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\begin{center}\Large
\includegraphics[width=5cm]{uibk_logo_4c_cmyk.pdf}\\[5mm]
\begin{large}\bf
PS 703301 -- WS 2021/22\\
Current Topics in Computer Science\\[5mm]
\end{large}
Final Report\\[20mm]
{\titlefont \huge Shaping Knowledge Graphs}\\[20mm]
Philipp Gritsch \\
Jamie Hochrainer \\
Kristina Magnussen \\
Danielle McKenney\\
Valerian Wintner\\[35mm]
supervised by\\
M.Sc. Elwin Huaman\\
\vfill
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\tableofcontents
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\todo{remove this part}
I added a comment colour for everyone.
\Jamie{Comment colour Jamie}
\Danielle{Comment colour Danielle}
\Philipp{Comment colour Philipp}
\Valerian{Comment colour Valerian}
\Kristina{Comment colour Kristina}
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\Jamie{We need an abstract!}
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Nowadays, more and more devices collect data very quickly. Since such a huge amount of data will get confusing, we need some way of representing this data in a useful way. This is where \emph{knowledge graphs} become important. There exist various definitions of \emph{knowledge graphs} but as the name indicates, they are basically a knowledge model that is structured as a graph. That knowledge model contains types, entities, literals as well as relationships. A \emph{knowledge graph} can make it easier to find and process facts in which one might be interested.
However, a problem that occurs when working with large datasets is that they can be inconsistent and might contain errors. In order to work with this data properly, it is necessary to shape the \emph{knowledge graph} in which this data is contained. This shaping is done by inferring constraints over the data and validating it based on these constraints. Validating a graph against constraints gives important insight into the structure of the data. For instance, when all nodes of a type conform to constraints, then it may be useful to define these as required attributes for all future nodes to ensure uniformity in the data. Non conforming nodes may also deliver important insight into where information is missing. For example, if 99\% of nodes of a given type conform to some constraints, it may be worthwhile to investigate the remaining 1\% to see if they are missing necessary information or are otherwise corrupt. \\
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Our task was to implement a framework for shaping \emph{knowledge graphs}. This consisted of three major steps, namely fetching \emph{knowledge graphs}, inferring constraints and verification of \emph{knowledge graphs}, for which we provide a user interface. These steps are described in Section~\ref{section:approach}.
The results of this approach are shown in Section~\ref{section:results}. Moreover, our evaluations are outlined in Section~\ref{section:evaluation}. A conclusion of our work is provided in Section~\ref{section:conclusion}.
\todo{Add thesis Werkmeister + RDF2Graph, also add another work, maybe from sources in thesis, done by Philipp}
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\section{Approach} \label{section:approach}
%You may add any subsections you deem appropriate for your specific project. Some examples for your reference: Technology stack, Training strategy, Data, Experiments, etc.
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Our framework offers a way to evaluate a \emph{knowledge graph} in an automated way. For this, we used \emph{knowledge graphs} from the \emph{CommonCrawl} datasets as a basis. The \emph{knowledge graphs} are imported as a static file. After this, our framework infers constraints over this data set (see Section~\ref{generatingconstraints}). These are validated automatically in the last step, see Section~\ref{validatingconstraints}. The user can interact with this framework over the front-end, see Section~\ref{frontend}. These different steps were implemented and tested separately. Once this was done, we consolidated them. The structure of our project can be seen in Fig.~\ref{fig:uml}. \todo{update figure}
\begin{figure}[ht]
\centering
\includegraphics[scale=0.35]{kg_shapes_uml.pdf}
\caption{UML diagram of the framework structure}
\label{fig:uml}
\end{figure}
\todo{refer to the readme here? Or should this happen somewhere else?}
\todo{add reference to our github repo!}
\subsection{Technology Stack}
\Jamie{In general, it would be nice to have an introductory sentence at the beginning of each section}
The framework was implemented in \emph{Java}. We used \emph{Maven} as a project management tool. We also used \emph{Jena}, which offers an \emph{RDF} API as well as support for \emph{SPARQL} queries and the \emph{ShEx} language. The front-end was implemented using \emph{Vue3}\cite{Vue} as a front-end framework and \emph{PrimeVue} as a library for the different UI components. For the deployment of our application we used a single virtual machine. Access to the front-end is done via a single \emph{Apache} server. The front-end accesses the back-end via an internal \emph{REST-API}.
