20 Search Results for "Fu, Bin"

Document
DOI: 10.4230/LIPIcs.SWAT.2026.3
Reachability with Restricted Reactions in Inhibitory Chemical Reaction Networks

Authors: Divya Bajaj, Bin Fu, Ryan Knobel, Austin Luchsinger, Aiden Massie, Pablo Santos, Ramiro Santos, Robert Schweller, Evan Tomai, and Tim Wylie

Published in: LIPIcs, Volume 370, 20th Scandinavian Symposium on Algorithm Theory (SWAT 2026)

Abstract
Chemical Reaction Networks (CRNs) are a well-established model of distributed computing characterized by quantities of molecular species that can transform or change through applications of reactions. A fundamental problem in CRNs is the reachability problem, which asks if an initial configuration of species can transition to a target configuration through an applicable sequence of reactions. It is well-known that the reachability problem in general CRNs was recently proven to be Ackermann-complete. However, if the CRN’s reactions are restricted in both power, such as only deleting species (deletion-only rules) or consuming and producing an equal number of species (volume-preserving rules), and size (unimolecular or bimolecular rules), then reachability falls below Ackermann-completeness, and is even solvable in polynomial time for deletion-only systems. In this paper, we investigate reachability under this set of restricted unimolecular and bimolecular reactions, but in the Priority-Inhibitory CRN and Inhibitory CRN models. These models extend a traditional CRN by allowing some reactions to be inhibited from firing in a configuration if certain species are present; the exact inhibition behavior varies between the models. We first show that reachability with Priority iCRNs mostly remains in P for deletion-only systems, but becomes NP-complete for one case. We then show that reachability with deletion-only reactions for iCRNs is mostly NP-complete, and PSPACE-complete even for (1,1)-size (general) reactions. We also provide FPT algorithms for solving most of the reachability problems for the iCRN model. Finally, we show reachability for CRNs with states is already NP-hard for the simplest deletion-only systems, and is PSPACE-complete even for (general) (1,1)-size reactions.
Cite as

Divya Bajaj, Bin Fu, Ryan Knobel, Austin Luchsinger, Aiden Massie, Pablo Santos, Ramiro Santos, Robert Schweller, Evan Tomai, and Tim Wylie. Reachability with Restricted Reactions in Inhibitory Chemical Reaction Networks. In 20th Scandinavian Symposium on Algorithm Theory (SWAT 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 370, pp. 3:1-3:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{bajaj_et_al:LIPIcs.SWAT.2026.3,
  author =	{Bajaj, Divya and Fu, Bin and Knobel, Ryan and Luchsinger, Austin and Massie, Aiden and Santos, Pablo and Santos, Ramiro and Schweller, Robert and Tomai, Evan and Wylie, Tim},
  title =	{{Reachability with Restricted Reactions in Inhibitory Chemical Reaction Networks}},
  booktitle =	{20th Scandinavian Symposium on Algorithm Theory (SWAT 2026)},
  pages =	{3:1--3:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-421-5},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{370},
  editor =	{Fraigniaud, Pierre},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SWAT.2026.3},
  URN =		{urn:nbn:de:0030-drops-260399},
  doi =		{10.4230/LIPIcs.SWAT.2026.3},
  annote =	{Keywords: Chemical Reaction Networks, Vector Addition Systems, Petri-nets, Reachability, Inhibitors, Void Reactions}
}
Document
DOI: 10.4230/OASIcs.PARMA-DITAM.2026.7
Linking High-Level Synthesis with FPGA Runtime Orchestration

Authors: Despoina Tomkou, Aggelos Ferikoglou, Dimosthenis Masouros, Sotirios Xydis, and Dimitrios Soudris

Published in: OASIcs, Volume 141, 17th Workshop on Parallel Programming and Run-Time Management Techniques for Many-Core Architectures and 15th Workshop on Design Tools and Architectures for Multicore Embedded Computing Platforms (PARMA-DITAM 2026)

Abstract
FPGAs are increasingly being adopted across the edge-to-cloud continuum due to their ability to provide both high performance and energy efficiency. However, the complexity of programming FPGAs often leads to deployed designs that underutilize available resources. FPGA multi-tenancy has been proposed to enhance resource utilization, yet monolithic designs and dynamic workload demands continue to challenge efficient FPGA usage and compliance with Quality of Service requirements. To address these issues, we propose a novel framework for the optimal orchestration of FPGAs across the edge-to-cloud continuum while meeting user demands. The framework generates approximations of Pareto-optimal designs for each application, capturing trade-offs between performance and resource usage with minimal bitstream generation. This information allows the runtime orchestrator to select the most suitable design based on available PR regions and the QoS requirements of each user. Experimental results demonstrate that the proposed approach achieves an average reduction of QoS violations by a factor of 8.1× across diverse workloads and baseline configurations. Overall, the framework offers a practical and effective solution for realizing FPGA-as-a-Service across the edge-to-cloud continuum.
Cite as

