=Paper=
{{Paper
|id=Vol-1799/Drift-a-LOD2016_paper_6
|storemode=property
|title=Visualizing the Drift of Linked Open Data Using Self-Organizing Maps
|pdfUrl=https://ceur-ws.org/Vol-1799/Drift-a-LOD2016_paper_6.pdf
|volume=Vol-1799
|authors=Albert Meroño-Peñuela,Peter Wittek,Sándor Darányi
|dblpUrl=https://dblp.org/rec/conf/ekaw/Merono-PenuelaW16
}}
==Visualizing the Drift of Linked Open Data Using Self-Organizing Maps==
https://ceur-ws.org/Vol-1799/Drift-a-LOD2016_paper_6.pdf
Visualizing the Drift of Linked Open Data Using
Self-Organizing Maps
Albert Meroño-Peñuela1 , Peter Wittek2,3 , and Sándor Darányi3
1
Department of Computer Science, Vrije Universiteit Amsterdam, NL
albert.merono@vu.nl
ICFO-The Institute of Photonic Sciences, ES
2
3
Swedish School of Library and Information Science, University of Borås, SE
Abstract. The urge for evolving the Web into a globally shared datas-
pace has turned the Linked Open Data (LOD) cloud into a massive plat-
form containing 100 billion machine-readable statements. Several factors
hamper a historical study of the evolution of the LOD cloud, and hence
forecast its future: its ever-growing scale, which makes a global analy-
sis difficult; its Web-distributed nature, which challenges the analysis of
its data; and the scarcity of regular and time-stamped archival dumps.
Recently, a scalable implementation of self-organizing maps (SOM) has
been developed to visualize the local topology of high-dimensional data.
We use this methodology to address scalability issues, and the Dynamic
Linked Data Observatory, a regular biweekly centralized sample of the
LOD cloud as a time-stamped collection. We visualize the drift of Linked
Datasets between 2012 and 2016, finding that datasets with high avail-
ability, high vocabulary reuse, and modeling with commonly used terms
in the LOD cloud are better traceable across time.
Keywords: Linked Data, Semantic Drift, Visualization
1 Introduction
The original vision of the Semantic Web [2] is becoming a reality by the publish-
ing paradigm of Linked Data, which so far consists of a global, Web-accessible
graph of knowledge of 100 billion RDF statements known as the Linked Open
Data (LOD) cloud 4 . In this Web dataspace, dynamics are the norm: new data
are added, old are removed, and schemata evolve to accommodate new require-
ments and changes in the domain. Terms like semantic drift are used to refer to
problems that arise as a consequence of these dynamics. One of the typical access
methods for Linked Data is SPARQL, a protocol and query language. Datasets
become inaccessible, for instance, due to query templates that no longer cor-
respond to the schema [8]. The maintainability of ontologies is cumbersome –
large change logs are costly and client applications cannot adapt to them. It is
4
http://lod-cloud.net/
impossible to have an abstract perception of the history of the LOD cloud, and
it is equally infeasible to forecast how it might evolve in the future.
Recent work addressing some areas of semantic drift shows that solutions
to specific problems in this domain can provide great real-world benefits, such
as automated maintenance of biomedical ontologies [10] and efficient update of
caches in applications using LOD [3]. However, the global challenge of semantic
drift is emphasized by three inherent factors of structured data on the Web:
(1) its unprecedented and unconstrained scale; (2) its highly distributed nature;
and (3) the scarcity of regular and systematic timestamped dumps. Several ap-
proaches study semantic drift over time in the context of LOD and the Semantic
Web, although none of them addresses all of these factors. For example, Wang et
al. [13] provide theoretical ground for heuristics under the assumption of existing
timestamped dumps, but do not address problems (1) and (2). Similarly, the well
established field of ontology evolution [12] has seen a rebirth in approaches that
model it using machine learning [9,10]. The Dynamic Linked Data Observatory
(DyLDO) [5] covers (2) and (3), but does not solve the problem of scale. Re-
cently, a massively parallel implementation of self-organizing maps (SOM) has
proven useful to model, reduce the dimensionality of, and visualize large scale
evolving data in an efficient way [6]). In this paper, we study the requirements
derived from problems (1), (2), and (3) for visualizing Linked Data that evolve
over time; and we argue that the combination of DyLDO and Somoclu fulfills
these requirements in a comprehensive and visually explicit manner. We find
that datasets published as LOD in the period 2012-2016 with high availability,
high reuse of vocabularies5 , and high adherence to commonly used terms are
better traceable in time. More specifically, the contributions of the paper are as
follows:
– We describe requirements for visualizing the temporal drift of datasets in
LOD (Section 3);
– We argue the convenience and describe the foundations of SOM techniques
to address these requirements (Sections 2 and 4);
– We use a scalable implementation of SOM over the DyLDO dataset, a large
crawl of timestamped LOD in the period 2012-2016 (Section 4). Datasets
that were highly available with online and de-referenceable URI resources,
reused existing vocabularies in the LOD cloud, and chose common and highly
used terms to describe their resources are better traceable over time in low-
dimensional representations of high-dimensional input Linked Data.
