14 Search Results for "Ryder, Nick"

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/OASIcs.DX.2025.10
Automating Control System Design: Using Language Models for Expert Knowledge in Decentralized Controller Auto-Tuning

Authors: Marlon J. Ares-Milian, Gregory Provan, and Marcos Quinones-Grueiro

Published in: OASIcs, Volume 136, 36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025)

Abstract
Fully-automated optimal controller design for engineering systems is a challenging task. While, optimization-based, automated control parameter tuning techniques have been widely discussed in the literature, most works do not discuss expert knowledge requirements for system design, which result in significant human intervention. In this work, we discuss a multistage controller tuning framework for decentralized control that highlights expert knowledge requirements in automated controller design. We propose a methodology to automate the input-output pairing and stage definition steps in the framework using Large Language Models (LLMs) for a family of multi-tank benchmarks. We achieve this by proposing a mathematical language to describe the system and design an algorithm to bind this mathematical representation to the input prompt space of an LLM. We demonstrate that our methodology can produce consistent expert knowledge outputs from the LLM with over 97% accuracy for the multi-tank benchmarks. We also empirically show that, correct stage definition by the LLM can improve tuned controller performance by up to 52%.
Cite as

Marlon J. Ares-Milian, Gregory Provan, and Marcos Quinones-Grueiro. Automating Control System Design: Using Language Models for Expert Knowledge in Decentralized Controller Auto-Tuning. In 36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025). Open Access Series in Informatics (OASIcs), Volume 136, pp. 10:1-10:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{aresmilian_et_al:OASIcs.DX.2025.10,
  author =	{Ares-Milian, Marlon J. and Provan, Gregory and Quinones-Grueiro, Marcos},
  title =	{{Automating Control System Design: Using Language Models for Expert Knowledge in Decentralized Controller Auto-Tuning}},
  booktitle =	{36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025)},
  pages =	{10:1--10:20},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-394-2},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{136},
  editor =	{Quinones-Grueiro, Marcos and Biswas, Gautam and Pill, Ingo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.DX.2025.10},
  URN =		{urn:nbn:de:0030-drops-247996},
  doi =		{10.4230/OASIcs.DX.2025.10},
  annote =	{Keywords: controller auto-tuning, automated system design, large language models}
}
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
RANDOM
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2025.39
Consumable Data via Quantum Communication

Authors: Dar Gilboa, Siddhartha Jain, and Jarrod R. McClean

Published in: LIPIcs, Volume 353, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)

Abstract
Classical data can be copied and re-used for computation, with adverse consequences economically and in terms of data privacy. Motivated by this, we formulate problems in one-way communication complexity where Alice holds some data x and Bob holds m inputs y_1, …, y_m. They want to compute m instances of a bipartite relation R(⋅,⋅) on every pair (x, y_1), …, (x, y_m). We call this the asymmetric direct sum question for one-way communication. We give examples where the quantum communication complexity of such problems scales polynomially with m, while the classical communication complexity depends at most logarithmically on m. Thus, for such problems, data behaves like a consumable resource that is effectively destroyed upon use when the owner stores and transmits it as quantum states, but not when transmitted classically. We show an application to a strategic data-selling game, and discuss other potential economic implications.
Cite as

Dar Gilboa, Siddhartha Jain, and Jarrod R. McClean. Consumable Data via Quantum Communication. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 39:1-39:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gilboa_et_al:LIPIcs.APPROX/RANDOM.2025.39,
  author =	{Gilboa, Dar and Jain, Siddhartha and McClean, Jarrod R.},
  title =	{{Consumable Data via Quantum Communication}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{39:1--39:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-397-3},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{353},
  editor =	{Ene, Alina and Chattopadhyay, Eshan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2025.39},
  URN =		{urn:nbn:de:0030-drops-244059},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.39},
  annote =	{Keywords: quantum communication, one-time programs, data markets}
}
Document
DOI: 10.4230/OASIcs.ICPEC.2025.4
Can Open Large Language Models Catch Vulnerabilities?

