12 Search Results for "Xu, Helen"

Document
Research
DOI: 10.4230/TGDK.3.3.4
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
DOI: 10.4230/LIPIcs.GD.2025.32
Planar Stories of Graph Drawings: Algorithms and Experiments

Authors: Carla Binucci, Sabine Cornelsen, Walter Didimo, Seok-Hee Hong, Eleni Katsanou, Maurizio Patrignani, Antonios Symvonis, and Samuel Wolf

Published in: LIPIcs, Volume 357, 33rd International Symposium on Graph Drawing and Network Visualization (GD 2025)

Abstract
We address the problem of computing a dynamic visualization of a geometric graph G as a sequence of frames. Each frame shows only a portion of the graph but their union covers G entirely. The two main requirements of our dynamic visualization are: (i) guaranteeing drawing stability, so to preserve the user’s mental map; (ii) keeping the visual complexity of each frame low. To satisfy the first requirement, we never change the position of the vertices. Regarding the second requirement, we avoid edge crossings in each frame. More precisely, in the first frame we visualize a suitable subset of non-crossing edges; in each subsequent frame, exactly one new edge enters the visualization and all the edges that cross with it are deleted. We call such a sequence of frames a planar story of G. Our goal is to find a planar story whose minimum number of edges contemporarily displayed is maximized (i.e., a planar story that maximizes the minimum frame size). Besides studying our model from a theoretical point of view, we also design and experimentally compare different algorithms, both exact techniques and heuristics. These algorithms provide an array of alternative trade-offs between efficiency and effectiveness, also depending on the structure of the input graph.
Cite as

Carla Binucci, Sabine Cornelsen, Walter Didimo, Seok-Hee Hong, Eleni Katsanou, Maurizio Patrignani, Antonios Symvonis, and Samuel Wolf. Planar Stories of Graph Drawings: Algorithms and Experiments. In 33rd International Symposium on Graph Drawing and Network Visualization (GD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 357, pp. 32:1-32:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{binucci_et_al:LIPIcs.GD.2025.32,
  author =	{Binucci, Carla and Cornelsen, Sabine and Didimo, Walter and Hong, Seok-Hee and Katsanou, Eleni and Patrignani, Maurizio and Symvonis, Antonios and Wolf, Samuel},
  title =	{{Planar Stories of Graph Drawings: Algorithms and Experiments}},
  booktitle =	{33rd International Symposium on Graph Drawing and Network Visualization (GD 2025)},
  pages =	{32:1--32:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-403-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{357},
  editor =	{Dujmovi\'{c}, Vida and Montecchiani, Fabrizio},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.GD.2025.32},
  URN =		{urn:nbn:de:0030-drops-250182},
  doi =		{10.4230/LIPIcs.GD.2025.32},
  annote =	{Keywords: Graph Drawing, Dynamic Graphs, Graph Stories, Heuristics, ILP}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.4
Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems

Authors: Inhoo Lee, Salvador Buse, and Erik Winfree

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract
Many molecular systems are best understood in terms of prototypical species and reactions. The central dogma and related biochemistry are rife with examples: gene i is transcribed into RNA i, which is translated into protein i; kinase n phosphorylates substrate m; protein p dimerizes with protein q. Engineered nucleic acid systems also often have this form: oligonucleotide i hybridizes to complementary oligonucleotide j; signal strand n displaces the output of seesaw gate m; hairpin p triggers the opening of target q. When there are many variants of a small number of prototypes, it can be conceptually cleaner and computationally more efficient to represent the full system in terms of indexed species (e.g. for dimerization, M_p, D_pq) and indexed reactions (M_p + M_q → D_pq). Here, we formalize the Indexed Chemical Reaction Network (ICRN) model and describe a Python software package designed to simulate such systems in the well-mixed and reaction-diffusion settings, using a differentiable programming framework originally developed for large-scale neural network models, taking advantage of GPU acceleration when available. Notably, this framework makes it straightforward to train the models’ initial conditions and rate constants to optimize a target behavior, such as matching experimental data, performing a computation, or exhibiting spatial pattern formation. The natural map of indexed chemical reaction networks onto neural network formalisms provides a tangible yet general perspective for translating concepts and techniques from the theory and practice of neural computation into the design of biomolecular systems.
Cite as