2 Related Work
The problems of semantic change and drift concern various research fields. In
the areas of Semantic Web and knowledge representation, ontology evolution [7]
addresses “the timely adaptation of an ontology and consistent propagation of
changes to dependent artifacts” [1]. Features of evolution have been studied [12]
and used for prediction using machine learning [10]. Gonçalves et al. [4] use
5
See http://lov.okfn.org/dataset/lov/
2
Description Logics to calculate differences between ontologies (so-called semantic
diffs). Wang et al. [13] define the semantics of concept change and drift, and how
to identify them. General surveys of semantic change in other fields, including
language, have recently appeared [11].
Caching Linked Data is the primary goal of repositories like LODCache6 . To
the best of our knowledge, the Dynamic Linked Data Observatory, DyLDO [5],
is the only available crawl of LOD with rigorous timestamps.
Dimensionality reduction is a standard technique in statistical data analysis
and machine learning. In sparse spaces, such as the ones we obtain from LOD, the
global topology of the space is often less important than the local regions where
many data instances have overlapping nonzero elements: techniques that focus
on preserving local topology are preferred. Self-organizing maps are an example
of this type [6]. They were introduced to the study of drifts [14] which was
enabled at scale by a massively parallel implementation of the methodology [15].
After training a map, each data instance will have a matching point called the
best matching unit (BMU) on the map – the immediate surroundings of this
point reflect the local topology of the original space. Intense colours on the map
indicate high distances between the original data points.
3 Requirements for Visualizing LOD Drifts Over Time
Table 1 compiles a set of requirements for visualizing the temporal drift of
datasets in the LOD cloud. For each requirement, we assign a name, a descrip-
tion, and whether it concerns the drift analysis algorithms or the analyzed data.
As a basis for this, we consider the following characteristics of the LOD cloud:
– High-scale. The size of the LOD cloud is large, counting 100 billion state-
ments in an unconstrained environment that allows for arbitrary growth;
– Distributed. LOD uses the Web as a publishing platform, meaning that
Linked Data can be potentially found in any node of the Web;
– Timestamped dumps. In LOD, temporal drifts may occur anytime. Since
a sound and complete version control that manages all changes in LOD is
currently impracticable, regular timestamped snapshots of the LOD cloud
(or a sample of it) are necessary to study drift.
4 Experiments
We describe an empirical application of SOM to different subsequent snapshots
of the LOD cloud over time, using the Somoclu algorithm [15] and the DyLDO [5]
dataset7,8 . Somoclu and DyLDO fulfill the requirements of Table 1, and hence
their combination poses a promising solution for visualizing LOD drifts. Somo-
clu fulfills the algorithm requirements in terms of efficiency, visualization, di-
mensionality reduction, topology preservation and unsupervised learning; while
DyLDO does for the requirements of centralization, sampling and provenance.
6
https://datahub.io/dataset/openlink-lod-cache
7
http://swse.deri.org/dyldo/
8
All experimental data and code are available online at https://github.com/
albertmeronyo/somoclu-dyldo
3
Name Description Alg./Data
Efficiency Solutions addressing semantic drift in LOD should be ef- Alg.
ficient in order to address its scale.
Centralization Linked Data is scattered over the Web, and analysis of Data
drift is impracticable in Web-distributed data. Datasets
to be analyzed need to be centralized.
Visualization The result of the analysis of drift in LOD should be an Alg.
understandable, meaningful and coherent visualization to
the human eye
Sampling The distributed architecture of the Web makes complete Data
studies of drift over all LOD very difficult. Samples of
different sizes are needed.
