8 Search Results for "Williams, Andy E."

Document
DOI: 10.4230/LIPIcs.ESA.2025.24
Fréchet Distance in Unweighted Planar Graphs

Authors: Ivor van der Hoog, Thijs van der Horst, Eva Rotenberg, and Lasse Wulf

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

Abstract
The Fréchet distance is a distance measure between trajectories in ℝ^d or walks in a graph G. Given constant-time shortest path queries, the Discrete Fréchet distance D_G(P, Q) between two walks P and Q can be computed in O(|P|⋅|Q|) time using a dynamic program. Driemel, van der Hoog, and Rotenberg [SoCG'22] show that for weighted planar graphs this approach is likely tight, as there can be no strongly-subquadratic algorithm to compute a 1.01-approximation of D_G(P, Q) unless the Orthogonal Vector Hypothesis (OVH) fails. Such quadratic-time conditional lower bounds are common to many Fréchet distance variants. However, they can be circumvented by assuming that the input comes from some well-behaved class: There exist (1+ε)-approximations, both in weighted graphs and in ℝ^d, that take near-linear time for c-packed or κ-straight walks in the graph. In ℝ^d there also exists a near-linear time algorithm to compute the Fréchet distance whenever all input edges are long compared to the distance. We consider computing the Fréchet distance in unweighted planar graphs. We show that there exist no strongly-subquadratic 1.25-approximations of the discrete Fréchet distance between two disjoint simple paths in an unweighted planar graph in strongly subquadratic time, unless OVH fails. This improves the previous lower bound, both in terms of generality and approximation factor. We subsequently show that adding graph structure circumvents this lower bound: If the graph is a regular tiling with unit-weighted edges, then there exists an Õ((|P|+|Q|)^{1.5})-time algorithm to compute D_G(P, Q). Our result has natural implications in the plane, as it allows us to define a new class of well-behaved curves that facilitate (1+ε)-approximations of their discrete Fréchet distance in subquadratic time.
Cite as

Ivor van der Hoog, Thijs van der Horst, Eva Rotenberg, and Lasse Wulf. Fréchet Distance in Unweighted Planar Graphs. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 24:1-24:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{vanderhoog_et_al:LIPIcs.ESA.2025.24,
  author =	{van der Hoog, Ivor and van der Horst, Thijs and Rotenberg, Eva and Wulf, Lasse},
  title =	{{Fr\'{e}chet Distance in Unweighted Planar Graphs}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{24:1--24:16},
  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.2025.24},
  URN =		{urn:nbn:de:0030-drops-244924},
  doi =		{10.4230/LIPIcs.ESA.2025.24},
  annote =	{Keywords: Fr\'{e}chet distance, planar graphs, lower bounds, approximation algorithms}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.4
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
DOI: 10.4230/LIPIcs.GIScience.2025.4
Precomputed Topological Relations for Integrated Geospatial Analysis Across Knowledge Graphs

Authors: Katrina Schweikert, David K. Kedrowski, Shirly Stephen, and Torsten Hahmann

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

Abstract
Geospatial Knowledge Graphs (GeoKGs) represent a significant advancement in the integration of AI-driven geographic information, facilitating interoperable and semantically rich geospatial analytics across various domains. This paper explores the use of topologically enriched GeoKGs, built on an explicit representation of S2 Geometry alongside precomputed topological relations, for constructing efficient geospatial analysis workflows within and across knowledge graphs (KGs). Using the SAWGraph knowledge graph as a case study focused on enviromental contamination by PFAS, we demonstrate how this framework supports fundamental GIS operations - such as spatial filtering, proximity analysis, overlay operations and network analysis - in a GeoKG setting while allowing for the easy linking of these operations with one another and with semantic filters. This enables the efficient execution of complex geospatial analyses as semantically-explicit queries and enhances the usability of geospatial data across graphs. Additionally, the framework eliminates the need for explicit support for GeoSPARQL’s topological operations in the utilized graph databases and better integrates spatial knowledge into the overall semantic inference process supported by RDFS and OWL ontologies.
Cite as

