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Data analytics is at the foundation of both high-quality products and services in modern economies and societies. Big data workloads run on complex large-scale computing clusters, which implies significant challenges for deeply understanding and characterizing overall system performance. In general, performance is affected by many factors at multiple layers in the system stack, hence it is challenging to identify the key metrics when understanding big data workload performance. In this paper, we propose a novel workload characterization methodology using ensemble learning, called Metric Importance Analysis (MIA), to quantify the respective importance of workload metrics. By focusing on the most important metrics, MIA reduces the complexity of the analysis without losing information. Moreover, we develop the MIA-based Kiviat Plot (MKP) and Benchmark Similarity Matrix (BSM) which provide more insightful information than the traditional linkage clustering based dendrogram to visualize program behavior (dis)similarity. To demonstrate the applicability of MIA, we use it to characterize three big data benchmark suites: HiBench, CloudRank-D and SZTS. The results show that MIA is able to characterize complex big data workloads in a simple, intuitive manner, and reveal interesting insights. Moreover, through a case study, we demonstrate that tuning the configuration parameters related to the important metrics found by MIA results in higher performance improvements than through tuning the parameters related to the less important ones.

In-Memory cluster Computing (IMC) frameworks (e.g., Spark) have become increasingly important because they typically achieve more than 10× speedups over the traditional On-Disk cluster Computing (ODC) frameworks for iterative and interactive applications. Like ODC, IMC frameworks typically run the same given programs repeatedly on a given cluster with similar input dataset size each time. It is challenging to build performance model for IMC program because: 1) the performance of IMC programs is more sensitive to the size of input dataset, which is known to be difficult to be incorporated into a performance model due to its complex effects on performance; 2) the number of performance-critical configuration parameters in IMC is much larger than ODC (more than 40 vs. around 10), the high dimensionality requires more sophisticated models to achieve high accuracy. To address this challenge, we propose DAC, a datasize-aware auto-tuning approach to efficiently identify the high dimensional configuration for a given IMC program to achieve optimal performance on a given cluster. DAC is a significant advance over the state-of-the-art because it can take the size of input dataset and 41 configuration parameters as the parameters of the performance model for a given IMC program, --- unprecedented in previous work. It is made possible by two key techniques: 1) Hierarchical Modeling (HM), which combines a number of individual sub-models in a hierarchical manner; 2) Genetic Algorithm (GA) is employed to search the optimal configuration. To evaluate DAC, we use six typical Spark programs, each with five different input dataset sizes. The evaluation results show that DAC improves the performance of six typical Spark programs, each with five different input dataset sizes compared to default configurations by a factor of 30.4x on average and up to 89x. We also report that the geometric mean speedups of DAC over configurations by default, expert, and RFHOC are 15.4x, 2.3x, and 1.5x, respectively.

Sequence-based residue contact prediction plays a crucial role in protein structure reconstruction. In recent years, the combination of evolutionary coupling analysis (ECA) and deep learning (DL) techniques has made tremendous progress for residue contact prediction, thus a comprehensive assessment of current methods based on a large-scale benchmark data set is very needed. In this study, we evaluate 18 contact predictors on 610 non-redundant proteins and 32 CASP13 targets according to a wide range of perspectives. The results show that different methods have different application scenarios: (1) DL methods based on multi-categories of inputs and large training sets are the best choices for low-contact-density proteins such as the intrinsically disordered ones and proteins with shallow multi-sequence alignments (MSAs). (2) With at least 5L (L is sequence length) effective sequences in the MSA, all the methods show the best performance, and methods that rely only on MSA as input can reach comparable achievements as methods that adopt multi-source inputs. (3) For top L/5 and L/2 predictions, DL methods can predict more hydrophobic interactions while ECA methods predict more salt bridges and disulfide bonds. (4) ECA methods can detect more secondary structure interactions, while DL methods can accurately excavate more contact patterns and prune isolated false positives. In general, multi-input DL methods with large training sets dominate current approaches with the best overall performance. Despite the great success of current DL methods must be stated the fact that there is still much room left for further improvement: (1) With shallow MSAs, the performance will be greatly affected. (2) Current methods show lower precisions for inter-domain compared with intra-domain contact predictions, as well as very high imbalances in precisions between intra-domains. (3) Strong prediction similarities between DL methods indicating more feature types and diversified models need to be developed. (4) The runtime of most methods can be further optimized., Author summary The amino acid sequence of a protein ultimately determines its tertiary structure, and the tertiary structure determines its function(s) and plays a key role in understanding biological processes and disease pathogenesis. Protein tertiary structure can be determined using experimental techniques such as cryo-electron microscopy, nuclear magnetic resonance and X-ray crystallography, which are very expensive and time-consuming. As an alternative, researchers are trying to use in silico methods to predict the 3D structures. Residue contact-assisted protein folding paves an avenue for sequence-based protein structure prediction and therefore has become one of the most challenging and promising problems in structural bioinformatics. Over the past years, contact prediction has undergone continuous evolution in techniques. Through a retrospective analysis of traditional machine learning /evolutionary coupling analysis methods/ consensus machine learning methods and a multi-perspective study on recently developed deep learning methods, we explore the most advanced contact predictors, pursue application scenarios for different methods, and seek prospective directions for further improvement. We anticipate that our study will serve as a practical and useful guide for the development of future approaches to contact prediction.

