Pipelined genetic propagation

© 2015 IEEE.Genetic Algorithms (GAs) are a class of numerical and combinatorial optimisers which are especially useful for solving complex non-linear and non-convex problems. However, the required execution time often limits their application to small-scale or latency-insensitive problems, so techniques to increase the computational efficiency of GAs are needed. FPGA-based acceleration has significant potential for speeding up genetic algorithms, but existing FPGA GAs are limited by the generational approaches inherited from software GAs. Many parts of the generational approach do not map well to hardware, such as the large shared population memory and intrinsic loop-carried dependency. To address this problem, this paper proposes a new hardware-oriented approach to GAs, called Pipelined Genetic Propagation (PGP), which is intrinsically distributed and pipelined. PGP represents a GA solver as a graph of loosely coupled genetic operators, which allows the solution to be scaled to the available resources, and also to dynamically change topology at run-time to explore different solution strategies. Experiments show that pipelined genetic propagation is effective in solving seven different applications. Our PGP design is 5 times faster than a recent FPGA-based GA system, and 90 times faster than a CPU-based GA system

Multidimensional Range Queries on Modern Hardware

Range queries over multidimensional data are an important part of database workloads in many applications. Their execution may be accelerated by using multidimensional index structures (MDIS), such as kd-trees or R-trees. As for most index structures, the usefulness of this approach depends on the selectivity of the queries, and common wisdom told that a simple scan beats MDIS for queries accessing more than 15%-20% of a dataset. However, this wisdom is largely based on evaluations that are almost two decades old, performed on data being held on disks, applying IO-optimized data structures, and using single-core systems. The question is whether this rule of thumb still holds when multidimensional range queries (MDRQ) are performed on modern architectures with large main memories holding all data, multi-core CPUs and data-parallel instruction sets. In this paper, we study the question whether and how much modern hardware influences the performance ratio between index structures and scans for MDRQ. To this end, we conservatively adapted three popular MDIS, namely the R*-tree, the kd-tree, and the VA-file, to exploit features of modern servers and compared their performance to different flavors of parallel scans using multiple (synthetic and real-world) analytical workloads over multiple (synthetic and real-world) datasets of varying size, dimensionality, and skew. We find that all approaches benefit considerably from using main memory and parallelization, yet to varying degrees. Our evaluation indicates that, on current machines, scanning should be favored over parallel versions of classical MDIS even for very selective queries

The detection of globular clusters in galaxies as a data mining problem

We present an application of self-adaptive supervised learning classifiers derived from the Machine Learning paradigm, to the identification of candidate Globular Clusters in deep, wide-field, single band HST images. Several methods provided by the DAME (Data Mining & Exploration) web application, were tested and compared on the NGC1399 HST data described in Paolillo 2011. The best results were obtained using a Multi Layer Perceptron with Quasi Newton learning rule which achieved a classification accuracy of 98.3%, with a completeness of 97.8% and 1.6% of contamination. An extensive set of experiments revealed that the use of accurate structural parameters (effective radius, central surface brightness) does improve the final result, but only by 5%. It is also shown that the method is capable to retrieve also extreme sources (for instance, very extended objects) which are missed by more traditional approaches.Comment: Accepted 2011 December 12; Received 2011 November 28; in original form 2011 October 1

Overview of Random Forest Methodology and Practical Guidance with Emphasis on Computational Biology and Bioinformatics

The Random Forest (RF) algorithm by Leo Breiman has become a standard data analysis tool in bioinformatics. It has shown excellent performance in settings where the number of variables is much larger than the number of observations, can cope with complex interaction structures as well as highly correlated variables and returns measures of variable importance. This paper synthesizes ten years of RF development with emphasis on applications to bioinformatics and computational biology. Special attention is given to practical aspects such as the selection of parameters, available RF implementations, and important pitfalls and biases of RF and its variable importance measures (VIMs). The paper surveys recent developments of the methodology relevant to bioinformatics as well as some representative examples of RF applications in this context and possible directions for future research

