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Documents authored by Lin, Yu

Found 6 Possible Name Variants:

Lin, Yu

Document
DOI: 10.4230/LIPIcs.WABI.2021.11
LRBinner: Binning Long Reads in Metagenomics Datasets

Authors: Anuradha Wickramarachchi and Yu Lin

Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)

Abstract
Advancements in metagenomics sequencing allow the study of microbial communities directly from their environments. Metagenomics binning is a key step in the species characterisation of microbial communities. Next-generation sequencing reads are usually assembled into contigs for metagenomics binning mainly due to the limited information within short reads. Third-generation sequencing provides much longer reads that have lengths similar to the contigs assembled from short reads. However, existing contig-binning tools cannot be directly applied on long reads due to the absence of coverage information and the presence of high error rates. The few existing long-read binning tools either use only composition or use composition and coverage information separately. This may ignore bins that correspond to low-abundance species or erroneously split bins that correspond to species with non-uniform coverages. Here we present a reference-free binning approach, LRBinner, that combines composition and coverage information of complete long-read datasets. LRBinner also uses a distance-histogram-based clustering algorithm to extract clusters with varying sizes. The experimental results on both simulated and real datasets show that LRBinner achieves the best binning accuracy against the baselines. Moreover, we show that binning reads using LRBinner prior to assembly reduces computational resources for assembly while attaining satisfactory assembly qualities.
Cite as

Anuradha Wickramarachchi and Yu Lin. LRBinner: Binning Long Reads in Metagenomics Datasets. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 11:1-11:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{wickramarachchi_et_al:LIPIcs.WABI.2021.11,
  author =	{Wickramarachchi, Anuradha and Lin, Yu},
  title =	{{LRBinner: Binning Long Reads in Metagenomics Datasets}},
  booktitle =	{21st International Workshop on Algorithms in Bioinformatics (WABI 2021)},
  pages =	{11:1--11:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-200-6},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{201},
  editor =	{Carbone, Alessandra and El-Kebir, Mohammed},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.11},
  URN =		{urn:nbn:de:0030-drops-143644},
  doi =		{10.4230/LIPIcs.WABI.2021.11},
  annote =	{Keywords: Metagenomics binning, long reads, machine learning, clustering}
}
Document
DOI: 10.4230/LIPIcs.WABI.2020.8
GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs

Authors: Vijini G. Mallawaarachchi, Anuradha S. Wickramarachchi, and Yu Lin

Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)

Abstract
Metagenomic sequencing allows us to study structure, diversity and ecology in microbial communities without the necessity of obtaining pure cultures. In many metagenomics studies, the reads obtained from metagenomics sequencing are first assembled into longer contigs and these contigs are then binned into clusters of contigs where contigs in a cluster are expected to come from the same species. As different species may share common sequences in their genomes, one assembled contig may belong to multiple species. However, existing tools for contig binning only support non-overlapped binning, i.e., each contig is assigned to at most one bin (species). In this paper, we introduce GraphBin2 which refines the binning results obtained from existing tools and, more importantly, is able to assign contigs to multiple bins. GraphBin2 uses the connectivity and coverage information from assembly graphs to adjust existing binning results on contigs and to infer contigs shared by multiple species. Experimental results on both simulated and real datasets demonstrate that GraphBin2 not only improves binning results of existing tools but also supports to assign contigs to multiple bins.
Cite as

Vijini G. Mallawaarachchi, Anuradha S. Wickramarachchi, and Yu Lin. GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 8:1-8:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{mallawaarachchi_et_al:LIPIcs.WABI.2020.8,
  author =	{Mallawaarachchi, Vijini G. and Wickramarachchi, Anuradha S. and Lin, Yu},
  title =	{{GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs}},
  booktitle =	{20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
  pages =	{8:1--8:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-161-0},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{172},
  editor =	{Kingsford, Carl and Pisanti, Nadia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.8},
  URN =		{urn:nbn:de:0030-drops-127974},
  doi =		{10.4230/LIPIcs.WABI.2020.8},
  annote =	{Keywords: Metagenomics binning, contigs, assembly graphs, overlapped binning}
}

