14863694
System level perspective on object locality
Performance of modern computers is tied closely to the effective use of cache because of the continually increasing speed discrepancy between processors and main memory. Optimum system performance is achieved when software and hardware work symbiotically to increase performance. This work focuses on identifying locality in object-oriented systems and developing techniques for approaching optimum performance with respect to the memory hierarchy.
9645285
Using scratchpad to exploit object locality in Java
Performance of modern computers is tied closely to the effective use of cache because of the continually increasing speed discrepancy between processors and main memory. We demonstrate that generational garbage collection employed by a system with cache and scratchpad memory can take advantage of the locality of small short-lived objects in Java and reduce memory traffic by as much as 20% when compared to a cache-only configuration. Converting half of the cache to scratchpad can be more effective at reducing memory traffic than doubling or even quadrupling the size of the cache for several of the applications in SPECjvm98.
1021056
A performance perspective on the Active Memory System
Abstract One major problem of using Java in real-time and embedded devices is the non-deterministic turnaround time of dynamic memory management systems (memory allocation and garbage collection). For the allocation, the non-determinism is often contributed by the time to perform searching, splitting, and coalescing. For the garbage collection, the turnaround time is usually determined by the size of the heap, the number of live objects, the number of object collected, and the amount of garbage collected. Even with the current state-of-the-art garbage collectors (generational and incremental schemes), they may or may not guarantee the worst-case latency. Moreover, such schemes often prolong overall garbage collection time. In this paper, the performance analysis of the proposed Active Memory Module (AMM) for embedded systems is presented. Unlike the software counterparts, the AMM can perform a memory allocation in a predictable and bounded fashion (14 cycles). Moreover, it can also yield a bounded sweeping time regardless of the number of live objects or heap size. By utilizing the proposed system, the overall speedup can be as high as 23% compared to the garbage collection system of the JDK 1.2.2 running in classic mode.
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.
39527990
FPGA-based reconfigurable computing
12198410
Scalable hardware-algorithm for mark-sweep garbage collection
The memory-intensive nature of object-oriented languages such as C++ and Java has created the need for high-performance dynamic memory management. Object-oriented applications often generate higher memory intensity in the heap region. Thus, a high-performance memory manager is needed to cope with such applications. As today's VLSI technology advances, it becomes increasingly attractive to map software algorithms such as malloc(), free() and garbage collection into hardware. This paper presents a hardware design of a sweeping function (for mark-and-sweep garbage collection) that fully utilizes the advantages of combinational logic. In our scheme, the bit sweep can detect and sweep the garbage in a constant time. Bit-map marking in software can improve the cache performance and reduce number of page faults; however, it often requires several instructions to perform a single mark. In our scheme, only one hardware instruction is required per mark. Moreover, since the complexity of the sweeping phase is often higher than the marking phase, the garbage collection time may be substantially improved. The hardware complexity of the proposed scheme (bit-sweeper) is O(n), where n represents the size of the bit map.
9345376
Finding recently frequent itemsets adaptively over online transactional data streams,
A data stream is a massive unbounded sequence of data elements continuously generated at a rapid rate. Consequently, the knowledge embedded in a data stream is more likely to be changed as time goes by. Identifying the recent change of a data stream, especially for an online data stream, can provide valuable information for the analysis of the data stream. However, most of mining algorithms or frequency approximation algorithms over a data stream do not differentiate the information of recently generated data elements from the obsolete information of old data elements which may be no longer useful or possibly invalid at present. Therefore, they are not able to extract the recent change of information in a data stream adaptively. This paper proposes a data mining method for finding recently frequent itemsets adaptively over an online transactional data stream. The effect of old transactions on the current mining result of a data steam is diminished by decaying the old occurrences of each itemset as time goes by. Furthermore, several optimization techniques are devised to minimize processing time as well as memory usage. Finally, the performance of the proposed method is analyzed by a series of experiments to identify its various characteristics.
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.
7532286
Finding recent frequent itemsets adaptively over online data streams
A data stream is a massive unbounded sequence of data elements continuously generated at a rapid rate. Consequently, the knowledge embedded in a data stream is more likely to be changed as time goes by. Identifying the recent change of a data stream, specially for an online data stream, can provide valuable information for the analysis of the data stream. In addition, monitoring the continuous variation of a data stream enables to find the gradual change of embedded knowledge. However, most of mining algorithms over a data stream do not differentiate the information of recently generated transactions from the obsolete information of old transactions which may be no longer useful or possibly invalid at present. This paper proposes a data mining method for finding recent frequent itemsets adaptively over an online data stream. The effect of old transactions on the mining result of the data steam is diminished by decaying the old occurrences of each itemset as time goes by. Furthermore, several optimization techniques are devised to minimize processing time as well as main memory usage. Finally, the proposed method is analyzed by a series of experiments.
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/
9862925
Powers of Asteroidal Triple-free Graphs with Applications
An asteroidal triple is an independent set of three vertices in a graph such that every two of them are joined by a path avoiding the closed neighborhood of the third. Graphs without asteroidal triples are called AT-free graphs. In this paper, we show that every AT-free graph admits a vertex ordering that we call a 2-cocomparability ordering. The new suggested ordering generalizes the cocomparability ordering achievable for cocomparability graphs. According to the property of this ordering, we show that every proper power G (k ≥ 2) of an AT-free graph G is a cocomparability graph. Moreover, we demonstrate that our results can be exploited for algorithmic purposes on AT-free graphs.