5 Search Results for "Goebel, Randy"

Document
Research
DOI: 10.4230/OASIcs.Grossi.20
Subsequence-Based Indices for Genome Sequence Analysis

Authors: Giovanni Buzzega, Alessio Conte, Veronica Guerrini, Giulia Punzi, Giovanna Rosone, and Lorenzo Tattini

Published in: OASIcs, Volume 132, From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday (2025)

Abstract
Compact indices are a fundamental tool in string analysis, even more so in bioinformatics, where genomic sequences can reach billions in length. This paper presents some recent results in which Roberto Grossi has been involved, showing how some of these indices do more than just efficiently represent data, but rather are able to bring out salient information within it, which can be exploited for their downstream analysis. Specifically, we first review a recently-introduced method [Guerrini et al., 2023] that employs the Burrows-Wheeler Transform to build reasonably accurate phylogenetic trees in an assembly-free scenario. We then describe a recent practical tool [Buzzega et al., 2025] for indexing Maximal Common Subsequences between strings, which can enable analysis of genomic sequence similarity. Experimentally, we show that the results produced by the one index are consistent with the expectations about the results of the other index.
Cite as

Giovanni Buzzega, Alessio Conte, Veronica Guerrini, Giulia Punzi, Giovanna Rosone, and Lorenzo Tattini. Subsequence-Based Indices for Genome Sequence Analysis. In From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 132, pp. 20:1-20:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{buzzega_et_al:OASIcs.Grossi.20,
  author =	{Buzzega, Giovanni and Conte, Alessio and Guerrini, Veronica and Punzi, Giulia and Rosone, Giovanna and Tattini, Lorenzo},
  title =	{{Subsequence-Based Indices for Genome Sequence Analysis}},
  booktitle =	{From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
  pages =	{20:1--20:21},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-391-1},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{132},
  editor =	{Conte, Alessio and Marino, Andrea and Rosone, Giovanna and Vitter, Jeffrey Scott},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Grossi.20},
  URN =		{urn:nbn:de:0030-drops-238199},
  doi =		{10.4230/OASIcs.Grossi.20},
  annote =	{Keywords: String Indices, Burrows-Wheeler Transform, Maximal Common Subsequences, Sequence Analysis, Phylogeny}
}
Document
Position
DOI: 10.4230/TGDK.2.1.5
Standardizing Knowledge Engineering Practices with a Reference Architecture

Authors: Bradley P. Allen and Filip Ilievski

Published in: TGDK, Volume 2, Issue 1 (2024): Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge, Volume 2, Issue 1

Abstract
Knowledge engineering is the process of creating and maintaining knowledge-producing systems. Throughout the history of computer science and AI, knowledge engineering workflows have been widely used given the importance of high-quality knowledge for reliable intelligent agents. Meanwhile, the scope of knowledge engineering, as apparent from its target tasks and use cases, has been shifting, together with its paradigms such as expert systems, semantic web, and language modeling. The intended use cases and supported user requirements between these paradigms have not been analyzed globally, as new paradigms often satisfy prior pain points while possibly introducing new ones. The recent abstraction of systemic patterns into a boxology provides an opening for aligning the requirements and use cases of knowledge engineering with the systems, components, and software that can satisfy them best, however, this direction has not been explored to date. This paper proposes a vision of harmonizing the best practices in the field of knowledge engineering by leveraging the software engineering methodology of creating reference architectures. We describe how a reference architecture can be iteratively designed and implemented to associate user needs with recurring systemic patterns, building on top of existing knowledge engineering workflows and boxologies. We provide a six-step roadmap that can enable the development of such an architecture, consisting of scope definition, selection of information sources, architectural analysis, synthesis of an architecture based on the information source analysis, evaluation through instantiation, and, ultimately, instantiation into a concrete software architecture. We provide an initial design and outcome of the definition of architectural scope, selection of information sources, and analysis. As the remaining steps of design, evaluation, and instantiation of the architecture are largely use-case specific, we provide a detailed description of their procedures and point to relevant examples. We expect that following through on this vision will lead to well-grounded reference architectures for knowledge engineering, will advance the ongoing initiatives of organizing the neurosymbolic knowledge engineering space, and will build new links to the software architectures and data science communities.
Cite as

Bradley P. Allen and Filip Ilievski. Standardizing Knowledge Engineering Practices with a Reference Architecture. In Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 1, pp. 5:1-5:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{allen_et_al:TGDK.2.1.5,
  author =	{Allen, Bradley P. and Ilievski, Filip},
  title =	{{Standardizing Knowledge Engineering Practices with a Reference Architecture}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{5:1--5:23},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.1.5},
  URN =		{urn:nbn:de:0030-drops-198623},
  doi =		{10.4230/TGDK.2.1.5},
  annote =	{Keywords: knowledge engineering, knowledge graphs, quality attributes, software architectures, sociotechnical systems}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2019.46
A 21/16-Approximation for the Minimum 3-Path Partition Problem

Authors: Yong Chen, Randy Goebel, Bing Su, Weitian Tong, Yao Xu, and An Zhang

Published in: LIPIcs, Volume 149, 30th International Symposium on Algorithms and Computation (ISAAC 2019)

Abstract
The minimum k-path partition (Min-k-PP for short) problem targets to partition an input graph into the smallest number of paths, each of which has order at most k. We focus on the special case when k=3. Existing literature mainly concentrates on the exact algorithms for special graphs, such as trees. Because of the challenge of NP-hardness on general graphs, the approximability of the Min-3-PP problem attracts researchers' attention. The first approximation algorithm dates back about 10 years and achieves an approximation ratio of 3/2, which was recently improved to 13/9 and further to 4/3. We investigate the 3/2-approximation algorithm for the Min-3-PP problem and discover several interesting structural properties. Instead of studying the unweighted Min-3-PP problem directly, we design a novel weight schema for l-paths, l in {1, 2, 3}, and investigate the weighted version. A greedy local search algorithm is proposed to generate a heavy path partition. We show the achieved path partition has the least 1-paths, which is also the key ingredient for the algorithms with ratios 13/9 and 4/3. When switching back to the unweighted objective function, we prove the approximation ratio 21/16 via amortized analysis.
Cite as