Despoina Tomkou, Aggelos Ferikoglou, Dimosthenis Masouros, Sotirios Xydis, and Dimitrios Soudris. Linking High-Level Synthesis with FPGA Runtime Orchestration. In 17th Workshop on Parallel Programming and Run-Time Management Techniques for Many-Core Architectures and 15th Workshop on Design Tools and Architectures for Multicore Embedded Computing Platforms (PARMA-DITAM 2026). Open Access Series in Informatics (OASIcs), Volume 141, pp. 7:1-7:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{tomkou_et_al:OASIcs.PARMA-DITAM.2026.7,
  author =	{Tomkou, Despoina and Ferikoglou, Aggelos and Masouros, Dimosthenis and Xydis, Sotirios and Soudris, Dimitrios},
  title =	{{Linking High-Level Synthesis with FPGA Runtime Orchestration}},
  booktitle =	{17th Workshop on Parallel Programming and Run-Time Management Techniques for Many-Core Architectures and 15th Workshop on Design Tools and Architectures for Multicore Embedded Computing Platforms (PARMA-DITAM 2026)},
  pages =	{7:1--7:14},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-416-1},
  ISSN =	{2190-6807},
  year =	{2026},
  volume =	{141},
  editor =	{Baroffio, Davide and Busia, Paola and Denisov, Lev and Shukla, Nitin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.PARMA-DITAM.2026.7},
  URN =		{urn:nbn:de:0030-drops-256746},
  doi =		{10.4230/OASIcs.PARMA-DITAM.2026.7},
  annote =	{Keywords: FPGA, Orchestration, Partial Reconfiguration, FPGAaaS}
}
Document
Survey
DOI: 10.4230/TGDK.4.1.2
Temporal Modelling in Cultural Heritage Knowledge Graphs: Use Cases, Requirements, Evaluation, and Decision Support

Authors: Oleksandra Bruns, Jörg Waitelonis, Jeff Z. Pan, and Harald Sack

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

Abstract
Our culture, history and world are in constant motion, continuously shaped by the flow of time, evolving narratives, and shifting relationships. Capturing this temporal complexity within cultural heritage (CH) knowledge graphs is essential for preserving the dynamic nature of human heritage. However, standard RDF predicates fail to effectively model the temporal aspects of cultural data, such as changing facts, evolving relationships, and temporal concepts. Over the past two decades, a variety of RDF-based approaches have been proposed to address this limitation, yet guidance is missing on which method best suits specific CH contexts. This paper presents a systematic evaluation of temporal RDF modelling approaches from a CH perspective. Based on an analysis of real-world CH use cases, core temporal requirements are identified that reflect both modelling expressivity and practical concerns. Six prominent approaches - RDF*, tRDF, Named Graphs, Singleton Property, N-ary Relations, and 4D Fluents - are assessed across these requirements. Our findings reveal that no single solution fits all scenarios, but suitable approaches can be selected based on project-specific priorities. To support practitioners, a decision-support tool is introduced to guide them in selecting the most suitable extension for their specific needs. This work provides practical guidance for CH modelling and contributes to the broader development of temporally aware Linked Data.
Cite as

Oleksandra Bruns, Jörg Waitelonis, Jeff Z. Pan, and Harald Sack. Temporal Modelling in Cultural Heritage Knowledge Graphs: Use Cases, Requirements, Evaluation, and Decision Support. In Transactions on Graph Data and Knowledge (TGDK), Volume 4, Issue 1, pp. 2:1-2:46, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@Article{bruns_et_al:TGDK.4.1.2,
  author =	{Bruns, Oleksandra and Waitelonis, J\"{o}rg and Pan, Jeff Z. and Sack, Harald},
  title =	{{Temporal Modelling in Cultural Heritage Knowledge Graphs: Use Cases, Requirements, Evaluation, and Decision Support}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{2:1--2:46},
  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.4.1.2},
  URN =		{urn:nbn:de:0030-drops-256871},
  doi =		{10.4230/TGDK.4.1.2},
  annote =	{Keywords: Temporal Data Representation, RDF Extensions, Cultural Heritage, Knowledge Graphs}
}
Document
DOI: 10.4230/OASIcs.NINeS.2026.18
TURBO: Utility-Aware Bandwidth Allocation for Cloud-Augmented Autonomous Control