Authors: Diogo Gaspar Lopes, Tiago Espinha Gasiba, Sathwik Amburi, and Maria Pinto-Albuquerque

Published in: OASIcs, Volume 133, 6th International Computer Programming Education Conference (ICPEC 2025)

Abstract
As Large Language Models (LLMs) become increasingly integrated into secure software development workflows, a critical question remains unanswered: can these models not only detect insecure code but also reliably classify vulnerabilities according to standardized taxonomies? In this work, we conduct a systematic evaluation of three state-of-the-art LLMs - Llama3, Codestral, and Deepseek R1 - using a carefully filtered subset of the Big-Vul dataset annotated with eight representative Common Weakness Enumeration categories. Adopting a closed-world classification setup, we assess each model’s performance in both identifying the presence of vulnerabilities and mapping them to the correct CWE label. Our findings reveal a sharp contrast between high detection rates and markedly poor classification accuracy, with frequent overgeneralization and misclassification. Moreover, we analyze model-specific biases and common failure modes, shedding light on the limitations of current LLMs in performing fine-grained security reasoning.These insights are especially relevant in educational contexts, where LLMs are being adopted as learning aids despite their limitations. A nuanced understanding of their behaviour is essential to prevent the propagation of misconceptions among students. Our results expose key challenges that must be addressed before LLMs can be reliably deployed in security-sensitive environments.
Cite as

Diogo Gaspar Lopes, Tiago Espinha Gasiba, Sathwik Amburi, and Maria Pinto-Albuquerque. Can Open Large Language Models Catch Vulnerabilities?. In 6th International Computer Programming Education Conference (ICPEC 2025). Open Access Series in Informatics (OASIcs), Volume 133, pp. 4:1-4:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gasparlopes_et_al:OASIcs.ICPEC.2025.4,
  author =	{Gaspar Lopes, Diogo and Espinha Gasiba, Tiago and Amburi, Sathwik and Pinto-Albuquerque, Maria},
  title =	{{Can Open Large Language Models Catch Vulnerabilities?}},
  booktitle =	{6th International Computer Programming Education Conference (ICPEC 2025)},
  pages =	{4:1--4:14},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-393-5},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{133},
  editor =	{Queir\'{o}s, Ricardo and Pinto, M\'{a}rio and Portela, Filipe and Sim\~{o}es, Alberto},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.ICPEC.2025.4},
  URN =		{urn:nbn:de:0030-drops-240340},
  doi =		{10.4230/OASIcs.ICPEC.2025.4},
  annote =	{Keywords: Large Language Models (LLMs), Secure Coding, CWE Classification, Machine Learning, Software Vulnerability Detection, Artificial Intelligence, Code Analysis, Big-Vul Dataset}
}
Document
DOI: 10.4230/OASIcs.ICPEC.2025.7
A Generative Artificial Intelligence Tool to Correct Programming Exercises

Authors: Filipe Portela

Published in: OASIcs, Volume 133, 6th International Computer Programming Education Conference (ICPEC 2025)

Abstract
This paper presents an innovative strategy for assessing programming exercises in higher education, leveraging generative artificial intelligence (GAI) to support automated grading while ensuring transparency, fairness, and pedagogical relevance. The proposed approach is framed within the TechTeach paradigm and integrates multiple tools - HackerRank for code development, Google Forms and Sheets for submission and prompt generation, and the ChatGPT API for intelligent evaluation. The correction process is personalised using student-specific variables (e.g., student ID, birth date, performance in group work), which are dynamically embedded into the statement and prompt. The GAI algorithm evaluates the code and performs authorship verification using peer-assessed effort data, enabling the detection of potential plagiarism or misuse of AI tools. A case study was conducted in the 2023/2024 edition of the Web Programming course at the University of Minho, which involved 118 students. Results indicate that the method produced consistent and meaningful grades, reflecting a balanced perception of difficulty from students. The system also includes a gamification mechanism (Grade Rescue) for managing contested cases. The achieved findings (>90% of students approved the exercise model) support the viability of GAI-based evaluation as a scalable and effective solution for programming education, while maintaining academic integrity and enhancing the student experience.
Cite as

Filipe Portela. A Generative Artificial Intelligence Tool to Correct Programming Exercises. In 6th International Computer Programming Education Conference (ICPEC 2025). Open Access Series in Informatics (OASIcs), Volume 133, pp. 7:1-7:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{portela:OASIcs.ICPEC.2025.7,
  author =	{Portela, Filipe},
  title =	{{A Generative Artificial Intelligence Tool to Correct Programming Exercises}},
  booktitle =	{6th International Computer Programming Education Conference (ICPEC 2025)},
  pages =	{7:1--7:16},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-393-5},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{133},
  editor =	{Queir\'{o}s, Ricardo and Pinto, M\'{a}rio and Portela, Filipe and Sim\~{o}es, Alberto},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.ICPEC.2025.7},
  URN =		{urn:nbn:de:0030-drops-240376},
  doi =		{10.4230/OASIcs.ICPEC.2025.7},
  annote =	{Keywords: TechTeach, Information Systems, Higher Education, Generative AI, Code Exercises}
}
Document
DOI: 10.4230/LIPIcs.GIScience.2025.3
Enriching Location Representation with Detailed Semantic Information

