6 Search Results for "Gu, Xinyu"

Document
DOI: 10.4230/OASIcs.AEiC.2026.4
HASCO: A Hybrid AI Simulation Compiler for Semantic Accident Reconstruction

Authors: Edin Jelačić, Rong Gu, Cristina Seceleanu, Ning Xiong, Peter Backeman, Tiberiu Seceleanu, Zhennan Fei, and Ali Nouri

Published in: OASIcs, Volume 143, 30th Ada-Europe International Conference on Reliable Software Technologies (AEiC 2026)

Abstract
The validation of Automated Driving Systems (ADSs) has shifted from distance-based metrics to Scenario-Based Testing (SBT). Large Language Models (LLMs) have emerged as powerful tools with potential for generating vehicular scenarios at scale. However, generative models, used for direct simulation synthesis, produce inadequate output, therefore necessitating a more structured compilation approach. In this regard, we present HASCO (Hybrid AI Simulation COmpiler), a system that translates natural-language driving scene specifications into executable simulation artifacts (XOSC/XODR files) for the esmini/OpenSCENARIO ecosystem. While LLMs excel at narrative parsing, we demonstrate that direct synthesis of simulation artifacts fails in the vast majority of cases due to hallucinated physics or schema violations. To resolve this, HASCO treats scenario creation as a compilation task rather than a generative one. The pipeline supports three compilation paths: direct synthesis, a Python intermediate (via scenariogeneration), and an ontology-guided path that grounds intent into an intermediate representation (IR) before compilation. We further evaluate a self-judging mechanism for automated repair. Across six operating modes evaluated on 40 real-world accident reports, the ontology-guided compiler and Python-based compiler achieve 95% and 90% executability rates, respectively (compared to 5% for direct synthesis). Additionally, we evaluate outputs on semantic fidelity, positioning HASCO as a robust tool for forensic scene reconstruction.
Cite as

Edin Jelačić, Rong Gu, Cristina Seceleanu, Ning Xiong, Peter Backeman, Tiberiu Seceleanu, Zhennan Fei, and Ali Nouri. HASCO: A Hybrid AI Simulation Compiler for Semantic Accident Reconstruction. In 30th Ada-Europe International Conference on Reliable Software Technologies (AEiC 2026). Open Access Series in Informatics (OASIcs), Volume 143, pp. 4:1-4:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{jelacic_et_al:OASIcs.AEiC.2026.4,
  author =	{Jela\v{c}i\'{c}, Edin and Gu, Rong and Seceleanu, Cristina and Xiong, Ning and Backeman, Peter and Seceleanu, Tiberiu and Fei, Zhennan and Nouri, Ali},
  title =	{{HASCO: A Hybrid AI Simulation Compiler for Semantic Accident Reconstruction}},
  booktitle =	{30th Ada-Europe International Conference on Reliable Software Technologies (AEiC 2026)},
  pages =	{4:1--4:22},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-425-3},
  ISSN =	{2190-6807},
  year =	{2026},
  volume =	{143},
  editor =	{Filieri, Antonio and Backeman, Peter},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.AEiC.2026.4},
  URN =		{urn:nbn:de:0030-drops-259220},
  doi =		{10.4230/OASIcs.AEiC.2026.4},
  annote =	{Keywords: Autonomous Driving, OpenSCENARIO, Large Language Models, Scenario Generation, Semantic Reconstruction}
}
Document
Invited Paper
DOI: 10.4230/OASIcs.RW.2024/2025.1
Rule-Based Knowledge Graph Completion (Invited Paper)

Authors: Patrick Betz, Christian Meilicke, and Heiner Stuckenschmidt

Published in: OASIcs, Volume 138, Joint Proceedings of the 20th and 21st Reasoning Web Summer Schools (RW 2024 & RW 2025)

Abstract
The field of knowledge graph completion is concerned with augmenting knowledge graphs with missing information. Symbolic rule-based approaches are not only efficient and interpretable but also competitive with embedding-based methods in regard to predictive quality. Rule-based knowledge graph completion can be separated into two stages, the learning stage and the application stage, which are both individually challenging. In the learning stage, horn rules are mined from a given knowledge graph. Given the vast size of the space of all possible rules, the mining approach must select relevant rules effectively. In the application stage, the mined rules are used to make new predictions which are assigned with plausibility scores. These scores need to be set by aggregating individual confidence values of rules that have the same consequence. This tutorial covers the fundamental aspects required to build a symbolic rule-based approach for knowledge graph completion. It will discuss the different rule types, mining strategies, and how to effectively apply the rules in different scenarios. Finally, we discuss practical examples for rule application by using the Python-based PyClause library.
Cite as

