Combined hardware–software multi-parallel prefiltering on the Convey HC-1 for fast homology detection

Protein databases used in research are huge and still grow at a fast pace. Many comparisons need to be done when searching similar (homologous) sequences for a given query sequence in these databases. Comparing a query sequence against all sequences of a huge database using the well-known Smith–Waterman algorithm is very time-consuming. Hidden Markov Models pose an opportunity for reducing the number of entries of a database and also enable to find distantly homologous sequences. Fewer entries are achieved by clustering similar sequences in a Hidden Markov Model. Such an approach is used by the bioinformatics tool HHblits. To further reduce the runtime, HHblits uses two-level prefiltering to reduce the number of time-consuming Viterbi comparisons. Still, prefiltering is very time-consuming. Highly parallel architectures and huge bandwidth are required for processing and transferring the massive amounts of data. In this article, we present an approach exploiting the reconfigurable, hybrid computer architecture Convey HC-1 for migrating the most time-consuming part. The Convey HC-1 with four FPGAs and high memory bandwidth of up to 76.8 GB/s serves as the platform of choice. Other bioinformatics applications have already been successfully supported by the HC-1. Limited by FPGA size only, we present a design that calculates four first-level prefiltering scores per FPGA concurrently, i.e. 16 calculations in total. This score calculation for the query profile against database sequences is done by a modified Smith–Waterman scheme that is internally parallelized 128 times in contrast to the original Streaming ‘Single Instruction Multiple Data (SIMD)’ Extensions (SSE)-supported implementation where only 16-fold parallelism can be exploited and where memory bandwidth poses the limiting factor. Preloading the query profile, we are able to transform the memory-bound implementation to a compute- and resource-bound FPGA design. We tightly integrated the FPGA-based coprocessor into the hybrid computing system by employing task-parallelism for the two-level prefiltering. Despite much lower clock rates, the FPGAs outperform SSE-based execution for the calculation of the prefiltering scores by a factor of 7.9.     

高温氢工质热物理性质计算分析

氢工质在新能源与动力、航天推进、化工材料等领域有着广泛应用。通过开展高温氢工质热力学与输运性质研究，建立了原子态氢、分子态氢、热解平衡态氢的热物理性质计算模型，开发了热物性计算程序Prop_H_H2，适用范围为温度100~3 500 K、压力104~5×107 Pa 。验证表明，Prop_H_H2在适用范围内计算氢工质的物性参数合理可靠，在温度200~3 000 K、压力104~107 Pa范围内，程序预测值更加准确，相对偏差在±5%左右。本研究可为氢工质相关的航天推进、应用物理学、能源动力等行业的科研和应用提供支持借鉴。     

Simplified anode architecture for PEMFC systems based on alternative fuel feeding: Experimental characterization and optimization for automotive applications

The need to reduce PEMFC systems cost as well as to increase their durability is crucial for their integration in various applications and especially for transport applications. A new simplified architecture of the anode circuit called Alternating Fuel Feeding (AFF) offers to reduce the development costs. Requiring a new stack concept, it combines the simplicity of Dead-End Anode (DEA) with the operation advantages of the hydrogen recirculation. The three architectures (DEA, recirculation and AFF) are compared in terms of performance on a 5-kW test bench in automotive conditions, through a sensitivity analysis. A gain of 17% on the system efficiency is observed when switching from DEA to AFF. Moreover, similar performances are obtained both for AFF and for recirculation after an accurate optimization of the AFF tuning parameters. Based on DoE data, a gain of 25% on the weight of the anodic line has been identified compared to pulsed ejector architecture and 43% with the classic recirculation architecture with blower only (Miraï).     

Parallel chaos optimization algorithm with migration and merging operation

Chaos optimization algorithm (COA) utilizes the chaotic maps to generate the pseudo-random sequences mapped as the decision variables for global optimization applications. A kind of parallel chaos optimization algorithm (PCOA) has been proposed in our former studies to improve COA. The salient feature of PCOA lies in its pseudo-parallel mechanism. However, all individuals in the PCOA search independently without utilizing the fitness and diversity information of the population. In view of the limitation of PCOA, a novel PCOA with migration and merging operation (denoted as MMO-PCOA) is proposed in this paper. Specifically, parallel individuals are randomly selected to be conducted migration and merging operation with the so far parallel solutions. Both migration and merging operation exchange information within population and produce new candidate individuals, which are different from those generated by stochastic chaotic sequences. Consequently, a good balance between exploration and exploitation can be achieved in the MMO-PCOA. The impacts of different one-dimensional maps and parallel numbers on the MMO-PCOA are also discussed. Benchmark functions and parameter identification problems are used to test the performance of the MMO-PCOA. Simulation results, compared with other optimization algorithms, show the superiority of the proposed MMO-PCOA algorithm.     