Lin, Yunfeng

Document
DOI: 10.4230/DagSemProc.05142.3
An Architecture for Tetherless Communication

Authors: Aaditeshwar Seth, Patrick Darragh, Suihong Liang, Yunfeng Lin, and Srinivasan Keshav

Published in: Dagstuhl Seminar Proceedings, Volume 5142, Disruption Tolerant Networking (2005)

Abstract
In the emerging paradigm of tetherless computing, client applications running on small, inexpensive, and smart mobile devices maintain opportunistic wireless connectivity with back-end services running on centralized computers, enabling novel classes of applications. These applications require a communications infrastrastructure that is mobility-aware, disconnection-resilient and provides support for an opportunistic style of communiction. It should even be able to function across network partitions that may arise when end-to-end communication is not possible. We outline, design, and evaluate the implementation of an architecture that provides this functionality. we shot that it is possible for next-generation mobile devices to obtain up to 80-fold improvement over conventional mechanisms by exploiting opportunistic WiFi links, and that this benefit can be delivered as an overlay that is compatible with the current Internet.
Cite as

Aaditeshwar Seth, Patrick Darragh, Suihong Liang, Yunfeng Lin, and Srinivasan Keshav. An Architecture for Tetherless Communication. In Disruption Tolerant Networking. Dagstuhl Seminar Proceedings, Volume 5142, pp. 1-13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2005)

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@InProceedings{seth_et_al:DagSemProc.05142.3,
  author =	{Seth, Aaditeshwar and Darragh, Patrick and Liang, Suihong and Lin, Yunfeng and Keshav, Srinivasan},
  title =	{{An Architecture for Tetherless Communication}},
  booktitle =	{Disruption Tolerant Networking},
  pages =	{1--13},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2005},
  volume =	{5142},
  editor =	{Marcus Brunner and Lars Eggert and Kevin Fall and J\"{o}rg Ott and Lars Wolf},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05142.3},
  URN =		{urn:nbn:de:0030-drops-3519},
  doi =		{10.4230/DagSemProc.05142.3},
  annote =	{Keywords: Delay tolerant networks, Opportunistic communication, Tetherless computing, Wireless, Mobile}
}

Lin, Cedric Yen-Yu

Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2019.27
Quantum SDP Solvers: Large Speed-Ups, Optimality, and Applications to Quantum Learning

Authors: Fernando G. S. L. Brandão, Amir Kalev, Tongyang Li, Cedric Yen-Yu Lin, Krysta M. Svore, and Xiaodi Wu

Published in: LIPIcs, Volume 132, 46th International Colloquium on Automata, Languages, and Programming (ICALP 2019)

Abstract
We give two new quantum algorithms for solving semidefinite programs (SDPs) providing quantum speed-ups. We consider SDP instances with m constraint matrices, each of dimension n, rank at most r, and sparsity s. The first algorithm assumes an input model where one is given access to an oracle to the entries of the matrices at unit cost. We show that it has run time O~(s^2 (sqrt{m} epsilon^{-10} + sqrt{n} epsilon^{-12})), with epsilon the error of the solution. This gives an optimal dependence in terms of m, n and quadratic improvement over previous quantum algorithms (when m ~~ n). The second algorithm assumes a fully quantum input model in which the input matrices are given as quantum states. We show that its run time is O~(sqrt{m}+poly(r))*poly(log m,log n,B,epsilon^{-1}), with B an upper bound on the trace-norm of all input matrices. In particular the complexity depends only polylogarithmically in n and polynomially in r. We apply the second SDP solver to learn a good description of a quantum state with respect to a set of measurements: Given m measurements and a supply of copies of an unknown state rho with rank at most r, we show we can find in time sqrt{m}*poly(log m,log n,r,epsilon^{-1}) a description of the state as a quantum circuit preparing a density matrix which has the same expectation values as rho on the m measurements, up to error epsilon. The density matrix obtained is an approximation to the maximum entropy state consistent with the measurement data considered in Jaynes' principle from statistical mechanics. As in previous work, we obtain our algorithm by "quantizing" classical SDP solvers based on the matrix multiplicative weight update method. One of our main technical contributions is a quantum Gibbs state sampler for low-rank Hamiltonians, given quantum states encoding these Hamiltonians, with a poly-logarithmic dependence on its dimension, which is based on ideas developed in quantum principal component analysis. We also develop a "fast" quantum OR lemma with a quadratic improvement in gate complexity over the construction of Harrow et al. [Harrow et al., 2017]. We believe both techniques might be of independent interest.
Cite as

