12 Search Results for "He, Shuai"

Document
Research
DOI: 10.4230/TGDK.4.1.1
On the Computational Cost of Knowledge Graph Embeddings

Authors: Victor Charpenay, Mansour Zoubeirou A Mayaki, and Antoine Zimmermann

Published in: TGDK, Volume 4, Issue 1 (2026). Transactions on Graph Data and Knowledge, Volume 4, Issue 1

Abstract
Over a decade, numerous Knowledge Graph Embedding (KGE) models have been designed and evaluated on reference datasets, always with increasing performance. In this paper, we re-evaluate these models with respect to their computational efficiency during training, by estimating the computational cost of the procedure expressed in floating-point operations. We design a cost model based on analytical expressions and apply it on a collection of 20 KGE models, representative of the state-of-the-art. We show that dimensionality or parameter efficiency, used in the literature to compare models with each other, are not suitable to evaluate the true cost of models. Through fixed-budget experiments, a novel approach to evaluate KGE models based on cost estimates, we re-assess the relative performance of model families compared to the state-of-the-art. Bilinear models such as ComplEx underperform with a low computational budget while hyperbolic linear models appear to offer no particular benefit compared to simpler Euclidian models, especially the MuRE model. Neural models, such as ConvE or CompGCN, achieve reasonable performance in the literature but their high computational cost appears unnecessary when compared with other models. The trade-off between efficiency and expressivity of both linear and neural models is to be further explored.
Cite as

Victor Charpenay, Mansour Zoubeirou A Mayaki, and Antoine Zimmermann. On the Computational Cost of Knowledge Graph Embeddings. In Transactions on Graph Data and Knowledge (TGDK), Volume 4, Issue 1, pp. 1:1-1:30, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@Article{charpenay_et_al:TGDK.4.1.1,
  author =	{Charpenay, Victor and Zoubeirou A Mayaki, Mansour and Zimmermann, Antoine},
  title =	{{On the Computational Cost of Knowledge Graph Embeddings}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{1:1--1:30},
  ISSN =	{2942-7517},
  year =	{2026},
  volume =	{4},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.4.1.1},
  URN =		{urn:nbn:de:0030-drops-256863},
  doi =		{10.4230/TGDK.4.1.1},
  annote =	{Keywords: Knowledge Graph Embedding, Parameter Efficiency, Computational Budget, Green AI}
}
Document
Survey
DOI: 10.4230/TGDK.3.2.1
Resilience in Knowledge Graph Embeddings

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

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

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

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

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@Article{sharma_et_al:TGDK.3.2.1,
  author =	{Sharma, Arnab and Kouagou, N'Dah Jean and Ngomo, Axel-Cyrille Ngonga},
  title =	{{Resilience in Knowledge Graph Embeddings}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{1:1--1:38},
  ISSN =	{2942-7517},
  year =	{2025},
  volume =	{3},
  number =	{2},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.3.2.1},
  URN =		{urn:nbn:de:0030-drops-248117},
  doi =		{10.4230/TGDK.3.2.1},
  annote =	{Keywords: Knowledge graphs, Resilience, Robustness}
}
Document
DOI: 10.4230/LIPIcs.GIScience.2025.18
U-Prithvi: Integrating a Foundation Model and U-Net for Enhanced Flood Inundation Mapping

Authors: Vit Kostejn, Yamil Essus, Jenna Abrahamson, and Ranga Raju Vatsavai

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

Abstract
In recent years, large pre-trained models, commonly referred to as foundation models, have become increasingly popular for various tasks leveraging transfer learning. This trend has expanded to remote sensing, where transformer-based foundation models such as Prithvi, msGFM, and SatSwinMAE have been utilized for a range of applications. While these transformer-based models, particularly the Prithvi model, exhibit strong generalization capabilities, they have limitations on capturing fine-grained details compared to convolutional neural network architectures like U-Net in segmentation tasks. In this paper, we propose a novel architecture, U-Prithvi, which combines the strengths of the Prithvi transformer with those of U-Net. We introduce a RandomHalfMaskLayer to ensure balanced learning from both models during training. Our approach is evaluated on the Sen1Floods11 dataset for flood inundation mapping, and experimental results demonstrate better performance of U-Prithvi over both individual models, achieving improved performance on out-of-sample data. While this principle is illustrated using the Prithvi model, it is easily adaptable to other foundation models.
Cite as

