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Mining Inter-Document Argument Structures in Scientific Papers for an Argument Web

Authors: Florian Ruosch, Cristina Sarasua, and Abraham Bernstein

Published in: TGDK, Volume 3, Issue 3 (2025). Transactions on Graph Data and Knowledge, Volume 3, Issue 3

Abstract

In Argument Mining, predicting argumentative relations between texts (or spans) remains one of the most challenging aspects, even more so in the cross-document setting. This paper makes three key contributions to advance research in this domain. We first extend an existing dataset, the Sci-Arg corpus, by annotating it with explicit inter-document argumentative relations, thereby allowing arguments to be distributed over several documents forming an Argument Web; these new annotations are published using Semantic Web technologies (RDF, OWL). Second, we explore and evaluate three automated approaches for predicting these inter-document argumentative relations, establishing critical baselines on the new dataset. We find that a simple classifier based on discourse indicators with access to context outperforms neural methods. Third, we conduct a comparative analysis of these approaches for both intra- and inter-document settings, identifying statistically significant differences in results that indicate the necessity of distinguishing between these two scenarios. Our findings highlight significant challenges in this complex domain and open crucial avenues for future research on the Argument Web of Science, particularly for those interested in leveraging Semantic Web technologies and knowledge graphs to understand scholarly discourse. With this, we provide the first stepping stones in the form of a benchmark dataset, three baseline methods, and an initial analysis for a systematic exploration of this field relevant to the Web of Data and Science.

Cite as

Florian Ruosch, Cristina Sarasua, and Abraham Bernstein. Mining Inter-Document Argument Structures in Scientific Papers for an Argument Web. In Transactions on Graph Data and Knowledge (TGDK), Volume 3, Issue 3, pp. 4:1-4:33, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{ruosch_et_al:TGDK.3.3.4,
  author =	{Ruosch, Florian and Sarasua, Cristina and Bernstein, Abraham},
  title =	{{Mining Inter-Document Argument Structures in Scientific Papers for an Argument Web}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{4:1--4:33},
  ISSN =	{2942-7517},
  year =	{2025},
  volume =	{3},
  number =	{3},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.3.3.4},
  URN =		{urn:nbn:de:0030-drops-252159},
  doi =		{10.4230/TGDK.3.3.4},
  annote =	{Keywords: Argument Mining, Large Language Models, Knowledge Graphs, Link Prediction}
}

Document

Survey

DOI: 10.4230/TGDK.3.2.1

Resilience in Knowledge Graph Embeddings

Authors: Arnab Sharma, N'Dah Jean Kouagou, and Axel-Cyrille Ngonga Ngomo

Published in: TGDK, Volume 3, Issue 2 (2025). Transactions on Graph Data and Knowledge, Volume 3, Issue 2

Abstract

In recent years, knowledge graphs have gained interest and witnessed widespread applications in various domains, such as information retrieval, question-answering, recommendation systems, amongst others. Large-scale knowledge graphs to this end have demonstrated their utility in effectively representing structured knowledge. To further facilitate the application of machine learning techniques, knowledge graph embedding models have been developed. Such models can transform entities and relationships within knowledge graphs into vectors. However, these embedding models often face challenges related to noise, missing information, distribution shift, adversarial attacks, etc. This can lead to sub-optimal embeddings and incorrect inferences, thereby negatively impacting downstream applications. While the existing literature has focused so far on adversarial attacks on KGE models, the challenges related to the other critical aspects remain unexplored. In this paper, we, first of all, give a unified definition of resilience, encompassing several factors such as generalisation, in-distribution generalization, distribution adaption, and robustness. After formalizing these concepts for machine learning in general, we define them in the context of knowledge graphs. To find the gap in the existing works on resilience in the context of knowledge graphs, we perform a systematic survey, taking into account all these aspects mentioned previously. Our survey results show that most of the existing works focus on a specific aspect of resilience, namely robustness. After categorizing such works based on their respective aspects of resilience, we discuss the challenges and future research directions.