Weighted Superposition Attraction (WSA): A swarm intelligence algorithm for optimization problems – Part 2: Constrained optimization

This paper is the second one of the two papers entitled “Weighted Superposition Attraction (WSA) Algorithm”, which is about the performance evaluation of the WSA algorithm in solving the constrained global optimization problems. For this purpose, the well-known mechanical design optimization problems, design of a tension/compression coil spring, design of a pressure vessel, design of a welded beam and design of a speed reducer, are selected as test problems. Since all these problems were formulated as constrained global optimization problems, WSA algorithm requires a constraint handling method for tackling them. For this purpose we have selected 6 formerly developed constraint handling methods for adapting into WSA algorithm and analyze the effect of the used constraint handling method on the performance of the WSA algorithm. In other words, we have the aim of producing concluding remarks over the performance and robustness of the WSA algorithm through a set of computational study in solving the constrained global optimization problems. Computational study indicates the robustness and the effectiveness of the WSA in terms of obtained results, reached level of convergence and the capability of coping with the problems of premature convergence, trapping in a local optima and stagnation.     

An unsupervised approach to generating generic summaries of documents

We present an optimization-based unsupervised approach to automatic document summarization. In the proposed approach, text summarization is modeled as a Boolean programming problem. This model generally attempts to optimize three properties, namely, (1) relevance: summary should contain informative textual units that are relevant to the user; (2) redundancy: summaries should not contain multiple textual units that convey the same information; and (3) length: summary is bounded in length. The approach proposed in this paper is applicable to both tasks: single- and multi-document summarization. In both tasks, documents are split into sentences in preprocessing. We select some salient sentences from document(s) to generate a summary. Finally, the summary is generated by threading all the selected sentences in the order that they appear in the original document(s). We implemented our model on multi-document summarization task. When comparing our methods to several existing summarization methods on an open DUC2005 and DUC2007 data sets, we found that our method improves the summarization results significantly. This is because, first, when extracting summary sentences, this method not only focuses on the relevance scores of sentences to the whole sentence collection, but also the topic representative of sentences. Second, when generating a summary, this method also deals with the problem of repetition of information. The methods were evaluated using ROUGE-1, ROUGE-2 and ROUGE-SU4 metrics. In this paper, we also demonstrate that the summarization result depends on the similarity measure. Results of the experiment showed that combination of symmetric and asymmetric similarity measures yields better result than their use separately.     

Systematic packaging design tools integrating functional and environmental consequences on product life cycle: Case studies on laundry detergent and milk

This study presents systematic packaging design tools integrating functional and environmental consequences on product life cycle. To design packaging for sustainability, the trade-offs between functional and environmental aspects of packaging throughout the product life cycle should be considered. However, it is difficult for packaging designers to understand the overall trade-offs because the extent of the design consequences on the entire life cycle of packaging and its contents is unclear. We developed two tools for packaging design: the Life Cycle Association Matrix (LCAM) and the Function Network Diagram (FND). The following three steps, based on literature reviews and interviews with industrial experts, were applied. Firstly, we listed the product functions and design variables related to the functions as the attributes allocated to the product life cycle. Secondly, the attributes were connected appropriately based on causal relationships. Lastly, we identified the factors to support decision making in the packaging design procedure. As a result, the LCAM depicts the design consequences on the life cycle, and the FND determines the stakeholders affected by the design consequences. Two case studies were demonstrated to analyze the trade-offs by using our tools. In the case studies, a liquid laundry detergent bottle and a milk carton were redesigned. The tools identified the design consequences and stakeholders affected by the redesign of the usability and protective function for the detergent and milk cases, respectively. The results showed the significance of understanding the design consequences on the product life cycle by integrating the functional and environmental aspects.     

Sensor network design based on system-wide reliability criteria. Part I: Objectives

Reliability based criteria are quite popular for optimal sensor network design. We present a modified definition of system reliability for sensor network design for two applications: reliable estimation of variables in a steady state linear flow process, and reliable fault detection and diagnosis for any process. Unlike the weakest-link based definition of system reliability in the literature, the proposed definition considers the entire system and is consistent with the reliability concept used in classical reliability literature. For each application, dual approaches for defining system reliability are proposed, and their analogy with the reliability problem in the classical reliability literature is established. Using examples and stochastic simulations, the advantage of using the proposed system reliability in contrast to the existing definition is illustrated. Part II of this series of articles presents methods for efficient generation of the system reliability function and its use in optimization-based approaches for designing optimal sensor networks.     

Fault handling in large water networks with online dictionary learning

Fault detection and isolation in water distribution networks is an active topic due to the nonlinearities of flow propagation and recent increases in data availability due to sensor deployment. Here, we propose an efficient two-step data driven alternative: first, we perform sensor placement taking the network topology into account; second, we use incoming sensor data to build a network model through online dictionary learning. Online learning is fast and allows tackling large networks as it processes small batches of signals at a time. This brings the benefit of continuous integration of new data into the existing network model, either in the beginning for training or in production when new data samples are gathered. The proposed algorithms show good performance in our simulations on both small and large-scale networks.