7 Search Results for "Ernst, Michael D."

Document
DOI: 10.4230/LIPIcs.WABI.2024.5
Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests

Authors: Lukas Hübner and Alexandros Stamatakis

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
The field of population genetics attempts to advance our understanding of evolutionary processes. It has applications, for example, in medical research, wildlife conservation, and - in conjunction with recent advances in ancient DNA sequencing technology - studying human migration patterns over the past few thousand years. The basic toolbox of population genetics includes genealogical trees, which describe the shared evolutionary history among individuals of the same species. They are calculated on the basis of genetic variations. However, in recombining organisms, a single tree is insufficient to describe the evolutionary history of the whole genome. Instead, a collection of correlated trees can be used, where each describes the evolutionary history of a consecutive region of the genome. The current corresponding state of-the-art data structure, tree sequences, compresses these genealogical trees via edit operations when moving from one tree to the next along the genome instead of storing the full, often redundant, description for each tree. We propose a new data structure, genealogical forests, which compresses the set of genealogical trees into a DAG. In this DAG identical subtrees that are shared across the input trees are encoded only once, thereby allowing for straight-forward memoization of intermediate results. Additionally, we provide a C++ implementation of our proposed data structure, called gfkit, which is 2.1 to 11.2 (median 4.0) times faster than the state-of-the-art tool on empirical and simulated datasets at computing important population genetics statistics such as the Allele Frequency Spectrum, Patterson’s f, the Fixation Index, Tajima’s D, pairwise Lowest Common Ancestors, and others. On Lowest Common Ancestor queries with more than two samples as input, gfkit scales asymptotically better than the state-of-the-art, and is thus up to 990 times faster. In conclusion, our proposed data structure compresses genealogical trees by storing shared subtrees only once, thereby enabling straight-forward memoization of intermediate results, yielding a substantial runtime reduction and a potentially more intuitive data representation over the state-of-the-art. Our improvements will boost the development of novel analyses and models in the field of population genetics and increases scalability to ever-growing genomic datasets.
Cite as

Lukas Hübner and Alexandros Stamatakis. Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 5:1-5:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{hubner_et_al:LIPIcs.WABI.2024.5,
  author =	{H\"{u}bner, Lukas and Stamatakis, Alexandros},
  title =	{{Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{5:1--5:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.5},
  URN =		{urn:nbn:de:0030-drops-206499},
  doi =		{10.4230/LIPIcs.WABI.2024.5},
  annote =	{Keywords: bioinformatics, population genetics, algorithms}
}
Document
DOI: 10.4230/OASIcs.FMBC.2024.7
Towards Formally Specifying and Verifying Smart Contract Upgrades in Coq

Authors: Derek Sorensen

Published in: OASIcs, Volume 118, 5th International Workshop on Formal Methods for Blockchains (FMBC 2024)

Abstract
Smart contract upgrades are costly from a verification perspective and can be a meaningful source of vulnerabilities when done incorrectly. Unfortunately, there is no established, formal framework through which one can reason about contracts as they undergo upgrades, though much work has been done to verify standalone smart contracts. Instead, one must repeat the full verification process for each contract upgrade, something which relies heavily on fallible intuition, can lead to unexpected vulnerabilities, and drives up the cost of formally verifying smart contracts. We propose a formal framework for contract upgrades in ConCert, a Coq-based smart contract verification tool. Central to this framework is our notion of a contract morphism, a theoretical tool which we introduce to formally encode structural relationships between smart contracts, and with which we can formally specify and verify an upgraded contract relative to its previous versions. We argue that ours is a natural framework for specifying and verifying contract upgrades, and hope to offer a first step towards rigorous, efficient specification and verification of contract upgrades.
Cite as