Hadoop is the most popular implementation framework of the MapReduce programming model, and it has a number of performance-critical configuration parameters. However, manually setting these parameters to their optimal values not only needs in-depth knowledge on Hadoop as well as the job itself, but also requires a large amount of time and efforts. Automatic approaches have therefore been proposed. Their usage, however, is still quite limited due to the intolerably long searching time. In this paper, we introduce MapreducE Self-Tuning (MEST), a framework that accelerates the searching process for the optimal configuration of a given Hadoop application. We have devised a novel mechanism by integrating the model trees algorithm with the genetic algorithm. As such, MEST significantly reduces the searching time by removing unnecessary profiling, modeling, and searching steps, which are mandatory for existing approaches. Our experiments using five benchmarks, each with two input data sets ( $DS1$ and $2\times DS1$ ) show that MEST improves the searching efficiency (SE) by factors of $1.37\times $ and $2.18\times $ on average respectively over the state-of-the-art approach.

At present, Spark is widely used in a number of enterprises. Although Spark is much faster than Hadoop for some applications, its configuration parameters can have a great impact on its performance due to the large number of the parameters, interaction between them, and various characteristics of applications as well. Unfortunately, there is not yet any research conducted to predict the performance of Spark based on its configuration sets.In this paper, we employ a machine learning method-Support Vector Machine(SVM) to build performance models for Spark. The input of configuration sets is collected by running Spark application previously with randomly modified and combined parameter values. In this way, we also determine the range of each property and gain a deeper understanding about how these properties work in Spark. We also use Artificial Neural Network to model the performance of Spark and find that the error rate of ANN is on average 1.98 times that of SVM for three workloads from HiBench.

Recently, big data has been evolved into a buzzword from academia to industry all over the world. Benchmarks are important tools for evaluating an IT system. However, benchmarking big data systems is much more challenging than ever before. First, big data systems are still in their infant stage and consequently they are not well understood. Second, big data systems are more complicated compared to previous systems such as a single node computing platform. While some researchers started to design benchmarks for big data systems, they do not consider the redundancy between their benchmarks. Moreover, they use artificial input data sets rather than real world data for their benchmarks. It is therefore unclear whether these benchmarks can be used to precisely evaluate the performance of big data systems. In this paper, we first analyze the redundancy among benchmarks from ICTBench, HiBench and typical workloads from real world applications: spatio-temporal data analysis for Shenzhen transportation system. Subsequently, we present an initial idea of a big data benchmark suite for spatio-temporal data. There are three findings in this work: (1) redundancy exists in these pioneering benchmark suites and some of them can be removed safely. (2) The workload behavior of trajectory data analysis applications is dramatically affected by their input data sets. (3) The benchmarks created for academic research cannot represent the cases of real world applications.

In this paper we address the problem of automated visual hull computation. This problem is important for various tasks from three dimensional object modeling to markerless motion capture. Different from classical visual hull method that are based on volume or surface, we compute the visual hull through operations on line segments. General intersection and surface reconstruction operations on line segments are proposed together with efficient algorithms. Experimental results demonstrate that the proposed approach can generate a robust and reliable visual hull.