An extensible automated protein annotation tool: standardizing input and output using validated XML

Motivation: There is a frequent need to apply a large range of local or remote prediction and annotation tools to one or more sequences. We have created a tool able to dispatch one or more sequences to assorted services by defining a consistent XML format for data and annotations. Results: By analyzing annotation tools, we have determined that annotations can be described using one or more of the six forms of data: numeric or textual annotation of residues, domains (residue ranges) or whole sequences. With this in mind, XML DTDs have been designed to store the input and output of any server. Plug-in wrappers to a number of services have been written which are called from a master script. The resulting APATML is then formatted for display in HTML. Alternatively further tools may be written to perform post-analysis.

Qualitative modelling of sustainable energy scenarios: An application and extension of the Bon Qualitative Input-Output model

Climate change is one of the major challenges facing economic systems at the start of the 21st century. Reducing greenhouse gas emissions will require both restructuring the energy supply system (production) and addressing the efficiency and sufficiency of the social uses of energy (consumption). The energy production system is a complicated supply network of interlinked sectors with 'knock-on' effects throughout the economy. End use energy consumption is governed by complex sets of interdependent cultural, social, psychological and economic variables driven by shifts in consumer preference and technological development trajectories. To date, few models have been developed for exploring alternative joint energy production-consumption systems. The aim of this work is to propose one such model. This is achieved in a methodologically coherent manner through integration of qualitative input-output models of production, with Bayesian belief network models of consumption, at point of final demand. The resulting integrated framework can be applied either (relatively) quickly and qualitatively to explore alternative energy scenarios, or as a fully developed quantitative model to derive or assess specific energy policy options. The qualitative applications are explored here.

The prompt hypothesis: clarification requests as corrective input for grammatical errors

The potential of clarification questions (CQs) to act as a form of corrective input for young children's grammatical errors was examined. Corrective responses were operationalized as those occasions when child speech shifted from erroneous to correct (E -> C) contingent on a clarification question. It was predicted that E -> C sequences would prevail over shifts in the opposite direction (C -> E), as can occur in the case of nonerror-contingent CQs. This prediction was tested via a standard intervention paradigm, whereby every 60s a sequence of two clarification requests (either specific or general) was introduced into conversation with a total of 45 2- and 4-year-old children. For 10 categories of grammatical structure, E -> C sequences predominated over their C -> E counterparts, with levels of E -> C shifts increasing after two clarification questions. Children were also more reluctant to repeat erroneous forms than their correct counterparts, following the intervention of CQs. The findings provide support for Saxton's prompt hypothesis, which predicts that error-contingent CQs bear the potential to cue recall of previously acquired grammatical forms.

Input and output modality effects in immediate serial recall

In immediate recall tasks, visual recency is substantially enhanced when output interference is low (Cowan, Saults, Elliott, & Moreno, 2002; Craik, 1969) whereas auditory recency remains high even under conditions of high output interference. Ibis auditory advantage has been interpreted in terms of auditory resistance to output interference (e.g., Neath & Surprenant, 2003). In this study the auditory-visual difference at low output interference re-emerged when ceiling effects were accounted for, but only with spoken output. With written responding the auditory advantage remained significantly larger with high than with low output interference. These new data suggest that both superior auditory encoding and modality-specific output interference contribute to the classic auditory-visual modality effect.

Input constraints handling in an MPC/feedback linearization scheme

The combination of model predictive control based on linear models (MPC) with feedback linearization (FL) has attracted interest for a number of years, giving rise to MPC+FL control schemes. An important advantage of such schemes is that feedback linearizable plants can be controlled with a linear predictive controller with a fixed model. Handling input constraints within such schemes is difficult since simple bound contraints on the input become state dependent because of the nonlinear transformation introduced by feedback linearization. This paper introduces a technique for handling input constraints within a real time MPC/FL scheme, where the plant model employed is a class of dynamic neural networks. The technique is based on a simple affine transformation of the feasible area. A simulated case study is presented to illustrate the use and benefits of the technique.

