Adaptive group mutation for tackling deception in genetic search

Copyright @ 2004 WSEASIn order to study the efficacy of genetic algorithms (GAs), a number of fitness landscapes have been designed and used as test functions. Among these functions a family of deceptive functions have been developed as difficult test functions for comparing different implementations of GAs. In this paper an adaptive group mutation (AGM), which can be combined with traditional bit mutation in GAs, is proposed to tackle the deception problem in genetic searching. Within the AGM, those genes that have converged to certain threshold degree are adaptively grouped together and subject to mutation together with a given probability. To test the performance of the AGM, experiments were carried out to compare GAs that combine the AGM and GAs that use only traditional bit mutation with a number of suggested “standard” fixed mutation rates over a set of deceptive functions as well as non-deceptive functions. The results demonstrate that GAs with the AGM perform better than GAs with only traditional bit mutation over deceptive functions and as well as GAs with only traditional bit mutation over non-deceptive functions. The results show that the AGM is a good choice for GAs since most problems may involve some degree of deception and deceptive functions are difficult for GAs

Intrinsically Evolvable Artificial Neural Networks

Dedicated hardware implementations of neural networks promise to provide faster, lower power operation when compared to software implementations executing on processors. Unfortunately, most custom hardware implementations do not support intrinsic training of these networks on-chip. The training is typically done using offline software simulations and the obtained network is synthesized and targeted to the hardware offline. The FPGA design presented here facilitates on-chip intrinsic training of artificial neural networks. Block-based neural networks (BbNN), the type of artificial neural networks implemented here, are grid-based networks neuron blocks. These networks are trained using genetic algorithms to simultaneously optimize the network structure and the internal synaptic parameters. The design supports online structure and parameter updates, and is an intrinsically evolvable BbNN platform supporting functional-level hardware evolution. Functional-level evolvable hardware (EHW) uses evolutionary algorithms to evolve interconnections and internal parameters of functional modules in reconfigurable computing systems such as FPGAs. Functional modules can be any hardware modules such as multipliers, adders, and trigonometric functions. In the implementation presented, the functional module is a neuron block. The designed platform is suitable for applications in dynamic environments, and can be adapted and retrained online. The online training capability has been demonstrated using a case study. A performance characterization model for RC implementations of BbNNs has also been presented

GPU acceleration for statistical gene classification

The use of Bioinformatic tools in routine clinical diagnostics is still facing a number of issues. The more complex and advanced bioinformatic tools become, the more performance is required by the computing platforms. Unfortunately, the cost of parallel computing platforms is usually prohibitive for both public and small private medical practices. This paper presents a successful experience in using the parallel processing capabilities of Graphical Processing Units (GPU) to speed up bioinformatic tasks such as statistical classification of gene expression profiles. The results show that using open source CUDA programming libraries allows to obtain a significant increase in performances and therefore to shorten the gap between advanced bioinformatic tools and real medical practic

Constrained and unconstrained evolution of “ LCR” low-pass filters with oscillating length representation

The unconstrained evolution has already been applied in the past towards design of digital circuits, and extraordinary results have been obtained, including generation of circuits with smaller number of electronic components. In this paper both constrained and unconstrained evolutions, blended with oscillating length genotype sweeping strategy, are applied towards design of analogue “ LCR” circuits. The comparison of both evolutions is made and the promising results are obtained. The new algorithm has produced the best results in terms of quality of the circuits evolved and evolutionary resources required. It differs from previous ones by its simplicity and represents one of the first attempts to apply Evolutionary Strategy towards the analogue circuit design. The obtained results are compared in details with low-pass filters previously designed

Second-generation PLINK: rising to the challenge of larger and richer datasets

PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for even faster and more scalable implementations of key functions. In addition, GWAS and population-genetic data now frequently contain probabilistic calls, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1's primary data format. To address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, O(sqrt(n))-time/constant-space Hardy-Weinberg equilibrium and Fisher's exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. This will be followed by PLINK 2.0, which will introduce (a) a new data format capable of efficiently representing probabilities, phase, and multiallelic variants, and (b) extensions of many functions to account for the new types of information. The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.Comment: 2 figures, 1 additional fil

DxNAT - Deep Neural Networks for Explaining Non-Recurring Traffic Congestion

Non-recurring traffic congestion is caused by temporary disruptions, such as accidents, sports games, adverse weather, etc. We use data related to real-time traffic speed, jam factors (a traffic congestion indicator), and events collected over a year from Nashville, TN to train a multi-layered deep neural network. The traffic dataset contains over 900 million data records. The network is thereafter used to classify the real-time data and identify anomalous operations. Compared with traditional approaches of using statistical or machine learning techniques, our model reaches an accuracy of 98.73 percent when identifying traffic congestion caused by football games. Our approach first encodes the traffic across a region as a scaled image. After that the image data from different timestamps is fused with event- and time-related data. Then a crossover operator is used as a data augmentation method to generate training datasets with more balanced classes. Finally, we use the receiver operating characteristic (ROC) analysis to tune the sensitivity of the classifier. We present the analysis of the training time and the inference time separately

An investigation of messy genetic algorithms

Genetic algorithms (GAs) are search procedures based on the mechanics of natural selection and natural genetics. They combine the use of string codings or artificial chromosomes and populations with the selective and juxtapositional power of reproduction and recombination to motivate a surprisingly powerful search heuristic in many problems. Despite their empirical success, there has been a long standing objection to the use of GAs in arbitrarily difficult problems. A new approach was launched. Results to a 30-bit, order-three-deception problem were obtained using a new type of genetic algorithm called a messy genetic algorithm (mGAs). Messy genetic algorithms combine the use of variable-length strings, a two-phase selection scheme, and messy genetic operators to effect a solution to the fixed-coding problem of standard simple GAs. The results of the study of mGAs in problems with nonuniform subfunction scale and size are presented. The mGA approach is summarized, both its operation and the theory of its use. Experiments on problems of varying scale, varying building-block size, and combined varying scale and size are presented

On-chip fully reconfigurable Artificial Neural Network in 16 nm FinFET for Positron Emission Tomography

Smarty is a fully-reconfigurable on-chip feed-forward artificial neural network (ANN) with ten integrated time-to-digital converters (TDCs) designed in a 16 nm FinFET CMOS technology node. The integration of TDCs together with an ANN aims to reduce system complexity and minimize data throughput requirements in positron emission tomography (PET) applications. The TDCs have an average LSB of 53.5 ps. The ANN is fully reconfigurable, the user being able to change its topology as desired within a set of constraints. The chip can execute 363 MOPS with a maximum power consumption of 1.9 mW, for an efficiency of 190 GOPS/W. The system performance was tested in a coincidence measurement setup interfacing Smarty with two groups of five 4 mm x 4 mm analog silicon photomultipliers (A-SiPMs) used as inputs for the TDCs. The ANN successfully distinguished between six different positions of a radioactive source placed between the two photodetector arrays by solely using the TDC timestamps.Comment: 13 pages, 24 Figure