Fernando G. S. L. Brandão, Amir Kalev, Tongyang Li, Cedric Yen-Yu Lin, Krysta M. Svore, and Xiaodi Wu. Quantum SDP Solvers: Large Speed-Ups, Optimality, and Applications to Quantum Learning. In 46th International Colloquium on Automata, Languages, and Programming (ICALP 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 132, pp. 27:1-27:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{brandao_et_al:LIPIcs.ICALP.2019.27,
  author =	{Brand\~{a}o, Fernando G. S. L. and Kalev, Amir and Li, Tongyang and Lin, Cedric Yen-Yu and Svore, Krysta M. and Wu, Xiaodi},
  title =	{{Quantum SDP Solvers: Large Speed-Ups, Optimality, and Applications to Quantum Learning}},
  booktitle =	{46th International Colloquium on Automata, Languages, and Programming (ICALP 2019)},
  pages =	{27:1--27:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-109-2},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{132},
  editor =	{Baier, Christel and Chatzigiannakis, Ioannis and Flocchini, Paola and Leonardi, Stefano},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2019.27},
  URN =		{urn:nbn:de:0030-drops-106036},
  doi =		{10.4230/LIPIcs.ICALP.2019.27},
  annote =	{Keywords: quantum algorithms, semidefinite program, convex optimization}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2018.4
A Complete Characterization of Unitary Quantum Space

Authors: Bill Fefferman and Cedric Yen-Yu Lin

Published in: LIPIcs, Volume 94, 9th Innovations in Theoretical Computer Science Conference (ITCS 2018)

Abstract
Motivated by understanding the power of quantum computation with restricted number of qubits, we give two complete characterizations of unitary quantum space bounded computation. First we show that approximating an element of the inverse of a well-conditioned efficiently encoded 2^k(n) x 2^k(n) matrix is complete for the class of problems solvable by quantum circuits acting on O(k(n)) qubits with all measurements at the end of the computation. Similarly, estimating the minimum eigenvalue of an efficiently encoded Hermitian 2^k(n) x 2^k(n) matrix is also complete for this class. In the logspace case, our results improve on previous results of Ta-Shma by giving new space-efficient quantum algorithms that avoid intermediate measurements, as well as showing matching hardness results. Additionally, as a consequence we show that preciseQMA, the version of QMA with exponentially small completeness-soundess gap, is equal to PSPACE. Thus, the problem of estimating the minimum eigenvalue of a local Hamiltonian to inverse exponential precision is PSPACE-complete, which we show holds even in the frustration-free case. Finally, we can use this characterization to give a provable setting in which the ability to prepare the ground state of a local Hamiltonian is more powerful than the ability to prepare PEPS states. Interestingly, by suitably changing the parameterization of either of these problems we can completely characterize the power of quantum computation with simultaneously bounded time and space.
Cite as

Bill Fefferman and Cedric Yen-Yu Lin. A Complete Characterization of Unitary Quantum Space. In 9th Innovations in Theoretical Computer Science Conference (ITCS 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 94, pp. 4:1-4:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{fefferman_et_al:LIPIcs.ITCS.2018.4,
  author =	{Fefferman, Bill and Lin, Cedric Yen-Yu},
  title =	{{A Complete Characterization of Unitary Quantum Space}},
  booktitle =	{9th Innovations in Theoretical Computer Science Conference (ITCS 2018)},
  pages =	{4:1--4:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-060-6},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{94},
  editor =	{Karlin, Anna R.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2018.4},
  URN =		{urn:nbn:de:0030-drops-83242},
  doi =		{10.4230/LIPIcs.ITCS.2018.4},
  annote =	{Keywords: Quantum complexity, space complexity, complete problems, QMA}
}
Document
DOI: 10.4230/LIPIcs.TQC.2015.1
Oracles with Costs