Design of a minimum variance multiple input-multiple output neuro self-tuning proportional-integral-derivative controller for non-linear dynamic systems

In this study a minimum variance neuro self-tuning proportional-integral-derivative (PID) controller is designed for complex multiple input-multiple output (MIMO) dynamic systems. An approximation model is constructed, which consists of two functional blocks. The first block uses a linear submodel to approximate dominant system dynamics around a selected number of operating points. The second block is used as an error agent, implemented by a neural network, to accommodate the inaccuracy possibly introduced by the linear submodel approximation, various complexities/uncertainties, and complicated coupling effects frequently exhibited in non-linear MIMO dynamic systems. With the proposed model structure, controller design of an MIMO plant with n inputs and n outputs could be, for example, decomposed into n independent single input-single output (SISO) subsystem designs. The effectiveness of the controller design procedure is initially verified through simulations of industrial examples.

Entropy versus APE production: on the buoyancy power input in the oceans energy cycle

This letter argues that the current controversy about whether Wbuoyancy, the power input due to the surface buoyancy fluxes, is large or small in the oceans stems from two distinct and incompatible views on how Wbuoyancy relates to the volume-integrated work of expansion/contraction B. The current prevailing view is that Wbuoyancy should be identified with the net value of B, which current theories estimate to be small. The alternative view, defended here, is that only the positive part of B, i.e., the one converting internal energy into mechanical energy, should enter the definition of Wbuoyancy, since the negative part of B is associated with the non-viscous dissipation of mechanical energy. Two indirect methods suggest that by contrast, the positive part of B is potentially large.

On the Kalman-Bucy filter with specified input

In a recent paper, Vathsal suggested that a new configuration had been obtained for linear filtering problems, which was distinctly different from the Kalman-Bucy filter. It is shown that this in fact is merely a special case of the filter with a specified input.

Weighted input predictive controller

A discrete-time algorithm is presented which is based on a predictive control scheme in the form of dynamic matrix control. A set of control inputs are calculated and made available at each time instant, the actual input applied being a weighted summation of the inputs within the set. The algorithm is directly applicable in a self-tuning format and is therefore suitable for slowly time-varying systems in a noisy environment.

Input/output linearization using dynamic recurrent neural networks

This paper brings together two areas of research that have received considerable attention during the last years, namely feedback linearization and neural networks. A proposition that guarantees the Input/Output (I/O) linearization of nonlinear control affine systems with Dynamic Recurrent Neural Networks (DRNNs) is formulated and proved. The proposition and the linearization procedure are illustrated with the simulation of a single link manipulator.

Control strategy for Boolean input systems

The purpose of this paper is to design a control law for continuous systems with Boolean inputs allowing the output to track a desired trajectory. Such systems are controlled by items of commutation. This type of systems, with Boolean inputs, has found increasing use in the electric industry. Power supplies include such systems and a power converter represents one of theses systems. For instance, in power electronics the control variable is the switching OFF and ON of components such as thyristors or transistors. In this paper, a method is proposed for the designing of a control law in state space for such systems. This approach is implemented in simulation for the control of an electronic circuit.

On the utility of input selection and pruning for financial distress prediction models

Analyzes the use of linear and neural network models for financial distress classification, with emphasis on the issues of input variable selection and model pruning. A data-driven method for selecting input variables (financial ratios, in this case) is proposed. A case study involving 60 British firms in the period 1997-2000 is used for illustration. It is shown that the use of the Optimal Brain Damage pruning technique can considerably improve the generalization ability of a neural model. Moreover, the set of financial ratios obtained with the proposed selection procedure is shown to be an appropriate alternative to the ratios usually employed by practitioners.

New developments in batch process input profile optimisation

A novel algorithm for solving nonlinear discrete time optimal control problems with model-reality differences is presented. The technique uses dynamic integrated system optimisation and parameter estimation (DISOPE) which achieves the correct optimal solution in spite of deficiencies in the mathematical model employed in the optimisation procedure. A new method for approximating some Jacobian trajectories required by the algorithm is introduced. It is shown that the iterative procedure associated with the algorithm naturally suits applications to batch chemical processes.