2468175
Optimal suffix selection
Given a string S[1·s n], the suffix selection problemis to find the kth lexicographically smallest amongst the n suffixes S[i·s n], for i=1,...,n. In particular, the fundamental question is if selection can be performed more efficiently than sorting all the suffixes.
 If one considered n numbers, they can be sorted using Θ(n log n) comparisonsand the classical result from 70's is that selection can be done using O(n) comparisons. Thus selection is provably more efficient than sorting, for n numbers.
 Suffix sorting can be done using Θ(n log n) comparisons, but does suffix selection need suffix sorting? We settle this fundamental problem by presenting an optimal, deterministic algorithm for suffix selection using O(n) comparisons.
2478393
Compressing and searching XML data via two zips
XML is fast becoming the standard format to store, exchange and publish over the web, and is getting embedded in applications. Two challenges in handling XML are its size (the XML representation of a document is significantly larger than its native state) and the complexity of its search (XML search involves path and content searches on labeled tree structures). We address the basic problems of compression, navigation and searching of XML documents. In particular, we adopt recently proposed theoretical algorithms [11] for succinct tree representations to design and implement a compressed index for XML, called XBZIPiNDEX, in which the XML document is maintained in a highly compressed format, and both navigation and searching can be done uncompressing only a tiny fraction of the data. This solution relies on compressing and indexing two arrays derived from the XML data. With detailed experiments we compare this with other compressed XML indexing and searching engines to show that XBZIPiNDEX has compression ratio up to 35% better than the ones achievable by those other tools, and its time performance on some path and content search operations is order of magnitudes faster: few milliseconds over hundreds of MBs of XML files versus tens of seconds, on standard XML data sources.
16380650
The Graham-Knowlton Problem Revisited
AbstractIn the late 60s Graham and Knowlton introduced the WIP (wire
identification problem) that affected electricians: match the wires in
the ceiling to those in the basement while making the fewest trips. We
revisit this problem and study its variants and generalizations; we
provide a combinatorial characterization of the solution(s) in terms of
an associated hypergraph and obtain nearly tight bounds on the minimum
number of trips.
1714371
Bidding to the Top: VCG and Equilibria of Position-Based Auctions
Many popular search engines run an auction to determine the placement of advertisements next to search results. Current auctions at Google and Yahoo! let advertisers specify a single amount as their bid in the auction. This bid is interpreted as the maximum amount the advertiser is willing to pay per click on its ad. When search queries arrive, the bids are used to rank the ads linearly on the search result page. Advertisers seek to be high on the list, as this attracts more attention and more clicks. The advertisers pay for each user who clicks on their ad, and the amount charged depends on the bids of all the advertisers participating in the auction. 
 
We study the problem of ranking ads and associated pricing mechanisms when the advertisers not only specify a bid, but additionally express their preference for positions in the list of ads. In particular, we study prefix position auctions where advertiser i can specify that she is interested only in the top κi positions. 
 
We present a simple allocation and pricing mechanism that generalizes the desirable properties of current auctions that do not have position constraints. In addition, we show that our auction has an envy-free [1] or symmetric [2] Nash equilibrium with the same outcome in allocation and pricing as the well-known truthful Vickrey-Clarke-Groves (VCG) auction. Furthermore, we show that this equilibrium is the best such equilibrium for the advertisers in terms of the profit made by each advertiser. We also discuss other position-based auctions.
2699773
Holistic UDAFs at streaming speeds
Many algorithms have been proposed to approximate holistic aggregates, such as quantiles and heavy hitters, over data streams. However, little work has been done to explore what techniques are required to incorporate these algorithms in a data stream query processor, and to make them useful in practice.In this paper, we study the performance implications of using user-defined aggregate functions (UDAFs) to incorporate selection-based and sketch-based algorithms for holistic aggregates into a data stream management system's query processing architecture. We identify key performance bottlenecks and tradeoffs, and propose novel techniques to make these holistic UDAFs fast and space-efficient for use in high-speed data stream applications. We evaluate performance using generated and actual IP packet data, focusing on approximating quantiles and heavy hitters. The best of our current implementations can process streaming queries at OC48 speeds (2x 2.4Gbps).
11291209
Randomization in Parallel Stringology
In this abstract, we provide an overview of our survey of randomized techniques for exploiting the parallelism in string matching problems. Broadly, the study of string matching falls into two categories: standard stringology and nonstandard stringology. Standard Stringology concerns the study of various exact matching problems. The fundamental problem here is the basic string matching problem where given a pattern string p 2 m and a text string t 2 n, the problem is to nd all occurrences i in t where the pattern occurs, that is, t[i i+m 1] = p[1 m]. Other well-studied problems within standard stringology include multiple pattern matching, dictionary matching, text indexing, etc. Non-standard Stringology concerns the study of various inexact matching problems. A fundamental problem here is string matching with wildcards where the problem, as before, is to nd all occurrences of the pattern within the text; however, some positions in the text and the pattern are marked as \wildcards"(denoted ), that is, these positions match whatever be the symbol in the string they align against. Formally, given p occurs in t at i if for all 1 j m, t[i+j 1] = p[j] if p[j] 6= and t[i+j 1] 6= . Another important problem here is the k-mismatches problem in which the goal is to determine all those positions in the text where the pattern occurs with at most k mismatches amongst the aligned symbols. Other problems here include subset matching, range matching etc. Stringology includes study of many other problems involving
14958117
Computational identification of novel chitinase-like proteins in the Drosophila melanogaster genome
MOTIVATION
Multiple chitinases as well as lectins closely related to them have been characterized previously from many insect species and the corresponding genes/cDNAs have been cloned. However, the identification of the entire assortment of genes for chitinase family proteins and their differences in biochemical properties have not been carried out in any individual insect species. The completion of the entire DNA sequence of Drosophila melanogaster (fruit fly) genome and identification of open reading frames presents an opportunity to study the structures and functions of chitinase-like proteins, and also to identify new members of this family in Drosophila. We are, therefore, interested in studying the functional genomics of chitinase-like gene families in insects.


METHODS
We searched the Drosophila protein sequences database using fully characterized insect chitinase sequences and BLASTP software, identified all the putative chitinase-like proteins encoded in Drosophila genome, and predicted their structures using domain analysis tools. A phylogenetic analysis of the chitinase-like proteins from Drosophila and several other insect species was carried out. The structures of these chitinases were modeled using homology modeling software.


RESULTS
Our analysis revealed the presence of 18 chitinase-like proteins in the Drosophila protein database. Among these are seven novel chitinase-like proteins that contain four signature amino acid sequences of chitinases belonging to family 18 glycosylhydrolases, including both acidic and hydrophobic amino acid residues critical for enzyme activity. All the proteins contain at least one catalytic domain with one having four catalytic domains. Phylogenetic analysis of chitinase-like proteins from Drosophila and other insects revealed an evolutionary relationship among all these proteins, which indicated gene duplication and domain shuffling to generate the observed diversity in the encoded proteins. Homology modeling showed that all the Drosophila chitinase-like proteins contain one or more catalytic domains with a (alpha/beta)8 barrel-like structure. Our results suggest that insects utilize multiple family 18 chitinolytic enzymes and also non-enzymatic chitinase-like proteins for degrading/remodeling/binding to chitin in different insect anatomical extracellular structures, such as the cuticle, peritrophic membrane, trachea and mouth parts during insect development, and possibly for other roles including chitin synthesis.


AVAILABILITY
Perl program and supplementary material are available at http://www.ksu.edu/bioinformatics/supplementary.htm