Katrina Schweikert, David K. Kedrowski, Shirly Stephen, and Torsten Hahmann. Precomputed Topological Relations for Integrated Geospatial Analysis Across Knowledge Graphs. In 13th International Conference on Geographic Information Science (GIScience 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 346, pp. 4:1-4:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{schweikert_et_al:LIPIcs.GIScience.2025.4,
  author =	{Schweikert, Katrina and Kedrowski, David K. and Stephen, Shirly and Hahmann, Torsten},
  title =	{{Precomputed Topological Relations for Integrated Geospatial Analysis Across Knowledge Graphs}},
  booktitle =	{13th International Conference on Geographic Information Science (GIScience 2025)},
  pages =	{4:1--4:22},
  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.2025.4},
  URN =		{urn:nbn:de:0030-drops-238332},
  doi =		{10.4230/LIPIcs.GIScience.2025.4},
  annote =	{Keywords: knowledge graph, GeoKG, spatial analysis, ontology, SPARQL, GeoSPARQL, discrete global grid system, S2 geometry, GeoAI, PFAS}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.11
Mutational Signature Refitting on Sparse Pan-Cancer Data

Authors: Gal Gilad, Teresa M. Przytycka, and Roded Sharan

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
Mutational processes shape cancer genomes, leaving characteristic marks that are termed signatures. The level of activity of each such process, or its signature exposure, provides important information on the disease, improving patient stratification and the prediction of drug response. Thus, there is growing interest in developing refitting methods that decipher those exposures. Previous work in this domain was unsupervised in nature, employing algebraic decomposition and probabilistic inference methods. Here we provide a supervised approach to the problem of signature refitting and show its superiority over current methods. Our method, SuRe, leverages a neural network model to capture correlations between signature exposures in real data. We show that SuRe outperforms previous methods on sparse mutation data from tumor type specific data sets, as well as pan-cancer data sets, with an increasing advantage as the data become sparser. We further demonstrate its utility in clinical settings.
Cite as

Gal Gilad, Teresa M. Przytycka, and Roded Sharan. Mutational Signature Refitting on Sparse Pan-Cancer Data. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 11:1-11:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gilad_et_al:LIPIcs.WABI.2025.11,
  author =	{Gilad, Gal and Przytycka, Teresa M. and Sharan, Roded},
  title =	{{Mutational Signature Refitting on Sparse Pan-Cancer Data}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{11:1--11:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.11},
  URN =		{urn:nbn:de:0030-drops-239374},
  doi =		{10.4230/LIPIcs.WABI.2025.11},
  annote =	{Keywords: mutational signatures, signature refitting, cancer genomics, genomic data analysis, somatic mutations}
}
Document
DOI: 10.4230/LIPIcs.STACS.2025.20
On Cascades of Reset Automata

Authors: Roberto Borelli, Luca Geatti, Marco Montali, and Angelo Montanari

Published in: LIPIcs, Volume 327, 42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025)

Abstract
The Krohn-Rhodes decomposition theorem is a pivotal result in automata theory. It introduces the concept of cascade product, where two semiautomata, that is, automata devoid of initial and final states, are combined in a feed-forward fashion. The theorem states that any semiautomaton can be decomposed into a sequence of permutation-reset semiautomata. For the counter-free case, this decomposition consists entirely of reset components with two states each. This decomposition has significantly impacted recent research in various areas of computer science, including the identification of a class of transformer encoders equivalent to star-free languages and the conversion of Linear Temporal Logic formulas into past-only expressions (pastification). The paper revisits the cascade product in the context of reset automata, thus considering each component of the cascade as a language acceptor. First, we give regular expression counterparts of cascades of reset automata. We then establish several expressiveness results, identifying hierarchies of languages based on the restriction of the height (number of components) of the cascade or of the number of states in each level. We also show that any cascade of reset automata can be transformed, with a quadratic increase in height, into a cascade that only includes two-state components. Finally, we show that some fundamental operations on cascades, like intersection, union, negation, and concatenation with a symbol to the left, can be directly and efficiently computed by adding a two-state component.
Cite as