Authors: Shelby Kimmel, Cedric Yen-Yu Lin, and Han-Hsuan Lin

Published in: LIPIcs, Volume 44, 10th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2015)

Abstract
While powerful tools have been developed to analyze quantum query complexity, there are still many natural problems that do not fit neatly into the black box model of oracles. We create a new model that allows multiple oracles with differing costs. This model captures more of the difficulty of certain natural problems. We test this model on a simple problem, Search with Two Oracles, for which we create a quantum algorithm that we prove is asymptotically optimal. We further give some evidence, using a geometric picture of Grover's algorithm, that our algorithm is exactly optimal.
Cite as

Shelby Kimmel, Cedric Yen-Yu Lin, and Han-Hsuan Lin. Oracles with Costs. In 10th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2015). Leibniz International Proceedings in Informatics (LIPIcs), Volume 44, pp. 1-26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2015)

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@InProceedings{kimmel_et_al:LIPIcs.TQC.2015.1,
  author =	{Kimmel, Shelby and Lin, Cedric Yen-Yu and Lin, Han-Hsuan},
  title =	{{Oracles with Costs}},
  booktitle =	{10th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2015)},
  pages =	{1--26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-96-5},
  ISSN =	{1868-8969},
  year =	{2015},
  volume =	{44},
  editor =	{Beigi, Salman and K\"{o}nig, Robert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TQC.2015.1},
  URN =		{urn:nbn:de:0030-drops-55459},
  doi =		{10.4230/LIPIcs.TQC.2015.1},
  annote =	{Keywords: Quantum Algorithms, Query Complexity, Amplitude Amplification}
}
Document
DOI: 10.4230/LIPIcs.CCC.2015.537
Upper Bounds on Quantum Query Complexity Inspired by the Elitzur-Vaidman Bomb Tester

Authors: Cedric Yen-Yu Lin and Han-Hsuan Lin

Published in: LIPIcs, Volume 33, 30th Conference on Computational Complexity (CCC 2015)

Abstract
Inspired by the Elitzur-Vaidman bomb testing problem [Elitzur/Vaidman 1993], we introduce a new query complexity model, which we call bomb query complexity B(f). We investigate its relationship with the usual quantum query complexity Q(f), and show that B(f)=Theta(Q(f)^2). This result gives a new method to upper bound the quantum query complexity: we give a method of finding bomb query algorithms from classical algorithms, which then provide nonconstructive upper bounds on Q(f)=Theta(sqrt(B(f))). We subsequently were able to give explicit quantum algorithms matching our upper bound method. We apply this method on the single-source shortest paths problem on unweighted graphs, obtaining an algorithm with O(n^(1.5)) quantum query complexity, improving the best known algorithm of O(n^(1.5) * sqrt(log(n))) [Furrow, 2008]. Applying this method to the maximum bipartite matching problem gives an O(n^(1.75)) algorithm, improving the best known trivial O(n^2) upper bound.
Cite as

Cedric Yen-Yu Lin and Han-Hsuan Lin. Upper Bounds on Quantum Query Complexity Inspired by the Elitzur-Vaidman Bomb Tester. In 30th Conference on Computational Complexity (CCC 2015). Leibniz International Proceedings in Informatics (LIPIcs), Volume 33, pp. 537-566, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2015)

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@InProceedings{lin_et_al:LIPIcs.CCC.2015.537,
  author =	{Lin, Cedric Yen-Yu and Lin, Han-Hsuan},
  title =	{{Upper Bounds on Quantum Query Complexity Inspired by the Elitzur-Vaidman Bomb Tester}},
  booktitle =	{30th Conference on Computational Complexity (CCC 2015)},
  pages =	{537--566},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-81-1},
  ISSN =	{1868-8969},
  year =	{2015},
  volume =	{33},
  editor =	{Zuckerman, David},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2015.537},
  URN =		{urn:nbn:de:0030-drops-50635},
  doi =		{10.4230/LIPIcs.CCC.2015.537},
  annote =	{Keywords: Quantum Algorithms, Query Complexity, Elitzur-Vaidman Bomb Tester, Adversary Method, Maximum Bipartite Matching}
}