Derek Sorensen. Towards Formally Specifying and Verifying Smart Contract Upgrades in Coq. In 5th International Workshop on Formal Methods for Blockchains (FMBC 2024). Open Access Series in Informatics (OASIcs), Volume 118, pp. 7:1-7:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{sorensen:OASIcs.FMBC.2024.7,
  author =	{Sorensen, Derek},
  title =	{{Towards Formally Specifying and Verifying Smart Contract Upgrades in Coq}},
  booktitle =	{5th International Workshop on Formal Methods for Blockchains (FMBC 2024)},
  pages =	{7:1--7:14},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-317-1},
  ISSN =	{2190-6807},
  year =	{2024},
  volume =	{118},
  editor =	{Bernardo, Bruno and Marmsoler, Diego},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.FMBC.2024.7},
  URN =		{urn:nbn:de:0030-drops-198728},
  doi =		{10.4230/OASIcs.FMBC.2024.7},
  annote =	{Keywords: smart contract verification, formal methods, interactive theorem prover, smart contract upgrades}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2022.10
Accumulation Analysis

Authors: Martin Kellogg, Narges Shadab, Manu Sridharan, and Michael D. Ernst

Published in: LIPIcs, Volume 222, 36th European Conference on Object-Oriented Programming (ECOOP 2022)

Abstract
A typestate specification indicates which behaviors of an object are permitted in each of the object’s states. In the general case, soundly checking a typestate specification requires precise information about aliasing (i.e., an alias or pointer analysis), which is computationally expensive. This requirement has hindered the adoption of sound typestate analyses in practice. This paper identifies accumulation typestate specifications, which are the subset of typestate specifications that can be soundly checked without any information about aliasing. An accumulation typestate specification can be checked instead by an accumulation analysis: a simple, fast dataflow analysis that conservatively approximates the operations that have been performed on an object. This paper formalizes the notions of accumulation analysis and accumulation typestate specification. It proves that accumulation typestate specifications are exactly those typestate specifications that can be checked soundly without aliasing information. Further, 41% of the typestate specifications that appear in the research literature are accumulation typestate specifications.
Cite as

Martin Kellogg, Narges Shadab, Manu Sridharan, and Michael D. Ernst. Accumulation Analysis. In 36th European Conference on Object-Oriented Programming (ECOOP 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 222, pp. 10:1-10:30, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{kellogg_et_al:LIPIcs.ECOOP.2022.10,
  author =	{Kellogg, Martin and Shadab, Narges and Sridharan, Manu and Ernst, Michael D.},
  title =	{{Accumulation Analysis}},
  booktitle =	{36th European Conference on Object-Oriented Programming (ECOOP 2022)},
  pages =	{10:1--10:30},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-225-9},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{222},
  editor =	{Ali, Karim and Vitek, Jan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2022.10},
  URN =		{urn:nbn:de:0030-drops-162381},
  doi =		{10.4230/LIPIcs.ECOOP.2022.10},
  annote =	{Keywords: Typestate, finite-state property}
}
Document
Artifact
DOI: 10.4230/DARTS.8.2.22
Accumulation Analysis (Artifact)

Authors: Martin Kellogg, Narges Shadab, Manu Sridharan, and Michael D. Ernst

Published in: DARTS, Volume 8, Issue 2, Special Issue of the 36th European Conference on Object-Oriented Programming (ECOOP 2022)

Abstract
This artifact contains the data and analysis supporting the literature survey in section 4 of [Kellogg et al., 2022]. In our literature survey, we examined 187 papers from the literature that mention "typestate" and analyzed the typestate specifications they contained to determine whether or not they are accumulation typestate specifications. Our purpose in doing this literature survey was to determine whether typestate FSMs were accumulation or not. However, we believe that the collection of typestate automata in typestates.pdf might be useful to anyone interested in the sort of typestate automata that appear in the literature. If we had had access to such a collection (gathered for a different purpose), our classification of whether these typestate automata were accumulation would have been much simpler. Anyone interested in properties of typestate automata can re-use our work.
Cite as