Dimensionality Most features of Linked Data are usually in a high- Alg.
reduction dimensional space (e.g. total number of URIs in predicate
position). Representing these in a lower-dimensional space
is necessary for human-understandable visualizations
Topology preser- Any technique reducing the dimensionality of the input Alg.
vation space must preserve its topology in order to faithfully rep-
resent the subtleties of drifts in LOD
Unsupervised The high-scale of LOD makes the manual annotation of Alg.
learning instances by humans impracticable, and algorithms ana-
lyzing drifts in LOD should operate in an unsupervised
manner.
Provenance The Linked Data subject to the study of drift should Data
have accurate and structured provenance information, es-
pecially regarding its collection time in the form of times-
tamps
Table 1: Requirements for visualizing LOD drifts, concerning algorithms and
data.
4.1 Preparation
We select 79 DyLDO snapshots comprised in the period from 2012-05-13 until
2016-03-27 (dates are in format YYYY-MM-DD). Since a study of drift that considers
RDF triples as units of analysis would be both cumbersome and superficial, we
consider URIs that appear in predicate position only. This allows us to simplify
the matrix construction process, at the time we focus the analysis on the usage
of vocabulary terms.
First, we build an index of common unique predicates (275,412) and common
unique graph names (4,506) in all these snapshots. All these predicates and graph
names occur in all snapshots. Secondly, for each snapshot we build a sparse
matrix that indicates the frequency of each predicate in each graph name. These
highly sparse vectors characterize the contents of the graphs: every instance
is a vector containing counts of each possible predicate in that graph name.
This means we generate 79 sparse matrices with 275,412 dimensions and 4,506
instances, with an average sparsity (i.e. non-zero elements) of 0.03%.
4.2 Training SOMs
Training self-organizing maps is a computationally expensive task. We rely on
a massively parallel implementation called Somoclu [15]9 . This implementation
9
See http://peterwittek.github.io/somoclu/. We use its Python interface for
visualization, which is available at https://pypi.python.org/pypi/somoclu/
4
can also handle sparse input data. Apart from the computational requirements, a
key challenge in using SOMs is the large number of parameters that require fine-
tuning. As a rule of thumb, toroid topology yields higher quality maps because we
avoid jamming best matching neurons along the edges as we would with a planar
layout. We seldom see fundamental topological differences between hexagonal
and square-shaped neurons, so we use the second for their easier visual treatment.
Due to memory limitations, we establish a map size of 15 rows and 25 columns.
To ensure a smooth initial map, we train it for a longer time (ten epochs instead
of three) and at a higher learning rate (0.1 instead of 0.05) than the rest. We
use the output neuron weights of snapshot t as a codebook to initialize the map
of snapshot t + 1.
4.3 Results
Figure 1 shows a summary of 6 key frames in the evolution of the vocabulary
terms in the DyLDO dataset from 2012-05-13 until 2016-03-27. The numbered
labels correspond to the named graph’s BMUs. Complete animations are avail-
able online10 . The output maps of Figure 1 display the following chronology:
– 2012-05-13: There are at least three recognizable clusters in the middle of the
map. Some BMUs arise in the centers of these clusters, while others appear
in their neighborhoods. The named graphs that correspond to these BMUs
are, by its proximity to the cluster’s center:
• 3987: http://www.bbc.co.uk/nature/life/Morelia_amethistina;
• 312: http://en.openei.org/wiki/Special:ExportRDF/Colorado’s_7th_
congressional_district;
• 4370: http://www.salon.com/writer/glenn_greenwald/;
• 335: http://en.openei.org/wiki/Special:ExportRDF/Property:Name;
• 4376: http://www.steelers.com/;
– These clusters move over the map, and get almost perfectly merged together
by 2013-04-07. At this point important BMUs in this area are:
• 3991: http://www.bbc.co.uk/nature/life/Myodes_glareolus;
• 313: http://en.openei.org/wiki/Special:ExportRDF/Colorado;
• 4373/2: http://www.sports-reference.com/olympics/athletes/br/heinz-brandt-1.
html / http://www.snee.com/bob/foaf.rdf;
• 3819: http://www.bbc.co.uk/nature/life/Gelada;
• 335: http://en.openei.org/wiki/Special:ExportRDF/Property:Name;
– 2013-8-11: The clusters have perfectly merged. The BMUs of the previous
key epochs continue appearing as “shared” cluster centers;
– End of 2013: BMUs that did qualify as important in the previous epochs,
but that did not make it as cluster centers, are not that obivously related to
the cluster centers anymore. At this point, the BBC BMU and the OpenEI
BMU seem to compete in importance in the unique remaining cluster;
– During 2014: BBC clusters get merged, so does the OpenEI by becoming
indistinguishable within the BBC cluster;
– This tendency continues until the final data epoch in 2016-03-27.
