Related papers: Compressed Indexing for Consecutive Occurrences
In this paper we study the fundamental problem of maintaining a dynamic collection of strings under the following operations: concat - concatenates two strings, split - splits a string into two at a given position, compare - finds the…
Domains like bioinformatics, version control systems, collaborative editing systems (wiki), and others, are producing huge data collections that are very repetitive. That is, there are few differences between the elements of the collection.…
The nature of the alignment with gaps corresponding to a longest common subsequence (LCS) of two independent iid random sequences drawn from a finite alphabet is investigated. It is shown that such an optimal alignment typically matches…
We present a new graph compressor that works by recursively detecting repeated substructures and representing them through grammar rules. We show that for a large number of graphs the compressor obtains smaller representations than other…
In optimization or machine learning problems we are given a set of items, usually points in some metric space, and the goal is to minimize or maximize an objective function over some space of candidate solutions. For example, in clustering…
We consider the problem of detecting data races in program traces that have been compressed using straight line programs (SLP), which are special context-free grammars that generate exactly one string, namely the trace that they represent.…
Sequential learning with Gaussian processes (GPs) is challenging when access to past data is limited, for example, in continual and active learning. In such cases, errors can accumulate over time due to inaccuracies in the posterior,…
Let S be a finite, ordered alphabet, and let x = x_1 x_2 ... x_n be a string over S. A "secondary index" for x answers alphabet range queries of the form: Given a range [a_l,a_r] over S, return the set I_{[a_l;a_r]} = {i |x_i \in [a_l;…
A linear parameter must be consumed exactly once in the body of its function. When declaring resources such as file handles and manually managed memory as linear arguments, a linear type system can verify that these resources are used…
Indexing intervals is a fundamental problem, finding a wide range of applications. Recent work on managing large collections of intervals in main memory focused on overlap joins and temporal aggregation problems. In this paper, we propose…
We consider the problem of learning overcomplete dictionaries in the context of sparse coding, where each sample selects a sparse subset of dictionary elements. Our main result is a strategy to approximately recover the unknown dictionary…
In this paper, we revisit the much studied problem of Pattern Matching with Swaps (Swap Matching problem, for short). We first present a graph-theoretic model, which opens a new and so far unexplored avenue to solve the problem. Then, using…
The constrained synchronization problem (CSP) asks for a synchronizing word of a given input automaton contained in a regular set of constraints. It could be viewed as a special case of synchronization of a discrete event system under…
The perfect phylogeny is one of the most used models in different areas of computational biology. In this paper we consider the problem of the Persistent Perfect Phylogeny (referred as P-PP) recently introduced to extend the perfect…
Advances in DNA sequencing mean databases of thousands of human genomes will soon be commonplace. In this paper we introduce a simple technique for reducing the size of conventional indexes on such highly repetitive texts. Given upper…
In this paper we present a new problem, the fast set intersection problem, which is to preprocess a collection of sets in order to efficiently report the intersection of any two sets in the collection. In addition we suggest new solutions…
We study strategies of approximate pattern matching that exploit bidirectional text indexes, extending and generalizing ideas of Lam et al. We introduce a formalism, called search schemes, to specify search strategies of this type, then…
Consistent sampling is a technique for specifying, in small space, a subset $S$ of a potentially large universe $U$ such that the elements in $S$ satisfy a suitably chosen sampling condition. Given a subset $\mathcal{I}\subseteq U$ it…
Search applications often display shortened sentences which must contain certain query terms and must fit within the space constraints of a user interface. This work introduces a new transition-based sentence compression technique developed…
Causal consistency is one of the most adopted consistency criteria for distributed implementations of data structures. It ensures that operations are executed at all sites according to their causal precedence. We address the issue of…