Cite as

Arnab Sharma, N'Dah Jean Kouagou, and Axel-Cyrille Ngonga Ngomo. Resilience in Knowledge Graph Embeddings. In Transactions on Graph Data and Knowledge (TGDK), Volume 3, Issue 2, pp. 1:1-1:38, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{sharma_et_al:TGDK.3.2.1,
  author =	{Sharma, Arnab and Kouagou, N'Dah Jean and Ngomo, Axel-Cyrille Ngonga},
  title =	{{Resilience in Knowledge Graph Embeddings}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{1:1--1:38},
  ISSN =	{2942-7517},
  year =	{2025},
  volume =	{3},
  number =	{2},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.3.2.1},
  URN =		{urn:nbn:de:0030-drops-248117},
  doi =		{10.4230/TGDK.3.2.1},
  annote =	{Keywords: Knowledge graphs, Resilience, Robustness}
}

Document

DOI: 10.4230/OASIcs.SpaceCHI.2025.23

(Can't) Fly Me to the Moon or Mars? Context of Use Analysis Approaches for Space Exploration

Authors: Tilo Mentler

Published in: OASIcs, Volume 130, Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)

Abstract

Contexts of use are a central concept of research and development in human-computer interaction (HCI). Their in-depth understanding is a key for usable and acceptable computer-aided solutions and a particular challenge in connection with space exploration. It is necessary to examine which of the established approaches can be implemented here and where methodological adjustments are necessary. This article provides a systematic consideration of three perspectives to understand space contexts of use: theory and literature, imparted experiential knowledge, and personal experience. Potentials and risks are evaluated. The findings of HCI research in safety-critical contexts and under COVID-19 conditions that can be transferred to space HCI are taken up.

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Tilo Mentler. (Can't) Fly Me to the Moon or Mars? Context of Use Analysis Approaches for Space Exploration. In Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025). Open Access Series in Informatics (OASIcs), Volume 130, pp. 23:1-23:7, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{mentler:OASIcs.SpaceCHI.2025.23,
  author =	{Mentler, Tilo},
  title =	{{(Can't) Fly Me to the Moon or Mars? Context of Use Analysis Approaches for Space Exploration}},
  booktitle =	{Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)},
  pages =	{23:1--23:7},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-384-3},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{130},
  editor =	{Bensch, Leonie and Nilsson, Tommy and Nisser, Martin and Pataranutaporn, Pat and Schmidt, Albrecht and Sumini, Valentina},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.SpaceCHI.2025.23},
  URN =		{urn:nbn:de:0030-drops-240135},
  doi =		{10.4230/OASIcs.SpaceCHI.2025.23},
  annote =	{Keywords: Context of Use, Experiential Knowledge, Remote Contextual Inquiry}
}

Document

DOI: 10.4230/LIPIcs.WABI.2025.17

An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT

Authors: Ahsan Sanaullah, Degui Zhi, and Shaojie Zhang

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract

String matching problems in bioinformatics are typically for finding exact substring matches between a query and a reference text. Previous formulations often focus on maximum exact matches (MEMs). However, multiple occurrences of substrings of the query in the text that are long enough but not maximal may not be captured by MEMs. Such long matches can be informative, especially when the text is a collection of similar sequences such as genomes. In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount of LEMs, so we only consider those above some length threshold ℒ. These are referred to as long LEMs. The purpose of long LEMs is to capture substring matches between a query and a text that are not necessarily maximal in the pattern but still long enough to be important. Therefore efficient long LEMs finding algorithms are desired for these datasets. However, these datasets are too large to query on traditional string indexes. Fortunately, these datasets are very repetitive. Recently, compressed string indexes that take advantage of the redundancy in the data but retain efficient querying capability have been proposed as a solution. We therefore give an efficient algorithm for computing all the long LEMs of a query and a text in a BWT runs compressed string index. We describe an O(m+occ) expected time algorithm that relies on an O(r) words space string index for outputting all long LEMs of a pattern with respect to a text given the matching statistics of the pattern with respect to the text. Here m is the length of the query, occ is the number of long LEMs outputted, and r is the number of runs in the BWT of the text. The O(r) space string index we describe relies on an adaptation of the move data structure by Nishimoto and Tabei. We are able to support LCP[i] queries in constant time given SA[i]. In other words, we answer PLCP[i] queries in constant time. These PLCP queries enable the efficient long LEM query. Long LEMs may provide useful similarity information between a pattern and a text that MEMs may ignore. This information is particularly useful in pangenome and biobank scale haplotype panel contexts.