Patrick Betz, Christian Meilicke, and Heiner Stuckenschmidt. Rule-Based Knowledge Graph Completion (Invited Paper). In Joint Proceedings of the 20th and 21st Reasoning Web Summer Schools (RW 2024 & RW 2025). Open Access Series in Informatics (OASIcs), Volume 138, pp. 1:1-1:45, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{betz_et_al:OASIcs.RW.2024/2025.1,
  author =	{Betz, Patrick and Meilicke, Christian and Stuckenschmidt, Heiner},
  title =	{{Rule-Based Knowledge Graph Completion}},
  booktitle =	{Joint Proceedings of the 20th and 21st Reasoning Web Summer Schools (RW 2024 \& RW 2025)},
  pages =	{1:1--1:45},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-405-5},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{138},
  editor =	{Artale, Alessandro and Bienvenu, Meghyn and Garc{\'\i}a, Yazm{\'\i}n Ib\'{a}\~{n}ez and Murlak, Filip},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.RW.2024/2025.1},
  URN =		{urn:nbn:de:0030-drops-250461},
  doi =		{10.4230/OASIcs.RW.2024/2025.1},
  annote =	{Keywords: Knowledge Graph Completion, Rule Learning, Symbolic AI}
}
Document
Research
DOI: 10.4230/TGDK.3.2.3
GraphRAG on Technical Documents - Impact of Knowledge Graph Schema

Authors: Henri Scaffidi, Melinda Hodkiewicz, Caitlin Woods, and Nicole Roocke

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

Abstract
Retrieval Augmented Generation (RAG) is seeing rapid adoption in industry to enable employees to query information captured in proprietary data for their organisation. In this work, we test the impact of domain-relevant knowledge graph schemas on the results of Microsoft’s GraphRAG pipeline. Our approach aims to address the poor quality of GraphRAG responses on technical reports rich in domain-specific terms. The use case involves technical reports about geology, chemistry and mineral processing published by the Minerals Research Institute of Western Australia (MRIWA). Four schemas are considered: a simple five-class minerals domain expert-developed schema, an expanded minerals domain schema, the Microsoft GraphRAG auto-generated schema, and a schema-less GraphRAG. These are compared to a conventional baseline RAG. Performance is evaluated using a scoring approach that accounts for the mix of correct, incorrect, additional, and missing content in RAG responses. The results show that the simple five-class minerals domain schema extracts approximately 10% more entities from the MRIWA reports than the other schema options. Additionally, both the five-class and the expanded eight-class minerals domain schemas produce the most factually correct answers and the fewest hallucinations. We attribute this to the minerals-specific schemas extracting more relevant, domain-specific information during the Indexing stage. As a result, the Query stage’s context window includes more high-value content. This contributes to the observed improvement in answer quality compared to the other pipelines. In contrast, pipelines with fewer domain-related entities in the KG retrieve less valuable information, leaving more room for irrelevant content in the context window. Baseline RAG responses were typically shorter, less complete, and contained more hallucinations compared to our GraphRAG pipelines. We provide a complete set of resources at https://github.com/nlp-tlp/GraphRAG-on-Minerals-Domain/tree/main. These resources include links to the MRIWA reports, a set of questions (from simple to challenging) along with domain-expert curated answers, schemas, and evaluations of the pipelines.
Cite as

Henri Scaffidi, Melinda Hodkiewicz, Caitlin Woods, and Nicole Roocke. GraphRAG on Technical Documents - Impact of Knowledge Graph Schema. In Transactions on Graph Data and Knowledge (TGDK), Volume 3, Issue 2, pp. 3:1-3:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{scaffidi_et_al:TGDK.3.2.3,
  author =	{Scaffidi, Henri and Hodkiewicz, Melinda and Woods, Caitlin and Roocke, Nicole},
  title =	{{GraphRAG on Technical Documents - Impact of Knowledge Graph Schema}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{3:1--3:24},
  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.3.2.3},
  URN =		{urn:nbn:de:0030-drops-248131},
  doi =		{10.4230/TGDK.3.2.3},
  annote =	{Keywords: RAG, minerals, local search, global search, entity extraction, competency questions}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2025.6
Detecting Functionality-Specific Vulnerabilities via Retrieving Individual Functionality-Equivalent APIs in Open-Source Repositories

Authors: Tianyu Chen, Zeyu Wang, Lin Li, Ding Li, Zongyang Li, Xiaoning Chang, Pan Bian, Guangtai Liang, Qianxiang Wang, and Tao Xie