Vit Kostejn, Yamil Essus, Jenna Abrahamson, and Ranga Raju Vatsavai. U-Prithvi: Integrating a Foundation Model and U-Net for Enhanced Flood Inundation Mapping. In 13th International Conference on Geographic Information Science (GIScience 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 346, pp. 18:1-18:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kostejn_et_al:LIPIcs.GIScience.2025.18,
  author =	{Kostejn, Vit and Essus, Yamil and Abrahamson, Jenna and Vatsavai, Ranga Raju},
  title =	{{U-Prithvi: Integrating a Foundation Model and U-Net for Enhanced Flood Inundation Mapping}},
  booktitle =	{13th International Conference on Geographic Information Science (GIScience 2025)},
  pages =	{18:1--18:17},
  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.2025.18},
  URN =		{urn:nbn:de:0030-drops-238479},
  doi =		{10.4230/LIPIcs.GIScience.2025.18},
  annote =	{Keywords: GeoAI, flood mapping, foundation model, U-Net, Prithvi}
}
Document
DOI: 10.4230/LIPIcs.CP.2025.3
Solving the Agile Earth Observation Satellite Scheduling Problem with CP and Local Search

Authors: Valentin Antuori, Damien T. Wojtowicz, and Emmanuel Hebrard

Published in: LIPIcs, Volume 340, 31st International Conference on Principles and Practice of Constraint Programming (CP 2025)

Abstract
The increasing hunger for remote sensing data fuels a boom in satellite imagery, leading to larger agile Earth observation satellite (AEOS) constellations. Therefore, instances of the AEOS scheduling problem (AEOSSP) has become harder to solve. As most existing approaches to solve AEOSSP are designed for a single spacecraft or smaller constellations in mind, they are not tailored to the need of our industrial partner that is about to launch a constellation of 20 AEOSs. Hence, we designed a local search solver able to schedule observations and downloads at such a scale. It relies on solving a series of sub-problems as travelling salesman problem with time windows (TSPTW), first greedily, then using a CP-SAT exact solver in order to find a solution when the greedy insertion fails. Lastly, it schedules downloads and enforces memory constraints with greedy algorithms. Experiments were carried out on instances from the literature as well as generated instances from a simulator we designed. Our experiments show that using CP to solve the sub-problem significantly improve the solutions, and overall our method is slightly better than state-of-the-art approaches.
Cite as

Valentin Antuori, Damien T. Wojtowicz, and Emmanuel Hebrard. Solving the Agile Earth Observation Satellite Scheduling Problem with CP and Local Search. In 31st International Conference on Principles and Practice of Constraint Programming (CP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 340, pp. 3:1-3:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{antuori_et_al:LIPIcs.CP.2025.3,
  author =	{Antuori, Valentin and Wojtowicz, Damien T. and Hebrard, Emmanuel},
  title =	{{Solving the Agile Earth Observation Satellite Scheduling Problem with CP and Local Search}},
  booktitle =	{31st International Conference on Principles and Practice of Constraint Programming (CP 2025)},
  pages =	{3:1--3:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-380-5},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{340},
  editor =	{de la Banda, Maria Garcia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CP.2025.3},
  URN =		{urn:nbn:de:0030-drops-238647},
  doi =		{10.4230/LIPIcs.CP.2025.3},
  annote =	{Keywords: Local Search, Greedy Algorithms, Aerospace Applications}
}
Document
DOI: 10.4230/LIPIcs.SEA.2025.11
CluStRE: Streaming Graph Clustering with Multi-Stage Refinement

Authors: Adil Chhabra, Shai Dorian Peretz, and Christian Schulz

Published in: LIPIcs, Volume 338, 23rd International Symposium on Experimental Algorithms (SEA 2025)

Abstract
We present CluStRE, a novel streaming graph clustering algorithm that balances computational efficiency with high-quality clustering using multi-stage refinement. Unlike traditional in-memory clustering approaches, CluStRE processes graphs in a streaming setting, significantly reducing memory overhead while leveraging re-streaming and evolutionary heuristics to improve solution quality. Our method dynamically constructs a quotient graph, enabling modularity-based optimization while efficiently handling large-scale graphs. We introduce multiple configurations of CluStRE to provide trade-offs between speed, memory consumption, and clustering quality. Experimental evaluations demonstrate that CluStRE improves solution quality by 89.8%, operates 2.6× faster, and uses less than two-thirds of the memory required by the state-of-the-art streaming clustering algorithm on average. Moreover, our strongest mode enhances solution quality by up to 150% on average. With this, CluStRE achieves comparable solution quality to in-memory algorithms, i.e. over 96% of the quality of clustering approaches, including Louvain, effectively bridging the gap between streaming and traditional clustering methods.
Cite as

