2412225
Dynamic Voltage Scaling for Multitasking Real-Time Systems With Uncertain Execution Time
Dynamic voltage and frequency scaling can save energy for real-time systems. Frequencies are generally assumed proportional to voltages. Previous studies consider the probabilistic distributions of tasks' execution time to assist dynamic voltage scaling in task scheduling. These studies use probability information for intratask voltage scheduling but do not sufficiently explore the opportunities for intertask scheduling to save more energy. This paper presents a new approach to combine intra- and intertask voltage scheduling for better energy savings in hard real-time systems with uncertain task execution time. Our approach takes three steps: 1) We calculate statistically the optimal voltage schedules for multiple concurrent tasks, using earliest deadline first scheduling for an ideal processor that can change the frequency continuously; 2) we then adapt the solution to a processor with a limited range of discrete frequencies, using a polynomial-time heuristic algorithm; and 3) finally, we improve our solution, considering the time and energy overheads of frequency switching for schedulability and energy reduction. Our simulation shows that the new approach can save more energy than existing solutions while meeting hard deadlines.
2733921
Joint power management of memory and disk
The paper presents a scheme to combine memory and power management for achieving better energy reduction. Our method periodically adjusts the size of physical memory and the timeout value to shut down a hard disk for reducing the average power consumption. We use Pareto distributions to model the distributions of idle time. The parameters of the distributions are adjusted at run-time for calculating the corresponding timeout value of the disk power management. The memory size is changed based on the inclusion property to predict the number of disk accesses at different memory sizes. Experimental results show more than 50% energy savings compared to a 2-competitive fixed-timeout method.
14287933
Statistically optimal dynamic power management for streaming data
This paper presents a method that uses data buffers to create long periods of idleness to exploit power management. This method considers the power consumed by the buffers and assigns an energy penalty for buffer underflow. Our approach provides analytic formulas for calculating the optimal buffer sizes without subjective or heuristic decisions. We simulate four different hardware configurations with MPEG-1, MPEG-2, and MPEG-4 formats as a case study. Our results indicate that the optimal buffer size varies significantly for different data formats on different hardware. Simulation results indicate that 16 MB buffers are sufficient for MPEG-1, MPEG-2, and MPEG-4 video streams from a microdrive or a network card, but transfers from an IDE disk require buffer sizes ranging from 16 MB to 176 MB, depending on each video's statistical properties.
161273
Dynamic power management for streaming data
This paper presents a method that uses data buffers to smoothen request variations and to create long idleness for power management. This method considers the power consumed by the buffers and assigns an energy penalty for buffer underflow. Our approach provides analytic formulas for calculating the optimal buffer sizes and the amount of data to store in the buffers. We use video prefetching as a case study and obtain power savings of more than 74% for MPEG-1 and 34% for MPEG-2 videos.
9215156
Energy management using buffer memory for streaming data
This work presents a new approach for energy management by inserting data buffers. The buffers are managed using the concept of inventory control by treating energy as cost and computation as production. The data stored in the buffers are considered as merchandise. Our method provides a mathematical framework to develop general strategies managing the energy consumption in computers. The approach can solve a wide range of problems. For example, it can calculate the needed buffer sizes to achieve optimal energy savings. It can derive the conditions when a standby state saves energy. The method also shows the effect of load balancing on energy conservation and can handle the variations of data rates. We use sensor networks as case studies and demonstrate more than 20% energy savings.
15594355
Replacing Failed Sensor Nodes by Mobile Robots
Sensor replacement is important for sensor networks to provide continuous sensing services. Existing approaches relocate redundant nodes to fill the holes created by failed sensors and require all or most sensor nodes to have mobility. However, mobility equipment is expensive while technology trends are scaling sensors to be smaller and cheaper. In this paper, we propose to use a small number of mobile robots to replace failed sensors in a large-scale static sensor network. We study algorithms for detecting and reporting sensor failures and coordinating the movement of robots that minimize the motion energy of mobile robots and the messaging overhead incurred to the sensor network. A manager receives failure reports and determines which robot to handle a failure. We study three algorithms: a centralized manager algorithm, a fixed distributed manager algorithm, and a dynamic distributed manager algorithm. Our simulations show that: (a) The centralized and the dynamic distributed algorithms have lower motion overhead than the fixed distributed algorithm. (b) The centralized algorithm is less scalable than the two distributed manager algorithms. (c) The two distributed algorithms have higher messaging cost than the centralized algorithm. Hence, the optimal choice of the coordination algorithm depends on the specific scenarios and objectives being optimized.