Authors: Peter Schafhalter, Alexander Krentsel, Hongbo Wei, Joseph E. Gonzalez, Sylvia Ratnasamy, Scott Shenker, and Ion Stoica

Published in: OASIcs, Volume 139, 1st New Ideas in Networked Systems (NINeS 2026)

Abstract
Autonomous driving system progress has been driven by improvements in machine learning (ML) models, whose computational demands now exceed what edge devices alone can provide. The cloud offers abundant compute, but the network has long been treated as an unreliable bottleneck rather than a co-equal part of the autonomous vehicle control loop. We argue that this separation is no longer tenable: safety-critical autonomy requires co-design of control, models, and network resource allocation itself. We introduce TURBO, a cloud-augmented control framework that addresses this challenge, formulating bandwidth allocation and control pipeline configuration across both the car and cloud as a joint optimization problem. TURBO maximizes benefit to the car while guaranteeing safety in the face of highly variable network conditions. We implement TURBO and evaluate it in both simulation and real-world deployment, showing it can improve average accuracy by up to 15.6%pt over existing on-vehicle-only pipelines. Our code is made available at www.github.com/NetSys/turbo.
Cite as

Peter Schafhalter, Alexander Krentsel, Hongbo Wei, Joseph E. Gonzalez, Sylvia Ratnasamy, Scott Shenker, and Ion Stoica. TURBO: Utility-Aware Bandwidth Allocation for Cloud-Augmented Autonomous Control. In 1st New Ideas in Networked Systems (NINeS 2026). Open Access Series in Informatics (OASIcs), Volume 139, pp. 18:1-18:34, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{schafhalter_et_al:OASIcs.NINeS.2026.18,
  author =	{Schafhalter, Peter and Krentsel, Alexander and Wei, Hongbo and Gonzalez, Joseph E. and Ratnasamy, Sylvia and Shenker, Scott and Stoica, Ion},
  title =	{{TURBO: Utility-Aware Bandwidth Allocation for Cloud-Augmented Autonomous Control}},
  booktitle =	{1st New Ideas in Networked Systems (NINeS 2026)},
  pages =	{18:1--18:34},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-414-7},
  ISSN =	{2190-6807},
  year =	{2026},
  volume =	{139},
  editor =	{Argyraki, Katerina and Panda, Aurojit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.NINeS.2026.18},
  URN =		{urn:nbn:de:0030-drops-256039},
  doi =		{10.4230/OASIcs.NINeS.2026.18},
  annote =	{Keywords: autonomous vehicles, bandwidth allocation, cloud computing, edge computing, machine learning}
}
Document
DOI: 10.4230/OASIcs.NINeS.2026.19
Simulate Before Sending: Rethinking Transport in Datacenter Networks

Authors: Dan Straussman, Isaac Keslassy, Alexander Shpiner, and Liran Liss

Published in: OASIcs, Volume 139, 1st New Ideas in Networked Systems (NINeS 2026)

Abstract
Existing transport protocols in commodity datacenter networks struggle to provide low collective completion times (CCTs) to AI training collectives, as packet losses and retransmissions significantly degrade performance. We propose dcSim, an efficient transport that achieves low CCTs and practically lossless performance with commodity switches. In dcSim, each packet first employs a small simulation probe to traverse the network and explore congestion along a candidate path. Only packets whose simulation probes succeed are then transmitted, expecting to succeed as well. Evaluations confirm that dcSim achieves faster CCTs than existing schemes, with small queues and virtually zero packet loss. Finally, dcSim also excels in adverse conditions, including oversubscribed topologies.
Cite as

Dan Straussman, Isaac Keslassy, Alexander Shpiner, and Liran Liss. Simulate Before Sending: Rethinking Transport in Datacenter Networks. In 1st New Ideas in Networked Systems (NINeS 2026). Open Access Series in Informatics (OASIcs), Volume 139, pp. 19:1-19:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{straussman_et_al:OASIcs.NINeS.2026.19,
  author =	{Straussman, Dan and Keslassy, Isaac and Shpiner, Alexander and Liss, Liran},
  title =	{{Simulate Before Sending: Rethinking Transport in Datacenter Networks}},
  booktitle =	{1st New Ideas in Networked Systems (NINeS 2026)},
  pages =	{19:1--19:22},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-414-7},
  ISSN =	{2190-6807},
  year =	{2026},
  volume =	{139},
  editor =	{Argyraki, Katerina and Panda, Aurojit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.NINeS.2026.19},
  URN =		{urn:nbn:de:0030-drops-256044},
  doi =		{10.4230/OASIcs.NINeS.2026.19},
  annote =	{Keywords: Datacenter networks, transport protocols, AI training, lossless networks}
}
Document
DOI: 10.4230/OASIcs.NINeS.2026.24
SwiftQueue: Optimizing Low-Latency Applications with Swift Packet Queuing