Martin Kellogg, Narges Shadab, Manu Sridharan, and Michael D. Ernst. Accumulation Analysis (Artifact). In Special Issue of the 36th European Conference on Object-Oriented Programming (ECOOP 2022). Dagstuhl Artifacts Series (DARTS), Volume 8, Issue 2, pp. 22:1-22:3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@Article{kellogg_et_al:DARTS.8.2.22,
  author =	{Kellogg, Martin and Shadab, Narges and Sridharan, Manu and Ernst, Michael D.},
  title =	{{Accumulation Analysis (Artifact)}},
  pages =	{22:1--22:3},
  journal =	{Dagstuhl Artifacts Series},
  ISSN =	{2509-8195},
  year =	{2022},
  volume =	{8},
  number =	{2},
  editor =	{Kellogg, Martin and Shadab, Narges and Sridharan, Manu and Ernst, Michael D.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DARTS.8.2.22},
  URN =		{urn:nbn:de:0030-drops-162209},
  doi =		{10.4230/DARTS.8.2.22},
  annote =	{Keywords: Typestate, finite-state property}
}
Document
DOI: 10.4230/LIPIcs.SNAPL.2017.4
Natural Language is a Programming Language: Applying Natural Language Processing to Software Development

Authors: Michael D. Ernst

Published in: LIPIcs, Volume 71, 2nd Summit on Advances in Programming Languages (SNAPL 2017)

Abstract
A powerful, but limited, way to view software is as source code alone. Treating a program as a sequence of instructions enables it to be formalized and makes it amenable to mathematical techniques such as abstract interpretation and model checking. A program consists of much more than a sequence of instructions. Developers make use of test cases, documentation, variable names, program structure, the version control repository, and more. I argue that it is time to take the blinders off of software analysis tools: tools should use all these artifacts to deduce more powerful and useful information about the program. Researchers are beginning to make progress towards this vision. This paper gives, as examples, four results that find bugs and generate code by applying natural language processing techniques to software artifacts. The four techniques use as input error messages, variable names, procedure documentation, and user questions. They use four different NLP techniques: document similarity, word semantics, parse trees, and neural networks. The initial results suggest that this is a promising avenue for future work.
Cite as

Michael D. Ernst. Natural Language is a Programming Language: Applying Natural Language Processing to Software Development. In 2nd Summit on Advances in Programming Languages (SNAPL 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 71, pp. 4:1-4:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{ernst:LIPIcs.SNAPL.2017.4,
  author =	{Ernst, Michael D.},
  title =	{{Natural Language is a Programming Language: Applying Natural Language Processing to Software Development}},
  booktitle =	{2nd Summit on Advances in Programming Languages (SNAPL 2017)},
  pages =	{4:1--4:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-032-3},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{71},
  editor =	{Lerner, Benjamin S. and Bod{\'\i}k, Rastislav and Krishnamurthi, Shriram},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SNAPL.2017.4},
  URN =		{urn:nbn:de:0030-drops-71357},
  doi =		{10.4230/LIPIcs.SNAPL.2017.4},
  annote =	{Keywords: natural language processing, program analysis, software development}
}
Document
DOI: 10.4230/LIPIcs.SNAPL.2015.103
Toward a Dependability Case Language and Workflow for a Radiation Therapy System

Authors: Michael D. Ernst, Dan Grossman, Jon Jacky, Calvin Loncaric, Stuart Pernsteiner, Zachary Tatlock, Emina Torlak, and Xi Wang

Published in: LIPIcs, Volume 32, 1st Summit on Advances in Programming Languages (SNAPL 2015)

Abstract
We present a near-future research agenda for bringing a suite of modern programming-languages verification tools - specifically interactive theorem proving, solver-aided languages, and formally defined domain-specific languages - to the development of a specific safety-critical system, a radiotherapy medical device. We sketch how we believe recent programming-languages research advances can merge with existing best practices for safety-critical systems to increase system assurance and developer productivity. We motivate hypotheses central to our agenda: That we should start with a single specific system and that we need to integrate a variety of complementary verification and synthesis tools into system development.
Cite as