\Valerian{Missing: Subsection about generating subgraph (with limit), starting from a certain type of node.} \Kristina{Wouldn't this be part of Generating constraints? I feel like that doesn't really fit into technology stack}
\label{generatingconstraints}
For the generation of constraints, we used the adaption of the tool \emph{RDF2Graph}\cite{original_rdf2graph_git} by Werkmeister\cite{werkmeister2018}\cite{werkmeister_rdf2graph_git}. \Valerian{(this is the old version, we use the fork)} \Kristina{I adapted the sentence, do you think this works now, Valerian?} and adapted it for our purposes. As input, \emph{RDF2Graph} takes a \emph{knowledge graph} from \emph{CommonCrawl}. The properties of the graph are read out with several \emph{SPARQL} queries. These properties are saved in a new \emph{RDF} graph. As output, we receive a graph containing constraints for the initial input data. We use a tool offered by \emph{RDF2Graph} to extract the constraints in \emph{ShEx} syntax. \Valerian{RDF2Graph offers a tool to export the constraints to ShEx syntax.} \Kristina{I adapted the sentence, do you think this is okay now, Valerian?}
\missingfigure{ add query to graph (chosen by Philipp), e.g. multiplicy of argument etc.}
\subsubsection{Integrating RDF2Graph with our framework}
We implemented the following steps in order to integrate \emph{RDF2Graph} into our project. We added \emph{RDF2graph} to our framework so that they could be compiled together\Valerian{, and in the process minimally updated it to be compatible with our version of Java and Jena}. \Kristina{I would leave out the minimally, no need to downplay the work you did on this here, I think. Apart from that, I like it, feel free to put it in} In addition, we changed some of the initial parameters of the \emph{RDF2Graph}, since it originally was intended as a stand-alone application. As we are handling \emph{Models} \todo{Add explanation for Model? Maybe in glossary?} in our software, we changed the input to \emph{RDF2Graph} to a \emph{Model}. In our application, \emph{RDF2Graph} does not use any other storage apart from the \emph{Model} data structure. Previously, such a Model needed to be created by \emph{RDF2Graph}, now it is provided by our framework. We did this so we could have full control over the files handled by \emph{RDF2Graph}. \emph{RDF2Graph} allows for multithreaded execution, which requires a thread pool. This thread pool was initially created by \emph{RDF2Graph}. In our framework, it is provided by our application. In addition, resources which are used by \emph{RDF2Graph} had to be provided in a different way so that they are still available when running from a server environment. We also changed some of the queries. \emph{RDF2Graph} supports multiple output graphs, however, this did not work \todo{should we explain this in more detail?}. As we only work on one Model at a time, we only use one output graph.
\todo{Add explanation of limit to this section?}
\label{validatingconstraints}
Given a \emph{RDF} graph and a set of constraints, the validation consists of verifying that every node in the graph fulfils the requirements given in the constraints. A graph consists of several different types. Each of those types must conform to its definition outlined in the constraints. The results of the validation output a boolean flag for every single node in the graph, indicating whether or not it conforms to its type's constraints. In case of nonconformity, a reason will be given. \\
In our code, this is implemented in the following way. As input, we receive a \emph{RDF} subgraph as well as a set of constraints. We use this to generate a \emph{shape map}, which contains all of the types which need to be validated. For the actual validation, the \emph{ShExValidator} provided by the \emph{Jena} library was used. \todo{add reference to Jena library here?} The validator requires a set of constraints defined in valid \emph{ShEx} syntax and a \emph{shape map}. The \emph{shape map} describes which types of nodes need to be validated against which \emph{ShEx} constraint definitions.