Roberto Borelli, Luca Geatti, Marco Montali, and Angelo Montanari. On Cascades of Reset Automata. In 42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 327, pp. 20:1-20:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{borelli_et_al:LIPIcs.STACS.2025.20,
  author =	{Borelli, Roberto and Geatti, Luca and Montali, Marco and Montanari, Angelo},
  title =	{{On Cascades of Reset Automata}},
  booktitle =	{42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025)},
  pages =	{20:1--20:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-365-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{327},
  editor =	{Beyersdorff, Olaf and Pilipczuk, Micha{\l} and Pimentel, Elaine and Thắng, Nguy\~{ê}n Kim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2025.20},
  URN =		{urn:nbn:de:0030-drops-228453},
  doi =		{10.4230/LIPIcs.STACS.2025.20},
  annote =	{Keywords: Automata, Cascade products, Regular expressions, Krohn-Rhodes theory}
}
Document
DOI: 10.4230/LIPIcs.OPODIS.2024.24
Hash & Adjust: Competitive Demand-Aware Consistent Hashing

Authors: Arash Pourdamghani, Chen Avin, Robert Sama, Maryam Shiran, and Stefan Schmid

Published in: LIPIcs, Volume 324, 28th International Conference on Principles of Distributed Systems (OPODIS 2024)

Abstract
Distributed systems often serve dynamic workloads and resource demands evolve over time. Such a temporal behavior stands in contrast to the static and demand-oblivious nature of most data structures used by these systems. In this paper, we are particularly interested in consistent hashing, a fundamental building block in many large distributed systems. Our work is motivated by the hypothesis that a more adaptive approach to consistent hashing can leverage structure in the demand, and hence improve storage utilization and reduce access time. We initiate the study of demand-aware consistent hashing. Our main contribution is H&A, a constant-competitive online algorithm (i.e., it comes with provable performance guarantees over time). H&A is demand-aware and optimizes its internal structure to enable faster access times, while offering a high utilization of storage. We further evaluate H&A empirically.
Cite as

Arash Pourdamghani, Chen Avin, Robert Sama, Maryam Shiran, and Stefan Schmid. Hash & Adjust: Competitive Demand-Aware Consistent Hashing. In 28th International Conference on Principles of Distributed Systems (OPODIS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 324, pp. 24:1-24:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{pourdamghani_et_al:LIPIcs.OPODIS.2024.24,
  author =	{Pourdamghani, Arash and Avin, Chen and Sama, Robert and Shiran, Maryam and Schmid, Stefan},
  title =	{{Hash \& Adjust: Competitive Demand-Aware Consistent Hashing}},
  booktitle =	{28th International Conference on Principles of Distributed Systems (OPODIS 2024)},
  pages =	{24:1--24:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-360-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{324},
  editor =	{Bonomi, Silvia and Galletta, Letterio and Rivi\`{e}re, Etienne and Schiavoni, Valerio},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.OPODIS.2024.24},
  URN =		{urn:nbn:de:0030-drops-225607},
  doi =		{10.4230/LIPIcs.OPODIS.2024.24},
  annote =	{Keywords: Consistent hashing, demand-awareness, online algorithms}
}
Document
Survey
DOI: 10.4230/TGDK.1.1.11
How Does Knowledge Evolve in Open Knowledge Graphs?