Cite as

Ahsan Sanaullah, Degui Zhi, and Shaojie Zhang. An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 17:1-17:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{sanaullah_et_al:LIPIcs.WABI.2025.17,
  author =	{Sanaullah, Ahsan and Zhi, Degui and Zhang, Shaojie},
  title =	{{An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{17:1--17:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.17},
  URN =		{urn:nbn:de:0030-drops-239433},
  doi =		{10.4230/LIPIcs.WABI.2025.17},
  annote =	{Keywords: BWT, LEM, Long LEM, MEM, Run Length Compressed BWT, Move Data Structure, Pangenome}
}

Document

Track B: Automata, Logic, Semantics, and Theory of Programming

DOI: 10.4230/LIPIcs.ICALP.2025.157

Bayesian Inference in Quantum Programs

Authors: Christina Gehnen, Dominique Unruh, and Joost-Pieter Katoen

Published in: LIPIcs, Volume 334, 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)

Abstract

Conditioning is a key feature in probabilistic programming to enable modeling the influence of data (also known as observations) to the probability distribution described by such programs. Determining the posterior distribution is also known as Bayesian inference. This paper equips a quantum while-language with conditioning, defines its denotational and operational semantics over infinite-dimensional Hilbert spaces, and shows their equivalence. We provide sufficient conditions for the existence of weakest (liberal) precondition-transformers and derive inductive characterizations of these transformers. It is shown how w(l)p-transformers can be used to assess the effect of Bayesian inference on (possibly diverging) quantum programs.

Cite as

Christina Gehnen, Dominique Unruh, and Joost-Pieter Katoen. Bayesian Inference in Quantum Programs. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 157:1-157:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gehnen_et_al:LIPIcs.ICALP.2025.157,
  author =	{Gehnen, Christina and Unruh, Dominique and Katoen, Joost-Pieter},
  title =	{{Bayesian Inference in Quantum Programs}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{157:1--157:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-372-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{334},
  editor =	{Censor-Hillel, Keren and Grandoni, Fabrizio and Ouaknine, Jo\"{e}l and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2025.157},
  URN =		{urn:nbn:de:0030-drops-235345},
  doi =		{10.4230/LIPIcs.ICALP.2025.157},
  annote =	{Keywords: Quantum Program Logics, Weakest Preconditions, Bayesian Inference, Program Semantics}
}

Document

Survey

DOI: 10.4230/TGDK.3.1.3

Uncertainty Management in the Construction of Knowledge Graphs: A Survey

Authors: Lucas Jarnac, Yoan Chabot, and Miguel Couceiro

Published in: TGDK, Volume 3, Issue 1 (2025). Transactions on Graph Data and Knowledge, Volume 3, Issue 1

