Generic systolic array for genetic algorithms

The authors present a systolic design for a simple GA mechanism which provides high throughput and unidirectional pipelining by exploiting the inherent parallelism in the genetic operators. The design computes in O(N+G) time steps using O(N2) cells where N is the population size and G is the chromosome length. The area of the device is independent of the chromosome length and so can be easily scaled by replicating the arrays or by employing fine-grain migration. The array is generic in the sense that it does not rely on the fitness function and can be used as an accelerator for any GA application using uniform crossover between pairs of chromosomes. The design can also be used in hybrid systems as an add-on to complement existing designs and methods for fitness function acceleration and island-style population management

A new linear initialization in SOM for biomolecular data

In the past decade, the amount of data in biological field has become larger and larger; Bio-techniques for analysis of biological data have been developed and new tools have been introduced. Several computational methods are based on unsupervised neural network algorithms that are widely used for multiple purposes including clustering and visualization, i.e. the Self Organizing Maps (SOM). Unfortunately, even though this method is unsupervised, the performances in terms of quality of result and learning speed are strongly dependent from the neuron weights initialization. In this paper we present a new initialization technique based on a totally connected undirected graph, that report relations among some intersting features of data input. Result of experimental tests, where the proposed algorithm is compared to the original initialization techniques, shows that our technique assures faster learning and better performance in terms of quantization error.

Parallel genetic algorithms for the tuning of a fuzzy AQM controller

This paper presents the results of the application of a parallel Genetic Algorithm (GA) in order to design a Fuzzy Proportional Integral (FPI) controller for active queue management on Internet routers. The Active Queue Management (AQM) policies are those policies of router queue management that allow the detection of network congestion, the notification of such occurrences to the hosts on the network borders, and the adoption of a suitable control policy. Two different parallel implementations of the genetic algorithm are adopted to determine an optimal configuration of the FPI controller parameters. Finally, the results of several experiments carried out on a forty nodes cluster of workstations are presented.

Implementing a generic systolic array for genetic algorithms

We have designed a highly parallel design for a simple genetic algorithm using a pipeline of systolic arrays. The systolic design provides high throughput and unidirectional pipelining by exploiting the implicit parallelism in the genetic operators. The design is significant because, unlike other hardware genetic algorithms, it is independent of both the fitness function and the particular chromosome length used in a problem. We have designed and simulated a version of the mutation array using Xilinix FPGA tools to investigate the feasibility of hardware implementation. A simple 5-chromosome mutation array occupies 195 CLBs and is capable of performing more than one million mutations per second. I. Introduction Genetic algorithms (GAs) are established search and optimization techniques which have been applied to a range of engineering and applied problems with considerable success [1]. They operate by maintaining a population of trial solutions encoded, using a suitable encoding scheme.

Systolic random number generation for genetic algorithms

A parallel hardware random number generator for use with a VLSI genetic algorithm processing device is proposed. The design uses an systolic array of mixed congruential random number generators. The generators are constantly reseeded with the outputs of the proceeding generators to avoid significant biasing of the randomness of the array which would result in longer times for the algorithm to converge to a solution. 1 Introduction In recent years there has been a growing interest in developing hardware genetic algorithm devices [1, 2, 3]. A genetic algorithm (GA) is a stochastic search and optimization technique which attempts to capture the power of natural selection by evolving a population of candidate solutions by a process of selection and reproduction [4]. In keeping with the evolutionary analogy, the solutions are called chromosomes with each chromosome containing a number of genes. Chromosomes are commonly simple binary strings, the bits being the genes.

Mapping and controlling molecular processes: The application of control theory and system identification algorithms to ASOPS and other fast pulse spectroscopies

Asynchronous Optical Sampling (ASOPS) [1,2] and frequency comb spectrometry [3] based on dual Ti:saphire resonators operated in a master/slave mode have the potential to improve signal to noise ratio in THz transient and IR sperctrometry. The multimode Brownian oscillator time-domain response function described by state-space models is a mathematically robust framework that can be used to describe the dispersive phenomena governed by Lorentzian, Debye and Drude responses. In addition, the optical properties of an arbitrary medium can be expressed as a linear combination of simple multimode Brownian oscillator functions. The suitability of a range of signal processing schemes adopted from the Systems Identification and Control Theory community for further processing the recorded THz transients in the time or frequency domain will be outlined [4,5]. Since a femtosecond duration pulse is capable of persistent excitation of the medium within which it propagates, such approach is perfectly justifiable. Several de-noising routines based on system identification will be shown. Furthermore, specifically developed apodization structures will be discussed. These are necessary because due to dispersion issues, the time-domain background and sample interferograms are non-symmetrical [6-8]. These procedures can lead to a more precise estimation of the complex insertion loss function. The algorithms are applicable to femtosecond spectroscopies across the EM spectrum. Finally, a methodology for femtosecond pulse shaping using genetic algorithms aiming to map and control molecular relaxation processes will be mentioned.