Adil Chhabra, Shai Dorian Peretz, and Christian Schulz. CluStRE: Streaming Graph Clustering with Multi-Stage Refinement. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 11:1-11:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chhabra_et_al:LIPIcs.SEA.2025.11,
  author =	{Chhabra, Adil and Dorian Peretz, Shai and Schulz, Christian},
  title =	{{CluStRE: Streaming Graph Clustering with Multi-Stage Refinement}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{11:1--11:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-375-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{338},
  editor =	{Mutzel, Petra and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2025.11},
  URN =		{urn:nbn:de:0030-drops-232493},
  doi =		{10.4230/LIPIcs.SEA.2025.11},
  annote =	{Keywords: graph clustering, community, streaming, online, memetic, evolutionary}
}
Document
DOI: 10.4230/LIPIcs.ECRTS.2025.10
LoRaHART: Hardware-Aware Real-Time Scheduling for LoRa

Authors: Soumya Ranjan Sahoo, Amalinda Gamage, Niraj Kumar, and Arvind Easwaran

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

Abstract
Time-sensitive data acquisition is critical for many Low-Power Wide-Area Network (LPWAN) applications, such as healthcare monitoring and industrial Internet of Things. Among the available LPWAN technologies, LoRa (Long Range) has emerged as a leading choice, offering kilometer-scale communication with minimal power consumption and enabling high-density deployments across large areas. However, the conventional ALOHA-based Medium Access Control (MAC) in LoRa is not designed to support real-time communication over large-scale networks. This paper introduces LoRaHART, a novel approach that overcomes two critical, under-explored limitations in Commercial Off The Shelf (COTS) LoRa gateways that impact real-time performance. LoRa gateways have limited capacity for demodulation of parallel transmissions and their antenna can either transmit or receive at any time instant. LoRaHART incorporates a hardware-aware super-frame structure, comprising both Time Division Multiple Access (TDMA) slots as well as opportunistic retransmissions using Carrier Sense Multiple Access (CSMA), designed to mitigate the above constraints. We use a partial packing and makespan minimization algorithm to schedule periodic real-time transmissions efficiently within the TDMA slots, and also develop a probabilistic node contention model for CSMA retransmissions, providing analytical guarantees for deadline satisfaction under ideal channel conditions. Our evaluation of LoRaHART on a 40-node LoRa testbed demonstrates significant improvements over existing solutions in practice, achieving an average Packet Reception Ratio of 98% and a 45% higher airtime utilization than the best performing baseline.
Cite as

Soumya Ranjan Sahoo, Amalinda Gamage, Niraj Kumar, and Arvind Easwaran. LoRaHART: Hardware-Aware Real-Time Scheduling for LoRa. In 37th Euromicro Conference on Real-Time Systems (ECRTS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 335, pp. 10:1-10:28, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{sahoo_et_al:LIPIcs.ECRTS.2025.10,
  author =	{Sahoo, Soumya Ranjan and Gamage, Amalinda and Kumar, Niraj and Easwaran, Arvind},
  title =	{{LoRaHART: Hardware-Aware Real-Time Scheduling for LoRa}},
  booktitle =	{37th Euromicro Conference on Real-Time Systems (ECRTS 2025)},
  pages =	{10:1--10:28},
  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.2025.10},
  URN =		{urn:nbn:de:0030-drops-235880},
  doi =		{10.4230/LIPIcs.ECRTS.2025.10},
  annote =	{Keywords: LoRa, LPWAN, Real-time Scheduling, Hardware Constraints}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2025.23
Wastrumentation: Portable WebAssembly Dynamic Analysis with Support for Intercession

Authors: Aäron Munsters, Angel Luis Scull Pupo, and Elisa Gonzalez Boix

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

Abstract
Dynamic program analyses help in understanding a program’s runtime behavior and detect issues related to security, program comprehension, or profiling. Instrumentation platforms aid analysis developers by offering a high-level API to write the analysis, and inserting the analysis into the target program. However, current instrumentation platforms for WebAssembly (Wasm) restrict analysis portability because they require concrete runtime environments. Moreover, their analysis API only allows the development of analyses that observe the target program but cannot modify it. As a result, many popular dynamic analyses present for other languages, such as runtime hardening, virtual patching or runtime optimization, cannot currently be implemented for Wasm atop a dynamic analysis platform. Instead, they need to be built manually, which requires knowledge of low-level details of the Wasm’s semantics and instruction set, and how to safely manipulate it. This paper introduces Wastrumentation, the first dynamic analysis platform for WebAssembly that supports intercession. Our solution, based on source code instrumentation, weaves the analysis code directly into the target program code. Inlining the analysis into the target’s source code avoids dependencies on the runtime environment, making analyses portable across Wasm VMs. Moreover, it enables the implementation of analyses in any Wasm-compatible language. We evaluate our solution in two ways. First, we compare it against a state-of-the-art source code instrumentation platform using the WasmR3 benchmarks. The results show improved memory consumption and competitive performance overhead. Second, we develop an extensive portfolio of dynamic analyses, including novel analyses previously unattainable with source code instrumentation platforms, such as memoization, safe heap access, and the removal of NaN non-determinism.
Cite as