\missingfigure{add picture/code snipped of shapeMap}
The class \emph{ShexValidationRecord} stores the result of the validation for every single node of the graph. Not only is the individual result of every node checked against its relevant constraints, but we also calculate the percentage of nodes that conform to their constraints.
\subsection{Front-end}
\label{frontend}
We implemented a front-end where the user can choose a \emph{knowledge graph} as well as a type of knowledge graph and its type. \todo{check whether this is what we are doing in the finished version} In addition, the user can also set a limit. \todo{explain this in more detail, maybe also put the explanation in query} As output, \emph{ShEx} constraints as well as a validation of those constraints are given. The constraints can be edited by the user and those edited constraints can be revalidated.
If a node is deemed invalid, a reason is given, e.g. "Cardinality violation (min=1): 0". The user can download the subset of the graph which was validated. The interaction between user, front-end and server can also be seen in Fig.~\ref{fig:sequence}.
\todo{explain how different limit influences data output}
\missingfigure{add screenshot of the front-end}
\todo{update and scale sequence diagram and refer to it}
\begin{figure}[ht]
\centering
\includegraphics[scale=0.5]{kgshapes_sequence.pdf}
\caption{Sequence diagram showing the interaction between web application, user and server}
\label{fig:sequence}
\end{figure}
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\section{Results} \label{section:results}
Our framework automatically infers constraints and validates the given data based on those constraints. This can be done on two different \emph{CommonCrawl} datasets. The user can choose one of those datasets and a limit \todo{explain this limit in more depth, maybe in front-end?} using the front-end. User can also edit constraints.
\missingfigure{Maybe add small figure that shows workflow of project here? Something similar like we did in presentation but more professional?}
\todo{describe results of benchmark tests here}
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\section{Evaluation} \label{section:evaluation}
\todo{add benchmarks here}
\todo{check what Elwin said concerning Evaluation on meeting 20.01.2022}
\subsection{Future work}
\todo{Possible future work could be: more data sets, more possibilities for user inputs}
Our application currently only handles two different datasets. For future work, this could be expanded so that the framework could handle more and bigger datasets. Currently, the size of the datasets that can be handled is limited by the RAM on the virtual machine. One possible solution for this could be to only work on parts of the graph.
One problem we encountered when handling datasets from \emph{CommonCrawl} was the quality of these datasets. Many datasets include \emph{non-unicode} characters, which are replaced by Jena with \emph{unicode} characters. This takes a lot of computing time. In addition, many files include invalid \emph{RDF} syntax or are otherwise damaged. This means that in order to handle additional datasets, some way of processing these datasets would have to be implemented. Processing could include filtering for broken files and invalid syntax and fixing this before handling the dataset in the framework.
\todo{Should we add proper SPARQL endpoints here? Might not be possible?}
In addition, more possibilities for user interaction could be added. For instance, a feature could be added where a user can upload their own dataset and have it validated.
\Philipp{i labeled all the included graphics with h!, when we have finished the report we might want to make it so, that one image is on the top and one on the bottom, if 2 pages are on the same page, for example}
For taking the measurements, the application was started locally on our hardware,\Kristina{I would put a full stop here and maybe start the next sentence like "This was done to minimise..} to minimize side-effects of other applications running on the virtual machine where the live-instance is deployed. The JVM was additionally setup \Kristina{Additionally, the JVM was set up..?} to use up to 16 GB of main memory for its heap to allow parallel queries without compromising the runtime of the executions, arising from extensive swap usage. \Kristina{This sentence is very long, maybe we can split it somehow?}
\subsection{Runtime}
Figures~\ref{fig:exec_times_per_limit} and \ref{fig:exec_times_per_triples} show our \Kristina{the?} measurements we obtained by changing the \emph{LIMIT} input parameter. This parameter limits the size of the start-node subset, from which connected nodes are queried. All the measurements are shown in Tables~\ref{table:runtimes_wo_limit} and \ref{table:runtimes_w_limit}.
