Archive for the ‘Data Aggregation’ Category

Data Provenance: A Short Bibliography

Tuesday, September 6th, 2016

The video Provenance for Database Transformations by Val Tannen ends with a short bibliography.

Links and abstracts for the items in Val’s bibliography:

Provenance Semirings by Todd J. Green, Grigoris Karvounarakis, Val Tannen. (2007)

We show that relational algebra calculations for incomplete databases, probabilistic databases, bag semantics and whyprovenance are particular cases of the same general algorithms involving semirings. This further suggests a comprehensive provenance representation that uses semirings of polynomials. We extend these considerations to datalog and semirings of formal power series. We give algorithms for datalog provenance calculation as well as datalog evaluation for incomplete and probabilistic databases. Finally, we show that for some semirings containment of conjunctive queries is the same as for standard set semantics.

Update Exchange with Mappings and Provenance by Todd J. Green, Grigoris Karvounarakis, Zachary G. Ives, Val Tannen. (2007)

We consider systems for data sharing among heterogeneous peers related by a network of schema mappings. Each peer has a locally controlled and edited database instance, but wants to ask queries over related data from other peers as well. To achieve this, every peer’s updates propagate along the mappings to the other peers. However, this update exchange is filtered by trust conditions — expressing what data and sources a peer judges to be authoritative — which may cause a peer to reject another’s updates. In order to support such filtering, updates carry provenance information. These systems target scientific data sharing applications, and their general principles and architecture have been described in [20].

In this paper we present methods for realizing such systems. Specifically, we extend techniques from data integration, data exchange, and incremental view maintenance to propagate updates along mappings; we integrate a novel model for tracking data provenance, such that curators may filter updates based on trust conditions over this provenance; we discuss strategies for implementing our techniques in conjunction with an RDBMS; and we experimentally demonstrate the viability of our techniques in the ORCHESTRA prototype system.

Annotated XML: Queries and Provenance by J. Nathan Foster, Todd J. Green, Val Tannen. (2008)

We present a formal framework for capturing the provenance of data appearing in XQuery views of XML. Building on previous work on relations and their (positive) query languages, we decorate unordered XML with annotations from commutative semirings and show that these annotations suffice for a large positive fragment of XQuery applied to this data. In addition to tracking provenance metadata, the framework can be used to represent and process XML with repetitions, incomplete XML, and probabilistic XML, and provides a basis for enforcing access control policies in security applications.

Each of these applications builds on our semantics for XQuery, which we present in several steps: we generalize the semantics of the Nested Relational Calculus (NRC) to handle semiring-annotated complex values, we extend it with a recursive type and structural recursion operator for trees, and we define a semantics for XQuery on annotated XML by translation into this calculus.

Containment of Conjunctive Queries on Annotated Relations by Todd J. Green. (2009)

We study containment and equivalence of (unions of) conjunctive queries on relations annotated with elements of a commutative semiring. Such relations and the semantics of positive relational queries on them were introduced in a recent paper as a generalization of set semantics, bag semantics, incomplete databases, and databases annotated with various kinds of provenance information. We obtain positive decidability results and complexity characterizations for databases with lineage, why-provenance, and provenance polynomial annotations, for both conjunctive queries and unions of conjunctive queries. At least one of these results is surprising given that provenance polynomial annotations seem “more expressive” than bag semantics and under the latter, containment of unions of conjunctive queries is known to be undecidable. The decision procedures rely on interesting variations on the notion of containment mappings. We also show that for any positive semiring (a very large class) and conjunctive queries without self-joins, equivalence is the same as isomorphism.

Collaborative Data Sharing with Mappings and Provenance by Todd J. Green, dissertation. (2009)

A key challenge in science today involves integrating data from databases managed by different collaborating scientists. In this dissertation, we develop the foundations and applications of collaborative data sharing systems (CDSSs), which address this challenge. A CDSS allows collaborators to define loose confederations of heterogeneous databases, relating them through schema mappings that establish how data should flow from one site to the next. In addition to simply propagating data along the mappings, it is critical to record data provenance (annotations describing where and how data originated) and to support policies allowing scientists to specify whose data they trust, and when. Since a large data sharing confederation is certain to evolve over time, the CDSS must also efficiently handle incremental changes to data, schemas, and mappings.

We focus in this dissertation on the formal foundations of CDSSs, as well as practical issues of its implementation in a prototype CDSS called Orchestra. We propose a novel model of data provenance appropriate for CDSSs, based on a framework of semiring-annotated relations. This framework elegantly generalizes a number of other important database semantics involving annotated relations, including ranked results, prior provenance models, and probabilistic databases. We describe the design and implementation of the Orchestra prototype, which supports update propagation across schema mappings while maintaining data provenance and filtering data according to trust policies. We investigate fundamental questions of query containment and equivalence in the context of provenance information. We use the results of these investigations to develop novel approaches to efficiently propagating changes to data and mappings in a CDSS. Our approaches highlight unexpected connections between the two problems and with the problem of optimizing queries using materialized views. Finally, we show that semiring annotations also make sense for XML and nested relational data, paving the way towards a future extension of CDSS to these richer data models.