10
See the videos at https://youtu.be/3nK3teAzzCM, https://youtu.be/
XTcsv2i2Hlg, and https://youtu.be/-UKKIdIyKGA
5
(a) Map for 2012-05-13. (b) Map for 2013-04-07.
(c) Map for 2013-08-11. (d) Map for 2013-12-29.
(e) Map for 2014-06-15. (f) Map for 2016-03-27.
Fig. 1: Snapshots of key phases in the evolving map of the DyLDO dataset in
the period from 2012-05-13 until 2016-03-27.
4.4 Discussion
The resulting maps described in Section 4.3 and the BMUs displayed therein
seem to indicate that certain named graphs cluster together around some very
specific datasets, namely:
– The BBC Nature data dataset. Some other BBC named graphs cluster to-
gether outside of the main cluster, but end up merging into one. The common
vocabularies and predicates that can be found in these are RDF (rdf:type),
RDFS (rdfs:label), the Wildlife Ontology, FOAF, and Dublin Core.
– The Open Energy Information wiki export as Linked Data. Like the BBC
graphs, some other OpenEI named graphs are clustered separately before
merging into one. The common vocabularies and predicates that are found in
6
these are RDF (rdf:type), Semantic MediaWiki terms, OWL (owl:imports,
owl:sameAs), RDFS (rdfs:label), and custom OpenEI ontological terms.
– Olympics athletes Linked Data / FOAF file of Bob DuCharme, and more
generally pages with personal details and FOAF data. In the olympics ath-
letes pages, the used vocabularies are Facebook, the Open Graph Protocol,
and XHTML; while in personal page’s Linked Data the most common are
RDFS (rdfs:seeAlso), RDF, and FOAF.
Besides the common usage of typical terms of RDF and RDFS, these datasets
represent some significant actors of the LOD cloud: life sciences data and BBC
datasets, encyclopedic knowledge coming from wikis, and RDF/RDFa data em-
bedded in personal pages describing personal profiles. Apart from their funda-
mental differences (e.g. usage of FOAF, MediaWiki), subsequent SOMs tend to
emphasize their common characteristics, grouping them. A fundamental question
is, though, what makes these datasets so different from the surrounding, planar
surface around the main clusters? We conjecture about plausible explanations
for this. First, the higher number of instances using these terms might lead to
a higher frequency in their sparse matrices. Second, the SOM maps reward the
stability of these datasets versus others that changed their used vocabularies over
time. Third, we observe that these datasets tend to reuse existing vocabularies,
instead of minting their own (with few exceptions). Finally, all of them reuse
very common terms that tend appear elsewhere in the LOD cloud. Anyhow,
Figure 1 highlights publishers that kept their data accessible and that did not
introduce new terminology nor removed it. We observe that this corroborates
how systematic the DyLDO crawls were.
5 Conclusions and Future Work
In this paper we studied the requirements for visualizing large amounts of Linked
Data that evolve over time, and proposed candidate solutions for fulfilling them.
These candidate solutions were Somoclu, an efficient parallel implementation of
self-organizing maps – an unsupervised dimensionality reduction technique; and
DyLDO, a timestamped and systematic sample of the LOD cloud between 2012
and 2016. Our findings arose from an animation that told a story of stability,
but that emphasized datasets with high availability, high vocabulary reuse, and
priority for frequently used terms.
Many paths remain open, and we plan on extending this work in several
ways. First, we will prepare the timestamped LOD with different assumptions
beyond usage of predicates in named graphs. Second, we will treat different scal-
able datasets as both content repositories and fodders for semantic reasoning.
Finally, we will integrate metadata of version control systems and data engi-
neering workflows to better visualize, and understand, the semantic drift of Web
data over time.
7
6 Acknowledgment
The second and third author acknowledge research funding by the European
Commission Seventh Framework Programme under Grant Agreement Number
FP7-601138 PERICLES.
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