43590220
Lower Bounds and Parameterized Approach for Longest Common Subsequence
In this paper, different parameterized versions of the longest common subsequence (LCS) problem are extensively investigated and computational lower bound results are derived based on current research progress in parameterized computation. For example, with the number of sequences as the parameter k, the problem is unlikely to be solvable in time f(k)no(k), where n is the length of each sequence and f is any recursive function. The lower bound result is asymptotically tight in consideration of the dynamic programming approach of time O(nk). Computational lower bounds for polynomial-time approximation schemes (PTAS) for the LCS problem are also derived. It is shown that the LCS problem has no PTAS of time f(1/ e)no(1/ e) for any recursive function f, unless all SNP problems are solvable in subexponential time. Compared with former results on this problem, this result has its significance. Finally a parameterized approach for the LCS problem is discussed, which is more efficient than the dynamic programming approach, especially when applied to large scale sequences.
37155625
Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment
Computational alignment of a biopolymer sequence (e.g., an RNA or a protein) to a structure is an effective approach to predict and search for the structure of new sequences. To identify the structure of remote homologs, the structure-sequence alignment has to consider not only sequence similarity but also spatially conserved conformations caused by residue interactions, and consequently is computationally intractable. It is difficult to cope with the inefficiency without compromising alignment accuracy, especially for structure search in genomes or large databases. This paper introduces a novel method and a parameterized algorithm for structure-sequence alignment. Both the structure and the sequence are represented as graphs, where in general the graph for a biopolymer structure has a naturally small tree width. The algorithm constructs an optimal alignment by finding in the sequence graph the maximum valued subgraph isomorphic to the structure graph. It has the computational time complexity O(k t N 2) for the structure of N residues and its tree decomposition of width t. The parameter k, small in nature, is determined by a statistical cutoff for the correspondence between the structure and the sequence. The paper demonstrates a successful application of the algorithm to developing a fast program for RNA structural homology search.
2218327
Strong computational lower bounds via parameterized complexity
We develop new techniques for deriving strong computational lower bounds for a class of well-known NP-hard problems. This class includes weighted satisfiability, dominating set, hitting set, set cover, clique, and independent set. For example, although a trivial enumeration can easily test in time O(n^k) if a given graph of n vertices has a clique of size k, we prove that unless an unlikely collapse occurs in parameterized complexity theory, the problem is not solvable in time f(k)n^o^(^k^) for any function f, even if we restrict the parameter values to be bounded by an arbitrarily small function of n. Under the same assumption, we prove that even if we restrict the parameter values k to be of the order @Q(@m(n)) for any reasonable function @m, no algorithm of running time n^o^(^k^) can test if a graph of n vertices has a clique of size k. Similar strong lower bounds on the computational complexity are also derived for other NP-hard problems in the above class. Our techniques can be further extended to derive computational lower bounds on polynomial time approximation schemes for NP-hard optimization problems. For example, we prove that the NP-hard distinguishing substring selection problem, for which a polynomial time approximation scheme has been recently developed, has no polynomial time approximation schemes of running time f(1/@e)n^o^(^1^/^@e^) for any function f unless an unlikely collapse occurs in parameterized complexity theory.
28347745
On global sequence alignment
We present a dynamic programming algorithm for computing a best global alignment of two sequences. The proposed algorithm is robust in identifying any of several global relationships between two sequences. The algorithm delivers a best alignment of two sequences in linear space and quadratic time. We also describe a multiple alignment algorithm based on the pairwise algorithm. Both algorithms have been implemented as portable C programs. Experimental results indicate that for a commonly used set of gap penalties, the new programs produce more satisfactory alignments on sequences of various lengths than some existing pairwise and multiple programs based on the dynamic programming algorithm of Needleman and Wunsch.
