On-Demand Big Data Integration: A Hybrid ETL Approach for Reproducible Scientific Research

Scientific research requires access, analysis, and sharing of data that is distributed across various heterogeneous data sources at the scale of the Internet. An eager ETL process constructs an integrated data repository as its first step, integrating and loading data in its entirety from the data sources. The bootstrapping of this process is not efficient for scientific research that requires access to data from very large and typically numerous distributed data sources. a lazy ETL process loads only the metadata, but still eagerly. Lazy ETL is faster in bootstrapping. However, queries on the integrated data repository of eager ETL perform faster, due to the availability of the entire data beforehand. In this paper, we propose a novel ETL approach for scientific data integration, as a hybrid of eager and lazy ETL approaches, and applied both to data as well as metadata. This way, Hybrid ETL supports incremental integration and loading of metadata and data from the data sources. We incorporate a human-in-the-loop approach, to enhance the hybrid ETL, with selective data integration driven by the user queries and sharing of integrated data between users. We implement our hybrid ETL approach in a prototype platform, Obidos, and evaluate it in the context of data sharing for medical research. Obidos outperforms both the eager ETL and lazy ETL approaches, for scientific research data integration and sharing, through its selective loading of data and metadata, while storing the integrated data in a scalable integrated data repository.Comment: Pre-print Submitted to the DMAH Special Issue of the Springer DAPD Journa

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

The Case for Learned Index Structures

Indexes are models: a B-Tree-Index can be seen as a model to map a key to the position of a record within a sorted array, a Hash-Index as a model to map a key to a position of a record within an unsorted array, and a BitMap-Index as a model to indicate if a data record exists or not. In this exploratory research paper, we start from this premise and posit that all existing index structures can be replaced with other types of models, including deep-learning models, which we term learned indexes. The key idea is that a model can learn the sort order or structure of lookup keys and use this signal to effectively predict the position or existence of records. We theoretically analyze under which conditions learned indexes outperform traditional index structures and describe the main challenges in designing learned index structures. Our initial results show, that by using neural nets we are able to outperform cache-optimized B-Trees by up to 70% in speed while saving an order-of-magnitude in memory over several real-world data sets. More importantly though, we believe that the idea of replacing core components of a data management system through learned models has far reaching implications for future systems designs and that this work just provides a glimpse of what might be possible

Efficient Spatial Keyword Search in Trajectory Databases

An increasing amount of trajectory data is being annotated with text descriptions to better capture the semantics associated with locations. The fusion of spatial locations and text descriptions in trajectories engenders a new type of top-$k$ queries that take into account both aspects. Each trajectory in consideration consists of a sequence of geo-spatial locations associated with text descriptions. Given a user location $\lambda$ and a keyword set $\psi$, a top-$k$ query returns $k$ trajectories whose text descriptions cover the keywords $\psi$ and that have the shortest match distance. To the best of our knowledge, previous research on querying trajectory databases has focused on trajectory data without any text description, and no existing work has studied such kind of top-$k$ queries on trajectories. This paper proposes one novel method for efficiently computing top-$k$ trajectories. The method is developed based on a new hybrid index, cell-keyword conscious B$^+$-tree, denoted by \cellbtree, which enables us to exploit both text relevance and location proximity to facilitate efficient and effective query processing. The results of our extensive empirical studies with an implementation of the proposed algorithms on BerkeleyDB demonstrate that our proposed methods are capable of achieving excellent performance and good scalability.Comment: 12 page

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

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