Authors: Siddhant Ray, Xi Jiang, Jack Luo, Nick Feamster, and Junchen Jiang

Published in: OASIcs, Volume 139, 1st New Ideas in Networked Systems (NINeS 2026)

Abstract
Low Latency, Low Loss, and Scalable Throughput (L4S), as an emerging router-queue management technique, has seen steady deployment in the industry. An L4S-enabled router assigns each packet to the queue based on the packet header marking. Currently, L4S employs per-flow queue selection, i.e., all packets of a flow are marked the same way and thus use the same queues, even though each packet is marked separately. However, this may hurt tail latency and latency-sensitive applications because transient congestion and queue buildups may only affect a fraction of packets in a flow. We present SwiftQueue, a new L4S queue-selection strategy in which a sender uses a novel per-packet latency predictor to pinpoint which packets likely have latency spikes or drops. The insight is that many packet-level latency variations result from complex interactions among recent packets at shared router queues. Yet, these intricate packet-level latency patterns are hard to learn efficiently by traditional models. Instead, SwiftQueue uses a custom Transformer, which is well-studied for its expressiveness on sequential patterns, to predict the next packet’s latency based on the latencies of recently received ACKs. Based on the predicted latency of each outgoing packet, SwiftQueue’s sender dynamically marks the L4S packet header to assign packets to potentially different queues, even within the same flow. Using real network traces, we show that SwiftQueue is 45-65% more accurate in predicting latency and its variations than state-of-art methods. Based on its latency prediction, SwiftQueue reduces the tail latency for L4S-enabled flows by 36-45%, compared with the existing L4S queue-selection method.
Cite as

Siddhant Ray, Xi Jiang, Jack Luo, Nick Feamster, and Junchen Jiang. SwiftQueue: Optimizing Low-Latency Applications with Swift Packet Queuing. In 1st New Ideas in Networked Systems (NINeS 2026). Open Access Series in Informatics (OASIcs), Volume 139, pp. 24:1-24:29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{ray_et_al:OASIcs.NINeS.2026.24,
  author =	{Ray, Siddhant and Jiang, Xi and Luo, Jack and Feamster, Nick and Jiang, Junchen},
  title =	{{SwiftQueue: Optimizing Low-Latency Applications with Swift Packet Queuing}},
  booktitle =	{1st New Ideas in Networked Systems (NINeS 2026)},
  pages =	{24:1--24:29},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-414-7},
  ISSN =	{2190-6807},
  year =	{2026},
  volume =	{139},
  editor =	{Argyraki, Katerina and Panda, Aurojit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.NINeS.2026.24},
  URN =		{urn:nbn:de:0030-drops-256093},
  doi =		{10.4230/OASIcs.NINeS.2026.24},
  annote =	{Keywords: Latency prediction, L4S Queue Management}
}
Document
DOI: 10.4230/OASIcs.NINeS.2026.28
CrowdLink: Unlocking Idle LEO Network Capacity with User Terminals

Authors: Lixin Liu, Jinyao Zhang, Bijia You, Yimei Chen, Jiabo Yang, Yuanjie Li, Hewu Li, Qian Wu, Zeqi Lai, and Jun Liu

Published in: OASIcs, Volume 139, 1st New Ideas in Networked Systems (NINeS 2026)

Abstract
The Low Earth Orbit (LEO) network is booming worldwide thanks to its unprecedented number of satellites. However, most of these satellites remain underutilized to connect more users or boost performance, posing tensions for their return on investment. A critical cause is that their gateways to the Internet (ground stations) are geographically skewed or even centralized, forming last-mile bottlenecks. We examine the potential of eliminating these bottlenecks with ubiquitous user terminals (UTs). Our solution, CrowdLink, reuses UTs as local access points to decentralize satellites' gateways to the Internet, and as relays to convert idle satellite radio links into additional paths for more network capacity. This user-centric paradigm is self-scaling to more UTs and satellites (akin to P2P networks), resilient to rapid satellite mobility, mutually beneficial for users and operators, and readily deployable in operational LEO networks. Our real tests with Starlink UTs across three countries and large-scale simulations show that CrowdLink can increase each UT’s throughput by 3.09× on average (up to 65.27×), double the LEO network capacity utilization, and unlock 2.05-7.99 million more users for Starlink without adding satellites/ground stations.
Cite as

