This article reviews machine learning methods for bioinformatics. It presents modelling methods, such as supervised classification, clustering and probabilistic graphical models for knowledge discovery, as well as deterministic and stochastic heuristics for optimization. Applications in genomics, proteomics, systems biology, evolution and text mining are also shown.

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Machine learning in bioinformatics

Neuromorphic computing has come to refer to a variety of brain-inspired computers, devices, and models that contrast the pervasive von Neumann computer architecture This biologically inspired approach has created highly connected synthetic neurons and synapses that can be used to model neuroscience theories as well as solve challenging machine learning problems The promise of the technology is to create a brain-like ability to learn and adapt, but the technical challenges are significant, starting with an accurate neuroscience model of how the brain works, to finding materials and engineering breakthroughs to build devices to support these models, to creating a programming framework so the systems can learn, to creating applications with brain-like capabilities In this work, we provide a comprehensive survey of the research and motivations for neuromorphic computing over its history We begin with a 35-year review of the motivations and drivers of neuromorphic computing, then look at the major research areas of the field, which we define as neuro-inspired models, algorithms and learning approaches, hardware and devices, supporting systems, and finally applications We conclude with a broad discussion on the major research topics that need to be addressed in the coming years to see the promise of neuromorphic computing fulfilled The goals of this work are to provide an exhaustive review of the research conducted in neuromorphic computing since the inception of the term, and to motivate further work by illuminating gaps in the field where new research is needed

A Survey of Neuromorphic Computing and Neural Networks in Hardware.

Multiple sequence alignment is one of the cornerstones of modern molecular biology. It is used to identify conserved motifs, to determine protein domains, in 2D/3D structure prediction by homology and in evolutionary studies. Recently, high-throughput technologies such as genome sequencing and structural proteomics have lead to an explosion in the amount of sequence and structure information available. In response, several new multiple alignment methods have been developed that improve both the efficiency and the quality of protein alignments. Consequently, the benchmarks used to evaluate and compare these methods must also evolve. We present here the latest release of the most widely used multiple alignment benchmark, BAliBASE, which provides high quality, manually refined, reference alignments based on 3D structural superpositions. Version 3.0 of BAliBASE includes new, more challenging test cases, representing the real problems encountered when aligning large sets of complex sequences. Using a novel, semiautomatic update protocol, the number of protein families in the benchmark has been increased and representative test cases are now available that cover most of the protein fold space. The total number of proteins in BAliBASE has also been significantly increased from 1444 to 6255 sequences. In addition, full-length sequences are now provided for all test cases, which represent difficult cases for both global and local alignment programs. Finally, the BAliBASE Web site (http://www-bio3d-igbmc.u-strasbg.fr/balibase) has been completely redesigned to provide a more user-friendly, interactive interface for the visualization of the BAliBASE reference alignments and the associated annotations.

BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark

In this paper, we present a new method, called the genetic simulated annealing ant colony system with particle swarm optimization techniques, for solving the traveling salesman problem. We also make experiments using the 25 data sets obtained from the TSPLIB (http://comopt.ifi.uni-heidelberg.de/software/TSPLIB95/) and compare the experimental results of the proposed method with the methods of Angeniol, Vaubois, and Texier (1988), Somhom, Modares, and Enkawa (1997), Masutti and Castro (2009) and Pasti and Castro (2006). The experimental results show that both the average solution and the percentage deviation of the average solution to the best known solution of the proposed method are better than the methods of Angeniol et al. (1988), Somhom et al. (1997), Masutti and Castro (2009) and Pasti and Castro (2006).