329318
The garbage collection advantage: improving program locality
As improvements in processor speed continue to outpace improvements in cache and memory speed, poor locality increasingly degrades performance. Because copying garbage collectors move objects, they have an opportunity to improve locality. However, no static copying order is guaranteed to match program traversal orders. This paper introduces <i>online object reordering</i> (OOR) which includes a new dynamic, online class analysis for Java that detects program traversal patterns and exploits them in a copying collector. OOR uses run-time method sampling that drives just-in-time (JIT) compilation. For each <i>hot</i> (frequently executed) method, OOR analysis identifies the hot field accesses. At garbage collection time, the OOR collector then copies referents of hot fields together with their parent. Enhancements include static analysis to exclude accesses in cold basic blocks, heuristics that decay heat to respond to phase changes, and a separate space for hot objects. The overhead of OOR is on average negligible and always less than 2% on Java benchmarks in Jikes RVM with MMTk. We compare program performance of OOR to static class-oblivious copying orders (e.g., breadth and depth first). Performance variation due to static orders is often low, but can be up to 25%. In contrast, OOR matches or improves upon the best static order since its history-based copying tunes memory layout to program traversal.
668000
Applying language modeling to session identification from database trace logs
A database session is a sequence of requests presented to the database system by a user or an application to achieve a certain task. Session identification is an important step in discovering useful patterns from database trace logs. The discovered patterns can be used to improve the performance of database systems by prefetching predicted queries, rewriting the current query or conducting effective cache replacement.In this paper, we present an application of a new session identification method based on statistical language modeling to database trace logs. Several problems of the language modeling based method are revealed in the application, which include how to select values for the parameters of the language model, how to evaluate the accuracy of the session identification result and how to learn a language model without well-labeled training data. All of these issues are important in the successful application of the language modeling based method for session identification. We propose solutions to these open issues. In particular, new methods for determining an entropy threshold and the order of the language model are proposed. New performance measures are presented to better evaluate the accuracy of the identified sessions. Furthermore, three types of learning methods, namely, learning from labeled data, learning from semi-labeled data and learning from unlabeled data, are introduced to learn language models from different types of training data. Finally, we report experimental results that show the effectiveness of the language model based method for identifying sessions from the trace logs of an OLTP database application and the TPC-C Benchmark.
17235430
A generalized global alignment algorithm
MOTIVATION
Homologous sequences are sometimes similar over some regions but different over other regions. Homologous sequences have a much lower global similarity if the different regions are much longer than the similar regions.


RESULTS
We present a generalized global alignment algorithm for comparing sequences with intermittent similarities, an ordered list of similar regions separated by different regions. A generalized global alignment model is defined to handle sequences with intermittent similarities. A dynamic programming algorithm is designed to compute an optimal general alignment in time proportional to the product of sequence lengths and in space proportional to the sum of sequence lengths. The algorithm is implemented as a computer program named GAP3 (Global Alignment Program Version 3). The generalized global alignment model is validated by experimental results produced with GAP3 on both DNA and protein sequences. The GAP3 program extends the ability of standard global alignment programs to recognize homologous sequences of lower similarity.


AVAILABILITY
The GAP3 program is freely available for academic use at http://bioinformatics.iastate.edu/aat/align/align.html.
17510008
Applying Machine Learning to Text Segmentation for Information Retrieval
We propose a self-supervised word segmentation technique for text segmentation in Chinese information retrieval. This method combines the advantages of traditional dictionary based, character based and mutual information based approaches, while overcoming many of their shortcomings. Experiments on TREC data show this method is promising. Our method is completely language independent and unsupervised, which provides a promising avenue for constructing accurate multi-lingual or cross-lingual information retrieval systems that are flexible and adaptive. We find that although the segmentation accuracy of self-supervised segmentation is not as high as some other segmentation methods, it is enough to give good retrieval performance. It is commonly believed that word segmentation accuracy is monotonically related to retrieval performance in Chinese information retrieval. However, for Chinese, we find that the relationship between segmentation and retrieval performance is in fact nonmonotonic; that is, at around 70% word segmentation accuracy an over-segmentation phenomenon begins to occur which leads to a reduction in information retrieval performance. We demonstrate this effect by presenting an empirical investigation of information retrieval on Chinese TREC data, using a wide variety of word segmentation algorithms with word segmentation accuracies ranging from 44% to 95%, including 70% word segmentation accuracy from our self-supervised word-segmentation approach. It appears that the main reason for the drop in retrieval performance is that correct compounds and collocations are preserved by accurate segmenters, while they are broken up by less accurate (but reasonable) segmenters, to a surprising advantage. This suggests that words themselves might be too broad a notion to conveniently capture the general semantic meaning of Chinese text. Our research suggests machine learning techniques can play an important role in building adaptable information retrieval systems and different evaluation standards for word segmentation should be given to different applications.