Provenance in Collaborative Data Sharing by Grigoris Karvounarakis, dissertation. (2009)

This dissertation focuses on recording, maintaining and exploiting provenance information in Collaborative Data Sharing Systems (CDSS). These are systems that support data sharing across loosely-coupled, heterogeneous collections of relational databases related by declarative schema mappings. A fundamental challenge in a CDSS is to support the capability of update exchange — which publishes a participant’s updates and then translates others’ updates to the participant’s local schema and imports them — while tolerating disagreement between them and recording the provenance of exchanged data, i.e., information about the sources and mappings involved in their propagation. This provenance information can be useful during update exchange, e.g., to evaluate provenance-based trust policies. It can also be exploited after update exchange, to answer a variety of user queries, about the quality, uncertainty or authority of the data, for applications such as trust assessment, ranking for keyword search over databases, or query answering in probabilistic databases.

To address these challenges, in this dissertation we develop a novel model of provenance graphs that is informative enough to satisfy the needs of CDSS users and captures the semantics of query answering on various forms of annotated relations. We extend techniques from data integration, data exchange, incremental view maintenance and view update to define the formal semantics of unidirectional and bidirectional update exchange. We develop algorithms to perform update exchange incrementally while maintaining provenance information. We present strategies for implementing our techniques over an RDBMS and experimentally demonstrate their viability in the ORCHESTRA prototype system. We define ProQL, iv a query language for provenance graphs that can be used by CDSS users to combine data querying with provenance testing as well as to compute annotations for their data, based on their provenance, that are useful for a variety of applications. Finally, we develop a prototype implementation ProQL over an RDBMS and indexing techniques to speed up provenance querying, evaluate experimentally the performance of provenance querying and the benefits of our indexing techniques.

Provenance for Aggregate Queries by Yael Amsterdamer, Daniel Deutch, Val Tannen. (2011)

We study in this paper provenance information for queries with aggregation. Provenance information was studied in the context of various query languages that do not allow for aggregation, and recent work has suggested to capture provenance by annotating the different database tuples with elements of a commutative semiring and propagating the annotations through query evaluation. We show that aggregate queries pose novel challenges rendering this approach inapplicable. Consequently, we propose a new approach, where we annotate with provenance information not just tuples but also the individual values within tuples, using provenance to describe the values computation. We realize this approach in a concrete construction, first for “simple” queries where the aggregation operator is the last one applied, and then for arbitrary (positive) relational algebra queries with aggregation; the latter queries are shown to be more challenging in this context. Finally, we use aggregation to encode queries with difference, and study the semantics obtained for such queries on provenance annotated databases.

Circuits for Datalog Provenance by Daniel Deutch, Tova Milo, Sudeepa Roy, Val Tannen. (2014)

The annotation of the results of database queries with provenance information has many applications. This paper studies provenance for datalog queries. We start by considering provenance representation by (positive) Boolean expressions, as pioneered in the theories of incomplete and probabilistic databases. We show that even for linear datalog programs the representation of provenance using Boolean expressions incurs a super-polynomial size blowup in data complexity. We address this with an approach that is novel in provenance studies, showing that we can construct in PTIME poly-size (data complexity) provenance representations as Boolean circuits. Then we present optimization techniques that embed the construction of circuits into seminaive datalog evaluation, and further reduce the size of the circuits. We also illustrate the usefulness of our approach in multiple application domains such as query evaluation in probabilistic databases, and in deletion propagation. Next, we study the possibility of extending the circuit approach to the more general framework of semiring annotations introduced in earlier work. We show that for a large and useful class of provenance semirings, we can construct in PTIME poly-size circuits that capture the provenance.

Incomplete but a substantial starting point exploring data provenance and its relationship/use with topic map merging.

To get a feel for “data provenance” just prior to the earliest reference here (2007), consider A Survey of Data Provenance Techniques by Yogesh L. Simmhan, Beth Plale, Dennis Gannon, published in 2005.

Data management is growing in complexity as large-scale applications take advantage of the loosely coupled resources brought together by grid middleware and by abundant storage capacity. Metadata describing the data products used in and generated by these applications is essential to disambiguate the data and enable reuse. Data provenance, one kind of metadata, pertains to the derivation history of a data product starting from its original sources.

The provenance of data products generated by complex transformations such as workflows is of considerable value to scientists. From it, one can ascertain the quality of the data based on its ancestral data and derivations, track back sources of errors, allow automated re-enactment of derivations to update a data, and provide attribution of data sources. Provenance is also essential to the business domain where it can be used to drill down to the source of data in a data warehouse, track the creation of intellectual property, and provide an audit trail for regulatory purposes.