Inhoo Lee, Salvador Buse, and Erik Winfree. Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 4:1-4:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lee_et_al:LIPIcs.DNA.31.4,
  author =	{Lee, Inhoo and Buse, Salvador and Winfree, Erik},
  title =	{{Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{4:1--4:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.4},
  URN =		{urn:nbn:de:0030-drops-238534},
  doi =		{10.4230/LIPIcs.DNA.31.4},
  annote =	{Keywords: Differentiable Programming, Chemical Reaction Networks, Reaction-Diffusion Systems}
}
Document
DOI: 10.4230/LIPIcs.GIScience.2025.13
Assessing Map Reproducibility with Visual Question-Answering: An Empirical Evaluation

Authors: Eftychia Koukouraki, Auriol Degbelo, and Christian Kray

Published in: LIPIcs, Volume 346, 13th International Conference on Geographic Information Science (GIScience 2025)

Abstract
Reproducibility is a key principle of the modern scientific method. Maps, as an important means of communicating scientific results in GIScience and across disciplines, should be reproducible. Currently, map reproducibility assessment is done manually, which makes the assessment process tedious and time-consuming, ultimately limiting its efficiency. Hence, this work explores the extent to which Visual Question-Answering (VQA) can be used to automate some tasks relevant to map reproducibility assessment. We selected five state-of-the-art vision language models (VLMs) and followed a three-step approach to evaluate their ability to discriminate between maps and other images, interpret map content, and compare two map images using VQA. Our results show that current VLMs already possess map-reading capabilities and demonstrate understanding of spatial concepts, such as cardinal directions, geographic scope, and legend interpretation. Our paper demonstrates the potential of using VQA to support reproducibility assessment and highlights the outstanding issues that need to be addressed to achieve accurate, trustworthy map descriptions, thereby reducing the time and effort required by human evaluators.
Cite as

Eftychia Koukouraki, Auriol Degbelo, and Christian Kray. Assessing Map Reproducibility with Visual Question-Answering: An Empirical Evaluation. In 13th International Conference on Geographic Information Science (GIScience 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 346, pp. 13:1-13:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{koukouraki_et_al:LIPIcs.GIScience.2025.13,
  author =	{Koukouraki, Eftychia and Degbelo, Auriol and Kray, Christian},
  title =	{{Assessing Map Reproducibility with Visual Question-Answering: An Empirical Evaluation}},
  booktitle =	{13th International Conference on Geographic Information Science (GIScience 2025)},
  pages =	{13:1--13:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-378-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{346},
  editor =	{Sila-Nowicka, Katarzyna and Moore, Antoni and O'Sullivan, David and Adams, Benjamin and Gahegan, Mark},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.GIScience.2025.13},
  URN =		{urn:nbn:de:0030-drops-238426},
  doi =		{10.4230/LIPIcs.GIScience.2025.13},
  annote =	{Keywords: map comparison, computational reproducibility, visual question answering, large language models, GeoAI}
}
Document
DOI: 10.4230/LIPIcs.GIScience.2025.5
Analysis of Points of Interests Recommended for Leisure Walk Descriptions

Authors: Ehsan Hamzei, Thi Minh Hoai Bui, Martin Tomko, and Stephan Winter

Published in: LIPIcs, Volume 346, 13th International Conference on Geographic Information Science (GIScience 2025)

Abstract
Leisure walking is a physical activity where locomotion through a natural or even urban environment is the goal in itself, e.g., in pursuit of health and wellbeing. In contrast to destination-oriented walks that are focused on navigation efficiency (i.e., shortest or simplest walk from source to destination), leisure walks emphasize experiencing the environment, engaging in activities, and discovering places that may be off route, or intermediate destinations en-route, summarily called points of interest (POIs). POIs are key for recommending leisure walks, yet a detailed analysis of POIs in the context of leisure walking is missing in the literature. This study extracts and annotates POIs of leisure walking recommendations available in WalkingMaps.com.au, creating an annotated dataset to address this research gap and provide a first analysis of leisure walking descriptions. We classify POIs using the verbal description provided in the dataset, match them with data available in OpenStreetMap (OSM), and compare the POIs with nearby alternatives in OSM. Our analysis reveals thematic and spatial patterns in POI selection, offering a machine learning approach to model POI choices for leisure walks. We further evaluate the availability of rich data in OSM for future automated leisure walking recommendation. This study contributes to automated systems for recommending leisure walks, tailoring suggestions based on available information in the spatial open data, and presents an annotated dataset to facilitate future research in this field.
Cite as