Authors: Axel Polleres, Romana Pernisch, Angela Bonifati, Daniele Dell'Aglio, Daniil Dobriy, Stefania Dumbrava, Lorena Etcheverry, Nicolas Ferranti, Katja Hose, Ernesto Jiménez-Ruiz, Matteo Lissandrini, Ansgar Scherp, Riccardo Tommasini, and Johannes Wachs

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
Openly available, collaboratively edited Knowledge Graphs (KGs) are key platforms for the collective management of evolving knowledge. The present work aims t o provide an analysis of the obstacles related to investigating and processing specifically this central aspect of evolution in KGs. To this end, we discuss (i) the dimensions of evolution in KGs, (ii) the observability of evolution in existing, open, collaboratively constructed Knowledge Graphs over time, and (iii) possible metrics to analyse this evolution. We provide an overview of relevant state-of-the-art research, ranging from metrics developed for Knowledge Graphs specifically to potential methods from related fields such as network science. Additionally, we discuss technical approaches - and their current limitations - related to storing, analysing and processing large and evolving KGs in terms of handling typical KG downstream tasks.
Cite as

Axel Polleres, Romana Pernisch, Angela Bonifati, Daniele Dell'Aglio, Daniil Dobriy, Stefania Dumbrava, Lorena Etcheverry, Nicolas Ferranti, Katja Hose, Ernesto Jiménez-Ruiz, Matteo Lissandrini, Ansgar Scherp, Riccardo Tommasini, and Johannes Wachs. How Does Knowledge Evolve in Open Knowledge Graphs?. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 11:1-11:59, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{polleres_et_al:TGDK.1.1.11,
  author =	{Polleres, Axel and Pernisch, Romana and Bonifati, Angela and Dell'Aglio, Daniele and Dobriy, Daniil and Dumbrava, Stefania and Etcheverry, Lorena and Ferranti, Nicolas and Hose, Katja and Jim\'{e}nez-Ruiz, Ernesto and Lissandrini, Matteo and Scherp, Ansgar and Tommasini, Riccardo and Wachs, Johannes},
  title =	{{How Does Knowledge Evolve in Open Knowledge Graphs?}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{11:1--11:59},
  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.1.1.11},
  URN =		{urn:nbn:de:0030-drops-194855},
  doi =		{10.4230/TGDK.1.1.11},
  annote =	{Keywords: KG evolution, temporal KG, versioned KG, dynamic KG}
}
Document
Poster
DOI: 10.4230/OASIcs.FAB.2022.10
Why General Collective Intelligence Must Be the Future of the Blockchain (Poster)

Authors: Andy E. Williams

Published in: OASIcs, Volume 101, 5th International Symposium on Foundations and Applications of Blockchain 2022 (FAB 2022)

Abstract
General Collective Intelligence or GCI is predicted to radically increase the speed and scale at which blockchain technology can be designed, developed, and deployed as well as being predicted to radically increase demand for those new blockchain based products and services where they don’t involve consumption of limited physical resources. Therefore, if a GCI can be implemented, it is predicted that GCI based platforms will quickly come to dominate the blockchain marketplace and that GCI is the future of the blockchain. But it also must be the case that GCI is the future of the blockchain because without it, through an effect called the "technology gravity well" blockchain and other technologies have the possibility of introducing an unprecedented degree of centralization, control, and abuse.
Cite as

Andy E. Williams. Why General Collective Intelligence Must Be the Future of the Blockchain (Poster). In 5th International Symposium on Foundations and Applications of Blockchain 2022 (FAB 2022). Open Access Series in Informatics (OASIcs), Volume 101, pp. 10:1-10:3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{williams:OASIcs.FAB.2022.10,
  author =	{Williams, Andy E.},
  title =	{{Why General Collective Intelligence Must Be the Future of the Blockchain}},
  booktitle =	{5th International Symposium on Foundations and Applications of Blockchain 2022 (FAB 2022)},
  pages =	{10:1--10:3},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-248-8},
  ISSN =	{2190-6807},
  year =	{2022},
  volume =	{101},
  editor =	{Tucci-Piergiovanni, Sara and Crooks, Natacha},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.FAB.2022.10},
  URN =		{urn:nbn:de:0030-drops-162774},
  doi =		{10.4230/OASIcs.FAB.2022.10},
  annote =	{Keywords: General Collective Intelligence, Human-Centric Functional Modeling, functional state space, conceptual space, blockchain state space, cooperation state space}
}
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