15675165
Maximum Common Subgraph: Upper Bound and Lower Bound Results
In bio informatics, the biological structure matching problems can be formulated as the problem of finding the maximum common subgraph. Among the many different variants of the maximum common subgraph problem, the maximum common induced subgraph of two graphs is of special interest. In this paper, first we derive the lower bound result for the exact algorithms of the maximum common induced subgraph of two graphs, based on the current research progress in the area of parameterized computation. Then we investigate the upper bound and design the approaches for addressing this problem. Basically, this problem can be reduced to find a maximum clique in the product graph of the two given graphs. In consideration of the upper bound result, the obtained lower bound result is asymptotically tight. We would like to point out that our lower bound result presented here is currently best-known
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.
42013296
On the computational hardness based on linear FPT-reductions
The notion of linear fpt-reductions has been recently introduced to derive strong computational lower bounds for well-known NP-hard problems. In this paper, we formally investigate the notion of W[t]-hardness under the linear fpt-reduction, and study the structural properties of the corresponding complexity classes. Additional complexity lower bounds on important computational problems are established. Some observations on structural properties of the standard parameterized hierarchy, the W -hierarchy, are also presented.
44298104
Tight Lower Bounds for Certain Parameterized NP-Hard Problems
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.
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.
16444798
Finding Similar Patterns in Microarray Data
In this paper we propose a clustering algorithm called s-Cluster for analysis of gene expression data based on pattern-similarity. The algorithm captures the tight clusters exhibiting strong similar expression patterns in Microarray data,and allows a high level of overlap among discovered clusters without completely grouping all genes like other algorithms. This reflects the biological fact that not all functions are turned on in an experiment, and that many genes are co-expressed in multiple groups in response to different stimuli. The experiments have demonstrated that the proposed algorithm successfully groups the genes with strong similar expression patterns and that the found clusters are interpretable.
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.
21231697
Finding and Analyzing Database User Sessions
A database user session is a sequence of queries issued by a user (or an application) to achieve a certain task. Analysis of task-oriented database user sessions provides useful insight into the query behavior of database users. In this paper, we describe novel algorithms for identifying sessions from database traces and for grouping the sessions different classes. We also present experimental results.
10948786
Boosting Prediction Accuracy on Imbalanced Datasets with SVM Ensembles
Learning from imbalanced datasets is inherently difficult due to lack of information about the minority class. In this paper, we study the performance of SVMs, which have gained great success in many real applications, in the imbalanced data context. Through empirical analysis, we show that SVMs suffer from biased decision boundaries, and that their prediction performance drops dramatically when the data is highly skewed. We propose to combine an integrated sampling technique with an ensemble of SVMs to improve the prediction performance. The integrated sampling technique combines both over-sampling and undersampling techniques. Through empirical study, we show that our method outperforms individual SVMs as well as several other state-of-the-art classifiers.
9414412
Concept-based biomedical text retrieval
One challenging problem for biomedical text retrieval is to find accurate synonyms or name variants for biomedical entities. In this paper, we propose a new concept-based approach to tackle this problem. In this approach, a set of concepts instead of keywords will be extracted from a query first. Then these concepts will be used for retrieval purpose. The experiment results show that the proposed approach can boost the retrieval performance and it generates very good results on 2005 TREC Genomics data sets.