8110517
FGKA: a Fast Genetic K-means Clustering Algorithm
In this paper, we propose a new clustering algorithm called Fast Genetic K-means Algorithm (FGKA). FGKA is inspired by the Genetic K-means Algorithm (GKA) proposed by Krishna and Murty in 1999 but features several improvements over GKA. Our experiments indicate that, while K-means algorithm might converge to a local optimum, both FGKA and GKA always converge to the global optimum eventually but FGKA runs much faster than GKA.
1552056
Pama: a Fast String Matching Algorithm
String matching is a fundamental operation in computer science, and its performance has great impact on many applications including database query, text processing, DNA and protein sequence analysis. In this paper, we propose a fast string matching algorithm, PAMA (PAttern MAtching). The shift rule used by PAMA not only subsumes both the bad character rule and the good suffix rule employed by the well-known Boyer-Moore algorithm, but also employs an additional key observation to enable faster shifting during the string matching process. Theoretically, we prove that from the same alignment, the next shift of PAMA will be at least as much as that of the Boyer-Moore algorithm. Experimentally, we show that PAMA indeed significantly outperforms the original Boyer-Moore algorithm in almost all cases, and outperforms other Boyer-Moore variants such as Tuned-BM, Turbo-BM and Horspool for long patterns (length ≥ 128) or for small alphabets (size < 8).
7907707
Fast search in DNA sequence databases using punctuation and indexing
Exact pattern searching in DNA sequence databases has applications in identification of highly conserved regulatory sequences, the design of hybridization probes, and improving performance of approximate homology searching tools such as BLAST and BLAT. We propose a new pattern searching algorithm, Compressed-Punctuated-Boyer-Moore (cp-BM), to enhance exact pattern match searches of DNA sequences. cp-BM encodes two bits to represent each A, T, C, G character (4-character 8 bit (4C8B) compression), plus punctuator characters to indicate unambiguously the encoding frame of the compressed target sequence, thereby solving the misalignment problem in searching patterns with ordinary 4C8B compression. cp-BM searches DNA patterns at least 6 times faster than AGREP for pattern lengths ≥ 128 and between 2-fold and 5-fold faster than d-BM for all pattern lengths. cp-BM's performance is enhanced by punctuator indexing and multiple punctuators, especially for short sequences, yielding greater than 10-fold enhancements compared to d-BM and AGREP. In addition, cp-BM outperformed BLAT for sequences 64 or more bases in length, and was more than three-fold faster for 256 base sequences.
7735246
Identifying cycling genes by combining sequence homology and expression data
MOTIVATION
The expression of genes during the cell division process has now been studied in many different species. An important goal of these studies is to identify the set of cycling genes. To date, this was done independently for each of the species studied. Due to noise and other data analysis problems, accurately deriving a set of cycling genes from expression data is a hard problem. This is especially true for some of the multicellular organisms, including humans.


RESULTS
Here we present the first algorithm that combines microarray expression data from multiple species for identifying cycling genes. Our algorithm represents genes from multiple species as nodes in a graph. Edges between genes represent sequence similarity. Starting with the measured expression values for each species we use Belief Propagation to determine a posterior score for genes. This posterior is used to determine a new set of cycling genes for each species. We applied our algorithm to improve the identification of the set of cell cycle genes in budding yeast and humans. As we show, by incorporating sequence similarity information we were able to obtain a more accurate set of genes compared to methods that rely on expression data alone. Our method was especially successful for the human dataset indicating that it can use a high quality dataset from one species to overcome noise problems in another.


AVAILABILITY
C implementation is available from the supporting website: http://www.cs.cmu.edu/~lyongu/pub/cellcycle/.
27140699
Differential Algebraic Method for Aberration Analysis of Electron Optical Systems
Differential algebraic method is a powerful technique in computer numerical analysis. It presents a straightforward method for computing arbitrary order derivatives of functions with extreme high accuracy limited only by the machine error. When applied to nonlinear dynamics systems, the arbitrary high order transfer properties of the system can be derived directly. In this paper, the principle of differential algebraic method is applied to calculate high order aberrations of electron optical systems. As an example, an electrostatic lens with an analytical expression has been calculated using this method. Relative errors of the Gaussian properties and spherical aberration coefficient of the lens compared with the analytic solutions are of the order 10− 11 or smaller. It is proved that differential algebraic aberration method is very helpful with high accuracy for high order aberration analysis and computation of electron optical systems.