8 Search Results for "Smith, Spencer W."


Document
Reconstructing Random Graphs from Distance Queries

Authors: Michael Krivelevich and Maksim Zhukovskii

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


Abstract
We estimate the minimum number of distance queries that is sufficient to reconstruct the binomial random graph G(n,p) with constant diameter with high probability. We get a tight (up to a constant factor) answer for all p > n^{-1+o(1)} outside "threshold windows" around n^{-k/(k+1)+o(1)}, k ∈ ℤ_{> 0}: with high probability the query complexity equals Θ(n^{4-d}p^{2-d}), where d is the diameter of the random graph. This demonstrates the following non-monotone behaviour: the query complexity jumps down at moments when the diameter gets larger; yet, between these moments the query complexity grows. We also show that there exists a non-adaptive algorithm that reconstructs the random graph with O(n^{4-d}p^{2-d}ln n) distance queries with high probability, and this is best possible.

Cite as

Michael Krivelevich and Maksim Zhukovskii. Reconstructing Random Graphs from Distance Queries. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 30:1-30:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{krivelevich_et_al:LIPIcs.ESA.2025.30,
  author =	{Krivelevich, Michael and Zhukovskii, Maksim},
  title =	{{Reconstructing Random Graphs from Distance Queries}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{30:1--30:17},
  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.2025.30},
  URN =		{urn:nbn:de:0030-drops-244982},
  doi =		{10.4230/LIPIcs.ESA.2025.30},
  annote =	{Keywords: random graphs, graph reconstruction, distance queries, query complexity}
}
Document
Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems

Authors: Inhoo Lee, Salvador Buse, and Erik Winfree

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


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

Cite as

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


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

Authors: Diego Díaz-Domínguez, Lavinia Egidi, Veronica Guerrini, Felipe A. Louza, and Giovanna Rosone

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


Abstract
The Burrows-Wheeler Transform (BWT) is a fundamental string transformation that, although initially introduced for data compression, has been extensively utilized across various domains, including text indexing and pattern matching within large datasets. Although the BWT construction is linear, the constants make the task impractical for large datasets, and as highlighted by Ferragina et al. [Paolo Ferragina et al., 2012], "to use it, one must first build it!". Thus, the construction of the BWT remains a significant challenge. For these reasons, during the past three decades there has been a succession of new algorithms for its construction using techniques that work in external memory or that use text compression. In this survey, we revise some of the most important advancements and tools presented in the past years for computing large BWTs exploiting external memory or text compression approaches without using additional information about the data.

Cite as

Diego Díaz-Domínguez, Lavinia Egidi, Veronica Guerrini, Felipe A. Louza, and Giovanna Rosone. Algorithms for Computing Very Large BWTs: a Short Survey. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 7:1-7:28, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{diazdominguez_et_al:OASIcs.Manzini.7,
  author =	{D{\'\i}az-Dom{\'\i}nguez, Diego and Egidi, Lavinia and Guerrini, Veronica and Louza, Felipe A. and Rosone, Giovanna},
  title =	{{Algorithms for Computing Very Large BWTs: a Short Survey}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{7:1--7:28},
  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.7},
  URN =		{urn:nbn:de:0030-drops-239151},
  doi =		{10.4230/OASIcs.Manzini.7},
  annote =	{Keywords: Burrows-Wheeler transform, Extended Burrows-Wheeler transform, external memory, text compression, longest common prefix}
}
Document
Vision
Machine Learning and Knowledge Graphs: Existing Gaps and Future Research Challenges

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

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


Abstract
The graph model is nowadays largely adopted to model a wide range of knowledge and data, spanning from social networks to knowledge graphs (KGs), representing a successful paradigm of how symbolic and transparent AI can scale on the World Wide Web. However, due to their unprecedented volume, they are generally tackled by Machine Learning (ML) and mostly numeric based methods such as graph embedding models (KGE) and deep neural networks (DNNs). The latter methods have been proved lately very efficient, leading the current AI spring. In this vision paper, we introduce some of the main existing methods for combining KGs and ML, divided into two categories: those using ML to improve KGs, and those using KGs to improve results on ML tasks. From this introduction, we highlight research gaps and perspectives that we deem promising and currently under-explored for the involved research communities, spanning from KG support for LLM prompting, integration of KG semantics in ML models to symbol-based methods, interpretability of ML models, and the need for improved benchmark datasets. In our opinion, such perspectives are stepping stones in an ultimate view of KGs as central assets for neuro-symbolic and explainable AI.

Cite as

Claudia d'Amato, Louis Mahon, Pierre Monnin, and Giorgos Stamou. Machine Learning and Knowledge Graphs: Existing Gaps and Future Research Challenges. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 8:1-8:35, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@Article{damato_et_al:TGDK.1.1.8,
  author =	{d'Amato, Claudia and Mahon, Louis and Monnin, Pierre and Stamou, Giorgos},
  title =	{{Machine Learning and Knowledge Graphs: Existing Gaps and Future Research Challenges}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{8:1--8:35},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.8},
  URN =		{urn:nbn:de:0030-drops-194824},
  doi =		{10.4230/TGDK.1.1.8},
  annote =	{Keywords: Graph-based Learning, Knowledge Graph Embeddings, Large Language Models, Explainable AI, Knowledge Graph Completion \& Curation}
}
Document
Vision
Knowledge Engineering Using Large Language Models

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

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


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

Cite as

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


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@Article{allen_et_al:TGDK.1.1.3,
  author =	{Allen, Bradley P. and Stork, Lise and Groth, Paul},
  title =	{{Knowledge Engineering Using Large Language Models}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{3:1--3:19},
  ISSN =	{2942-7517},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.3},
  URN =		{urn:nbn:de:0030-drops-194777},
  doi =		{10.4230/TGDK.1.1.3},
  annote =	{Keywords: knowledge engineering, large language models}
}
Document
APPROX
The (Im)possibility of Simple Search-To-Decision Reductions for Approximation Problems