Aäron Munsters, Angel Luis Scull Pupo, and Elisa Gonzalez Boix. Wastrumentation: Portable WebAssembly Dynamic Analysis with Support for Intercession. In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 23:1-23:29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{munsters_et_al:LIPIcs.ECOOP.2025.23,
  author =	{Munsters, A\"{a}ron and Scull Pupo, Angel Luis and Gonzalez Boix, Elisa},
  title =	{{Wastrumentation: Portable WebAssembly Dynamic Analysis with Support for Intercession}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{23:1--23:29},
  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.2025.23},
  URN =		{urn:nbn:de:0030-drops-233153},
  doi =		{10.4230/LIPIcs.ECOOP.2025.23},
  annote =	{Keywords: WebAssembly, dynamic analysis, instrumentation platform, intercession}
}
Document
DOI: 10.4230/OASIcs.FMBC.2025.3
Formal Verification in Solidity and Move: Insights from a Comparative Analysis

Authors: Massimo Bartoletti, Silvia Crafa, and Enrico Lipparini

Published in: OASIcs, Volume 129, 6th International Workshop on Formal Methods for Blockchains (FMBC 2025)

Abstract
Formal verification plays a crucial role in making smart contracts safer, being able to find bugs or to guarantee their absence, as well as checking whether the business logic is correctly implemented. For Solidity, even though there already exist several mature verification tools, the semantical quirks of the language can make verification quite hard in practice. Move, on the other hand, has been designed with security and verification in mind, and it has been accompanied since its early stages by a formal verification tool, the Move Prover. In this paper, we investigate through a comparative analysis: 1) how the different designs of the two contract languages impact verification, and 2) what is the state-of-the-art of verification tools for the two languages, and how do they compare on three paradigmatic use cases. Our investigation is supported by an open dataset of verification tasks performed in Certora and in the Aptos Move Prover.
Cite as

Massimo Bartoletti, Silvia Crafa, and Enrico Lipparini. Formal Verification in Solidity and Move: Insights from a Comparative Analysis. In 6th International Workshop on Formal Methods for Blockchains (FMBC 2025). Open Access Series in Informatics (OASIcs), Volume 129, pp. 3:1-3:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bartoletti_et_al:OASIcs.FMBC.2025.3,
  author =	{Bartoletti, Massimo and Crafa, Silvia and Lipparini, Enrico},
  title =	{{Formal Verification in Solidity and Move: Insights from a Comparative Analysis}},
  booktitle =	{6th International Workshop on Formal Methods for Blockchains (FMBC 2025)},
  pages =	{3:1--3:18},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-371-3},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{129},
  editor =	{Marmsoler, Diego and Xu, Meng},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.FMBC.2025.3},
  URN =		{urn:nbn:de:0030-drops-230302},
  doi =		{10.4230/OASIcs.FMBC.2025.3},
  annote =	{Keywords: Smart contracts, Solidity, Move, Verification, Blockchain}
}
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
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
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2020.96
Contraction: A Unified Perspective of Correlation Decay and Zero-Freeness of 2-Spin Systems

Authors: Shuai Shao and Yuxin Sun

Published in: LIPIcs, Volume 168, 47th International Colloquium on Automata, Languages, and Programming (ICALP 2020)

Abstract
We study complex zeros of the partition function of 2-spin systems, viewed as a multivariate polynomial in terms of the edge interaction parameters and the uniform external field. We obtain new zero-free regions in which all these parameters are complex-valued. Crucially based on the zero-freeness, we are able to extend the existence of correlation decay to these complex regions from real parameters. As a consequence, we obtain an FPTAS for computing the partition function of 2-spin systems on graphs of bounded degree for these parameter settings. We introduce the contraction property as a unified sufficient condition to devise FPTAS via either Weitz’s algorithm or Barvinok’s algorithm. Our main technical contribution is a very simple but general approach to extend any real parameter of which the 2-spin system exhibits correlation decay to its complex neighborhood where the partition function is zero-free and correlation decay still exists. This result formally establishes the inherent connection between two distinct notions of phase transition for 2-spin systems: the existence of correlation decay and the zero-freeness of the partition function via a unified perspective, contraction.
Cite as

