Daniel Valenzuela

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We give new space/time tradeoffs for compressed indexes that answer document retrieval queries on general sequences. On a collection of D documents of total length n, current approaches require at least |CSA| + O(n lgD lg lgD ) or 2|CSA| + o(n) bits of space, where CSA is a full-text index. Using monotone minimum perfect hash functions, we give new(More)
Supporting top-k document retrieval queries on general text databases, that is, finding the k documents where a given pattern occurs most frequently, has become a topic of interest with practical applications. While the problem has been solved in optimal time and linear space, the actual space usage is a serious concern. In this paper we study various(More)
Given a collection of documents and a query pattern, <i>document retrieval</i> is the problem of obtaining documents that are relevant to the query. The collection is available beforehand so that a data structure, called an index, can be built on it to speed up queries. While initially restricted to natural language text collections, document retrieval(More)
In the classical interval scheduling type of problems, a set of n jobs, characterized by their start and end time, need to be executed by a set of machines, under various constraints. In this paper we study a new variant in which the jobs need to be assigned to at most k identical machines, such that the minimum number of machines that are busy at the same(More)
Traditionally biological similarity search has been studied under the abstraction of a single string to represent each genome. The more realistic representation of diploid genomes, with two strings defining the genome, has so far been largely omitted in this context. With the development of sequencing techniques and better phasing routines through haplotype(More)
Detection of genomic variants is commonly conducted by aligning a set of reads sequenced from an individual to the reference genome of the species and analyzing the resulting read pileup. Typically, this process finds a subset of variants already reported in databases and additional novel variants characteristic to the sequenced individual. Most of the(More)