Ehsan Hamzei, Thi Minh Hoai Bui, Martin Tomko, and Stephan Winter. Analysis of Points of Interests Recommended for Leisure Walk Descriptions. In 13th International Conference on Geographic Information Science (GIScience 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 346, pp. 5:1-5:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{hamzei_et_al:LIPIcs.GIScience.2025.5,
  author =	{Hamzei, Ehsan and Bui, Thi Minh Hoai and Tomko, Martin and Winter, Stephan},
  title =	{{Analysis of Points of Interests Recommended for Leisure Walk Descriptions}},
  booktitle =	{13th International Conference on Geographic Information Science (GIScience 2025)},
  pages =	{5:1--5:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-378-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{346},
  editor =	{Sila-Nowicka, Katarzyna and Moore, Antoni and O'Sullivan, David and Adams, Benjamin and Gahegan, Mark},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.GIScience.2025.5},
  URN =		{urn:nbn:de:0030-drops-238341},
  doi =		{10.4230/LIPIcs.GIScience.2025.5},
  annote =	{Keywords: leisure walks, points of interest, places, platial information}
}
Document
DOI: 10.4230/LIPIcs.ECRTS.2025.7
Period Assignment for Real-Time Cascade Control Tasks Under Stability and Schedulability Constraints

Authors: Ismail Hawila, Liliana Cucu-Grosjean, and Slim Ben Amor

Published in: LIPIcs, Volume 335, 37th Euromicro Conference on Real-Time Systems (ECRTS 2025)

Abstract
Existing results for cyber-physical systems have been proposed to merge the requirements associated to the stability of the physical components and the schedulability of the cyber components. Nevertheless, none of the existing results has studied these requirements for multiple real-time cascade control tasks where their periods choice are dependent and affect stability. In this paper, we propose a methodology to evaluate the periods of the real-time cascade control tasks that ensures stability of the physical components, then we present a co-design problem for the period choice that guarantees good performance of the physical components and schedulability of the cyber components under fixed-priority scheduling. We then evaluate this methodology on a real use-case of a drone system. Results show the importance of studying these requirements together as their relation has an impact on stable periods range.
Cite as

Ismail Hawila, Liliana Cucu-Grosjean, and Slim Ben Amor. Period Assignment for Real-Time Cascade Control Tasks Under Stability and Schedulability Constraints. In 37th Euromicro Conference on Real-Time Systems (ECRTS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 335, pp. 7:1-7:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{hawila_et_al:LIPIcs.ECRTS.2025.7,
  author =	{Hawila, Ismail and Cucu-Grosjean, Liliana and Ben Amor, Slim},
  title =	{{Period Assignment for Real-Time Cascade Control Tasks Under Stability and Schedulability Constraints}},
  booktitle =	{37th Euromicro Conference on Real-Time Systems (ECRTS 2025)},
  pages =	{7:1--7:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-377-5},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{335},
  editor =	{Mancuso, Renato},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2025.7},
  URN =		{urn:nbn:de:0030-drops-235858},
  doi =		{10.4230/LIPIcs.ECRTS.2025.7},
  annote =	{Keywords: Real-time Systems, Cascade Control, Physical Stability, Control Performance}
}
Document
DOI: 10.4230/LIPIcs.FSCD.2025.25
Completeness of the Decreasing Diagrams Method for Proving Confluence of Rewriting Systems of the Least Uncountable Cardinality

Authors: Ievgen Ivanov

Published in: LIPIcs, Volume 337, 10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025)