Shuai Shao and Yuxin Sun. Contraction: A Unified Perspective of Correlation Decay and Zero-Freeness of 2-Spin Systems. In 47th International Colloquium on Automata, Languages, and Programming (ICALP 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 168, pp. 96:1-96:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{shao_et_al:LIPIcs.ICALP.2020.96,
  author =	{Shao, Shuai and Sun, Yuxin},
  title =	{{Contraction: A Unified Perspective of Correlation Decay and Zero-Freeness of 2-Spin Systems}},
  booktitle =	{47th International Colloquium on Automata, Languages, and Programming (ICALP 2020)},
  pages =	{96:1--96:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-138-2},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{168},
  editor =	{Czumaj, Artur and Dawar, Anuj and Merelli, Emanuela},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2020.96},
  URN =		{urn:nbn:de:0030-drops-125036},
  doi =		{10.4230/LIPIcs.ICALP.2020.96},
  annote =	{Keywords: 2-Spin system, Correlation decay, Zero-freeness, Phase transition, Contraction}
}
Document
Short Paper
DOI: 10.4230/LIPIcs.GISCIENCE.2018.35
Multimodal-Transport Collaborative Evacuation Strategies for Urban Serious Emergency Incidents Based on Multi-Sources Spatiotemporal Data (Short Paper)

Authors: Jincheng Jiang, Yang Yue, and Shuai He

Published in: LIPIcs, Volume 114, 10th International Conference on Geographic Information Science (GIScience 2018)

Abstract
When serious emergency events happen in metropolitan cities where pedestrians and vehicles are in high-density, single modal-transport cannot meet the requirements of quick evacuations. Existing mixed modes of transportation lacks spatiotemporal collaborative ability, which cannot work together to accomplish evacuation tasks in a safe and efficient way. It is of great scientific significance and application value for emergency response to adopt multimodal-transport evacuations and improve their spatial-temporal collaboration ability. However, multimodal-transport evacuation strategies for urban serious emergency event are great challenge to be solved. The reasons lie in that: (1) large-scale urban emergency environment are extremely complicated involving many geographical elements (e.g., road, buildings, over-pass, square, hydrographic net, etc.); (2) Evacuated objects are dynamic and hard to be predicted. (3) the distributions of pedestrians and vehicles are unknown. To such issues, this paper reveals both collaborative and competitive mechanisms of multimodal-transport, and further makes global optimal evacuation strategies from the macro-optimization perspective. Considering detailed geographical environment, pedestrian, vehicle and urban rail transit, a multi-objective multi-dynamic-constraints optimization model for multimodal-transport collaborative emergency evacuation is constructed. Take crowd incidents in Shenzhen as example, empirical experiments with real-world data are conducted to evaluate the evacuation strategies and path planning. It is expected to obtain innovative research achievements on theory and method of urban emergency evacuation in serious emergency events. Moreover, this research results provide spatial-temporal decision support for urban emergency response, which is benefit to constructing smart and safe cities.
Cite as

Jincheng Jiang, Yang Yue, and Shuai He. Multimodal-Transport Collaborative Evacuation Strategies for Urban Serious Emergency Incidents Based on Multi-Sources Spatiotemporal Data (Short Paper). In 10th International Conference on Geographic Information Science (GIScience 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 114, pp. 35:1-35:8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{jiang_et_al:LIPIcs.GISCIENCE.2018.35,
  author =	{Jiang, Jincheng and Yue, Yang and He, Shuai},
  title =	{{Multimodal-Transport Collaborative Evacuation Strategies for Urban Serious Emergency Incidents Based on Multi-Sources Spatiotemporal Data}},
  booktitle =	{10th International Conference on Geographic Information Science (GIScience 2018)},
  pages =	{35:1--35:8},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-083-5},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{114},
  editor =	{Winter, Stephan and Griffin, Amy and Sester, Monika},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.GISCIENCE.2018.35},
  URN =		{urn:nbn:de:0030-drops-93630},
  doi =		{10.4230/LIPIcs.GISCIENCE.2018.35},
  annote =	{Keywords: evacuation, multimodal-transport, path planning, disaster system modeling, time geography}
}
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