GeneMCL in microarray analysis

Accurately and reliably identifying the actual number of clusters present with a dataset of gene expression profiles, when no additional information on cluster structure is available, is a problem addressed by few algorithms. GeneMCL transforms microarray analysis data into a graph consisting of nodes connected by edges, where the nodes represent genes, and the edges represent the similarity in expression of those genes, as given by a proximity measurement. This measurement is taken to be the Pearson correlation coefficient combined with a local non-linear rescaling step. The resulting graph is input to the Markov Cluster (MCL) algorithm, which is an elegant, deterministic, non-specific and scalable method, which models stochastic flow through the graph. The algorithm is inherently affected by any cluster structure present, and rapidly decomposes a graph into cohesive clusters. The potential of the GeneMCL algorithm is demonstrated with a 5730 gene subset (IGS) of the Van't Veer breast cancer database, for which the clusterings are shown to reflect underlying biological mechanisms. (c) 2005 Elsevier Ltd. All rights reserved.

Advanced scalable algorithms for advanced architectures

With the latest advances in the area of advanced computer architectures we are seeing already large scale machines at petascale level and we are discussing exascale computing. All these require efficient scalable algorithms in order to bridge the performance gap. In this paper examples of various approaches of designing scalable algorithms for such advanced architectures will be given and the corresponding properties of these algorithms will be outlined and discussed. Examples will outline such scalable algorithms applied to large scale problems in the area Computational Biology, Environmental Modelling etc. The key properties of such advanced and scalable algorithms will be outlined.

Economic models and algorithms for distributed systems

Distributed computing paradigms for sharing resources such as Clouds, Grids, Peer-to-Peer systems, or voluntary computing are becoming increasingly popular. While there are some success stories such as PlanetLab, OneLab, BOINC, BitTorrent, and SETI@home, a widespread use of these technologies for business applications has not yet been achieved. In a business environment, mechanisms are needed to provide incentives to potential users for participating in such networks. These mechanisms may range from simple non-monetary access rights, monetary payments to specific policies for sharing. Although a few models for a framework have been discussed (in the general area of a "Grid Economy"), none of these models has yet been realised in practice. This book attempts to fill this gap by discussing the reasons for such limited take-up and exploring incentive mechanisms for resource sharing in distributed systems. The purpose of this book is to identify research challenges in successfully using and deploying resource sharing strategies in open-source and commercial distributed systems.

An analysis of real time implementation of Fourier transform-based frequency recognition algorithms

Frequency recognition is an important task in many engineering fields such as audio signal processing and telecommunications engineering, for example in applications like Dual-Tone Multi-Frequency (DTMF) detection or the recognition of the carrier frequency of a Global Positioning, System (GPS) signal. This paper will present results of investigations on several common Fourier Transform-based frequency recognition algorithms implemented in real time on a Texas Instruments (TI) TMS320C6713 Digital Signal Processor (DSP) core. In addition, suitable metrics are going to be evaluated in order to ascertain which of these selected algorithms is appropriate for audio signal processing(1).

Verification and FPGA circuits of a block-2 fast path-based predictor

This paper formally derives a new path-based neural branch prediction algorithm (FPP) into blocks of size two for a lower hardware solution while maintaining similar input-output characteristic to the algorithm. The blocked solution, here referred to as B2P algorithm, is obtained using graph theory and retiming methods. Verification approaches were exercised to show that prediction performances obtained from the FPP and B2P algorithms differ within one mis-prediction per thousand instructions using a known framework for branch prediction evaluation. For a chosen FPGA device, circuits generated from the B2P algorithm showed average area savings of over 25% against circuits for the FPP algorithm with similar time performances thus making the proposed blocked predictor superior from a practical viewpoint.

Pulse shaping using state space algorithms

We discuss the use of pulse shaping for optimal excitation of samples in time-domain THz spectroscopy. Pulse shaping can be performed in a 4f optical system to specifications from state space models of the system's dynamics. Subspace algorithms may be used for the identification of the state space models.