Abstract
We show that every confluent abstract rewriting system (ARS) of the cardinality that does not exceed the first uncountable cardinal belongs to the class DCR₃, i.e. the class of confluent ARS for which confluence can be proved with the the help of the decreasing diagrams method using the set of labels {0,1,2} ordered in such a way that 0<1<2 (in the general case, the decreasing diagrams method with two labels is not sufficient for proving confluence of such ARS). Under the Continuum Hypothesis this result implies that the decreasing diagrams method is sufficient for establishing confluence of ARS on many structures of interest to applied mathematics and various interdisciplinary fields (confluence of ARS on real numbers, continuous real functions, etc.). We provide a machine-checked formal proof of a formalized version of the main result in Isabelle proof assistant using HOL logic and the HOL-Cardinals theory. An extended version of this formalization is available in the Archive of Formal Proofs.
Cite as

Ievgen Ivanov. Completeness of the Decreasing Diagrams Method for Proving Confluence of Rewriting Systems of the Least Uncountable Cardinality. In 10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 337, pp. 25:1-25:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ivanov:LIPIcs.FSCD.2025.25,
  author =	{Ivanov, Ievgen},
  title =	{{Completeness of the Decreasing Diagrams Method for Proving Confluence of Rewriting Systems of the Least Uncountable Cardinality}},
  booktitle =	{10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025)},
  pages =	{25:1--25:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-374-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{337},
  editor =	{Fern\'{a}ndez, Maribel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2025.25},
  URN =		{urn:nbn:de:0030-drops-236404},
  doi =		{10.4230/LIPIcs.FSCD.2025.25},
  annote =	{Keywords: confluence, decreasing diagrams method, rewriting systems, reduction, formal methods, formal proofs, formal verification, non-discrete models, nondeterministic models, interval models}
}
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
Resource Paper
DOI: 10.4230/TGDK.2.2.7
Whelk: An OWL EL+RL Reasoner Enabling New Use Cases

Authors: James P. Balhoff and Christopher J. Mungall

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
Many tasks in the biosciences rely on reasoning with large OWL terminologies (Tboxes), often combined with even larger databases. In particular, a common task is retrieval queries that utilize relational expressions; for example, “find all genes expressed in the brain or any part of the brain”. Automated reasoning on these ontologies typically relies on scalable reasoners targeting the EL subset of OWL, such as ELK. While the introduction of ELK has been transformative in the incorporation of reasoning into bio-ontology quality control and production pipelines, we have encountered limitations when applying it to use cases involving high throughput query answering or reasoning about datasets describing instances (Aboxes). Whelk is a fast OWL reasoner for combined EL+RL reasoning. As such, it is particularly useful for many biological ontology tasks, particularly those characterized by large Tboxes using the EL subset of OWL, combined with Aboxes targeting the RL subset of OWL. Whelk is implemented in Scala and utilizes immutable functional data structures, which provides advantages when performing incremental or dynamic reasoning tasks. Whelk supports querying complex class expressions at a substantially greater rate than ELK, and can answer queries or perform incremental reasoning tasks in parallel, enabling novel applications of OWL reasoning.
Cite as

James P. Balhoff and Christopher J. Mungall. Whelk: An OWL EL+RL Reasoner Enabling New Use Cases. In Special Issue on Resources for Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 2, pp. 7:1-7:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{balhoff_et_al:TGDK.2.2.7,
  author =	{Balhoff, James P. and Mungall, Christopher J.},
  title =	{{Whelk: An OWL EL+RL Reasoner Enabling New Use Cases}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{7:1--7:17},
  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.2.2.7},
  URN =		{urn:nbn:de:0030-drops-225918},
  doi =		{10.4230/TGDK.2.2.7},
  annote =	{Keywords: Web Ontology Language, OWL, Semantic Web, ontology, reasoner}
}
Document
Vision
DOI: 10.4230/TGDK.1.1.9
Trust, Accountability, and Autonomy in Knowledge Graph-Based AI for Self-Determination

Authors: Luis-Daniel Ibáñez, John Domingue, Sabrina Kirrane, Oshani Seneviratne, Aisling Third, and Maria-Esther Vidal

