External Memory Three-Sided Range Reporting and Top-k Queries with Sublogarithmic Updates

An external memory data structure is presented for maintaining a dynamic set of N two-dimensional points under the insertion and deletion of points, and supporting unsorted 3-sided range reporting queries and top-k queries, where top-k queries report the k points with highest y-value within a given x-range. For any constant 0 < epsilon <= 1/2, a data structure is constructed that supports updates in amortized O(1/(epsilon * B^{1-epsilon}) * log_B(N)) IOs and queries in amortized O(1/epsilon * log_B(N+K/B)) IOs, where B is the external memory block size, and K is the size of the output to the query (for top-k queries K is the minimum of k and the number of points in the query interval). The data structure uses linear space. The update bound is a significant factor B^{1-epsilon} improvement over the previous best update bounds for these two query problems, while staying within the same query and space bounds

Sparse Dynamic Programming on DAGs with Small Width

The minimum path cover problem asks us to find a minimum-cardinality set of paths that cover all the nodes of a directed acyclic graph (DAG). We study the case when the size k of a minimum path cover is small, that is, when the DAG has a small width. This case is motivated by applications in pan-genomics, where the genomic variation of a population is expressed as a DAG. We observe that classical alignment algorithms exploiting sparse dynamic programming can be extended to the sequence-against-DAG case by mimicking the algorithm for sequences on each path of a minimum path cover and handling an evaluation order anomaly with reachability queries. Namely, we introduce a general framework for DAG-extensions of sparse dynamic programming. This framework produces algorithms that are slower than their counterparts on sequences only by a factor k. We illustrate this on two classical problems extended to DAGs: longest increasing subsequence and longest common subsequence. For the former, we obtain an algorithm with running time O(k vertical bar E vertical bar log vertical bar V vertical bar). This matches the optimal solution to the classical problem variant when the input sequence is modeled as a path. We obtain an analogous result for the longest common subsequence problem. We then apply this technique to the co-linear chaining problem, which is a generalization of the above two problems. The algorithm for this problem turns out to be more involved, needing further ingredients, such as an FM-index tailored for large alphabets and a two-dimensional range search tree modified to support range maximum queries. We also study a general sequence-to-DAG alignment formulation that allows affine gap costs in the sequence. The main ingredient of the proposed framework is a new algorithm for finding a minimum path cover of a DAG (V, E) in O(k vertical bar E vertical bar log vertical bar V vertical bar) time, improving all known time-bounds when k is small and the DAG is not too dense. In addition to boosting the sparse dynamic programming framework, an immediate consequence of this new minimum path cover algorithm is an improved space/time tradeoff for reachability queries in arbitrary directed graphs.Peer reviewe

Linear-Space Data Structures for Range Mode Query in Arrays

A mode of a multiset $S$ is an element $a \in S$ of maximum multiplicity; that is, $a$ occurs at least as frequently as any other element in $S$. Given a list $A[1:n]$ of $n$ items, we consider the problem of constructing a data structure that efficiently answers range mode queries on $A$. Each query consists of an input pair of indices $(i, j)$ for which a mode of $A[i:j]$ must be returned. We present an $O(n^{2-2\epsilon})$-space static data structure that supports range mode queries in $O(n^\epsilon)$ time in the worst case, for any fixed $\epsilon \in [0,1/2]$. When $\epsilon = 1/2$, this corresponds to the first linear-space data structure to guarantee $O(\sqrt{n})$ query time. We then describe three additional linear-space data structures that provide $O(k)$, $O(m)$, and $O(|j-i|)$ query time, respectively, where $k$ denotes the number of distinct elements in $A$ and $m$ denotes the frequency of the mode of $A$. Finally, we examine generalizing our data structures to higher dimensions.Comment: 13 pages, 2 figure

Location-based indexing for mobile context-aware access to a digital library

Mobile information systems need to collaborate with each other to provide seamless information access to the user. Information about the user and their context provides the points of contact between the systems. Location is the most basic user context. TIP is a mobile tourist information system that provides location-based access to documents in the digital library Greenstone. This paper identifies the challenges for providing effcient access to location-based information using the various access modes a tourist requires on their travels. We discuss our extended 2DR-tree approach to meet these challenges