Solving the traveling salesman problem based on the genetic simulated annealing ant colony system with particle swarm optimization techniques

A one-of-a-kind survey of the field of Reconfigurable Computing Gives a comprehensive introduction to a discipline that offers a 10X-100X acceleration of algorithms over microprocessors Discusses the impact of reconfigurable hardware on a wide range of applications: signal and image processing, network security, bioinformatics, and supercomputing Includes the history of the field as well as recent advances Includes an extensive bibliography of primary sources

Reconfigurable Computing: Accelerating Computation with Field-Programmable Gate Arrays

This correspondence describes a hybrid genetic algorithm (GA) to find high-quality solutions for the traveling salesman problem (TSP). The proposed method is based on a parallel implementation of a multipopulation steady-state GA involving local search heuristics. It uses a variant of the maximal preservative crossover and the double-bridge move mutation. An effective implementation of the Lin-Kernighan heuristic (LK) is incorporated into the method to compensate for the GA's lack of local search ability. The method is validated by comparing it with the LK-Helsgaun method (LKH), which is one of the most effective methods for the TSP. Experimental results with benchmarks having up to 316 228 cities show that the proposed method works more effectively and efficiently than LKH when solving large-scale problems. Finally, the method is used together with the implementation of the iterated LK to find a new best tour (as of June 2, 2003) for a 1 904 711-city TSP challenge

Implementation of an Effective Hybrid GA for Large-Scale Traveling Salesman Problems

This paper presents a parallel hybrid genetic algorithm (GA) for solving the sum-of-pairs multiple protein sequence alignment. A new chromosome representation and its corresponding genetic operators are proposed. A multi-population GENITOR-type GA is combined with local search heuristics. It is then extended to run in parallel on a multiprocessor system for speeding up. Experimental results of benchmarks from the BAliBASE show that the proposed method is superior to MSA, OMA, and SAGA methods with regard to quality of solution and running time. It can be used for finding multiple sequence alignment as well as testing cost functions.

Aligning multiple protein sequences by parallel hybrid genetic algorithm.

This paper presents a parallel hybrid genetic algorithm (GA) for solving sum-of-pairs multiple protein sequence alignment. The method is based on a multiple population GENITOR-type GA and involves local search heuristics. It is then extended to parallel to exploit the benefit of a multiprocessor system. Benchmarks from the BAliBASE library are used to validate the method.

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A parallel hybrid genetic algorithm for multiple protein sequence alignment

In this paper, we propose a new logic circuit design methodology for pattern recognition chips using the genetic algorithms. In the proposed design methodology, pattern data are transformed into the truth tables and the truth tables are generalized to adapt the unknown pattern data. The genetic algorithm is used to choose the generalization operators. The generalized, or evolved truth tables are then synthesized to logic circuits. Because of this data direct implementation approach, no floating point numerical circuits are required and the intrinsic parallelism in the data is embedded into the circuits. Consequently, high speed recognition systems can be realized with acceptable small circuit size. We have applied this methodology to the face image recognition and the sonar spectrum recognition tasks, and implemented them onto the developed FPGA-based reconfigurable pattern recognition board. The developed system demonstrates high recognition accuracy and much higher processing speed than the conventional approaches.

Genetic Algorithm-Based Methodology for Pattern Recognition Hardware

We propose a new logic circuit design methodology for kernel-based pattern recognition hardware using a genetic algorithm. In the proposed design methodology, pattern data are transformed into the truth tables and the truth tables are evolved to represent kernels in the discrimination functions for pattern recognition. The evolved truth tables are then synthesized to logic circuits. Because of this data direct implementation approach, no floating point numerical circuits are required and the intrinsic parallelism in the pattern data set is embedded into the circuits. Consequently, high speed recognition systems can be realized with acceptable small circuit size. We have applied this methodology to the image recognition and the sonar spectrum recognition tasks, and implemented them onto the newly developed FPGA-based reconfigurable pattern recognition board. The developed system demonstrates higher recognition accuracy and much faster processing speed than the conventional approaches.

Ikuo Yoshihara

Papers

Implementation of an Effective Hybrid GA for Large-Scale Traveling Salesman Problems

Aligning multiple protein sequences by parallel hybrid genetic algorithm.

A parallel hybrid genetic algorithm for multiple protein sequence alignment

Genetic Algorithm-Based Methodology for Pattern Recognition Hardware

Kernel-based pattern recognition hardware: its design methodology using evolved truth tables