40872599
Timestamp consistency and trace-driven analysis for distributed parallel systems
A continuous stream of event data describing the progress of parallel program execution is realized for trace-driven analysis. Unfortunately, it is often the case that separate streams are produced independently by multiple processors in the system, and the logical order of events cannot be guaranteed due to discrepancy among local clocks. We present an integrated approach for timestamp consistency and performance analysis techniques for IBM SPn systems. The trace facility requires no source code modification, and can generate message passing and system events with minimal trace overhead. Trace-driven analysis tools are developed to extract useful information. Analysis results for NAS kernel benchmarks are reported.<<ETX>>
38476421
Design Trade-offs for Process Scheduling in Tightly Coupled Multiprocessor Systems
14149213
Efficient Stack Simulation for Shared Memory Set-Associative Multiprocessor Caches
We propose efficient stack simulation algorithms for shared memory multiprocessor (MP) caches. A stack simulation algorithm for write-updated MP caches is first presented. It produces the number of write-updates as well as misses for all cache configurations in a single run. We then devise a new stack simulation algorithm for writeinvalidate MP caches. Our algorithm takes into account cross-invalidation among processors, and generates the number of invalidations as well as misses for all cache configurations in a single run. A cache simulator based on our algorithms for MP caches is developed and the results on sample traces are reported. Our results show that effi cient stack simulation is a powerful technique for multi processor cache analysis.
463160
A Rule-Based Circuit Representation for Automated CMOS Design and Verification
A novel rule-based circuit representation is proposed to describe the connectivities of CMOS circuits at the transistor level. The unique feature of the rule-based representation is its ability to automate CMOS circuit design and verification. A precise symbolic description of the functionality of a transistor-level circuit can be derived based on a set of production rules in linear time. Automated synthesis and verification of CMOS logic circuits are demonstrated.
6100465
A distributed connection manager interface for web services on IBM SP systems
In essence, the World Wide Web is a worldwide string of computer databases using a common information retrieval architecture. With the increasing popularity of the World Wide Web, more and more functions have been added to retrieve not only documents written in HTML (Hypertext Markup Language), but also those in other forms through the Common Gateway Interface (CGI), by constructing HTML documents dynamically. Dynamic construction of HTML documents for handling information such as digital libraries is slow and requires much more computer power. A significant performance bottleneck is the initialization and setup phase for a CGI process to gain access to the system containing the data. In this paper we describe the design and implementation of a Connection Manager Interface on IBM SP systems. The Connection Manager provides cliette processes to serve CGI requests and eliminates such bottlenecks. An IBM SP system is used for this emerging area to show that our design and implementation is flexible enough to take advantage of the High-Performance Switch in an IBM SP system. We trace and monitor this scalable Web services using UTE (Unified Trace Environment) tools, and present its performance analysis and visualization.
11414897
Trace-based analysis and tuning for distributed parallel applications
We present an integrated approach to deal with timestamp consistency, and trace based performance analysis techniques for distributed parallel applications. Our trace generation facility captures message passing and system events such as process dispatch with minimal trace overhead. Trace driven analysis tools are developed for post execution analysis, reporting information such as the time stolen by other processes in each node, and the observed message passing time and local wait time for each message. We then present our techniques to reduce total elapsed times based on observed message passing times and local wait times.
53305921
Substring selection for biomedical document classification
Motivation: Attribute selection is a critical step in development of document classification systems. As a standard practice, words are stemmed and the most informative ones are used as attributes in classification. Owing to high complexity of biomedical terminology, general-purpose stemming algorithms are often conservative and could also remove informative stems. This can lead to accuracy reduction, especially when the number of labeled documents is small. To address this issue, we propose an algorithm that omits stemming and, instead, uses the most discriminative substrings as attributes. 
 
Results: The approach was tested on five annotated sets of abstracts from iProLINK that report on the experimental evidence about five types of protein post-translational modifications. The experiments showed that Naive Bayes and support vector machine classifiers perform consistently better [with area under the ROC curve (AUC) accuracy in range 0.92--0.97] when using the proposed attribute selection than when using attributes obtained by the Porter stemmer algorithm (AUC in 0.86--0.93 range). The proposed approach is particularly useful when labeled datasets are small. 
 
Contact: vucetic@ist.temple.edu 
 
Supplementary Information: The supplementary data are available from www.ist.temple.edu/PIRsupplement
6353106
The Universal Protein Resource (UniProt): an expanding universe of protein information
The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at or downloaded at .
26993316
Construction of Cryptographically Important Boolean Permutations
Abstract.In this paper a new general methodology is developed to construct Boolean permutations such that any non-trivial linear combination of their components has the largest algebraic degree.
3641866
The iProClass integrated database for protein functional analysis
Increasingly, scientists have begun to tackle gene functions and other complex regulatory processes by studying organisms at the global scales for various levels of biological organization, ranging from genomes to metabolomes and physiomes. Meanwhile, new bioinformatics methods have been developed for inferring protein function using associative analysis of functional properties to complement the traditional sequence homology-based methods. To fully exploit the value of the high-throughput system biology data and to facilitate protein functional studies requires bioinformatics infrastructures that support both data integration and associative analysis. The iProClass database, designed to serve as a framework for data integration in a distributed networking environment, provides comprehensive descriptions of all proteins, with rich links to over 50 databases of protein family, function, pathway, interaction, modification, structure, genome, ontology, literature, and taxonomy. In particular, the database is organized with PIRSF family classification and maps to other family, function, and structure classification schemes. Coupled with the underlying taxonomic information for complete genomes, the iProClass system (http://pir.georgetown.edu/iproclass/) supports associative studies of protein family, domain, function, and structure. A case study of the phosphoglycerate mutases illustrates a systematic approach for protein family and phylogenetic analysis. Such studies may serve as a basis for further analysis of protein functional evolution, and its relationship to the co-evolution of metabolic pathways, cellular networks, and organisms.
29409365
A Parallel Asynchronous Garbage Collection Algorithm for Distributed Systems
The problem of distributed garbage collection is discussed. An algorithm for parallel distributed asynchronous garbage collection is presented. The liveness and safety properties of this method are demonstrated. The algorithm does not require a global clock, complex termination detection methods, or distributed synchronization techniques. A new color code is introduced to distinguish between local cells (black) and those that are exclusively accessible from the remote pointers (gray). The mutator operation is revised to handle a multiple mutator scheme on a given local memory. Simulation results show that the developed distributed and parallel algorithm performs much better than the sequential method as tested on a Balance 8000 computer. >