Authors: Junyuan Liu, Xinglei Wang, and Tao Cheng

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

Abstract
Spatial representations that capture both structural and semantic characteristics of urban environments are essential for urban modeling. Traditional spatial embeddings often prioritize spatial proximity while underutilizing fine-grained contextual information from places. To address this limitation, we introduce CaLLiPer+, an extension of the CaLLiPer model that systematically integrates Point-of-Interest (POI) names alongside categorical labels within a multimodal contrastive learning framework. We evaluate its effectiveness on two downstream tasks - land use classification and socioeconomic status distribution mapping - demonstrating consistent performance gains of 4% to 11% over baseline methods. Additionally, we show that incorporating POI names enhances location retrieval, enabling models to capture complex urban concepts with greater precision. Ablation studies further reveal the complementary role of POI names and the advantages of leveraging pretrained text encoders for spatial representations. Overall, our findings highlight the potential of integrating fine-grained semantic attributes and multimodal learning techniques to advance the development of urban foundation models.
Cite as

Junyuan Liu, Xinglei Wang, and Tao Cheng. Enriching Location Representation with Detailed Semantic Information. In 13th International Conference on Geographic Information Science (GIScience 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 346, pp. 3:1-3:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{liu_et_al:LIPIcs.GIScience.2025.3,
  author =	{Liu, Junyuan and Wang, Xinglei and Cheng, Tao},
  title =	{{Enriching Location Representation with Detailed Semantic Information}},
  booktitle =	{13th International Conference on Geographic Information Science (GIScience 2025)},
  pages =	{3:1--3:15},
  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.2025.3},
  URN =		{urn:nbn:de:0030-drops-238322},
  doi =		{10.4230/LIPIcs.GIScience.2025.3},
  annote =	{Keywords: Location Embedding, Contrastive Learning, Pretrained Model}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2025.35
Chain of Grounded Objectives: Concise Goal-Oriented Prompting for Code Generation

Authors: Sangyeop Yeo, Seung-Won Hwang, and Yu-Seung Ma

Published in: LIPIcs, Volume 333, 39th European Conference on Object-Oriented Programming (ECOOP 2025)

Abstract
The use of Large Language Models (LLMs) for code generation has gained significant attention in recent years. Existing methods often aim to improve the quality of generated code by incorporating additional contextual information or guidance into input prompts. Many of these approaches adopt process-oriented reasoning strategies, mimicking human-like step-by-step thinking; however, they may not always align with the structured nature of programming languages. This paper introduces Chain of Grounded Objectives (CGO), a concise goal-oriented prompting approach that embeds functional objectives into prompts to enhance code generation. By focusing on precisely defined objectives rather than explicit procedural steps, CGO aligns more naturally with programming tasks while retaining flexibility. Empirical evaluations on HumanEval, MBPP, their extended versions, and LiveCodeBench show that CGO achieves accuracy comparable to or better than existing methods while using fewer tokens, making it a more efficient approach to LLM-based code generation.
Cite as

Sangyeop Yeo, Seung-Won Hwang, and Yu-Seung Ma. Chain of Grounded Objectives: Concise Goal-Oriented Prompting for Code Generation. In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 35:1-35:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{yeo_et_al:LIPIcs.ECOOP.2025.35,
  author =	{Yeo, Sangyeop and Hwang, Seung-Won and Ma, Yu-Seung},
  title =	{{Chain of Grounded Objectives: Concise Goal-Oriented Prompting for Code Generation}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{35:1--35:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-373-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{333},
  editor =	{Aldrich, Jonathan and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2025.35},
  URN =		{urn:nbn:de:0030-drops-233271},
  doi =		{10.4230/LIPIcs.ECOOP.2025.35},
  annote =	{Keywords: Artificial Intelligence, Natural Language Processing, Prompt Design, Large Language Models, Code Generation}
}
Document
Vision
DOI: 10.4230/TGDK.1.1.3
Knowledge Engineering Using Large Language Models

Authors: Bradley P. Allen, Lise Stork, and Paul Groth

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 engineering is a discipline that focuses on the creation and maintenance of processes that generate and apply knowledge. Traditionally, knowledge engineering approaches have focused on knowledge expressed in formal languages. The emergence of large language models and their capabilities to effectively work with natural language, in its broadest sense, raises questions about the foundations and practice of knowledge engineering. Here, we outline the potential role of LLMs in knowledge engineering, identifying two central directions: 1) creating hybrid neuro-symbolic knowledge systems; and 2) enabling knowledge engineering in natural language. Additionally, we formulate key open research questions to tackle these directions.
Cite as