Abstract

Knowledge Graphs (KGs) are a major asset for companies thanks to their great flexibility in data representation and their numerous applications, e.g., vocabulary sharing, Q&A or recommendation systems. To build a KG, it is a common practice to rely on automatic methods for extracting knowledge from various heterogeneous sources. However, in a noisy and uncertain world, knowledge may not be reliable and conflicts between data sources may occur. Integrating unreliable data would directly impact the use of the KG, therefore such conflicts must be resolved. This could be done manually by selecting the best data to integrate. This first approach is highly accurate, but costly and time-consuming. That is why recent efforts focus on automatic approaches, which represent a challenging task since it requires handling the uncertainty of extracted knowledge throughout its integration into the KG. We survey state-of-the-art approaches in this direction and present constructions of both open and enterprise KGs. We then describe different knowledge extraction methods and discuss downstream tasks after knowledge acquisition, including KG completion using embedding models, knowledge alignment, and knowledge fusion in order to address the problem of knowledge uncertainty in KG construction. We conclude with a discussion on the remaining challenges and perspectives when constructing a KG taking into account uncertainty.

Cite as

Lucas Jarnac, Yoan Chabot, and Miguel Couceiro. Uncertainty Management in the Construction of Knowledge Graphs: A Survey. In Transactions on Graph Data and Knowledge (TGDK), Volume 3, Issue 1, pp. 3:1-3:48, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{jarnac_et_al:TGDK.3.1.3,
  author =	{Jarnac, Lucas and Chabot, Yoan and Couceiro, Miguel},
  title =	{{Uncertainty Management in the Construction of Knowledge Graphs: A Survey}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{3:1--3:48},
  ISSN =	{2942-7517},
  year =	{2025},
  volume =	{3},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.3.1.3},
  URN =		{urn:nbn:de:0030-drops-233733},
  doi =		{10.4230/TGDK.3.1.3},
  annote =	{Keywords: Knowledge reconciliation, Uncertainty, Heterogeneous sources, Knowledge graph construction}
}

Document

DOI: 10.4230/LIPIcs.FORC.2025.8

Differential Privacy Under Multiple Selections

Authors: Ashish Goel, Zhihao Jiang, Aleksandra Korolova, Kamesh Munagala, and Sahasrajit Sarmasarkar

Published in: LIPIcs, Volume 329, 6th Symposium on Foundations of Responsible Computing (FORC 2025)

Abstract

We consider the setting where a user with sensitive features wishes to obtain a recommendation from a server in a differentially private fashion. We propose a "multi-selection" architecture where the server can send back multiple recommendations and the user chooses one from these that matches best with their private features. When the user feature is one-dimensional - on an infinite line - and the accuracy measure is defined w.r.t some increasing function 𝔥(.) of the distance on the line, we precisely characterize the optimal mechanism that satisfies differential privacy. The specification of the optimal mechanism includes both the distribution of the noise that the user adds to its private value, and the algorithm used by the server to determine the set of results to send back as a response. We show that Laplace is an optimal noise distribution in this setting. Furthermore, we show that this optimal mechanism results in an error that is inversely proportional to the number of results returned when the function 𝔥(.) is the identity function.

Cite as

Ashish Goel, Zhihao Jiang, Aleksandra Korolova, Kamesh Munagala, and Sahasrajit Sarmasarkar. Differential Privacy Under Multiple Selections. In 6th Symposium on Foundations of Responsible Computing (FORC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 329, pp. 8:1-8:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{goel_et_al:LIPIcs.FORC.2025.8,
  author =	{Goel, Ashish and Jiang, Zhihao and Korolova, Aleksandra and Munagala, Kamesh and Sarmasarkar, Sahasrajit},
  title =	{{Differential Privacy Under Multiple Selections}},
  booktitle =	{6th Symposium on Foundations of Responsible Computing (FORC 2025)},
  pages =	{8:1--8:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-367-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{329},
  editor =	{Bun, Mark},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FORC.2025.8},
  URN =		{urn:nbn:de:0030-drops-231353},
  doi =		{10.4230/LIPIcs.FORC.2025.8},
  annote =	{Keywords: Differential Privacy, Mechanism Design and Multi-Selection}
}