Lixin Liu, Jinyao Zhang, Bijia You, Yimei Chen, Jiabo Yang, Yuanjie Li, Hewu Li, Qian Wu, Zeqi Lai, and Jun Liu. CrowdLink: Unlocking Idle LEO Network Capacity with User Terminals. In 1st New Ideas in Networked Systems (NINeS 2026). Open Access Series in Informatics (OASIcs), Volume 139, pp. 28:1-28:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{liu_et_al:OASIcs.NINeS.2026.28,
  author =	{Liu, Lixin and Zhang, Jinyao and You, Bijia and Chen, Yimei and Yang, Jiabo and Li, Yuanjie and Li, Hewu and Wu, Qian and Lai, Zeqi and Liu, Jun},
  title =	{{CrowdLink: Unlocking Idle LEO Network Capacity with User Terminals}},
  booktitle =	{1st New Ideas in Networked Systems (NINeS 2026)},
  pages =	{28:1--28:26},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-414-7},
  ISSN =	{2190-6807},
  year =	{2026},
  volume =	{139},
  editor =	{Argyraki, Katerina and Panda, Aurojit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.NINeS.2026.28},
  URN =		{urn:nbn:de:0030-drops-256130},
  doi =		{10.4230/OASIcs.NINeS.2026.28},
  annote =	{Keywords: LEO Satellite Networks, User Terminal Relaying, Capacity Utilization}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2025.7
Polynomial Equivalence of Extended Chemical Reaction Models

Authors: Divya Bajaj, Jose-Luis Castellanos, Ryan Knobel, Austin Luchsinger, Aiden Massie, Adrian Salinas, Pablo Santos, Ramiro Santos, Robert Schweller, and Tim Wylie

Published in: LIPIcs, Volume 359, 36th International Symposium on Algorithms and Computation (ISAAC 2025)

Abstract
The ability to detect whether a species (or dimension) is zero in Chemical Reaction Networks (CRN), Vector Addition Systems, or Petri Nets is known to increase the power of these models - making them capable of universal computation. While this ability may appear in many forms, such as extending the models to allow transitions to be inhibited, prioritized, or synchronized, we present an extension that directly performs this zero checking. We introduce a new void genesis CRN variant with a simple design that merely increments the count of a specific species when any other species' count goes to zero. As with previous extensions, we show that the model is Turing Universal. We then analyze several other studied CRN variants and show that they are all equivalent through a polynomial simulation with the void genesis model, which does not merely follow from Turing-universality. Thus, inhibitor species, reactions that occur at different rates, being allowed to run reactions in parallel, or even being allowed to continually add more volume to the CRN, does not add additional simulation power beyond simply detecting if a species count becomes zero.
Cite as

Divya Bajaj, Jose-Luis Castellanos, Ryan Knobel, Austin Luchsinger, Aiden Massie, Adrian Salinas, Pablo Santos, Ramiro Santos, Robert Schweller, and Tim Wylie. Polynomial Equivalence of Extended Chemical Reaction Models. In 36th International Symposium on Algorithms and Computation (ISAAC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 359, pp. 7:1-7:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bajaj_et_al:LIPIcs.ISAAC.2025.7,
  author =	{Bajaj, Divya and Castellanos, Jose-Luis and Knobel, Ryan and Luchsinger, Austin and Massie, Aiden and Salinas, Adrian and Santos, Pablo and Santos, Ramiro and Schweller, Robert and Wylie, Tim},
  title =	{{Polynomial Equivalence of Extended Chemical Reaction Models}},
  booktitle =	{36th International Symposium on Algorithms and Computation (ISAAC 2025)},
  pages =	{7:1--7:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-408-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{359},
  editor =	{Chen, Ho-Lin and Hon, Wing-Kai and Tsai, Meng-Tsung},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2025.7},
  URN =		{urn:nbn:de:0030-drops-249158},
  doi =		{10.4230/LIPIcs.ISAAC.2025.7},
  annote =	{Keywords: Chemical Reaction Networks, Simulations, Petri-nets, Vector Addition Systems, Bi-simulation, Turing-universality, Inhibitors}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.110
Faster Exponential Algorithms for Cut Problems via Geometric Data Structures

