1069327
DWE: Discriminating Word Enumerator
MOTIVATION
Tissue-specific transcription factor binding sites give insight into tissue-specific transcription regulation.


RESULTS
We describe a word-counting-based tool for de novo tissue-specific transcription factor binding site discovery using expression information in addition to sequence information. We incorporate tissue-specific gene expression through gene classification to positive expression and repressed expression. We present a direct statistical approach to find overrepresented transcription factor binding sites in a foreground promoter sequence set against a background promoter sequence set. Our approach naturally extends to synergistic transcription factor binding site search. We find putative transcription factor binding sites that are overrepresented in the proximal promoters of liver-specific genes relative to proximal promoters of liver-independent genes. Our results indicate that binding sites for hepatocyte nuclear factors (especially HNF-1 and HNF-4) and CCAAT/enhancer-binding protein (C/EBPbeta) are the most overrepresented in proximal promoters of liver-specific genes. Our results suggest that HNF-4 has strong synergistic relationships with HNF-1, HNF-4 and HNF-3beta and with C/EBPbeta.


AVAILABILITY
Programs are available for use over the Web at http://rulai.cshl.edu/tools/dwe.
12035419
A Transition Probability Model for Amino Acid Substitutions from Blocks
Substitution matrices have been useful for sequence alignment and protein sequence comparisons. The BLOSUM series of matrices, which had been derived from a database of alignments of protein blocks, improved the accuracy of alignments previously obtained from the PAM-type matrices estimated from only closely related sequences. Although BLOSUM matrices are scoring matrices now widely used for protein sequence alignments, they do not describe an evolutionary model. BLOSUM matrices do not permit the estimation of the actual number of amino acid substitutions between sequences by correcting for multiple hits. The method presented here uses the Blocks database of protein alignments, along with the additivity of evolutionary distances, to approximate the amino acid substitution probabilities as a function of actual evolutionary distance. The PMB (Probability Matrix from Blocks) defines a new evolutionary model for protein evolution that can be used for evolutionary analyses of protein sequences. Our model is directly derived from, and thus compatible with, the BLOSUM matrices. The model has the additional advantage of being easily implemented.
5737475
Toward Optimal Motif Enumeration
We present algorithms that reduce the time and space needed to solve problems of finding all motifs common to a set of sequences. In particular, we give algorithms that (1) require time and space linear in the size of the input, (2) succinctly encode the output so that the time and space requirements depend on the number of motifs, not directly on motif length, and (3) efficiently parallelize the enumeration.
14423694
Characteristics of I/O traffic in personal computer and server workloads
Understanding the characteristics of I/O traffic is increasingly important as the performance gap between the processor and disk-based storage continues to widen. Moreover, recent advances in technology, coupled with market demands, have led to new and exciting developments in storage systems, particularly network storage, storage utilities, and intelligent self-optimizing storage. In this paper, we empirically examine the physical I/O traffic of a wide range of server and personal computer (PC) workloads, focusing on how these workloads will be affected by the recent developments in storage systems. As part of our analysis, we compare our results with historical data and re-examine some rules of thumb (e.g., one bit of I/O per second for each instruction per second of processing power) that have been widely used for designing computer systems. We find that the I/O traffic is bursty and appears to exhibit self-similar characteristics. Our analysis also indicates that there is little cross-correlation between traffic volumes of server workloads, which suggests that aggregating these workloads will likely help to smooth out the traffic and enable more efficient utilization of resources. We discover that there is significant potential for harnessing "free" system resources to perform background tasks such as optimization of disk block layout. In general, we observe that the characteristics of the I/O traffic are relatively insensitive to the extent of upstream caching, and thus our results still apply, on a qualitative level, when the upstream cache is increased in size.
8448410
Measuring the Performance of Multimedia Instruction Sets
Many microprocessor instruction sets include instructions for accelerating multimedia applications such as DVD playback, speech recognition, and 3D graphics. Despite general agreement on the need to support this emerging workload, there are considerable differences between the instruction sets that have been designed to do so. In this paper, we study the performance of five instruction sets on kernels extracted from a broad multimedia workload. We compare the performance of contemporary implementations of each extension against each other as well as to the original compiled C performance. From our analysis, we determine how well multimedia workloads map to current instruction sets, noting what was useful and what was not. We also propose two enhancements: fat subwords and strided memory operations.
17481018
Analysis of benchmark characteristics and benchmark performance prediction
Standard benchmarking provides to run-times for given programs on given machines, but fails to provide insight as to why those results were obtained (either in terms of machine or program characteristics) and fails to provide run-times for that program on some other machine, or some other programs on that machine. We have developed a machine-imdependent model of program execution to characterize both machine performance and program execution. By merging these machine and program characterizations, we can estimate execution time for arbitrary machine/program combinations. Our technique allows us to identify those operations, either on the machine or in the programs, which dominate the benchmark results. This information helps designers in improving the performance of future machines and users in tuning their applications to better utilize the performance of existing machines. Here we apply our methodology to characterize benchmarks and predict their execution times. We present extensive run-time statistics for a large set of benchmarks including the SPEC and Perfect Club suites. We show how these statistics can be used to identify important shortcoming in the programs. In addition, we give execution time estimates for a large sample of programs and machines and compare these against benchmark results. Finally, we develop a metric for program similarity that makes it possible to classify benchmarks with respect to a large set of characteristics.
589196
Using user interface event information in dynamic voltage scaling algorithms
Increasingly, mobile computers use dynamic voltage scaling (DVS) to reduce CPU voltage and speed and thereby increase battery life. To determine how to change voltage and speed when responding to user interface events, we analyze traces of real user workloads. We evaluate a new heuristic for inferring when user interface tasks complete and find it is more efficient and nearly as effective as other approaches. We compare DVS algorithms and find that for a given performance level, the PACE algorithm uses the least energy and the Stepped algorithm uses the second least. We find that different types of user interface event (mouse movements, mouse clicks, and keystrokes) trigger tasks with significantly different CPU use, suggesting one should use different speeds for different event types. We also find differences in CPU use between categories of the same event type, e.g., between pressing spacebar and pressing enter, and between events of different applications. Thus, it is better to predict task CPU use based solely on tasks of the same category and application. However, energy savings from such improved predictions are small.
38568062
Multiprocessor memory reference generation using Cerberus
Presents Cerberus, an efficient system for simulating the execution of shared-memory, multiprocessor programs on a uniprocessor workstation. Using EDS (execution-driven simulation), it generates address traces which can be used to drive cache simulations on-the-fly, eliminating the large disk space requirements needed by trace files. It is fast because it links the program to be traced together with the cache or statistics gathering tool into a single executable, which eliminates the context switching needed by communicating processes. It is flexible because it has a simple interface which allows users to easily add any kind of module to use the generated trace information. It compares favorably to other existing tracers; it runs on a commonly available workstation and it is accurate, allowing cycle-by-cycle interactions between the simulated processors. The resulting slowdown from Cerberus is approximately 31 in uniprocessor mode and 45-50 in multiprocessor mode, relative to the workloads run natively on the same machines. We demonstrate that EDS uses only 5% of the total execution cycles when combined with a cache simulator, and we show that EDS is just as efficient as using trace-driven simulation.