Authors: Alexander Golovnev, Siyao Guo, Spencer Peters, and Noah Stephens-Davidowitz

Published in: LIPIcs, Volume 275, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2023)


Abstract
We study the question of when an approximate search optimization problem is harder than the associated decision problem. Specifically, we study a natural and quite general model of black-box search-to-decision reductions, which we call branch-and-bound reductions (in analogy with branch-and-bound algorithms). In this model, an algorithm attempts to minimize (or maximize) a function f: D → ℝ_{≥ 0} by making oracle queries to h_f : 𝒮 → ℝ_{≥ 0} satisfying min_{x ∈ S} f(x) ≤ h_f(S) ≤ γ ⋅ min_{x ∈ S} f(x) (*) for some γ ≥ 1 and any subset S in some allowed class of subsets 𝒮 of the domain D. (When the goal is to maximize f, h_f instead yields an approximation to the maximal value of f over S.) We show tight upper and lower bounds on the number of queries q needed to find even a γ'-approximate minimizer (or maximizer) for quite large γ' in a number of interesting settings, as follows. - For arbitrary functions f : {0,1}ⁿ → ℝ_{≥ 0}, where 𝒮 contains all subsets of the domain, we show that no branch-and-bound reduction can achieve γ' ≲ γ^{n/log q}, while a simple greedy approach achieves essentially γ^{n/log q}. - For a large class of MAX-CSPs, where 𝒮 := {S_w} contains each set of assignments to the variables induced by a partial assignment w, we show that no branch-and-bound reduction can do significantly better than essentially a random guess, even when the oracle h_f guarantees an approximation factor of γ ≈ 1+√{log(q)/n}. - For the Traveling Salesperson Problem (TSP), where 𝒮 := {S_p} contains each set of tours extending a path p, we show that no branch-and-bound reduction can achieve γ' ≲ (γ-1) n/log q. We also prove a nearly matching upper bound in our model. These results show an oracle model in which approximate search and decision are strongly separated. (In particular, our result for TSP can be viewed as a negative answer to a question posed by Bellare and Goldwasser (SIAM J. Comput. 1994), though only in an oracle model.) We also note two alternative interpretations of our results. First, if we view h_f as a data structure, then our results unconditionally rule out black-box search-to-decision reductions for certain data structure problems. Second, if we view h_f as an efficiently computable heuristic, then our results show that any reasonably efficient branch-and-bound algorithm requires more guarantees from its heuristic than simply Eq. (*). Behind our results is a "useless oracle lemma," which allows us to argue that under certain conditions the oracle h_f is "useless," and which might be of independent interest. See also the full version [Alexander Golovnev et al., 2022].

Cite as

Alexander Golovnev, Siyao Guo, Spencer Peters, and Noah Stephens-Davidowitz. The (Im)possibility of Simple Search-To-Decision Reductions for Approximation Problems. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 275, pp. 10:1-10:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{golovnev_et_al:LIPIcs.APPROX/RANDOM.2023.10,
  author =	{Golovnev, Alexander and Guo, Siyao and Peters, Spencer and Stephens-Davidowitz, Noah},
  title =	{{The (Im)possibility of Simple Search-To-Decision Reductions for Approximation Problems}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2023)},
  pages =	{10:1--10:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-296-9},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{275},
  editor =	{Megow, Nicole and Smith, Adam},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2023.10},
  URN =		{urn:nbn:de:0030-drops-188351},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2023.10},
  annote =	{Keywords: search-to-decision reductions, oracles, constraint satisfaction, traveling salesman, discrete optimization}
}
Document
Generating Software for Well-Understood Domains

Authors: Jacques Carette, Spencer W. Smith, and Jason Balaci

Published in: OASIcs, Volume 109, Eelco Visser Commemorative Symposium (EVCS 2023)


Abstract
Current software development is often quite code-centric and aimed at short-term deliverables, due to various contextual forces (such as the need for new revenue streams from many individual buyers). We're interested in software where different forces drive the development. Well understood domains and long-lived software provide one such context. A crucial observation is that software artifacts that are currently handwritten contain considerable duplication. By using domain-specific languages and generative techniques, we can capture the contents of many of the artifacts of such software. Assuming an appropriate codification of domain knowledge, we find that the resulting de-duplicated sources are shorter and closer to the domain. Our prototype, Drasil, indicates improvements to traceability and change management. We're also hopeful that this could lead to long-term productivity improvements for software where these forces are at play.

Cite as

Jacques Carette, Spencer W. Smith, and Jason Balaci. Generating Software for Well-Understood Domains. In Eelco Visser Commemorative Symposium (EVCS 2023). Open Access Series in Informatics (OASIcs), Volume 109, pp. 7:1-7:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{carette_et_al:OASIcs.EVCS.2023.7,
  author =	{Carette, Jacques and Smith, Spencer W. and Balaci, Jason},
  title =	{{Generating Software for Well-Understood Domains}},
  booktitle =	{Eelco Visser Commemorative Symposium (EVCS 2023)},
  pages =	{7:1--7:12},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-267-9},
  ISSN =	{2190-6807},
  year =	{2023},
  volume =	{109},
  editor =	{L\"{a}mmel, Ralf and Mosses, Peter D. and Steimann, Friedrich},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.EVCS.2023.7},
  URN =		{urn:nbn:de:0030-drops-177776},
  doi =		{10.4230/OASIcs.EVCS.2023.7},
  annote =	{Keywords: code generation, document generation, knowledge capture, software engineering}
}
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