3018061
Instruction Balance and Its Relation to Program Energy Consumption
A computer consists of multiple components such as functional units, cache and main memory. At each moment of execution, a program may have a varied amount of work for each component. Recent development has exploited this imbalance to save energy by slowing the components that have a lower load. Example techniques include dynamic scaling and clock gating used in processors from Transmeta and Intel. Symmetrical to reconfiguring hardware is reorganizing software. We can alter program demand for different components by reordering program instructions. This paper explores the theoretical lower bound of energy consumption assuming that both a program and a machine are fully adjustable. It shows that a program with a balanced load always consumes less energy than the same program with uneven loads under the same execution speed. In addition, the paper examines the relation between energy consumption and program performance. It shows that reducing power is a different problem than that of improving performance. Finally, the paper presents empirical evidence showing that a program may be transformed to have a balanced demand in most parts of its execution.
654543
A survey on wavelet applications in data mining
Recently there has been significant development in the use of wavelet methods in various data mining processes. However, there has been written no comprehensive survey available on the topic. The goal of this is paper to fill the void. First, the paper presents a high-level data-mining framework that reduces the overall process into smaller components. Then applications of wavelets for each component are reviewd. The paper concludes by discussing the impact of wavelets on data mining research and outlining potential future research directions and applications.
8121416
Biclustering Protein Complex Interactions with a Biclique Finding Algorithm
Biclustering has many applications in text mining, Web clickstream mining, and bioinformatics. When data entries are binary, the tightest biclusters become bicliques. We propose a flexible and highly efficient algorithm to compute bicliques. We first generalize the Motzkin-Straus formalism for computing the maximal clique from L1 constraint to Lp constraint, which enables us to provide a generalized Motzkin-Straus formalism for computing maximal-edge bicliques. By adjusting parameters, the algorithm can favor biclusters with more rows less columns, or vice verse, thus increasing the flexibility of the targeted biclusters. We then propose an algorithm to solve the generalized Motzkin-Straus optimization problem. The algorithm is provably convergent and has a computational complexity of O(/E/) where /E/ is the number of edges. Using this algorithm, we bicluster the yeast protein complex interaction network. We find that biclustering protein complexes at the protein level does not clearly reflect the functional linkage among protein complexes in many cases, while biclustering at protein domain level can reveal many underlying linkages. We show several new biologically significant results.
26202322
Searching the web using composed pages
Given a user keyword query, current Web search engines return a list of pages ranked by their “goodness” with respect to the query. However, this technique misses results whose contents are distributed across multiple physical pages and are connected via hyperlinks and frames [3]. That is, it is often the case that no single page contains all query keywords. Li et al. [3] make a first step towards this problem by returning a tree of hyperlinked pages that collectively contain all query keywords. The limitation of this approach is that it operates at the page-level granularity, which ignores the specific context where the keywords are found within the pages. More importantly, it is cumbersome for the user to locate the most desirable tree of pages due to the amount of data in each page tree and a large number of page trees.
15267641
Estimating Joint Probabilities from Marginal Ones
Estimating joint probabilities plays an important role in many data mining and machine learning tasks. In this paper we introduce two methods, minAB and prodAB, to estimate joint probabilities. Both methods are based on a light-weight structure, partition support. The core idea is to maintain the partition support of itemsets over logically disjoint partitions and then use it to estimate joint probabilities of item-sets of higher cardinalitiess. We present extensive mathematical analyses on both methods and compare their performances on synthetic datasets. We also demonstrate a case study of using the estimation methods in Apriori algorithm for fast association mining. Moreover, we explore the usefulness of the estimation methods in other mining/learning tasks. Experimental results show the effectiveness of the estimation methods.
217251
On combining multiple clusterings
Many problems can be reduced to the problem of combining multiple clusterings. In this paper, we first summarize different application scenarios of combining multiple clusterings and provide a new perspective of viewing the problem as a categorical clustering problem. We then show the connections between various consensus and clustering criteria and discuss the complexity results of the problem. Finally we propose a new method to determine the final clustering. Experiments on kinship terms and clustering popular music from heterogeneous feature sets show the effectiveness of combining multiple clusterings.