Document

DOI: 10.4230/LIPIcs.FORC.2025.2

Smooth Sensitivity Revisited: Towards Optimality

Authors: Richard Hladík and Jakub Tětek

Published in: LIPIcs, Volume 329, 6th Symposium on Foundations of Responsible Computing (FORC 2025)

Abstract

Smooth sensitivity is one of the most commonly used techniques for designing practical differentially private mechanisms. In this approach, one computes the smooth sensitivity of a given query q on the given input D and releases q(D) with noise added proportional to this smooth sensitivity. One question remains: what distribution should we pick the noise from? In this paper, we give a new class of distributions suitable for the use with smooth sensitivity, which we name the PolyPlace distribution. This distribution improves upon the state-of-the-art Student’s T distribution in terms of standard deviation by arbitrarily large factors, depending on a "smoothness parameter" γ, which one has to set in the smooth sensitivity framework. Moreover, our distribution is defined for a wider range of parameter γ, which can lead to significantly better performance. Furthermore, we prove that the PolyPlace distribution converges for γ → 0 to the Laplace distribution and so does its variance. This means that the Laplace mechanism is a limit special case of the PolyPlace mechanism. This implies that our mechanism is in a certain sense optimal for γ → 0.

Cite as

Richard Hladík and Jakub Tětek. Smooth Sensitivity Revisited: Towards Optimality. In 6th Symposium on Foundations of Responsible Computing (FORC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 329, pp. 2:1-2:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{hladik_et_al:LIPIcs.FORC.2025.2,
  author =	{Hlad{\'\i}k, Richard and T\v{e}tek, Jakub},
  title =	{{Smooth Sensitivity Revisited: Towards Optimality}},
  booktitle =	{6th Symposium on Foundations of Responsible Computing (FORC 2025)},
  pages =	{2:1--2:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-367-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{329},
  editor =	{Bun, Mark},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FORC.2025.2},
  URN =		{urn:nbn:de:0030-drops-231292},
  doi =		{10.4230/LIPIcs.FORC.2025.2},
  annote =	{Keywords: differential privacy, smooth sensitivity}
}

Document

DOI: 10.4230/LIPIcs.CSL.2025.31

Simple Types for Probabilistic Termination

Authors: Willem Heijltjes and Georgina Majury

Published in: LIPIcs, Volume 326, 33rd EACSL Annual Conference on Computer Science Logic (CSL 2025)

Abstract

We present a new typing discipline to guarantee the probability of termination in probabilistic lambda-calculi. The main contribution is a particular naturality and simplicity: our probabilistic types are as simple types, but generated from probabilities as base types, representing a least probability of termination. Simple types are recovered by restricting probabilities to one. Our vehicle is the Probabilistic Event Lambda-Calculus by Dal Lago, Guerrieri, and Heijltjes, which presents a solution to the issue of confluence in probabilistic lambda-calculi. Our probabilistic type system provides an alternative solution to that using counting quantifiers by Antonelli, Dal Lago, and Pistone, for the same calculus. The problem that both type systems address is to give a lower bound on the probability that terms head-normalize. Following the recent Functional Machine Calculus by Heijltjes, our development takes the (simplified) Krivine machine as primary, and proceeds via an extension of the calculus with sequential composition and identity on the machine. Our type system then gives a natural account of termination probability on the Krivine machine, reflected back onto head-normalization for the original calculus. In this way we are able to avoid the use of counting quantifiers, while improving on the termination bounds given by Antonelli, Dal Lago, and Pistone.