In this paper we create a taxonomy of data provenance techniques, and apply the classification to current research efforts in the field. The main aspect of our taxonomy categorizes provenance systems based on why they record provenance, what they describe, how they represent and store provenance, and ways to disseminate it. Our synthesis can help those building scientific and business metadata-management systems to understand existing provenance system designs. The survey culminates with an identification of open research problems in the field.

Another rich source of reading material!

Exploring and Visualizing Pre-Topic Map Data

Monday, November 2nd, 2015

AggreSet: Rich and Scalable Set Exploration using Visualizations of Element Aggregations by M. Adil Yalçın, Niklas Elmqvist, and Benjamin B. Bederson.

Abstract:

Datasets commonly include multi-value (set-typed) attributes that describe set memberships over elements, such as genres per movie or courses taken per student. Set-typed attributes describe rich relations across elements, sets, and the set intersections. Increasing the number of sets results in a combinatorial growth of relations and creates scalability challenges. Exploratory tasks (e.g. selection, comparison) have commonly been designed in separation for set-typed attributes, which reduces interface consistency. To improve on scalability and to support rich, contextual exploration of set-typed data, we present AggreSet. AggreSet creates aggregations for each data dimension: sets, set-degrees, set-pair intersections, and other attributes. It visualizes the element count per aggregate using a matrix plot for set-pair intersections, and histograms for set lists, set-degrees and other attributes. Its non-overlapping visual design is scalable to numerous and large sets. AggreSet supports selection, filtering, and comparison as core exploratory tasks. It allows analysis of set relations inluding subsets, disjoint sets and set intersection strength, and also features perceptual set ordering for detecting patterns in set matrices. Its interaction is designed for rich and rapid data exploration. We demonstrate results on a wide range of datasets from different domains with varying characteristics, and report on expert reviews and a case study using student enrollment and degree data with assistant deans at a major public university.

These two videos will give you a better overview of AggreSet than I can. The first one is about 30 seconds and the second one about 5 minutes.

The visualization of characters from Les Misérables (the second video) is a dynamite demonstration of how you could explore pre-topic map data with an eye towards creating roles and associations between characters as well as with the text.

First use case that pops to mind would be harvesting the fan posts on Harry Potter and crossing them with a similar listing of characters from the Harry Potter book series. With author, date, book, character, etc., relationships.

While you are at the GitHub site: https://github.com/adilyalcin/Keshif/tree/master/AggreSet, be sure to bounce up a level to Keshif:

Keshif is a web-based tool that lets you browse and understand datasets easily.

To start using Keshif:

  • Get the source code from github,
  • Explore the existing datasets and their source codes, and
  • Check out the wiki.

Or just go directly to the Keshif site, with 110 datasets (as of today)>

For the impatient, see Loading Data.

For the even more impatient:

You can load data to Keshif from :

  • Google Sheets
  • Text File
    • On Google Drive
    • On Dropbox
    • File on your webserver

Text File Types

Keshif can be used with the following data file types:

  • CSV / TSV
  • JSON
  • XML
  • Any other file type that you can load and parse in JavaScript. See Custom Data Loading

Hint: The dataset explorer at the frontpage indexes demos by file type and resource. Filter by data source to find example source code on how to apply a specific file loading approach.

The critical factor, in addition to its obvious usefulness, is that it works in a web browser. You don’t have to install software, set Java paths, download additional libraries, etc.

Are you using the modern web browser as your target for user facing topic map applications?

I first saw this in a tweet by Christophe Lalanne.

Gathering, Extracting, Analyzing Chemistry Datasets

Wednesday, April 22nd, 2015

Activities at the Royal Society of Chemistry to gather, extract and analyze big datasets in chemistry by Antony Williams.

If you are looking for a quick summary of efforts to combine existing knowledge resources in chemistry, you can do far worse than Antony’s 118 slides on the subject (2015).

I want to call special attention to Slide 107 in his slide deck:

chemistry-antony-22April2015

True enough, extraction is problematic, expensive, inaccurate, etc., all the things Antony describes. And I would strongly second all of what he implies is the better practice.

However, extraction isn’t just a necessity for today or for a few years, extraction is going to be necessary so long as we keep records about chemistry or any other subject.

Think about all the legacy materials on chemistry that exist in hard copy format just for the past two centuries. To say nothing of all of still older materials. It is more than unfortunate to abandon all that information simply because “modern” digital formats are easier to manipulate.

That was’t what Antony meant to imply but even after all materials have been extracted and exist in some form of digital format, that doesn’t mean the era of “extraction” will have ended.