Yong Chen, Randy Goebel, Bing Su, Weitian Tong, Yao Xu, and An Zhang. A 21/16-Approximation for the Minimum 3-Path Partition Problem. In 30th International Symposium on Algorithms and Computation (ISAAC 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 149, pp. 46:1-46:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{chen_et_al:LIPIcs.ISAAC.2019.46,
  author =	{Chen, Yong and Goebel, Randy and Su, Bing and Tong, Weitian and Xu, Yao and Zhang, An},
  title =	{{A 21/16-Approximation for the Minimum 3-Path Partition Problem}},
  booktitle =	{30th International Symposium on Algorithms and Computation (ISAAC 2019)},
  pages =	{46:1--46:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-130-6},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{149},
  editor =	{Lu, Pinyan and Zhang, Guochuan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2019.46},
  URN =		{urn:nbn:de:0030-drops-115422},
  doi =		{10.4230/LIPIcs.ISAAC.2019.46},
  annote =	{Keywords: 3-path partition, exact set cover, approximation algorithm, local search, amortized analysis}
}
Document
DOI: 10.4230/DagRep.5.2.128
Smart Buildings and Smart Grids (Dagstuhl Seminar 15091)

Authors: Hans-Arno Jacobsen, Randy H. Katz, Hartmut Schmeck, and Christoph Goebel

Published in: Dagstuhl Reports, Volume 5, Issue 2 (2015)

Abstract
This report provides an overview of the program, discussions, and outcomes of Dagstuhl Seminar 15091 "Smart Buildings and Smart Grids", which took place from 22-27 February 2015 at Schloss Dagstuhl - Leibniz Center for Informatics. The main goal of the seminar was to provide a forum for leading Energy Informatics (EI) researchers to discuss their recent research on Smart Buildings and Smart Grids, to further elaborate EI research agenda and methods, and to kick-start new research projects with industry. The report contains abstracts of talks that were held by the participants and the outcomes of several discussion sessions on the focal topics of the seminar (e.g., information technology driven developments in building and power system management, as well as cross-cutting topics, such as computer networks, data management, and system design.
Cite as

Hans-Arno Jacobsen, Randy H. Katz, Hartmut Schmeck, and Christoph Goebel. Smart Buildings and Smart Grids (Dagstuhl Seminar 15091). In Dagstuhl Reports, Volume 5, Issue 2, pp. 128-175, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2015)

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@Article{jacobsen_et_al:DagRep.5.2.128,
  author =	{Jacobsen, Hans-Arno and Katz, Randy H. and Schmeck, Hartmut and Goebel, Christoph},
  title =	{{Smart Buildings and Smart Grids (Dagstuhl Seminar 15091)}},
  pages =	{128--175},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2015},
  volume =	{5},
  number =	{2},
  editor =	{Jacobsen, Hans-Arno and Katz, Randy H. and Schmeck, Hartmut and Goebel, Christoph},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.5.2.128},
  URN =		{urn:nbn:de:0030-drops-52109},
  doi =		{10.4230/DagRep.5.2.128},
  annote =	{Keywords: Energy Informatics, Smart Grids, Smart Buildings, Cyber-Physical Systems}
}
Document
DOI: 10.4230/DagSemProc.05321.11
Iterated Belief Change and the Levi Identity

Authors: Abhaya Nayak, Randy Goebel, Mehmet Orgun, and Tam Pham

Published in: Dagstuhl Seminar Proceedings, Volume 5321, Belief Change in Rational Agents: Perspectives from Artificial Intelligence, Philosophy, and Economics (2005)

Abstract
Most works on iterated belief change have focussed on iterated belief revision, namely, on how to compute (K star x) star y. However, historically, belief revision has been defined in terms of belief expansion and belief contraction that have been viewed as primary operations. Accordingly, what we should be looking at are constructions like: (K+x)+y, (K-x)+y, (K-x)+y and (K-x)-y. The first two constructions are relatively innocuous. The last two are, however, more problematic. We look at these sequential operations. In the process, we use the Levi Identity as the guiding principle behind state changes (as opposed to belief set changes).
Cite as

Abhaya Nayak, Randy Goebel, Mehmet Orgun, and Tam Pham. Iterated Belief Change and the Levi Identity. In Belief Change in Rational Agents: Perspectives from Artificial Intelligence, Philosophy, and Economics. Dagstuhl Seminar Proceedings, Volume 5321, pp. 1-16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2005)

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@InProceedings{nayak_et_al:DagSemProc.05321.11,
  author =	{Nayak, Abhaya and Goebel, Randy and Orgun, Mehmet and Pham, Tam},
  title =	{{Iterated Belief Change and the Levi Identity}},
  booktitle =	{Belief Change in Rational Agents: Perspectives from Artificial Intelligence, Philosophy, and Economics},
  pages =	{1--16},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2005},
  volume =	{5321},
  editor =	{James Delgrande and Jerome Lang and Hans Rott and Jean-Marc Tallon},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05321.11},
  URN =		{urn:nbn:de:0030-drops-3317},
  doi =		{10.4230/DagSemProc.05321.11},
  annote =	{Keywords: Iterated belief change, iterated belief contraction, Levi Identity}
}
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