Cite as

Willem Heijltjes and Georgina Majury. Simple Types for Probabilistic Termination. In 33rd EACSL Annual Conference on Computer Science Logic (CSL 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 326, pp. 31:1-31:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{heijltjes_et_al:LIPIcs.CSL.2025.31,
  author =	{Heijltjes, Willem and Majury, Georgina},
  title =	{{Simple Types for Probabilistic Termination}},
  booktitle =	{33rd EACSL Annual Conference on Computer Science Logic (CSL 2025)},
  pages =	{31:1--31:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-362-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{326},
  editor =	{Endrullis, J\"{o}rg and Schmitz, Sylvain},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CSL.2025.31},
  URN =		{urn:nbn:de:0030-drops-227885},
  doi =		{10.4230/LIPIcs.CSL.2025.31},
  annote =	{Keywords: lambda-calculus, probabilistic termination, simple types}
}

Document

Resource Paper

DOI: 10.4230/TGDK.2.2.4

FAIR Jupyter: A Knowledge Graph Approach to Semantic Sharing and Granular Exploration of a Computational Notebook Reproducibility Dataset

Authors: Sheeba Samuel and Daniel Mietchen

Published in: TGDK, Volume 2, Issue 2 (2024): Special Issue on Resources for Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 2, Issue 2

Abstract

The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. The original dataset is about the computational reproducibility of GitHub-hosted Jupyter notebooks associated with biomedical publications. It contains rich metadata about the publications, associated GitHub repositories and Jupyter notebooks, and the notebooks' reproducibility. We took this dataset, converted it into semantic triples and loaded these into a triple store to create a knowledge graph - FAIR Jupyter - that we made accessible via a web service. This enables granular data exploration and analysis through queries that can be tailored to specific use cases. Such queries may provide details about any of the variables from the original dataset, highlight relationships between them or combine some of the graph’s content with materials from corresponding external resources. We provide a collection of example queries addressing a range of use cases in research and education. We also outline how sets of such queries can be used to profile specific content types, either individually or by class. We conclude by discussing how such a semantically enhanced sharing of complex datasets can both enhance their FAIRness - i.e., their findability, accessibility, interoperability, and reusability - and help identify and communicate best practices, particularly with regards to data quality, standardization, automation and reproducibility.

Cite as

Sheeba Samuel and Daniel Mietchen. FAIR Jupyter: A Knowledge Graph Approach to Semantic Sharing and Granular Exploration of a Computational Notebook Reproducibility Dataset. In Special Issue on Resources for Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 2, pp. 4:1-4:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{samuel_et_al:TGDK.2.2.4,
  author =	{Samuel, Sheeba and Mietchen, Daniel},
  title =	{{FAIR Jupyter: A Knowledge Graph Approach to Semantic Sharing and Granular Exploration of a Computational Notebook Reproducibility Dataset}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{4:1--4:24},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{2},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.2.4},
  URN =		{urn:nbn:de:0030-drops-225886},
  doi =		{10.4230/TGDK.2.2.4},
  annote =	{Keywords: Knowledge Graph, Computational reproducibility, Jupyter notebooks, FAIR data, PubMed Central, GitHub, Python, SPARQL}
}

Document

Survey

DOI: 10.4230/TGDK.2.1.3

Semantic Web: Past, Present, and Future

Authors: Ansgar Scherp, Gerd Groener, Petr Škoda, Katja Hose, and Maria-Esther Vidal

Published in: TGDK, Volume 2, Issue 1 (2024): Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge, Volume 2, Issue 1

Abstract

Ever since the vision was formulated, the Semantic Web has inspired many generations of innovations. Semantic technologies have been used to share vast amounts of information on the Web, enhance them with semantics to give them meaning, and enable inference and reasoning on them. Throughout the years, semantic technologies, and in particular knowledge graphs, have been used in search engines, data integration, enterprise settings, and machine learning. In this paper, we recap the classical concepts and foundations of the Semantic Web as well as modern and recent concepts and applications, building upon these foundations. The classical topics we cover include knowledge representation, creating and validating knowledge on the Web, reasoning and linking, and distributed querying. We enhance this classical view of the so-called "Semantic Web Layer Cake" with an update of recent concepts that include provenance, security and trust, as well as a discussion of practical impacts from industry-led contributions. We conclude with an outlook on the future directions of the Semantic Web. This is a living document. If you like to contribute, please contact the first author and visit: https://github.com/ascherp/semantic-web-primer