Michael D. Ernst, Dan Grossman, Jon Jacky, Calvin Loncaric, Stuart Pernsteiner, Zachary Tatlock, Emina Torlak, and Xi Wang. Toward a Dependability Case Language and Workflow for a Radiation Therapy System. In 1st Summit on Advances in Programming Languages (SNAPL 2015). Leibniz International Proceedings in Informatics (LIPIcs), Volume 32, pp. 103-112, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2015)

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@InProceedings{ernst_et_al:LIPIcs.SNAPL.2015.103,
  author =	{Ernst, Michael D. and Grossman, Dan and Jacky, Jon and Loncaric, Calvin and Pernsteiner, Stuart and Tatlock, Zachary and Torlak, Emina and Wang, Xi},
  title =	{{Toward a Dependability Case Language and Workflow for a Radiation Therapy System}},
  booktitle =	{1st Summit on Advances in Programming Languages (SNAPL 2015)},
  pages =	{103--112},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-80-4},
  ISSN =	{1868-8969},
  year =	{2015},
  volume =	{32},
  editor =	{Ball, Thomas and Bodík, Rastislav and Krishnamurthi, Shriram and Lerner, Benjamin S. and Morriset, Greg},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SNAPL.2015.103},
  URN =		{urn:nbn:de:0030-drops-50208},
  doi =		{10.4230/LIPIcs.SNAPL.2015.103},
  annote =	{Keywords: Synthesis, Proof Assistants, Verification, Dependability Cases, Domain Specific Languages, Radiation Therapy}
}
Document
DOI: 10.4230/LIPIcs.STACS.2015.197
Arc Diagrams, Flip Distances, and Hamiltonian Triangulations

Authors: Jean Cardinal, Michael Hoffmann, Vincent Kusters, Csaba D. Tóth, and Manuel Wettstein

Published in: LIPIcs, Volume 30, 32nd International Symposium on Theoretical Aspects of Computer Science (STACS 2015)

Abstract
We show that every triangulation (maximal planar graph) on n\ge 6 vertices can be flipped into a Hamiltonian triangulation using a sequence of less than n/2 combinatorial edge flips. The previously best upper bound uses 4-connectivity as a means to establish Hamiltonicity. But in general about 3n/5 flips are necessary to reach a 4-connected triangulation. Our result improves the upper bound on the diameter of the flip graph of combinatorial triangulations on n vertices from 5.2n-33.6 to 5n-23. We also show that for every triangulation on n vertices there is a simultaneous flip of less than 2n/3 edges to a 4-connected triangulation. The bound on the number of edges is tight, up to an additive constant. As another application we show that every planar graph on n vertices admits an arc diagram with less than n/2 biarcs, that is, after subdividing less than n/2 (of potentially 3n-6) edges the resulting graph admits a 2-page book embedding.
Cite as

Jean Cardinal, Michael Hoffmann, Vincent Kusters, Csaba D. Tóth, and Manuel Wettstein. Arc Diagrams, Flip Distances, and Hamiltonian Triangulations. In 32nd International Symposium on Theoretical Aspects of Computer Science (STACS 2015). Leibniz International Proceedings in Informatics (LIPIcs), Volume 30, pp. 197-210, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2015)

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@InProceedings{cardinal_et_al:LIPIcs.STACS.2015.197,
  author =	{Cardinal, Jean and Hoffmann, Michael and Kusters, Vincent and T\'{o}th, Csaba D. and Wettstein, Manuel},
  title =	{{Arc Diagrams, Flip Distances, and Hamiltonian Triangulations}},
  booktitle =	{32nd International Symposium on Theoretical Aspects of Computer Science (STACS 2015)},
  pages =	{197--210},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-78-1},
  ISSN =	{1868-8969},
  year =	{2015},
  volume =	{30},
  editor =	{Mayr, Ernst W. and Ollinger, Nicolas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2015.197},
  URN =		{urn:nbn:de:0030-drops-49141},
  doi =		{10.4230/LIPIcs.STACS.2015.197},
  annote =	{Keywords: graph embeddings, edge flips, flip graph, separating triangles}
}
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