Published in: TGDK, Volume 1, Issue 1 (2023): Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 1, Issue 1

Abstract
Knowledge Graphs (KGs) have emerged as fundamental platforms for powering intelligent decision-making and a wide range of Artificial Intelligence (AI) services across major corporations such as Google, Walmart, and AirBnb. KGs complement Machine Learning (ML) algorithms by providing data context and semantics, thereby enabling further inference and question-answering capabilities. The integration of KGs with neuronal learning (e.g., Large Language Models (LLMs)) is currently a topic of active research, commonly named neuro-symbolic AI. Despite the numerous benefits that can be accomplished with KG-based AI, its growing ubiquity within online services may result in the loss of self-determination for citizens as a fundamental societal issue. The more we rely on these technologies, which are often centralised, the less citizens will be able to determine their own destinies. To counter this threat, AI regulation, such as the European Union (EU) AI Act, is being proposed in certain regions. The regulation sets what technologists need to do, leading to questions concerning How the output of AI systems can be trusted? What is needed to ensure that the data fuelling and the inner workings of these artefacts are transparent? How can AI be made accountable for its decision-making? This paper conceptualises the foundational topics and research pillars to support KG-based AI for self-determination. Drawing upon this conceptual framework, challenges and opportunities for citizen self-determination are illustrated and analysed in a real-world scenario. As a result, we propose a research agenda aimed at accomplishing the recommended objectives.
Cite as

Luis-Daniel Ibáñez, John Domingue, Sabrina Kirrane, Oshani Seneviratne, Aisling Third, and Maria-Esther Vidal. Trust, Accountability, and Autonomy in Knowledge Graph-Based AI for Self-Determination. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 9:1-9:32, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{ibanez_et_al:TGDK.1.1.9,
  author =	{Ib\'{a}\~{n}ez, Luis-Daniel and Domingue, John and Kirrane, Sabrina and Seneviratne, Oshani and Third, Aisling and Vidal, Maria-Esther},
  title =	{{Trust, Accountability, and Autonomy in Knowledge Graph-Based AI for Self-Determination}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{9:1--9:32},
  ISSN =	{2942-7517},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.9},
  URN =		{urn:nbn:de:0030-drops-194839},
  doi =		{10.4230/TGDK.1.1.9},
  annote =	{Keywords: Trust, Accountability, Autonomy, AI, Knowledge Graphs}
}
Document
Position
DOI: 10.4230/TGDK.1.1.5
Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities

Authors: Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma

Published in: TGDK, Volume 1, Issue 1 (2023): Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 1, Issue 1

Abstract
The term life sciences refers to the disciplines that study living organisms and life processes, and include chemistry, biology, medicine, and a range of other related disciplines. Research efforts in life sciences are heavily data-driven, as they produce and consume vast amounts of scientific data, much of which is intrinsically relational and graph-structured. The volume of data and the complexity of scientific concepts and relations referred to therein promote the application of advanced knowledge-driven technologies for managing and interpreting data, with the ultimate aim to advance scientific discovery. In this survey and position paper, we discuss recent developments and advances in the use of graph-based technologies in life sciences and set out a vision for how these technologies will impact these fields into the future. We focus on three broad topics: the construction and management of Knowledge Graphs (KGs), the use of KGs and associated technologies in the discovery of new knowledge, and the use of KGs in artificial intelligence applications to support explanations (explainable AI). We select a few exemplary use cases for each topic, discuss the challenges and open research questions within these topics, and conclude with a perspective and outlook that summarizes the overarching challenges and their potential solutions as a guide for future research.
Cite as

Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma. Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 5:1-5:33, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{chen_et_al:TGDK.1.1.5,
  author =	{Chen, Jiaoyan and Dong, Hang and Hastings, Janna and Jim\'{e}nez-Ruiz, Ernesto and L\'{o}pez, Vanessa and Monnin, Pierre and Pesquita, Catia and \v{S}koda, Petr and Tamma, Valentina},
  title =	{{Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{5:1--5:33},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.5},
  URN =		{urn:nbn:de:0030-drops-194791},
  doi =		{10.4230/TGDK.1.1.5},
  annote =	{Keywords: Knowledge graphs, Life science, Knowledge discovery, Explainable AI}
}
Document
DOI: 10.4230/LIPIcs.ESA.2022.16
When Are Cache-Oblivious Algorithms Cache Adaptive? A Case Study of Matrix Multiplication and Sorting