Cite as

Ansgar Scherp, Gerd Groener, Petr Škoda, Katja Hose, and Maria-Esther Vidal. Semantic Web: Past, Present, and Future. In Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 1, pp. 3:1-3:37, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{scherp_et_al:TGDK.2.1.3,
  author =	{Scherp, Ansgar and Groener, Gerd and \v{S}koda, Petr and Hose, Katja and Vidal, Maria-Esther},
  title =	{{Semantic Web: Past, Present, and Future}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{3:1--3:37},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.1.3},
  URN =		{urn:nbn:de:0030-drops-198607},
  doi =		{10.4230/TGDK.2.1.3},
  annote =	{Keywords: Linked Open Data, Semantic Web Graphs, Knowledge Graphs}
}

Document

Invited Talk

DOI: 10.4230/LIPIcs.CSL.2022.2

How to Develop an Intuition for Risk... and Other Invisible Phenomena (Invited Talk)

Authors: Natasha Fernandes, Annabelle McIver, and Carroll Morgan

Published in: LIPIcs, Volume 216, 30th EACSL Annual Conference on Computer Science Logic (CSL 2022)

Abstract

The study of quantitative risk in security systems is often based around complex and subtle mathematical ideas involving probabilities. The notations for these ideas can pose a communication barrier between collaborating researchers even when those researchers are working within a similar framework. This paper describes the use of geometrical representation and reasoning as a way to share ideas using the minimum of notation so as to build intuition about what kinds of properties might or might not be true. We describe a faithful geometrical setting for the channel model of quantitative information flow (QIF) and demonstrate how it can facilitate "proofs without words" for problems in the QIF setting.

Cite as

Natasha Fernandes, Annabelle McIver, and Carroll Morgan. How to Develop an Intuition for Risk... and Other Invisible Phenomena (Invited Talk). In 30th EACSL Annual Conference on Computer Science Logic (CSL 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 216, pp. 2:1-2:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{fernandes_et_al:LIPIcs.CSL.2022.2,
  author =	{Fernandes, Natasha and McIver, Annabelle and Morgan, Carroll},
  title =	{{How to Develop an Intuition for Risk... and Other Invisible Phenomena}},
  booktitle =	{30th EACSL Annual Conference on Computer Science Logic (CSL 2022)},
  pages =	{2:1--2:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-218-1},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{216},
  editor =	{Manea, Florin and Simpson, Alex},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CSL.2022.2},
  URN =		{urn:nbn:de:0030-drops-157227},
  doi =		{10.4230/LIPIcs.CSL.2022.2},
  annote =	{Keywords: Geometry, Quantitative Information Flow, Proof, Explainability, Privacy}
}

Document

DOI: 10.4230/OASIcs.Gabbrielli.11

Derivation of Constraints from Machine Learning Models and Applications to Security and Privacy

Authors: Moreno Falaschi, Catuscia Palamidessi, and Marco Romanelli

Published in: OASIcs, Volume 86, Recent Developments in the Design and Implementation of Programming Languages (2020)

Abstract

This paper shows how we can combine the power of machine learning with the flexibility of constraints. More specifically, we show how machine learning models can be represented by first-order logic theories, and how to derive these theories. The advantage of this representation is that it can be augmented with additional formulae, representing constraints of some kind on the data domain. For instance, new knowledge, or potential attackers, or fairness desiderata. We consider various kinds of learning algorithms (neural networks, k-nearest-neighbours, decision trees, support vector machines) and for each of them we show how to infer the FOL formulae. Then we focus on one particular application domain, namely the field of security and privacy. The idea is to represent the potentialities and goals of the attacker as a set of constraints, then use a constraint solver (more precisely, a solver modulo theories) to verify the satisfiability. If a solution exists, then it means that an attack is possible, otherwise, the system is safe. We show various examples from different areas of security and privacy; specifically, we consider a side-channel attack on a password checker, a malware attack on smart health systems, and a model-inversion attack on a neural network.