\begin{figure}[h!]
\begin{subfigure}{\textwidth}
\centering
\includegraphics[width=0.65\linewidth]{img/limit_legend.pdf}
\end{subfigure}
\begin{subfigure}{0.33\textwidth}
\includegraphics[width=0.9\linewidth]{img/Canal_limit.pdf}
\caption{RDFType = Canal}
\label{fig:limit_canal}
\end{subfigure}
\begin{subfigure}{0.33\textwidth}
\includegraphics[width=0.9\linewidth]{img/RiverBodyOfWater_limit.pdf}
\caption{RDFType = RiverBodyOfWater}
\label{fig:limit_rbow}
\end{subfigure}
\begin{subfigure}{0.33\textwidth}
\includegraphics[width=0.9\linewidth]{img/Service_limit.pdf}
\caption{RDFType = Service}
\label{fig:limit_service}
\end{subfigure}
\caption{Execution times per RDFType, per size of start-node subset on RiverBodyOfWater dataset}
\label{fig:exec_times_per_limit}
\end{figure}
The results shown in Figure~\ref{fig:exec_times_per_limit} were to be expected. First of all, the runtime of constructing the desired subset of the graph is considerably larger than the time needed to create the \emph{ShEx} constraints, or to validate the constraints on the graph.
Secondly, the runtime of constructing the subgraph scales with the \emph{LIMIT}. This becomes especially evident in Figures~\ref{fig:limit_canal} and \ref{fig:limit_service}.
To understand the behaviour shown in Figure~\ref{fig:limit_rbow}, we want to look at Figure~\ref{fig:exec_times_per_triples}, which shows the same runtimes, but grouped by the number of triples in the subgraph, on which the constraints are created. Unlike in Figures~\ref{fig:triple_canal} and \ref{fig:triple_service} the maximum number of triples (shown in the x-coordinate in Figure~\ref{fig:triple_rbow}), is 1769.
This is also the amrefer to figures paperount \Kristina{What does this mean?} of triples contained in the subgraph that we get without providing any limit. Therefore, providing a limit larger than 200 won't enrich the constructed graph, keeping the time almost constant in regards to the \emph{LIMIT} parameter.
\begin{figure}[h!]
\begin{subfigure}{\textwidth}
\centering
\includegraphics[width=0.65\linewidth]{img/triple_legend.pdf}
\end{subfigure}
\begin{subfigure}{0.33\textwidth}
\includegraphics[width=0.9\linewidth]{img/Canal_triple.pdf}
\caption{RDFType = Canal}
\label{fig:triple_canal}
\end{subfigure}
\begin{subfigure}{0.33\textwidth}
\includegraphics[width=0.9\linewidth]{img/RiverBodyOfWater_triple.pdf}
\caption{RDFType = RiverBodyOfWater}
\label{fig:triple_rbow}
\end{subfigure}
\begin{subfigure}{0.33\textwidth}
\includegraphics[width=0.9\linewidth]{img/Service_triple.pdf}
\caption{RDFType = Service}
\label{fig:triple_service}
\end{subfigure}
\caption{Execution times per RDFType, per number of triples on RiverBodyOfWater dataset}
\label{fig:exec_times_per_triples}
Figure \ref{fig:exec_times_no_limit} shows the runtime without limiting the construction of the subgraph. Note the much larger runtime needed for querying the graph, despite resulting in the same amount of triples when providing a large enough \emph{LIMIT}.
\begin{figure}[h!]
\begin{subfigure}{\textwidth}
\centering
\includegraphics[width=0.65\linewidth]{img/no_limit_legend.pdf}
\end{subfigure}
\begin{subfigure}{\textwidth}
\centering
\includegraphics[width=0.6\linewidth]{img/no_limit.pdf}
\end{subfigure}
\caption{Execution times per RDFType of the RiverBodyOfWater dataset (containing 49915 triples)}
\label{fig:exec_times_no_limit}
\end{figure}
\subsection{Correctness}
We thought \emph{Shexer}, which was already mentioned in Section~\ref{section:related_work}, was a good fit for cross validating our \emph{ShEx}-generation. However, due to our limited knowledge of operating this tool, we did not manage to generate proper constraints for our RiverBodyOfWater-dataset. Our attempt at using this tool is shown in Figure~\ref{code:shexer}, which generated the trivial, non-restrictive constraints shown in Figure~\ref{fig:shexer_output}.