14562465
Bioinformatics on Embedded Systems: A Case Study of Computational Biology Applications on VLIW Architecture
Bioinformatics applications represent the increasingly important workloads. Their characteristics and implications on the underlying hardware design, however, are largely unknown. Currently, biological data processing ubiquitously relies on the high-end systems equipped with expensive, general-purpose processors. The future generation of bioinformatics requires the more flexible and cost-effective computing platforms to meet its rapidly growing market. The programmable, application-specific embedded systems appear to be an attractive solution in terms of easy of programming, design cost, power, portability and time-to-market. The first step towards such systems is to characterize bioinformatics applications on the target architecture. Such studies can help in understanding the design issues and the trade-offs in specializing hardware and software systems to meet the needs of bioinformatics market. This paper evaluates several representative bioinformatics tools on the VLIW based embedded systems. We investigate the basic characteristics of the benchmarks, impact of function units, the efficiency of VLIW execution, cache behavior and the impact of compiler optimizations. The architectural implications observed from this study can be applied to the design optimizations. To the best of our knowledge, this is one of the first such studies that have ever been attempted.
10443056
A large, fast instruction window for tolerating cache misses
Instruction window size is an important design parameter for many modern processors. Large instruction windows offer the potential advantage of exposing large amounts of instruction level parallelism. Unfortunately naively scaling conventional window designs can significantly degrade clock cycle time, undermining the benefits of increased parallelism.This paper presents a new instruction window design targeted at achieving the latency tolerance of large windows with the clock cycle time of small windows. The key observation is that instructions dependent on a long latency operation (e.g., cache miss) cannot execute until that source operation completes. These instructions are moved out of the conventional, small, issue queue to a much larger waiting instruction buffer (WIB). When the long latency operation completes, the instructions are reinserted into the issue queue. In this paper, we focus specifically on load cache misses and their dependent instructions. Simulations reveal that, for an 8-way processor, a 2K-entry WIB with a 32-entry issue queue can achieve speedups of 20%, 84%, and 50% over a conventional 32-entry issue queue for a subset of the SPEC CINT2000, SPEC CFP2000, and Olden benchmarks, respectively.
3381503
Finite-alphabet information and multivariate blind deconvolution and identification of linear systems
This article addresses the problem of estimating a multivariate linear system from its output when the input is an unobservable sequence of random vectors with finite-alphabet distribution. By explicitly utilizing the finite-alphabet property, an estimation method is proposed under the traditional inverse filtering paradigm as a generalization of a univariate method that has been studied previously. Identifiability of multivariate systems by the proposed method is proved mathematically under very mild conditions that can be satisfied even if the input is nonstationary and has both cross-channel and serial statistical dependencies. Statistical super-efficiency in estimating both parametric and nonparametric systems is also established for an alphabet-based cost function.
6096323
Quantifying instruction criticality for shared memory multiprocessors
Recent research on processor microarchitecture suggests using instruction criticality as a metric to guide hardware control policies. Fields et al. [3, 4] have proposed a directed acyclic graph (DAG) model for characterizing program microexecutions on uniprocessors. Under such a model, critical path analysis can be applied and instructions' slack values can be used to quantify instruction criticality. In this paper, we extend the uniprocessor DAG model to characterize parallel program executions on shared memory multiprocessor systems. We describe how critical path analysis can be applied, at a fine grain, in a multiprocessor system running both finite and continuous workloads. We provide detailed evaluations for various aspects of multiprocessor executions under the DAG model. To enable efficient offline critical path analysis, we propose a novel graph reduction technique that reduces a DAG to an equivalent but significantly smaller DAG.
200438
Nanoparticle-enhanced proton computed tomography: a Monte Carlo simulation study
Proton computed tomography (pCT) has the potential to improve the accuracy of proton treatment planning, which is currently based on X-ray computed tomography (XCT). However, at this time no method exists for pCT to selectively increase the contrast of tumor tissues with respect to normal tissues. One possibility to achieve this goal is to bind gold-nanoparticles, i.e., microscopic structures in the size range of 1 nm to several hundred nanometers, to the surface of tumor cells with cell-seeking antibodies conjugated to the surface of the nanoparticles. In order to test the suitability of this approach, we used the Monte Carlo transport code GEANT4, to provide simulated histories of 200 MeV protons going through a cylindrical water phantom with embedded inhomogeneities enhanced with traces of gold. The energy loss of several million protons traversing the cylinder from 180 different angles formed the basis for reconstructing the single proton CT image representing the relative volume electron density map of the phantom using an approximate filtered back projection algorithm. Our results demonstrate that with hundred nanoparticles of 100 nm diameters per tumor cell, it may be possible to enhance the visibility of tumors in pCT.