Cite as

Moreno Falaschi, Catuscia Palamidessi, and Marco Romanelli. Derivation of Constraints from Machine Learning Models and Applications to Security and Privacy. In Recent Developments in the Design and Implementation of Programming Languages. Open Access Series in Informatics (OASIcs), Volume 86, pp. 11:1-11:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{falaschi_et_al:OASIcs.Gabbrielli.11,
  author =	{Falaschi, Moreno and Palamidessi, Catuscia and Romanelli, Marco},
  title =	{{Derivation of Constraints from Machine Learning Models and Applications to Security and Privacy}},
  booktitle =	{Recent Developments in the Design and Implementation of Programming Languages},
  pages =	{11:1--11:20},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-171-9},
  ISSN =	{2190-6807},
  year =	{2020},
  volume =	{86},
  editor =	{de Boer, Frank S. and Mauro, Jacopo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Gabbrielli.11},
  URN =		{urn:nbn:de:0030-drops-132338},
  doi =		{10.4230/OASIcs.Gabbrielli.11},
  annote =	{Keywords: Constraints, machine learning, privacy, security}
}

Document

DOI: 10.4230/LIPIcs.ITP.2019.27

Verifying That a Compiler Preserves Concurrent Value-Dependent Information-Flow Security

Authors: Robert Sison and Toby Murray

Published in: LIPIcs, Volume 141, 10th International Conference on Interactive Theorem Proving (ITP 2019)

Abstract

It is common to prove by reasoning over source code that programs do not leak sensitive data. But doing so leaves a gap between reasoning and reality that can only be filled by accounting for the behaviour of the compiler. This task is complicated when programs enforce value-dependent information-flow security properties (in which classification of locations can vary depending on values in other locations) and complicated further when programs exploit shared-variable concurrency. Prior work has formally defined a notion of concurrency-aware refinement for preserving value-dependent security properties. However, that notion is considerably more complex than standard refinement definitions typically applied in the verification of semantics preservation by compilers. To date it remains unclear whether it can be applied to a realistic compiler, because there exist no general decomposition principles for separating it into smaller, more familiar, proof obligations. In this work, we provide such a decomposition principle, which we show can almost halve the complexity of proving secure refinement. Further, we demonstrate its applicability to secure compilation, by proving in Isabelle/HOL the preservation of value-dependent security by a proof-of-concept compiler from an imperative While language to a generic RISC-style assembly language, for programs with shared-memory concurrency mediated by locking primitives. Finally, we execute our compiler in Isabelle on a While language model of the Cross Domain Desktop Compositor, demonstrating to our knowledge the first use of a compiler verification result to carry an information-flow security property down to the assembly-level model of a non-trivial concurrent program.

Cite as

Robert Sison and Toby Murray. Verifying That a Compiler Preserves Concurrent Value-Dependent Information-Flow Security. In 10th International Conference on Interactive Theorem Proving (ITP 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 141, pp. 27:1-27:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{sison_et_al:LIPIcs.ITP.2019.27,
  author =	{Sison, Robert and Murray, Toby},
  title =	{{Verifying That a Compiler Preserves Concurrent Value-Dependent Information-Flow Security}},
  booktitle =	{10th International Conference on Interactive Theorem Proving (ITP 2019)},
  pages =	{27:1--27:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-122-1},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{141},
  editor =	{Harrison, John and O'Leary, John and Tolmach, Andrew},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITP.2019.27},
  URN =		{urn:nbn:de:0030-drops-110829},
  doi =		{10.4230/LIPIcs.ITP.2019.27},
  annote =	{Keywords: Secure compilation, Information flow security, Concurrency, Verification}
}

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