MESSM: a framework for protein threading by neural networks and support vector machines

Protein threading, which is also referred to as fold recognition, aligns a probe amino acid sequence onto a library of representative folds of known structure to identify a structural similarity. Following the threading technique of the structural profile approach, this research focused on developing and evaluating a new framework - Mixed Environment Specific Substitution Mapping (MESSM) - for protein threading by artificial neural networks (ANNs) and support vector machines (SVMs). The MESSM presents a new process to develop an efficient tool for protein fold recognition. It achieved better efficiency while retained the effectiveness on protein prediction. The MESSM has three key components, each of which is a step in the protein threading framework. First, building the fold profile library-given a protein structure with a residue level environmental description, Neural Networks are used to generate an environment-specific amino acid substitution (3D-1D) mapping. Second, mixed substitution mapping--a mixed environment-specific substitution mapping is developed by combing the structural-derived substitution score with sequence profile from well-developed amino acid substitution matrices. Third, confidence evaluation--a support vector machine is employed to measure the significance of the sequence-structure alignment. Four computational experiments are carried out to verify the performance of the MESSM. They are Fischer, ProSup, Lindahl and Wallner benchmarks. Tested on Fischer, Lindahl and Wallner benchmarks, MESSM achieved a comparable performance on fold recognition to those energy potential based threading models. For Fischer benchmark, MESSM correctly recognise 56 out of 68 pairs, which has the same performance as that of COBLATH and SPARKS. The computational experiments show that MESSM is a fast program. It could make an alignment between probe sequence (150 amino acids) and a profile of 4775 template proteins in 30 seconds on a PC with IG memory Pentium IV. Also, tested on ProSup benchmark, the MESSM achieved alignment accuracy of 59.7%, which is better than current models. The research work was extended to develop a threading score following the threading technique of the contact potential approach. A TES (Threading with Environment-specific Score) model is constructed by neural networks

Solar-Sailing Trajectory Design for Close-Up NEA Observations Mission

Near-Earth Asteroids (NEAs) are an extremely valuable resource to study the origin and evolution of the Solar System more in depth. At the same time, they constitute a serious risk for the Earth in the not-so-remote case of an impact. In order to mitigate the hazard of a potential impact with the Earth, several techniques have been studied so far and, for the majority of them, a good knowledge about the chemical and physical composition of the target object is extremely helpful for the success of the mission. A multiple-rendezvous mission with NEAs, with close-up observations, can help the scientific community to improve the overall knowledge about these objects and to support any mitigation strategy. Because of the cost of this kind of mission in terms of Dv, a solar sail spacecraft is proposed in this study, in order to take advantage of the propellantless characteristic of this system. As part of the DLR/ESA Gossamer roadmap, and thus considering the sailcraft based on this technology, the present work is focused on the search of possible sequences of encounters, with priority on Potentially Hazardous Asteroids (PHAs). Because of the huge amount of NEAs, the selection of the candidates for a multiple rendezvous is firstly a combinatorial problem, with more than a billion of possible sequences for only three consecutive encounters. Moreover, an optimization problem should be solved in order to find a feasible solar-sail trajectory for each leg of the sequence. In order to tackle this mixed combinatorial/optimization problem, the strategy used is divided into two main steps: a sequence search by means of heuristic rules and simplified trajectory models, and a subsequent optimization phase. Preliminary results were presented previously by the authors, demonstrating that this kind of mission is promising. In this paper, we aim to find new sequences by introducing a different approach on the sequence search algorithm and by reducing the area-to-mass ratio of the solar sail. A smaller area-to-mass ratio entails either the possibility to carry on more payload or to reduce the sail area, raising the TRL. A grid search over 10 years of launching dates is carried out, resulting in different sequences of objects depending on the departing date. Two sequences are fully studied and optimized. The mission parameters and trajectories of the sequences found are shown and explained