Bradley P. Allen, Lise Stork, and Paul Groth. Knowledge Engineering Using Large Language Models. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 3:1-3:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{allen_et_al:TGDK.1.1.3,
  author =	{Allen, Bradley P. and Stork, Lise and Groth, Paul},
  title =	{{Knowledge Engineering Using Large Language Models}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{3:1--3:19},
  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.1.1.3},
  URN =		{urn:nbn:de:0030-drops-194777},
  doi =		{10.4230/TGDK.1.1.3},
  annote =	{Keywords: knowledge engineering, large language models}
}
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
Position
DOI: 10.4230/TGDK.1.1.2
Large Language Models and Knowledge Graphs: Opportunities and Challenges

Authors: Jeff Z. Pan, Simon Razniewski, Jan-Christoph Kalo, Sneha Singhania, Jiaoyan Chen, Stefan Dietze, Hajira Jabeen, Janna Omeliyanenko, Wen Zhang, Matteo Lissandrini, Russa Biswas, Gerard de Melo, Angela Bonifati, Edlira Vakaj, Mauro Dragoni, and Damien Graux

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
Large Language Models (LLMs) have taken Knowledge Representation - and the world - by storm. This inflection point marks a shift from explicit knowledge representation to a renewed focus on the hybrid representation of both explicit knowledge and parametric knowledge. In this position paper, we will discuss some of the common debate points within the community on LLMs (parametric knowledge) and Knowledge Graphs (explicit knowledge) and speculate on opportunities and visions that the renewed focus brings, as well as related research topics and challenges.
Cite as

Jeff Z. Pan, Simon Razniewski, Jan-Christoph Kalo, Sneha Singhania, Jiaoyan Chen, Stefan Dietze, Hajira Jabeen, Janna Omeliyanenko, Wen Zhang, Matteo Lissandrini, Russa Biswas, Gerard de Melo, Angela Bonifati, Edlira Vakaj, Mauro Dragoni, and Damien Graux. Large Language Models and Knowledge Graphs: Opportunities and Challenges. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 2:1-2:38, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{pan_et_al:TGDK.1.1.2,
  author =	{Pan, Jeff Z. and Razniewski, Simon and Kalo, Jan-Christoph and Singhania, Sneha and Chen, Jiaoyan and Dietze, Stefan and Jabeen, Hajira and Omeliyanenko, Janna and Zhang, Wen and Lissandrini, Matteo and Biswas, Russa and de Melo, Gerard and Bonifati, Angela and Vakaj, Edlira and Dragoni, Mauro and Graux, Damien},
  title =	{{Large Language Models and Knowledge Graphs: Opportunities and Challenges}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{2:1--2:38},
  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.1.1.2},
  URN =		{urn:nbn:de:0030-drops-194766},
  doi =		{10.4230/TGDK.1.1.2},
  annote =	{Keywords: Large Language Models, Pre-trained Language Models, Knowledge Graphs, Ontology, Retrieval Augmented Language Models}
}
Document
Vision
DOI: 10.4230/TGDK.1.1.8
Machine Learning and Knowledge Graphs: Existing Gaps and Future Research Challenges

Authors: Claudia d'Amato, Louis Mahon, Pierre Monnin, and Giorgos Stamou

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 graph model is nowadays largely adopted to model a wide range of knowledge and data, spanning from social networks to knowledge graphs (KGs), representing a successful paradigm of how symbolic and transparent AI can scale on the World Wide Web. However, due to their unprecedented volume, they are generally tackled by Machine Learning (ML) and mostly numeric based methods such as graph embedding models (KGE) and deep neural networks (DNNs). The latter methods have been proved lately very efficient, leading the current AI spring. In this vision paper, we introduce some of the main existing methods for combining KGs and ML, divided into two categories: those using ML to improve KGs, and those using KGs to improve results on ML tasks. From this introduction, we highlight research gaps and perspectives that we deem promising and currently under-explored for the involved research communities, spanning from KG support for LLM prompting, integration of KG semantics in ML models to symbol-based methods, interpretability of ML models, and the need for improved benchmark datasets. In our opinion, such perspectives are stepping stones in an ultimate view of KGs as central assets for neuro-symbolic and explainable AI.
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Claudia d'Amato, Louis Mahon, Pierre Monnin, and Giorgos Stamou. Machine Learning and Knowledge Graphs: Existing Gaps and Future Research Challenges. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 8:1-8:35, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{damato_et_al:TGDK.1.1.8,
  author =	{d'Amato, Claudia and Mahon, Louis and Monnin, Pierre and Stamou, Giorgos},
  title =	{{Machine Learning and Knowledge Graphs: Existing Gaps and Future Research Challenges}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{8:1--8:35},
  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.1.1.8},
  URN =		{urn:nbn:de:0030-drops-194824},
  doi =		{10.4230/TGDK.1.1.8},
  annote =	{Keywords: Graph-based Learning, Knowledge Graph Embeddings, Large Language Models, Explainable AI, Knowledge Graph Completion \& Curation}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2023.42
Bit Complexity of Jordan Normal Form and Polynomial Spectral Factorization

