The problems of finding a longest common subsequence of two sequences A and B and a shortest edit script for transforming A into B have long been known to be dual problems. In this paper, they are shown to be equivalent to finding a shortest/longest path in an edit graph. Using this perspective, a simple O(ND) time and space algorithm is developed where N is the sum of the lengths of A and B and D is the size of the minimum edit script for A and B. The algorithm performs well when differences are small (sequences are similar) and is consequently fast in typical applications. The algorithm is shown to have O(N +D expected-time performance under a basic stochastic model. A refinement of the algorithm requires only O(N) space, and the use of suffix trees leads to an O(NlgN +D ) time variation.

On-line forums for the collaborative creation of bodies of information are a phenomenon of rising importance; the Wikipedia is one of the best-known examples. The open nature of such forums could benefit from a notion of reputation for its authors. Author reputation could be used to flag new contributions from low-reputation authors, and it could be used to allow only authors with good reputation to contribute to controversial or critical pages. A reputation system for the Wikipedia would also provide an incentive to give high-quality contributions. We present in this paper a novel type of contentdriven reputation system for Wikipedia authors. In our system, authors gain reputation when the edits and text additions they perform to Wikipedia articles are longlived, and they lose reputation when their changes are undone in short order. We have implemented the proposed system, and we have used it to analyze the entire Italian and French Wikipedias, consisting of a total of 691,551 pages and 5,587,523 revisions. Our results show that our notion of reputation has good predictive value: changes performed by low-reputation authors have a significantly larger than average probability of having poor quality, and of being undone.

XML has become the de facto standard format for web publishing and data transportation. Since online information changes frequently, being able to quickly detect changes in XML documents is important to Internet query systems, search engines, and continuous query systems. Previous work in change detection on XML, or other hierarchically structured documents, used an ordered tree model, in which left-to-right order among siblings is important and it can affect the change result. This paper argues that an unordered model (only ancestor relationships are significant) is more suitable for most database applications. Using an unordered model, change detection is substantially harder than using the ordered model, but the change result that it generates is more accurate. This paper proposes X-Diff, an effective algorithm that integrates key XML structure characteristics with standard tree-to-tree correction techniques. The algorithm is analyzed and compared with XyDiff [CAM02], a published XML diff algorithm. An experimental evaluation on both algorithms is provided.

this paper is organized into five sections, as follows. The internal form of a program, which is a variant of a parse tree, is discussed in the next section. Then the tree-matching algorithm and the synchronous pretty-printing technique are described. Experience with the comparator for the C language and some performance measurements are also presented. The last section discusses related work and concludes this paper

Categorizing visitors based on their interactions with a website is a key problem in web usage mining. The clickstreams generated by various users often follow distinct patterns, the knowledge of which may help in providing customized content. In this paper, we propose a novel and effective algorithm for clustering webusers based on a function of the longest common subsequence of their clickstreams that takes into account both the trajectory taken through a website and the time spent at each page. Results are presented on weblogs of www.sulekha.com to illustrate the techniques.

To improve software productivity, when constructing new software systems, developers often reuse existing class libraries or frameworks by invoking their APIs. Those APIs, however, are often complex and not well documented, posing barriers for developers to use them in new client code. To get familiar with how those APIs are used, developers may search the Web using a general search engine to find relevant documents or code examples. Developers can also use a source code search engine to search open source repositories for source files that use the same APIs. Nevertheless, the number of returned source files is often large. It is difficult for developers to learn API usages from a large number of returned results. In order to help developers understand API usages and write API client code more effectively, we have developed an API usage mining framework and its supporting tool called MAPO (for Mining API usages from Open source repositories). Given a query that describes a method, class, or package for an API, MAPO leverages the existing source code search engines to gather relevant source files and conducts data mining. The mining leads to a short list of frequent API usages for developers to inspect. MAPO currently consists of five components: a code search engine, a source code analyzer, a sequence preprocessor, a frequent sequence miner, and a frequent sequence postprocessor. We have examined the effectiveness of MAPO using a set of various queries. The preliminary results show that the framework is practical for providing informative and succinct API usage patterns.

The AT&T Internet Difference Engine (aide) is a system that finds and displays changes to pages on the World Wide Web. The system consists of several components, including a webcrawler that detects changes, an archive of past versions of pages, a tool called HtmlDiff to highlight changes between versions of a page, and a graphical interface to view the relationship between pages over time. This paper describes aide, with an emphasis on the evolution of the system and experiences with it. It also raises some sociological and legal issues.

Molecular biologists use algorithms that compare and otherwise analyze sequences that represent genetic and protein molecules. Most of these algorithms, however, operate on the basic sequence and do not incorporate the additional information that is often known about the molecule and its pieces. This research describes schemes to combinatorially annotate this information onto sequences so that it can be analyzed in tandem with the sequence; the overall result would thus reflect both types of information about the sequence. These annotation schemes include adding colours and arcs to the sequence. Colouring a sequence would produce a same-length sequence of colours or other symbols that highlight or label parts of the sequence. Arcs can be used to link sequence symbols (or coloured substrings) to indicate molecular bonds or other relationships. Adding these annotations to sequence analysis problems such as sequence alignment or finding the longest common subsequence can make the problem more complex, often depending on the complexity of the annotation scheme. This research examines the different annotation schemes and the corresponding problems of verifying annotations, creating annotations, and finding the longest common subsequence of pairs of sequences with annotations. This work involves both the conventional complexity framework and parameterized complexity, and includes algorithms and hardness results for both frameworks. Automata and transducers are created for some annotation verification and creation problems. Different restrictions on layered substring and arc annotation are considered to de- iii termine what properties an annotation scheme must have to make its incorporation feasible. Extensions to the algorithms that use weighting schemes are explored. Examin...

The problem of comparing two sequences A and B to determine their LCS or the edit distance between them has been much studied. In this paper we consider the following incremental version of these problems: given an appropriate encoding of a comparison between A and B, can one incrementally compute the answer for A and bB, and the answer for A and Bb with equal efficiency, where b is an additional symbol? Our main result is a theorem exposing a surprising relationship between the dynamic programming solutions for two such "adjacent" problems. Given a threshold k on the number of differences to be permitted in an alignment, the theorem leads directly to an O(k) algorithm for incrementally computing a new solution from an old one, as contrasts the O(k²) time required to compute a solution from scratch. We further show with a series of applications that this algorithm is indeed more powerful than its non-incremental counterpart by solving the applications with greater asymptotic ef...

. Arc-annotated sequences are useful in representing the structural information of RNA and protein sequences. Recently, the longest arc-preserving common subsequence problem has been introduced in [6, 7] as a framework for studying the similarity of arc-annotated sequences. In this paper, we consider arc-annotated sequences with various arc structures and present some new algorithmic and complexity results on the longest arc-preserving common subsequence problem. Some of our results answer an open question in [6, 7] and some others improve the hardness results in [6, 7]. Keywords: sequence annotation, longest common subsequence, approximation algorithm, maximum independent set, MAX SNP-hard, dynamic programming. 1