Authors: László Kozma and Junqi Tan

Published in: LIPIcs, Volume 351, 33rd Annual European Symposium on Algorithms (ESA 2025)

Abstract
For many hard computational problems, simple algorithms that run in time 2ⁿ ⋅ n^O(1) arise, say, from enumerating all subsets of a size-n set. Finding (exponentially) faster algorithms is a natural goal that has driven much of the field of exact exponential algorithms (e.g., see Fomin and Kratsch, 2010). In this paper we obtain algorithms with running time O(1.9999977ⁿ) on input graphs with n vertices, for the following well-studied problems: - d-Cut: find a proper cut in which no vertex has more than d neighbors on the other side of the cut; - Internal Partition: find a proper cut in which every vertex has at least as many neighbors on its side of the cut as on the other side; and - (α,β)-Domination: given intervals α,β ⊆ [0,n], find a subset S of the vertices, so that for every vertex v ∈ S the number of neighbors of v in S is from α and for every vertex v ∉ S, the number of neighbors of v in S is from β. Our algorithms are exceedingly simple, combining the split and list technique (Horowitz and Sahni, 1974; Williams, 2005) with a tool from computational geometry: orthogonal range searching in the moderate dimensional regime (Chan, 2017). Our technique is applicable to the decision, optimization and counting versions of these problems and easily extends to various generalizations with more fine-grained, vertex-specific constraints, as well as to directed, balanced, and other variants. Algorithms with running times of the form cⁿ, for c < 2, were known for the first problem only for constant d, and for the third problem for certain special cases of α and β; for the second problem we are not aware of such results.
Cite as

László Kozma and Junqi Tan. Faster Exponential Algorithms for Cut Problems via Geometric Data Structures. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 110:1-110:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kozma_et_al:LIPIcs.ESA.2025.110,
  author =	{Kozma, L\'{a}szl\'{o} and Tan, Junqi},
  title =	{{Faster Exponential Algorithms for Cut Problems via Geometric Data Structures}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{110:1--110:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2025.110},
  URN =		{urn:nbn:de:0030-drops-245796},
  doi =		{10.4230/LIPIcs.ESA.2025.110},
  annote =	{Keywords: graph algorithms, cuts, exponential time, data structures}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.3
Reachability in Deletion-Only Chemical Reaction Networks

Authors: Bin Fu, Timothy Gomez, Ryan Knobel, Austin Luchsinger, Aiden Massie, Marco Rodriguez, Adrian Salinas, Robert Schweller, and Tim Wylie

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

Abstract
For general discrete Chemical Reaction Networks (CRNs), the fundamental problem of reachability - the question of whether a target configuration can be produced from a given initial configuration - was recently shown to be Ackermann-complete. However, many open questions remain about which features of the CRN model drive this complexity. We study a restricted class of CRNs with void rules, reactions that only decrease species counts. We further examine this regime in the motivated model of step CRNs, which allow additional species to be introduced in discrete stages. With and without steps, we characterize the complexity of the reachability problem for CRNs with void rules. We show that, without steps, reachability remains polynomial-time solvable for bimolecular systems but becomes NP-complete for larger reactions. Conversely, with just a single step, reachability becomes NP-complete even for bimolecular systems. Our results provide a nearly complete classification of void-rule reachability problems into tractable and intractable cases, with only a single exception.
Cite as

Bin Fu, Timothy Gomez, Ryan Knobel, Austin Luchsinger, Aiden Massie, Marco Rodriguez, Adrian Salinas, Robert Schweller, and Tim Wylie. Reachability in Deletion-Only Chemical Reaction Networks. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 3:1-3:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{fu_et_al:LIPIcs.DNA.31.3,
  author =	{Fu, Bin and Gomez, Timothy and Knobel, Ryan and Luchsinger, Austin and Massie, Aiden and Rodriguez, Marco and Salinas, Adrian and Schweller, Robert and Wylie, Tim},
  title =	{{Reachability in Deletion-Only Chemical Reaction Networks}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{3:1--3:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.3},
  URN =		{urn:nbn:de:0030-drops-238521},
  doi =		{10.4230/LIPIcs.DNA.31.3},
  annote =	{Keywords: CRN, Chemical Reaction Network, Reachability, Void Reactions}
}
Document
DOI: 10.4230/LIPIcs.GIScience.2025.12
Large Multi-Modal Model Cartographic Map Comprehension for Textual Locality Georeferencing

