16579446
Mining Correlation between Motifs and Gene Expression
One of the major challenges in the post-genomic era is to determine all DNA-binding transcription factors (TFs) and their regulatory binding sites (motifs) within the genomes. To discover the relationship between the motifs and changes in gene expression, we propose a new algorithm, co-miner (correlation miner). Correlation rules are generated based on the expression profiles of genes with significant expression change through the time course of gene expression. Thus, we may consider the change in gene expression to be causatively associated with the transcription binding sites in the upstream sequences. In addition, we introduce partition and constraint pushing techniques to improve the performance and demonstrate their effectiveness by our experiments. By applying co-miner to a yeast dataset, the relationships between motifs and gene expression revealed by co-miner are confirmed in the literature.
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.
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).
18404090
Dynamic frequency scaling with buffer insertion for mixed workloads
This paper presents a method to reduce the energy of interactive systems for mixed workloads: multimedia applications that require constant output rates and sporadic jobs that need prompt responses. The authors' method divides multimedia programs into stages and inserts data buffers between them. Data buffering has three purposes: (1) to support constant output rates; (2) to allow frequency scaling for energy reduction; and (3) to shorten the response times of sporadic jobs. The authors construct frequency-assignment graphs. Each vertex represents the current state of the buffers and the frequencies of the processor. The authors develop an efficient graph-walk algorithm that assigns frequencies to reduce energy. The same method. can be applied to perform voltage scaling and the combination of frequency and voltage scaling. The authors' experimental results on a Strong-ARM-based computer show that four discrete frequencies are sufficient to achieve nearly maximum energy saving. The method reduces the power consumption of an MPEG program by 46%. The authors also demonstrate a case that shortens the response time of a sporadic job by 55%.
7818893
Performance Benefits of Monolithically Stacked 3-D FPGA
The performance benefits of a monolithically stacked three-dimensional (3-D) field-programmable gate array (FPGA), whereby the programming overhead of an FPGA is stacked on top of a standard CMOS layer containing logic blocks (LBs) and interconnects, are investigated. A Virtex-II-style two-dimensional (2-D) FPGA fabric is used as a baseline architecture to quantify the relative improvements in logic density, delay, and power consumption achieved by such a 3-D FPGA. It is assumed that only the switch transistor and configuration memory cells can be moved to the top layers and that the 3-D FPGA employs the same LB and programmable interconnect architecture as the baseline 2-D FPGA. Assuming they are les 0.7, the area of a static random-access memory cell and switch transistors having the same characteristics as n-channel metal-oxide-semiconductor devices in the CMOS layer are used. It is shown that a monolithically stacked 3-D FPGA can achieve 3.2 times higher logic density, 1.7 times lower critical path delay, and 1.7 times lower total dynamic power consumption than the baseline 2-D FPGA fabricated in the same 65-nm technology node
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/.
11944586
Comparing System-Level Power Management Policies
Reducing power consumption is a challenge to system designers. Portable systems, such as laptop computers and personal digital assistants (PDAs), draw power from batteries, so reducing power consumption extends their operating times. For desktop computers or servers, high power consumption raises temperature and deteriorates performance and reliability. Soaring energy prices and rising concern about the environmental impact of electronics systems further highlight the importance of low power consumption. Power reduction techniques can be classified as static and dynamic. Static techniques, such as synthesis and compilation for low power, are applied at design time. In contrast, dynamic techniques use runtime behavior to reduce power when systems are serving light workloads or are idle. These techniques are known as dynamic power management (DPM). DPM can be achieved in different ways; for example, dynamic voltage scaling (DVS) changes supply voltage at runtime as a method of power management. Here, we use DPM specifically for shutting down unused I/O devices. We built an experimental environment on a laptop computer running Microsoft Windows. We implemented existing power management policies and quantitatively compared their effects on power saving and performance degradation.
6121809
Tree-like counterexamples in model checking
Counter examples for specification violations provide engineers with important debugging information. Although counterexamples are considered one of the main advantages of model checking, state-of the art model checkers are restricted to relatively simple counterexamples, and surprisingly little research effort has been put into counterexamples. In this paper, we introduce a new general framework for counterexamples. The paper has three main contributions: (i) We determine the general form of ACTL counterexamples. To this end, we investigate the notion of counterexample and show that a large class of temporal logics beyond ACTL admits counterexamples with a simple tree-like transition relation. We show that the existence of tree-like counterexamples is related to a universal fragment of extended branching time logic based on w-regular temporal operators. (ii) We present new symbolic algorithms to generate tree-like counterexamples for ACTL specifications. (iii) Based on tree-like counterexamples we extend the abstraction refinement methodology developed recently by Clarke et al. (CAV'2000) to full ACTL. This demonstrates the conceptual simplicity and elegance of tree-like counterexamples.