (FSM), the generation of test suites which guarantee full fault detection, known as complete test suites, has been a long-standing research topic. In this paper, we present conditions that are sufficient for a test suite to be complete. We demonstrate that the existing conditions are special cases of the proposed ones. An algorithm that checks whether a given test suite is complete is given. The experimental results show that the algorithm can be used for relatively large FSMs and test suites.