Approximating the Set of Local Minima in Partial RNA Folding Landscapes

Motivation: We study a stochastic method for approximating the set of local minima in partial RNA folding landscapes associated with a bounded-distance neighbourhood of folding conformations. The conformations are limited to RNA secondary structures without pseudoknots. The method aims at exploring partial energy landscapes pL induced by folding simulations and their underlying neighbourhood relations. It combines an approximation of the number of local optima devised by Garnier and Kallel (2002) with a run-time estimation for identifying sets of local optima established by Reeves and Eremeev (2004).

Results: The method is tested on nine sequences of length between 50 nt and 400 nt, which allows us to compare the results with data generated by RNAsubopt and subsequent barrier tree calculations. On the nine sequences, the method captures on average 92% of local minima with settings designed for a target of 95%. The run-time of the heuristic can be estimated by O(n2D?ln?), where n is the sequence length, ? is the number of local minima in the partial landscape pL under consideration and D is the maximum number of steepest descent steps in attraction basins associated with pL.

On generating set index functions for randomized caches

Caches hide the growing latency of accesses to the main memory from the processor by storing the most recently used data on-chip. To limit the search time through the caches, they are organized in a direct mapped or set-associative way. Such an organization introduces many conflict misses that hamper performance. This paper studies randomizing set index functions, a technique to place the data in the cache in such a way that conflict misses are avoided. The performance of such a randomized cache strongly depends on the randomization function. This paper discusses a methodology to generate randomization functions that perform well over a broad range of benchmarks. The methodology uses profiling information to predict the conflict miss rate of randomization functions. Then, using this information, a search algorithm finds the best randomization function. Due to implementation issues, it is preferable to use a randomization function that is extremely simple and can be evaluated in little time. For these reasons, we use randomization functions where each randomized address bit is computed as the XOR of a subset of the original address bits. These functions are chosen such that they operate on as few address bits as possible and have few inputs to each XOR. This paper shows that to index a 2(m)-set cache, it suffices to randomize m+2 or m+3 address bits and to limit the number of inputs to each XOR to 2 bits to obtain the full potential of randomization. Furthermore, it is shown that the randomization function that we generate for one set of benchmarks also works well for an entirely different set of benchmarks. Using the described methodology, it is possible to reduce the implementation cost of randomization functions with only an insignificant loss in conflict reduction.

Highly accurate and efficient evaluation of randomising set index functions

Randomising set index functions can reduce the number of conflict misses in data caches by spreading the cache blocks uniformly over all sets. Typically, the randomisation functions compute the exclusive ors of several address bits. Not all randomising set index functions perform equally well, which calls for the evaluation of many set index functions. This paper discusses and improves a technique that tackles this problem by predicting the miss rate incurred by a randomisation function, based on profiling information. A new way of looking at randomisation functions is used, namely the null space of the randomisation function. The members of the null space describe pairs of cache blocks that are mapped to the same set. This paper presents an analytical model of the error made by the technique and uses this to propose several optimisations to the technique. The technique is then applied to generate a conflict-free randomisation function for the SPEC benchmarks. (C) 2003 Elsevier Science B.V. All rights reserved.

Improved structure optimization for fuzzy-neural networks

Fuzzy-neural-network-based inference systems are well-known universal approximators which can produce linguistically interpretable results. Unfortunately, their dimensionality can be extremely high due to an excessive number of inputs and rules, which raises the need for overall structure optimization. In the literature, various input selection methods are available, but they are applied separately from rule selection, often without considering the fuzzy structure. This paper proposes an integrated framework to optimize the number of inputs and the number of rules simultaneously. First, a method is developed to select the most significant rules, along with a refinement stage to remove unnecessary correlations. An improved information criterion is then proposed to find an appropriate number of inputs and rules to include in the model, leading to a balanced tradeoff between interpretability and accuracy. Simulation results confirm the efficacy of the proposed method.

Feedforward Control of Shape Memory Alloy Actuators Using Fuzzy-Based Inverse Preisach Model

This brief investigates a possible application of the inverse Preisach model in combination with the feedforward and feedback control strategies to control shape memory alloy actuators. In the feedforward control design, a fuzzy-based inverse Preisach model is used to compensate for the hysteresis nonlinearity effect. An extrema input history and a fuzzy inference is utilized to replace the inverse classical Preisach model. This work allows for a reduction in the number of experimental parameters and computation time for the inversion of the classical Preisach model. A proportional-integral-derivative (PID) controller is used as a feedback controller to regulate the error between the desired output and the system output. To demonstrate the effectiveness of the proposed controller, real-time control experiment results are presented.

Position control of shape memory alloy actuators using self tuning fuzzy PID controller

Shape Memory Alloy (SMA) actuators, which have the ability to return to a predetermined shape when heated, have many potential applications such as aeronautics, surgical tools, robotics and so on. Although the conventional PID controller can be used with slow response systems, there has been limited success in precise motion control of SMA actuators, since the systems are disturbed by unknown factors beside their inherent nonlinear hysteresis and changes in the surrounding environment of the systems. This paper presents a new development of a SMA position control system by using a self-tuning fuzzy PID controller. This control algorithm is used by tuning the parameters of the PID controller thereby integrating fuzzy inference and producing a fuzzy adaptive PID controller, which can then be used to improve the control performance of nonlinear systems. The experimental results of position control of SMA actuators using conventional and self-tuning fuzzy PID controllers are both included in this paper.

Internal model control for shape memory alloy actuators using fuzzy based Preisach model

This paper investigates a possible application of Preisach model to control shape memory alloy (SMA) actuators using an internal model control strategy. The developed strategy consists in including the Preisach hysteresis model of SMA actuator and the inverse Preisach model within the control structure. In this work, an extrema input hystory and a fuzzy inference is utilized to replace the classical Preisach model. This allows to reduce a large amount of experimental parameters and computation time of the classical Preisach model. To demonstrate the effectiveness of the proposed controller in improving control performance and hysteresis compensation of SMA actuators, experimental results from real time control are presented.

Trajectory Control of Electro Hydraulic Excavator using Fuzzy Self Tuning Algorithm with Neural Network

This paper presents the trajectory control of a 2DOF mini electro-hydraulic excavator by using fuzzy self tuning with neural network algorithm. First, the mathematical model is derived for the 2DOF mini electro-hydraulic excavator. The fuzzy PID and fuzzy self tuning with neural network are designed for circle trajectory following. Its two links are driven by an electric motor controlled pump system. The experimental results demonstrated that the proposed controllers have better control performance than the conventional controller.

Modelling and Control of Shape Memory Alloy Actuators by using Preisach Model, Genetic Algorithm and Fuzzy Logic

Shapememoryalloy (SMA) actuators, which have the ability to return to a predetermined shape when heated, have many potential applications in aeronautics, surgical tools, robotics and so on. Nonlinearity hysteresis effects existing in SMA actuators present a problem in the motion control of these smart actuators. This paper investigates the control problem of SMA actuators in both simulation and experiment. In the simulation, the numerical Preisachmodel with geometrical interpretation is used for hysteresis modeling of SMA actuators. This model is then incorporated in a closed loop PID control strategy. The optimal values of PID parameters are determined by using geneticalgorithm to minimize the mean squared error between desired output displacement and simulated output. However, the control performance is not good compared with the simulation results when these parameters are applied to the real SMA control since the system is disturbed by unknown factors and changes in the surrounding environment of the system. A further automated readjustment of the PID parameters using fuzzylogic is proposed for compensating the limitation. To demonstrate the effectiveness of the proposed controller, real time control experiment results are presented.