Therefore, we checked the generated constraints manually for small subgraphs (see Figures~\ref{fig:shex_canal_50}, \ref{fig:shex_rbow_50} and \ref{fig:shex_service_50}) and identified two issues with our tool.
Firstly, if the dataset consists of only stand-alone blank nodes, as seen in Figure~\ref{code:blank_nodes}, then \emph{Rdf2Graph} does not infer any \emph{ShEx}-constraints. This was the case for the generated subgraph using RiverBodyOfWater with a \emph{LIMIT} of 50, and the resulting \emph{ShEx} can be seen in Figure~\ref{fig:shex_rbow_50}.
Secondly, optional properties are not always inferred and therefore missing from the generated \emph{ShEx}-constraints. This also happens for unlimited subgraphs (see Figures~\ref{fig:shex_canal_wo_limit}, \ref{fig:shex_rbow_wo_limit} and \ref{fig:shex_service_wo_limit}), with the exception of the RiverBodyOfWater-RDFtype, where it looks like the constraints are complete, \Kristina{Would put a full stop here and start new sentence "However,..."} however due to the large graph manually checking for correctness is infeasible. We did not see a correlation between missing constraint-properties and the shape of the graph.
The generated \emph{ShEx}-constraints for small subgraphs (Canal with \emph{LIMIT} 50, Service with \emph{LIMIT} 50) were cross validated using the online-tool \emph{RDFShape}\cite{RDFShape}. The validation result was the same as in our tool.
\begin{figure}
\centering
\lstinputlisting{code_snippets/blank_nodes.ttl}
\caption{Blank Nodes in Turtle File}
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\section{Conclusion} \label{section:conclusion}
\todo{Which challenges did we face during the implementation? (Maybe depth of SPARQL query, outdated RDF2Graph?)}
\todo{Did we achieve what we wanted to do? How well and reliably does the framework work?}
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% Bibliography
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\bibliography{bibliography}
\bibliographystyle{abbrv}
\appendix
\section{Contribution Statements}
Please write down a short contribution statement for each member of your group. You may evaluate the contribution along the three common categories:
i) conception (i.\,e., problem framing, ideation, validation, and method selection), ii) operational work (e.\,g., setting up your tech stack, algorithm implementation, data analysis, and interpretation), and iii) writing \& reporting (i.\,e., report drafting, literature review, revision of comments, presentation preparations, etc.).
\section{Appendix}
You may use appendices to include any auxiliary results you would like to share, however cannot insert in the main text due to the page limit.