Authors: Kalana Wijegunarathna, Kristin Stock, and Christopher B. Jones

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

Abstract
Millions of biological sample records collected in the last few centuries archived in natural history collections are un-georeferenced. Georeferencing complex locality descriptions associated with these collection samples is a highly labour-intensive task collection agencies struggle with. None of the existing automated methods exploit maps that are an essential tool for georeferencing complex relations. We present preliminary experiments and results of a novel method that exploits multi-modal capabilities of recent Large Multi-Modal Models (LMM). This method enables the model to visually contextualize spatial relations it reads in the locality description. We use a grid-based approach to adapt these auto-regressive models for this task in a zero-shot setting. Our experiments conducted on a small manually annotated dataset show impressive results for our approach (∼1 km Average distance error) compared to uni-modal georeferencing with Large Language Models and existing georeferencing tools. The paper also discusses the findings of the experiments in light of an LMM’s ability to comprehend fine-grained maps. Motivated by these results, a practical framework is proposed to integrate this method into a georeferencing workflow.
Cite as

Kalana Wijegunarathna, Kristin Stock, and Christopher B. Jones. Large Multi-Modal Model Cartographic Map Comprehension for Textual Locality Georeferencing. In 13th International Conference on Geographic Information Science (GIScience 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 346, pp. 12:1-12:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{wijegunarathna_et_al:LIPIcs.GIScience.2025.12,
  author =	{Wijegunarathna, Kalana and Stock, Kristin and Jones, Christopher B.},
  title =	{{Large Multi-Modal Model Cartographic Map Comprehension for Textual Locality Georeferencing}},
  booktitle =	{13th International Conference on Geographic Information Science (GIScience 2025)},
  pages =	{12:1--12:19},
  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.2025.12},
  URN =		{urn:nbn:de:0030-drops-238412},
  doi =		{10.4230/LIPIcs.GIScience.2025.12},
  annote =	{Keywords: Large Multi-Modal Models, Large Language Models, LLM, Georeferencing, Natural History collections}
}
Document
DOI: 10.4230/OASIcs.Manzini.9
Search Schemes for Approximate Pattern Matching: An Overview

Authors: Lore Depuydt, Jan Fostier, Simon Gottlieb, Gregory Kucherov, Knut Reinert, and Luca Renders

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
We provide a brief survey of results on solving the approximate pattern matching problem using search schemes, as introduced by Kucherov et al. (2016). We demonstrate that search schemes constitute a flexible and versatile tool that enable the specification of various search strategies, including several known filtering methods. We present approaches for designing efficient search schemes and for implementing them effectively. Finally, we conclude with experimental results comparing multiple search schemes on DNA sequencing data using the Columba software by Renders et al. (2021).
Cite as

Lore Depuydt, Jan Fostier, Simon Gottlieb, Gregory Kucherov, Knut Reinert, and Luca Renders. Search Schemes for Approximate Pattern Matching: An Overview. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 9:1-9:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{depuydt_et_al:OASIcs.Manzini.9,
  author =	{Depuydt, Lore and Fostier, Jan and Gottlieb, Simon and Kucherov, Gregory and Reinert, Knut and Renders, Luca},
  title =	{{Search Schemes for Approximate Pattern Matching: An Overview}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{9:1--9:16},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.9},
  URN =		{urn:nbn:de:0030-drops-239172},
  doi =		{10.4230/OASIcs.Manzini.9},
  annote =	{Keywords: FM-index, bidirectional index, approximate pattern matching, search scheme}
}
Document
Survey
DOI: 10.4230/TGDK.3.1.3
Uncertainty Management in the Construction of Knowledge Graphs: A Survey

Authors: Lucas Jarnac, Yoan Chabot, and Miguel Couceiro

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

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

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

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@Article{jarnac_et_al:TGDK.3.1.3,
  author =	{Jarnac, Lucas and Chabot, Yoan and Couceiro, Miguel},
  title =	{{Uncertainty Management in the Construction of Knowledge Graphs: A Survey}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{3:1--3:48},
  ISSN =	{2942-7517},
  year =	{2025},
  volume =	{3},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.3.1.3},
  URN =		{urn:nbn:de:0030-drops-233733},
  doi =		{10.4230/TGDK.3.1.3},
  annote =	{Keywords: Knowledge reconciliation, Uncertainty, Heterogeneous sources, Knowledge graph construction}
}
Document
Brief Announcement
DOI: 10.4230/LIPIcs.SAND.2025.23
Brief Announcement: Reachability in Deletion-Only Chemical Reaction Networks

