2829100
GAPSCORE: finding gene and protein names one word at a time
MOTIVATION
New high-throughput technologies have accelerated the accumulation of knowledge about genes and proteins. However, much knowledge is still stored as written natural language text. Therefore, we have developed a new method, GAPSCORE, to identify gene and protein names in text. GAPSCORE scores words based on a statistical model of gene names that quantifies their appearance, morphology and context.


RESULTS
We evaluated GAPSCORE against the Yapex data set and achieved an F-score of 82.5% (83.3% recall, 81.5% precision) for partial matches and 57.6% (58.5% recall, 56.7% precision) for exact matches. Since the method is statistical, users can choose score cutoffs that adjust the performance according to their needs.


AVAILABILITY
GAPSCORE is available at http://bionlp.stanford.edu/gapscore/
4458929
Including Biological Literature Improves Homology Search
Annotating the tremendous amount of sequence information being generated requires accurate automated methods for recognizing homology. Although sequence similarity is only one of many indicators of evolutionary homology, it is often the only one used. Here we find that supplementing sequence similarity with information from biomedical literature is successful in increasing the accuracy of homology search results. We modified the PSI-BLAST algorithm to use literature similarity in each iteration of its database search. The modified algorithm is evaluated and compared to standard PSI-BLAST in searching for homologous proteins. The performance of the modified algorithm achieved 32% recall with 95% precision, while the original one achieved 33% recall with 84% precision; the literature similarity requirement preserved the sensitive characteristic of the PSI-BLAST algorithm while improving the precision.
18001825
Architectural support for dynamic memory management
Recent advances in software engineering, such as graphical user interfaces and object-oriented programming, have caused applications to become more memory intensive. These applications tend to allocate dynamic memory prolifically. Moreover, automatic dynamic memory reclamation (garbage collection, GC) has become a popular feature in modern programming languages. As a result, the time consumed by dynamic storage management can be up to one-third of the program execution time. This illustrates the need for a high-performance memory management scheme. This paper presents a top-level design and evaluation of the proposed instruction extensions to facilitate heap management.
40774984
Performance enhancements to the Active Memory System
The Active Memory System - a garbage collected memory module - was introduced as a way to provide hardware support for garbage collection in embedded systems. The major component in the design was the Active Memory Processor (AMP) that utilized a set of bit-maps and a combinational circuit to perform mark-sweep garbage collection. The design can achieve constant time for both allocation and sweeping. In this paper two enhancements are made to the design of AMP so that it can perform one-bit reference counting that postpones the need to perform garbage collection. Moreover, a caching mechanism is also introduced to reduce the hardware cost of the design. The experimental results show that the proposed modification can reduce the number of garbage collection invocations by 76%. The speed-up in marking time can be as much as 5.81. With the caching mechanism, the hardware cost can be as small as 27 K gates and 6 KB of SRAM.
17166482
Benchmarking the effectiveness of sequential pattern mining methods
Recently, there is an increasing interest in new intelligent mining methods to find more meaningful and compact results. In intelligent data mining research, accessing the quality and usefulness of the results from different mining methods is essential. However, there is no general benchmarking criteria to evaluate whether these new methods are indeed more effective compared to the traditional methods. Here we propose a novel benchmarking criteria that can systematically evaluate the effectiveness of any sequential pattern mining method under a variety of situations. The benchmark evaluates how well a mining method finds known common patterns in synthetic data. Such an evaluation provides a comprehensive understanding of the resulting patterns generated from any mining method empirically. In this paper, the criteria are applied to conduct a detailed comparison study of the support-based sequential pattern model with an approximate pattern model based on sequence alignment. The study suggests that the alignment model will give a good summary of the sequential data in the form of a set of common patterns in the data. In contrast, the support model generates massive amounts of frequent patterns with much redundancy. This suggests that the results of the support model require more post processing before it can be of actual use in real applications.
27069893
Advanced POC model-based Java instruction folding mechanism
Ever since Java was introduced world wide, the execution performance has always been a problem. As one of the solutions, a bytecode instruction folding process for Java processors was developed in a PicoJava model and a Producer, Operator and Consumer (POC) model, but it could not handle certain types of instruction sequences. In this paper, a new instruction folding scheme based on a new, advanced POC model is proposed and demonstrates improvement in bytecode execution. The proposed POC model is able to detect and fold all possible instruction sequence types dynamically in hardware, including a sequence that is separated by other bytecode instructions. SPEC JMV98 benchmark results show that the proposed POC model-based folder can save more than 90% of folding operations. In addition, a design of the proposed POC model-based folding process in hardware is much smaller and more efficient than traditional folding mechanisms.
13312657
Feedback vertex sets in star graphs
In a graph G = (V, E), a subset F ⊂ V(G) is a feedback vertex set of G if the subgraph induced by V(G) \ F is acyclic. In this paper, we propose an algorithm for finding a small feedback vertex set of a star graph. Indeed, our algorithm can derive an upper bound to the size of the feedback vertex set for star graphs. Also by applying the properties of regular graphs, a lower bound can easily be achieved for star graphs.