Authors: Papri Dey, Ravi Kannan, Nick Ryder, and Nikhil Srivastava

Published in: LIPIcs, Volume 251, 14th Innovations in Theoretical Computer Science Conference (ITCS 2023)

Abstract
We study the bit complexity of two related fundamental computational problems in linear algebra and control theory. Our results are: (1) An Õ(n^{ω+3}a+n⁴a²+n^ωlog(1/ε)) time algorithm for finding an ε-approximation to the Jordan Normal form of an integer matrix with a-bit entries, where ω is the exponent of matrix multiplication. (2) An Õ(n⁶d⁶a+n⁴d⁴a²+n³d³log(1/ε)) time algorithm for ε-approximately computing the spectral factorization P(x) = Q^*(x)Q(x) of a given monic n× n rational matrix polynomial of degree 2d with rational a-bit coefficients having a-bit common denominators, which satisfies P(x)⪰0 for all real x. The first algorithm is used as a subroutine in the second one. Despite its being of central importance, polynomial complexity bounds were not previously known for spectral factorization, and for Jordan form the best previous best running time was an unspecified polynomial in n of degree at least twelve [Cai, 1994]. Our algorithms are simple and judiciously combine techniques from numerical and symbolic computation, yielding significant advantages over either approach by itself.
Cite as

Papri Dey, Ravi Kannan, Nick Ryder, and Nikhil Srivastava. Bit Complexity of Jordan Normal Form and Polynomial Spectral Factorization. In 14th Innovations in Theoretical Computer Science Conference (ITCS 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 251, pp. 42:1-42:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{dey_et_al:LIPIcs.ITCS.2023.42,
  author =	{Dey, Papri and Kannan, Ravi and Ryder, Nick and Srivastava, Nikhil},
  title =	{{Bit Complexity of Jordan Normal Form and Polynomial Spectral Factorization}},
  booktitle =	{14th Innovations in Theoretical Computer Science Conference (ITCS 2023)},
  pages =	{42:1--42:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-263-1},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{251},
  editor =	{Tauman Kalai, Yael},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2023.42},
  URN =		{urn:nbn:de:0030-drops-175450},
  doi =		{10.4230/LIPIcs.ITCS.2023.42},
  annote =	{Keywords: Symbolic algorithms, numerical algorithms, linear algebra}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2017.5
Real Stability Testing

Authors: Prasad Raghavendra, Nick Ryder, and Nikhil Srivastava

Published in: LIPIcs, Volume 67, 8th Innovations in Theoretical Computer Science Conference (ITCS 2017)

Abstract
We give a strongly polynomial time algorithm which determines whether or not a bivariate polynomial is real stable. As a corollary, this implies an algorithm for testing whether a given linear transformation on univariate polynomials preserves real-rootedness. The proof exploits properties of hyperbolic polynomials to reduce real stability testing to testing nonnegativity of a finite number of polynomials on an interval.
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Prasad Raghavendra, Nick Ryder, and Nikhil Srivastava. Real Stability Testing. In 8th Innovations in Theoretical Computer Science Conference (ITCS 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 67, pp. 5:1-5:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{raghavendra_et_al:LIPIcs.ITCS.2017.5,
  author =	{Raghavendra, Prasad and Ryder, Nick and Srivastava, Nikhil},
  title =	{{Real Stability Testing}},
  booktitle =	{8th Innovations in Theoretical Computer Science Conference (ITCS 2017)},
  pages =	{5:1--5:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-029-3},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{67},
  editor =	{Papadimitriou, Christos H.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2017.5},
  URN =		{urn:nbn:de:0030-drops-81965},
  doi =		{10.4230/LIPIcs.ITCS.2017.5},
  annote =	{Keywords: real stable polynomials, hyperbolic polynomials, real rootedness, moment matrix, sturm sequence}
}
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