1882756
Automatic Run-Time Selection of Power Policies for Operating Systems
A significant volume of research has concentrated on operating-system directed power management (OSPM). The primary focus of previous research has been the development of OSPM policies. Under different conditions, one policy may outperform another and vice versa. In this paper, we explain how to select the best policies at run-time without user or administrator intervention. We present a hardware-neutral architecture portable across different platforms running Linux. Our experiments reveal that changing policies at run-time can adapt to workloads more quickly than using any of the policies individually
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.
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.
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.
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.
18145477
Wyner-Ziv Video Coding Based on Set Partitioning in Hierarchical Tree
In this paper, we propose a Wyner-Ziv video coding scheme based on set-partitioning in hierarchical trees (SPIHT) which can utilizing not only the spatial and temporal correlations but also the high-order statistical correlations. Wyner-Ziv theory on source coding with side information is employed as the basic coding principle, which makes the independent encoding and joint decoding become possible. In the proposed scheme, wavelet transform is first used to de-correlate the spatial dependency of a Wyner-Ziv frame. Then the quantized transform coefficients are organized by using magnitude with a set partitioning sorting algorithm. The ordered bit planes are coded using the Wyner-Ziv coding based on turbo codes. At the decoder, side information generated by motion compensated interpolation is used to conditionally decode the Wyner-Ziv frame. Since the high order statistical correlation is used, the proposed algorithm owns advantages over the traditional pixel-domain and transform-domain Wyner-ziv video coding schemes.
11276211
PDC: Pattern discovery with confidence in DNA sequences
Pattern discovery in DNA sequences is one of the most challenging tasks in molecular biology and computer science. The main goal of pattern discovery in DNA sequences is to identify sequences of important biological function hidden in the huge amounts of genomic sequences. Several methods and techniques have been proposed and implemented in this field. However, in order to reduce computational time and complexity, most of them either focus on finding short DNA patterns or require explicit specification of pattern lengths in advance. Scientists need to find longer patterns without specifying pattern lengths in advance and still have good performance.In this paper, we propose a pattern discovery algorithm called Pattern Discovery with Confidence (PDC). Based on biological studies, we propose a new measurement system that can identify overrepresented patterns inside DNA sequences. Using this measurement, PDC algorithm can narrow the search space by checking dependency along the pattern, thus extending the pattern as long as possible without the need to restrict or specify the length of a pattern in advance. Experimental tests demonstrate that this approach can find long, interesting patterns within a reasonable computation time.
7665820
Equivalence checking using abstract BDDs
We introduce a new equivalence checking method based on abstract BDDs (aBDDs). The basic idea is the following: given an abstraction function, aBDDs reduce the size of BDDs by merging nodes that have the same abstract value. An aBDD has bounded size and can be constructed without constructing the original BDD. We show that this method of equivalence checking is always sound. It is complete for an important class of arithmetic circuits that includes integer multiplication. We also suggest heuristics for findings suitable abstraction functions based on the structure of the circuit. The efficiency of this technique is illustrated by experiments on ISCAS'85 benchmark circuits.
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/.
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).