Authors: Arghya Bhattacharya, Abiyaz Chowdhury, Helen Xu, Rathish Das, Rezaul A. Chowdhury, Rob Johnson, Rishab Nithyanand, and Michael A. Bender

Published in: LIPIcs, Volume 244, 30th Annual European Symposium on Algorithms (ESA 2022)

Abstract
Cache-adaptive algorithms are a class of algorithms that achieve optimal utilization of dynamically changing memory. These memory fluctuations are the norm in today’s multi-threaded shared-memory machines and time-sharing caches. Bender et al. [Bender et al., 2014] proved that many cache-oblivious algorithms are optimally cache-adaptive, but that some cache-oblivious algorithms can be relatively far from optimally cache-adaptive on worst-case memory fluctuations. This worst-case gap between cache obliviousness and cache adaptivity depends on a highly-structured, adversarial memory profile. Existing cache-adaptive analysis does not predict the relative performance of cache-oblivious and cache-adaptive algorithms on non-adversarial profiles. Does the worst-case gap appear in practice, or is it an artifact of an unrealistically powerful adversary? This paper sheds light on the question of whether cache-oblivious algorithms can effectively adapt to realistically fluctuating memory sizes; the paper focuses on matrix multiplication and sorting. The two matrix-multiplication algorithms in this paper are canonical examples of "(a, b, c)-regular" cache-oblivious algorithms, which underlie much of the existing theory on cache-adaptivity. Both algorithms have the same asymptotic I/O performance when the memory size remains fixed, but one is optimally cache-adaptive, and the other is not. In our experiments, we generate both adversarial and non-adversarial memory workloads. The performance gap between the algorithms for matrix multiplication grows with problem size (up to 3.8×) on the adversarial profiles, but the gap does not grow with problem size (stays at 2×) on non-adversarial profiles. The sorting algorithms in this paper are not "(a, b, c)-regular," but they have been well-studied in the classical external-memory model when the memory size does not fluctuate. The relative performance of a non-oblivious (cache-aware) sorting algorithm degrades with the problem size: it incurs up to 6 × the number of disk I/Os compared to an oblivious adaptive algorithm on both adversarial and non-adversarial profiles. To summarize, in all our experiments, the cache-oblivious matrix-multiplication and sorting algorithms that we tested empirically adapt well to memory fluctuations. We conjecture that cache-obliviousness will empirically help achieve adaptivity for other problems with similar structures.
Cite as

Arghya Bhattacharya, Abiyaz Chowdhury, Helen Xu, Rathish Das, Rezaul A. Chowdhury, Rob Johnson, Rishab Nithyanand, and Michael A. Bender. When Are Cache-Oblivious Algorithms Cache Adaptive? A Case Study of Matrix Multiplication and Sorting. In 30th Annual European Symposium on Algorithms (ESA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 244, pp. 16:1-16:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{bhattacharya_et_al:LIPIcs.ESA.2022.16,
  author =	{Bhattacharya, Arghya and Chowdhury, Abiyaz and Xu, Helen and Das, Rathish and Chowdhury, Rezaul A. and Johnson, Rob and Nithyanand, Rishab and Bender, Michael A.},
  title =	{{When Are Cache-Oblivious Algorithms Cache Adaptive? A Case Study of Matrix Multiplication and Sorting}},
  booktitle =	{30th Annual European Symposium on Algorithms (ESA 2022)},
  pages =	{16:1--16:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-247-1},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{244},
  editor =	{Chechik, Shiri and Navarro, Gonzalo and Rotenberg, Eva and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2022.16},
  URN =		{urn:nbn:de:0030-drops-169543},
  doi =		{10.4230/LIPIcs.ESA.2022.16},
  annote =	{Keywords: Cache-adaptive algorithms, cache-oblivious algorithms}
}
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