2 Search Results for "Chen, Brian Y."


Document
A Graphical User Interface Framework for Formal Verification

Authors: Edward W. Ayers, Mateja Jamnik, and W. T. Gowers

Published in: LIPIcs, Volume 193, 12th International Conference on Interactive Theorem Proving (ITP 2021)


Abstract
We present the "ProofWidgets" framework for implementing general user interfaces (UIs) within an interactive theorem prover. The framework uses web technology and functional reactive programming, as well as metaprogramming features of advanced interactive theorem proving (ITP) systems to allow users to create arbitrary interactive UIs for representing the goal state. Users of the framework can create GUIs declaratively within the ITP’s metaprogramming language, without having to develop in multiple languages and without coordinated changes across multiple projects, which improves development time for new designs of UI. The ProofWidgets framework also allows UIs to make use of the full context of the theorem prover and the specialised libraries that ITPs offer, such as methods for dealing with expressions and tactics. The framework includes an extensible structured pretty-printing engine that enables advanced interaction with expressions such as interactive term rewriting. We exemplify the framework with an implementation for the https://leanprover-community.github.io. The framework is already in use by hundreds of contributors to the Lean mathematical library.

Cite as

Edward W. Ayers, Mateja Jamnik, and W. T. Gowers. A Graphical User Interface Framework for Formal Verification. In 12th International Conference on Interactive Theorem Proving (ITP 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 193, pp. 4:1-4:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)


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@InProceedings{ayers_et_al:LIPIcs.ITP.2021.4,
  author =	{Ayers, Edward W. and Jamnik, Mateja and Gowers, W. T.},
  title =	{{A Graphical User Interface Framework for Formal Verification}},
  booktitle =	{12th International Conference on Interactive Theorem Proving (ITP 2021)},
  pages =	{4:1--4:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-188-7},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{193},
  editor =	{Cohen, Liron and Kaliszyk, Cezary},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ITP.2021.4},
  URN =		{urn:nbn:de:0030-drops-138996},
  doi =		{10.4230/LIPIcs.ITP.2021.4},
  annote =	{Keywords: User Interfaces, ITP}
}
Document
pClay: A Precise Parallel Algorithm for Comparing Molecular Surfaces

Authors: Georgi D. Georgiev, Kevin F. Dodd, and Brian Y. Chen

Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)


Abstract
Comparing binding sites as geometric solids can reveal conserved features of protein structure that bind similar molecular fragments and varying features that select different partners. Due to the subtlety of these features, algorithmic efficiency and geometric precision are essential for comparison accuracy. For these reasons, this paper presents pClay, the first structure comparison algorithm to employ fine-grained parallelism to enhance both throughput and efficiency. We evaluated the parallel performance of pClay on both multicore workstation CPUs and a 61-core Xeon Phi, observing scaleable speedup in many thread configurations. Parallelism unlocked levels of precision that were not practical with existing methods. This precision has important applications, which we demonstrate: A statistical model of steric variations in binding cavities, trained with data at the level of precision typical of existing work, can overlook 46% of authentic steric influences on specificity (p <= .02). The same model, trained with more precise data from pClay, overlooked 0% using the same standard of statistical significance. These results demonstrate how enhanced efficiency and precision can advance the detection of binding mechanisms that influence specificity.

Cite as

Georgi D. Georgiev, Kevin F. Dodd, and Brian Y. Chen. pClay: A Precise Parallel Algorithm for Comparing Molecular Surfaces. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 6:1-6:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


Copy BibTex To Clipboard

@InProceedings{georgiev_et_al:LIPIcs.WABI.2019.6,
  author =	{Georgiev, Georgi D. and Dodd, Kevin F. and Chen, Brian Y.},
  title =	{{pClay: A Precise Parallel Algorithm for Comparing Molecular Surfaces}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{6:1--6:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-123-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{143},
  editor =	{Huber, Katharina T. and Gusfield, Dan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.6},
  URN =		{urn:nbn:de:0030-drops-110365},
  doi =		{10.4230/LIPIcs.WABI.2019.6},
  annote =	{Keywords: Specificity Annotation, Structure Comparison, Cavity Analysis}
}
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