You may not remember when atomic chemistry used “punch cards” to record isotopes:

isotope-punch-card

An isotope file on punched cards. George M. Murphy J. Chem. Educ., 1947, 24 (11), p 556 DOI: 10.1021/ed024p556 Publication Date: November 1947.

Today we would represent that record in…NoSQL?

Are you confident that in another sixty-eight (68) years we will still be using NoSQL?

We have to choose from the choices available to us today, but we should not deceive ourselves into thinking our solution will be seen as the “best” solution in the future. New data will be discovered, new processes invented, new requirements will emerge, all of which will be clamoring for a “new” solution.

Extraction will persist as long as we keep recording information in the face of changing formats and requirements. We can improve that process but I don’t think we will ever completely avoid it.

Federal Data Integration: Dengue Fever

Tuesday, April 7th, 2015

The White House issued a press release today (April 7, 2015) titled: FACT SHEET: Administration Announces Actions To Protect Communities From The Impacts Of Climate Change.

That press release reads in part:


Unleashing Data: As part of the Administration’s Predict the Next Pandemic Initiative, in May 2015, an interagency working group co-chaired by OSTP, the CDC, and the Department of Defense will launch a pilot project to simulate efforts to forecast epidemics of dengue – a mosquito-transmitted viral disease affecting millions of people every year, including U.S. travelers and residents of the tropical regions of the U.S. such as Puerto Rico. The pilot project will consolidate data sets from across the federal government and academia on the environment, disease incidence, and weather, and challenge the research and modeling community to develop predictive models for dengue and other infectious diseases based on those datasets. In August 2015, OSTP plans to convene a meeting to evaluate resulting models and showcase this effort as a “proof-of-concept” for similar forecasting efforts for other infectious diseases.

I tried finding more details on earlier workshops in this effort but limiting the search to “Predict the Next Pandemic Initiative” and the domain to “.gov,” I got two “hits.” One of which was the press release I cite above.

I sent a message (webform) to the White House Office of Science and Technology Policy office and will update you with any additional information that arrives.

Of course my curiosity is about the means used to integrate the data sets. Once integrated, such data sets can be re-used, at least until it is time to integrate additional data sets. Bearing in mind that dirty data can lead to poor decision making, I would rather not duplicate the cleaning of data time after time.

Data Inte-Aggregration [Heads Up!]

Monday, February 4th, 2013

Data Inte-Aggregration by David Loshin.

From the post:

One of our clients is a government agency that, among many other directives, is tasked with collecting data from many sources, merging that data into a single asset and then making that collected data set available to the public. Interestingly, the source data sets themselves represent aggregations pulled from different collections of internal transactions between any particular company and a domain of individuals within a particular industry.

The agency must then collect the data from the many different companies and then link the records for each individual from each company, sum the totals for the sets of transactions and then present the collected totals for each individual.

This scenario poses a curious challenge: there is an integration, an aggregation, another integration, then another aggregation. But the first sets of integration and aggregation occur behind the corporate firewall while the second set is performed by a third party. That is the reason that I titled this blog post “Data Inte-Aggregation,” in reference to this dual-phased data consolidation that crosses administrative barriers.

David is starting a series of posts on aggregating data that crosses “administrative barriers.”

Looking forward to this series and so should you!

OData Extensions for Data Aggregation

Friday, June 15th, 2012

OData Extensions for Data Aggregation by Chris Webb.

Chris writes:

I was just reading the following blog post on the OASIS OData Technical Committee Call for Participation: http://www.odata.org/blog/2012/6/11/oasis-odata-technical-committee-call-for-participation

…when I saw this:

In addition to the core OData version 3.0 protocol found here, the Technical Committee will be defining some key extensions in the first version of the OASIS Standard:

OData Extensions for Data Aggregation – Business Intelligence provides the ability to get the right set of aggregated results from large data warehouses. OData Extensions for Analytics enable OData to support Business Intelligence by allowing services to model data analytic “cubes” (dimensions, hierarchies, measures) and consumers to query aggregated data

Follow the link in the quoted text – it’s very interesting reading! Here’s just one juicy quote:

You have to go to Chris’ post to see the “juicy quote.” 😉

With more data becoming available, at higher speeds, data aggregation is going to be the norm.

Some people will do it well. Some people will do it not so well.

Which one will describe you?

Participation in the OData TC at OASIS may help shape that answer: http://www.odata.org/blog/2012/6/11/oasis-odata-technical-committee-call-for-participation

First meeting details:

The first meeting of the Technical Committee will be a face-to-face meeting to be held in Redmond, Washington on July 26-27, 2012 from 9 AM PT to 5 PM PT. This meeting will be sponsored by Microsoft. Dial-in conference calling bridge numbers will be available for those unable to attend in person.

At least the meeting is on a Thursday/Friday slot! Any comments on the weather to expect in late July?