Authors: Bin Fu, Timothy Gomez, Ryan Knobel, Austin Luchsinger, Aiden Massie, Marco Rodriguez, Adrian Salinas, Robert Schweller, and Tim Wylie

Published in: LIPIcs, Volume 330, 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)

Abstract
For general discrete Chemical Reaction Networks (CRNs), the fundamental problem of reachability - the question of whether a target configuration can be produced from a given initial configuration - was recently shown to be Ackermann-complete. However, many open questions remain about which features of the CRN model drive this complexity. We study a restricted class of CRNs with void rules, reactions that only decrease species counts. We further examine this regime in the motivated model of step CRNs, which allow additional species to be introduced in discrete stages. With and without steps, we characterize the complexity of the reachability problem for CRNs with void rules. We show that, without steps, reachability remains polynomial-time solvable for bimolecular systems but becomes NP-complete for larger reactions. Conversely, with just a single step, reachability becomes NP-complete even for bimolecular systems. Beyond what is contained in this brief announcement, we also investigate optimization variants of reachability, provide approximation results for maximizing species deletion, establish ETH-based lower bounds for NP-complete cases, and prove hardness for counting reaction sequences.
Cite as

Bin Fu, Timothy Gomez, Ryan Knobel, Austin Luchsinger, Aiden Massie, Marco Rodriguez, Adrian Salinas, Robert Schweller, and Tim Wylie. Brief Announcement: Reachability in Deletion-Only Chemical Reaction Networks. In 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 330, pp. 23:1-23:6, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{fu_et_al:LIPIcs.SAND.2025.23,
  author =	{Fu, Bin and Gomez, Timothy and Knobel, Ryan and Luchsinger, Austin and Massie, Aiden and Rodriguez, Marco and Salinas, Adrian and Schweller, Robert and Wylie, Tim},
  title =	{{Brief Announcement: Reachability in Deletion-Only Chemical Reaction Networks}},
  booktitle =	{4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)},
  pages =	{23:1--23:6},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-368-3},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{330},
  editor =	{Meeks, Kitty and Scheideler, Christian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2025.23},
  URN =		{urn:nbn:de:0030-drops-230768},
  doi =		{10.4230/LIPIcs.SAND.2025.23},
  annote =	{Keywords: CRN, Chemical Reaction Network, Reachability, Void Reactions}
}
Document
DOI: 10.4230/LIPIcs.SAND.2025.11
Hardness of Traversing Gadget Systems with Small Bandwidth

Authors: MIT Gadgets Group, Erik D. Demaine, Jenny Diomidova, Timothy Gomez, Markus Hecher, and Jayson Lynch

Published in: LIPIcs, Volume 330, 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)

Abstract
The motion-planning-through-gadgets framework has enabled proofs of PSPACE-completeness for many motion-planning problems, ranging from swarm and modular robotics to DNA computing to video games. In this paper, we strengthen this framework to show that, for several useful gadgets and gadget families, motion planning remains PSPACE-complete even when gadgets are connected together into a graph of constant bandwidth (which implies constant pathwidth, treewidth, and cliquewidth). We then show how this result applies to several geometric/grid-based motion-planning problems, establishing PSPACE-completeness even when restricted to a rectangle/box where only one dimension is large (superconstant). On the positive side, we find one family of gadgets (DAG gadgets) for which motion planning is fixed-parameter tractable with respect to bandwidth.
Cite as

MIT Gadgets Group, Erik D. Demaine, Jenny Diomidova, Timothy Gomez, Markus Hecher, and Jayson Lynch. Hardness of Traversing Gadget Systems with Small Bandwidth. In 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 330, pp. 11:1-11:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{mitgadgetsgroup_et_al:LIPIcs.SAND.2025.11,
  author =	{MIT Gadgets Group and Demaine, Erik D. and Diomidova, Jenny and Gomez, Timothy and Hecher, Markus and Lynch, Jayson},
  title =	{{Hardness of Traversing Gadget Systems with Small Bandwidth}},
  booktitle =	{4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)},
  pages =	{11:1--11:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-368-3},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{330},
  editor =	{Meeks, Kitty and Scheideler, Christian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2025.11},
  URN =		{urn:nbn:de:0030-drops-230648},
  doi =		{10.4230/LIPIcs.SAND.2025.11},
  annote =	{Keywords: Gadgets, Motion Planning, Parameterized Complexity, Hardness}
}
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