\subsection{Code listings and additional data}
\begin{figure}
\centering
\lstinputlisting[language=python]{code_snippets/shexer.py}
\caption{Running shexer on the full graph}
\label{code:shexer}
\end{figure}
\begin{figure}
\centering
\lstinputlisting{code_snippets/shexer_out.shex}
\caption{Shexer output}
\label{fig:shexer_output}
\end{figure}
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\begin{figure}
\centering
\lstinputlisting{code_snippets/RiverBodyOfWater_Canal_50.shex}
\caption{Generated \emph{ShEx}-constraints of Canal with \emph{LIMIT} 50}
\label{fig:shex_canal_50}
\end{figure}
\begin{figure}
\centering
\lstinputlisting{code_snippets/RiverBodyOfWater_RiverBodyOfWater_50.shex}
\caption{Generated \emph{ShEx}-constraints of RiverBodyOfWater with \emph{LIMIT} 50}
\label{fig:shex_rbow_50}
\end{figure}
\begin{figure}
\centering
\lstinputlisting{code_snippets/RiverBodyOfWater_Service_50.shex}
\caption{Generated \emph{ShEx}-constraints of Service with \emph{LIMIT} 50}
\label{fig:shex_service_50}
\end{figure}
\begin{figure}
\centering
\lstinputlisting{code_snippets/RiverBodyOfWater_Canal_null.shex}
\caption{Generated \emph{ShEx}-constraints of Canal without a \emph{LIMIT}}
\label{fig:shex_canal_wo_limit}
\end{figure}
\begin{figure}
\centering
\lstinputlisting{code_snippets/RiverBodyOfWater_RiverBodyOfWater_null.shex}
\caption{Generated \emph{ShEx}-constraints of RiverBodyOfWater without a \emph{LIMIT}}
\label{fig:shex_rbow_wo_limit}
\end{figure}
\begin{figure}
\centering
\lstinputlisting{code_snippets/RiverBodyOfWater_Service_null.shex}
\caption{Generated \emph{ShEx}-constraints of Service without a \emph{LIMIT}}
\label{fig:shex_service_wo_limit}
\end{figure}
\begin{table}[!ht]
\centering
\begin{tabular}{|l|r|r|r|r|}
\hline
Rdftype & Triples & [$t_{graph}$] = ms & [$t_{shex}$] = ms & [$t_{validation}$] = ms \\ \hline
Canal & 16961 & 360000 & 737 & 45 \\ \hline
GeoCoordinates & 204 & 468000 & 585 & 4 \\ \hline
RiverBodyOfWater & 1769 & 468000 & 613 & 15 \\ \hline
Service & 7334 & 462000 & 618 & 19 \\ \hline
\end{tabular}
\caption{Execution times per RDF-Type, queried on full graph of the RiverBodyOfWater dataset (containing 49915 triples)}
\label{table:runtimes_wo_limit}
\end{table}
\begin{table}
\centering
\begin{tabular}{|l|r|r|r|r|r|}
\hline
Rdftype & Limit & Triples & [$t_{graph}$] = ms & [$t_{shex}$] = ms & [$t_{validation}$] = ms \\ \hline
Canal & 50 & 226 & 2420 & 923 & 44 \\ \hline
Canal & 100 & 328 & 2260 & 709 & 13 \\ \hline
Canal & 200 & 765 & 1740 & 637 & 8 \\ \hline
Canal & 400 & 1588 & 2020 & 559 & 9 \\ \hline
Canal & 800 & 3176 & 3270 & 661 & 8 \\ \hline
Canal & 1600 & 6817 & 5030 & 654 & 17 \\ \hline
Canal & 3200 & 13504 & 9100 & 736 & 33 \\ \hline
Canal & 6400 & 16961 & 10790 & 665 & 25 \\ \hline
RiverBodyOfWater & 50 & 192 & 2680 & 615 & 5 \\ \hline
RiverBodyOfWater & 75 & 291 & 2490 & 586 & 4 \\ \hline
RiverBodyOfWater & 100 & 1187 & 2700 & 624 & 7 \\ \hline
RiverBodyOfWater & 200 & 1769 & 4890 & 643 & 17 \\ \hline
RiverBodyOfWater & 400 & 1769 & 4840 & 641 & 8 \\ \hline
RiverBodyOfWater & 800 & 1769 & 4980 & 619 & 18 \\ \hline
Service & 50 & 615 & 1640 & 602 & 7 \\ \hline
Service & 100 & 1022 & 1790 & 562 & 6 \\ \hline
Service & 200 & 1852 & 2300 & 577 & 9 \\ \hline
Service & 400 & 3041 & 2880 & 601 & 6 \\ \hline
Service & 800 & 5437 & 4500 & 674 & 30 \\ \hline
Service & 1600 & 7334 & 5350 & 639 & 26 \\ \hline
\end{tabular}
\caption{Execution times per RDF-Type, limited size of start-node subset (using the RiverBodyOfWater dataset)}
\label{table:runtimes_w_limit}
\end{table}