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

Abstract
Functionality-specific vulnerabilities, which mainly occur in Application Programming Interfaces (APIs) with specific functionalities, are crucial for software developers to detect and avoid. When detecting individual functionality-specific vulnerabilities, the existing two categories of approaches are ineffective because they consider only the API bodies and are unable to handle diverse implementations of functionality-equivalent APIs. To effectively detect functionality-specific vulnerabilities, we propose APISS, the first approach to utilize API doc strings and signatures instead of API bodies. APISS first retrieves functionality-equivalent APIs for APIs with existing vulnerabilities and then migrates Proof-of-Concepts (PoCs) of the existing vulnerabilities for newly detected vulnerable APIs. To retrieve functionality-equivalent APIs, we leverage a Large Language Model for API embedding to improve the accuracy and address the effectiveness and scalability issues suffered by the existing approaches. To migrate PoCs of the existing vulnerabilities for newly detected vulnerable APIs, we design a semi-automatic schema to substantially reduce manual costs. We conduct a comprehensive evaluation to empirically compare APISS with four state-of-the-art approaches of detecting vulnerabilities and two state-of-the-art approaches of retrieving functionality-equivalent APIs. The evaluation subjects include 180 widely used Java repositories using 10 existing vulnerabilities, along with their PoCs. The results show that APISS effectively retrieves functionality-equivalent APIs, achieving a Top-1 Accuracy of 0.81 while the best of the baselines under comparison achieves only 0.55. APISS is highly efficient: the manual costs are within 10 minutes per vulnerability and the end-to-end runtime overhead of testing one candidate API is less than 2 hours. APISS detects 179 new vulnerabilities and receives 60 new CVE IDs, bringing high value to security practice.
Cite as

Tianyu Chen, Zeyu Wang, Lin Li, Ding Li, Zongyang Li, Xiaoning Chang, Pan Bian, Guangtai Liang, Qianxiang Wang, and Tao Xie. Detecting Functionality-Specific Vulnerabilities via Retrieving Individual Functionality-Equivalent APIs in Open-Source Repositories. In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 6:1-6:27, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chen_et_al:LIPIcs.ECOOP.2025.6,
  author =	{Chen, Tianyu and Wang, Zeyu and Li, Lin and Li, Ding and Li, Zongyang and Chang, Xiaoning and Bian, Pan and Liang, Guangtai and Wang, Qianxiang and Xie, Tao},
  title =	{{Detecting Functionality-Specific Vulnerabilities via Retrieving Individual Functionality-Equivalent APIs in Open-Source Repositories}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{6:1--6:27},
  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.2025.6},
  URN =		{urn:nbn:de:0030-drops-232999},
  doi =		{10.4230/LIPIcs.ECOOP.2025.6},
  annote =	{Keywords: Application Security, Vulnerability Detection, Large Language Model}
}
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.WABI.2023.21
Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design

Authors: Xinyu Gu, Yuanyuan Qi, and Mohammed El-Kebir

Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)

Abstract
The problem of designing an RNA sequence v that encodes for a given target protein w plays an important role in messenger RNA (mRNA) vaccine design. Due to codon degeneracy, there exist exponentially many RNA sequences for a single target protein. These candidate RNA sequences may adopt different secondary structure conformations with varying minimum free energy (MFE), affecting their thermodynamic stability and consequently mRNA half-life. In addition, species-specific codon usage bias, as measured by the codon adaptation index (CAI), also plays an essential role in translation efficiency. While previous works have focused on optimizing either MFE or CAI, more recent works have shown the merits of optimizing both objectives. Importantly, there is a trade-off between MFE and CAI, i.e. optimizing one objective is at the expense of the other. Here, we formulate the Pareto Optimal RNA Design problem, seeking the set of Pareto optimal solutions for which no other solution exists that is better in terms of both MFE and CAI. We introduce DERNA (DEsign RNA), which uses the weighted sum method to enumerate the Pareto front by optimizing convex combinations of both objectives. DERNA uses dynamic programming to solve each convex combination in O(|w|³) time and O(|w|²) space. Compared to a previous approach that only optimizes MFE, we show on a benchmark dataset that DERNA obtains solutions with identical MFE but superior CAI. Additionally, we show that DERNA matches the performance in terms of solution quality of LinearDesign, a recent approach that similarly seeks to balance MFE and CAI. Finally, we demonstrate our method’s potential for mRNA vaccine design using SARS-CoV-2 spike as the target protein.
Cite as

Xinyu Gu, Yuanyuan Qi, and Mohammed El-Kebir. Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 21:1-21:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{gu_et_al:LIPIcs.WABI.2023.21,
  author =	{Gu, Xinyu and Qi, Yuanyuan and El-Kebir, Mohammed},
  title =	{{Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{21:1--21:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-294-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{273},
  editor =	{Belazzougui, Djamal and Ouangraoua, A\"{i}da},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.21},
  URN =		{urn:nbn:de:0030-drops-186479},
  doi =		{10.4230/LIPIcs.WABI.2023.21},
  annote =	{Keywords: Multi-objective optimization, dynamic programming, RNA sequence design, reverse translation, mRNA vaccine design}
}
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