RkNN Query Processing in Distributed Spatial Infrastructures: A Performance Study

The Reverse k-Nearest Neighbor (RkNN) problem, i.e. finding all objects in a dataset that have a given query point among their corresponding k-nearest neighbors, has received increasing attention in the past years. RkNN queries are of particular interest in a wide range of applications such as decision support systems, resource allocation, profile-based marketing, location-based services, etc. With the current increasing volume of spatial data, it is difficult to perform RkNN queries efficiently in spatial data-intensive applications, because of the limited computational capability and storage resources. In this paper, we investigate how to design and implement distributed RkNN query algorithms using shared-nothing spatial cloud infrastructures as SpatialHadoop and LocationSpark. SpatialHadoop is a framework that inherently supports spatial indexing on top of Hadoop to perform efficiently spatial queries. LocationSpark is a recent spatial data processing system built on top of Spark. We have evaluated the performance of the distributed RkNN query algorithms on both SpatialHadoop and LocationSpark with big real-world datasets. The experiments have demonstrated the efficiency and scalability of our proposal in both distributed spatial data management systems, showing the performance advantages of LocationSpark

Indexing arbitrary-length kk-mers in sequencing reads

We propose a lightweight data structure for indexing and querying collections of NGS reads data in main memory. The data structure supports the interface proposed in the pioneering work by Philippe et al. for counting and locating $k$-mers in sequencing reads. Our solution, PgSA (pseudogenome suffix array), based on finding overlapping reads, is competitive to the existing algorithms in the space use, query times, or both. The main applications of our index include variant calling, error correction and analysis of reads from RNA-seq experiments

Universal Indexes for Highly Repetitive Document Collections

Indexing highly repetitive collections has become a relevant problem with the emergence of large repositories of versioned documents, among other applications. These collections may reach huge sizes, but are formed mostly of documents that are near-copies of others. Traditional techniques for indexing these collections fail to properly exploit their regularities in order to reduce space. We introduce new techniques for compressing inverted indexes that exploit this near-copy regularity. They are based on run-length, Lempel-Ziv, or grammar compression of the differential inverted lists, instead of the usual practice of gap-encoding them. We show that, in this highly repetitive setting, our compression methods significantly reduce the space obtained with classical techniques, at the price of moderate slowdowns. Moreover, our best methods are universal, that is, they do not need to know the versioning structure of the collection, nor that a clear versioning structure even exists. We also introduce compressed self-indexes in the comparison. These are designed for general strings (not only natural language texts) and represent the text collection plus the index structure (not an inverted index) in integrated form. We show that these techniques can compress much further, using a small fraction of the space required by our new inverted indexes. Yet, they are orders of magnitude slower.Comment: This research has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sk{\l}odowska-Curie Actions H2020-MSCA-RISE-2015 BIRDS GA No. 69094

Reverse-Safe Data Structures for Text Indexing

We introduce the notion of reverse-safe data structures. These are data structures that prevent the reconstruction of the data they encode (i.e., they cannot be easily reversed). A data structure D is called z-reverse-safe when there exist at least z datasets with the same set of answers as the ones stored by D. The main challenge is to ensure that D stores as many answers to useful queries as possible, is constructed efficiently, and has size close to the size of the original dataset it encodes. Given a text of length n and an integer z, we propose an algorithm which constructs a z-reverse-safe data structure that has size O(n) and answers pattern matching queries of length at most d optimally, where d is maximal for any such z-reverse-safe data structure. The construction algorithm takes O(n ω log d) time, where ω is the matrix multiplication exponent. We show that, despite the n ω factor, our engineered implementation takes only a few minutes to finish for million-letter texts. We further show that plugging our method in data analysis applications gives insignificant or no data utility loss. Finally, we show how our technique can be extended to support applications under a realistic adversary model

A Density-Based Approach to the Retrieval of Top-K Spatial Textual Clusters

Keyword-based web queries with local intent retrieve web content that is relevant to supplied keywords and that represent points of interest that are near the query location. Two broad categories of such queries exist. The first encompasses queries that retrieve single spatial web objects that each satisfy the query arguments. Most proposals belong to this category. The second category, to which this paper's proposal belongs, encompasses queries that support exploratory user behavior and retrieve sets of objects that represent regions of space that may be of interest to the user. Specifically, the paper proposes a new type of query, namely the top-k spatial textual clusters (k-STC) query that returns the top-k clusters that (i) are located the closest to a given query location, (ii) contain the most relevant objects with regard to given query keywords, and (iii) have an object density that exceeds a given threshold. To compute this query, we propose a basic algorithm that relies on on-line density-based clustering and exploits an early stop condition. To improve the response time, we design an advanced approach that includes three techniques: (i) an object skipping rule, (ii) spatially gridded posting lists, and (iii) a fast range query algorithm. An empirical study on real data demonstrates that the paper's proposals offer scalability and are capable of excellent performance

Improved ESP-index: a practical self-index for highly repetitive texts

While several self-indexes for highly repetitive texts exist, developing a practical self-index applicable to real world repetitive texts remains a challenge. ESP-index is a grammar-based self-index on the notion of edit-sensitive parsing (ESP), an efficient parsing algorithm that guarantees upper bounds of parsing discrepancies between different appearances of the same subtexts in a text. Although ESP-index performs efficient top-down searches of query texts, it has a serious issue on binary searches for finding appearances of variables for a query text, which resulted in slowing down the query searches. We present an improved ESP-index (ESP-index-I) by leveraging the idea behind succinct data structures for large alphabets. While ESP-index-I keeps the same types of efficiencies as ESP-index about the top-down searches, it avoid the binary searches using fast rank/select operations. We experimentally test ESP-index-I on the ability to search query texts and extract subtexts from real world repetitive texts on a large-scale, and we show that ESP-index-I performs better that other possible approaches.Comment: This is the full version of a proceeding accepted to the 11th International Symposium on Experimental Algorithms (SEA2014