Protein Tertiary Model Assessment Using Granular Machine Learning Techniques

The automatic prediction of protein three dimensional structures from its amino acid sequence has become one of the most important and researched fields in bioinformatics. As models are not experimental structures determined with known accuracy but rather with prediction it’s vital to determine estimates of models quality. We attempt to solve this problem using machine learning techniques and information from both the sequence and structure of the protein. The goal is to generate a machine that understands structures from PDB and when given a new model, predicts whether it belongs to the same class as the PDB structures (correct or incorrect protein models). Different subsets of PDB (protein data bank) are considered for evaluating the prediction potential of the machine learning methods. Here we show two such machines, one using SVM (support vector machines) and another using fuzzy decision trees (FDT). First using a preliminary encoding style SVM could get around 70% in protein model quality assessment accuracy, and improved Fuzzy Decision Tree (IFDT) could reach above 80% accuracy. For the purpose of reducing computational overhead multiprocessor environment and basic feature selection method is used in machine learning algorithm using SVM. Next an enhanced scheme is introduced using new encoding style. In the new style, information like amino acid substitution matrix, polarity, secondary structure information and relative distance between alpha carbon atoms etc is collected through spatial traversing of the 3D structure to form training vectors. This guarantees that the properties of alpha carbon atoms that are close together in 3D space and thus interacting are used in vector formation. With the use of fuzzy decision tree, we obtained a training accuracy around 90%. There is significant improvement compared to previous encoding technique in prediction accuracy and execution time. This outcome motivates to continue to explore effective machine learning algorithms for accurate protein model quality assessment. Finally these machines are tested using CASP8 and CASP9 templates and compared with other CASP competitors, with promising results. We further discuss the importance of model quality assessment and other information from proteins that could be considered for the same

Performance and Optimization Abstractions for Large Scale Heterogeneous Systems in the Cactus/Chemora Framework

We describe a set of lower-level abstractions to improve performance on modern large scale heterogeneous systems. These provide portable access to system- and hardware-dependent features, automatically apply dynamic optimizations at run time, and target stencil-based codes used in finite differencing, finite volume, or block-structured adaptive mesh refinement codes. These abstractions include a novel data structure to manage refinement information for block-structured adaptive mesh refinement, an iterator mechanism to efficiently traverse multi-dimensional arrays in stencil-based codes, and a portable API and implementation for explicit SIMD vectorization. These abstractions can either be employed manually, or be targeted by automated code generation, or be used via support libraries by compilers during code generation. The implementations described below are available in the Cactus framework, and are used e.g. in the Einstein Toolkit for relativistic astrophysics simulations

A Survey on Compiler Autotuning using Machine Learning

Since the mid-1990s, researchers have been trying to use machine-learning based approaches to solve a number of different compiler optimization problems. These techniques primarily enhance the quality of the obtained results and, more importantly, make it feasible to tackle two main compiler optimization problems: optimization selection (choosing which optimizations to apply) and phase-ordering (choosing the order of applying optimizations). The compiler optimization space continues to grow due to the advancement of applications, increasing number of compiler optimizations, and new target architectures. Generic optimization passes in compilers cannot fully leverage newly introduced optimizations and, therefore, cannot keep up with the pace of increasing options. This survey summarizes and classifies the recent advances in using machine learning for the compiler optimization field, particularly on the two major problems of (1) selecting the best optimizations and (2) the phase-ordering of optimizations. The survey highlights the approaches taken so far, the obtained results, the fine-grain classification among different approaches and finally, the influential papers of the field.Comment: version 5.0 (updated on September 2018)- Preprint Version For our Accepted Journal @ ACM CSUR 2018 (42 pages) - This survey will be updated quarterly here (Send me your new published papers to be added in the subsequent version) History: Received November 2016; Revised August 2017; Revised February 2018; Accepted March 2018