Lin, Chengyu

Document
DOI: 10.4230/LIPIcs.ICALP.2017.51
Sensitivity Conjecture and Log-Rank Conjecture for Functions with Small Alternating Numbers

Authors: Chengyu Lin and Shengyu Zhang

Published in: LIPIcs, Volume 80, 44th International Colloquium on Automata, Languages, and Programming (ICALP 2017)

Abstract
The Sensitivity Conjecture and the Log-rank Conjecture are among the most important and challenging problems in concrete complexity. Incidentally, the Sensitivity Conjecture is known to hold for monotone functions, and so is the Log-rank Conjecture for f(x and y) and f(x xor y) with monotone functions f, where and and xor are bit-wise AND and XOR , respectively. In this paper, we extend these results to functions f which alternate values for a relatively small number of times on any monotone path from 0^n to 1^n. These deepen our understandings of the two conjectures, and contribute to the recent line of research on functions with small alternating numbers.
Cite as

Chengyu Lin and Shengyu Zhang. Sensitivity Conjecture and Log-Rank Conjecture for Functions with Small Alternating Numbers. In 44th International Colloquium on Automata, Languages, and Programming (ICALP 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 80, pp. 51:1-51:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{lin_et_al:LIPIcs.ICALP.2017.51,
  author =	{Lin, Chengyu and Zhang, Shengyu},
  title =	{{Sensitivity Conjecture and Log-Rank Conjecture for Functions with Small Alternating Numbers}},
  booktitle =	{44th International Colloquium on Automata, Languages, and Programming (ICALP 2017)},
  pages =	{51:1--51:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-041-5},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{80},
  editor =	{Chatzigiannakis, Ioannis and Indyk, Piotr and Kuhn, Fabian and Muscholl, Anca},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2017.51},
  URN =		{urn:nbn:de:0030-drops-74045},
  doi =		{10.4230/LIPIcs.ICALP.2017.51},
  annote =	{Keywords: Analysis of Boolean functions, Sensitivity Conjecture, Log-rank Conjecture, Alternating Number}
}

Lin, Yu-Yang

Document
DOI: 10.4230/LIPIcs.FSCD.2020.27
Symbolic Execution Game Semantics

Authors: Yu-Yang Lin and Nikos Tzevelekos

Published in: LIPIcs, Volume 167, 5th International Conference on Formal Structures for Computation and Deduction (FSCD 2020)

Abstract
We present a framework for symbolically executing and model checking higher-order programs with external (open) methods. We focus on the client-library paradigm and in particular we aim to check libraries with respect to any definable client. We combine traditional symbolic execution techniques with operational game semantics to build a symbolic execution semantics that captures arbitrary external behaviour. We prove the symbolic semantics to be sound and complete. This yields a bounded technique by imposing bounds on the depth of recursion and callbacks. We provide an implementation of our technique in the 𝕂 framework and showcase its performance on a custom benchmark based on higher-order coding errors such as reentrancy bugs.
Cite as

Yu-Yang Lin and Nikos Tzevelekos. Symbolic Execution Game Semantics. In 5th International Conference on Formal Structures for Computation and Deduction (FSCD 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 167, pp. 27:1-27:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{lin_et_al:LIPIcs.FSCD.2020.27,
  author =	{Lin, Yu-Yang and Tzevelekos, Nikos},
  title =	{{Symbolic Execution Game Semantics}},
  booktitle =	{5th International Conference on Formal Structures for Computation and Deduction (FSCD 2020)},
  pages =	{27:1--27:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-155-9},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{167},
  editor =	{Ariola, Zena M.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2020.27},
  URN =		{urn:nbn:de:0030-drops-123493},
  doi =		{10.4230/LIPIcs.FSCD.2020.27},
  annote =	{Keywords: game semantics, symbolic execution, higher-order open programs}
}

Yu, Xilin

Document
DOI: 10.4230/LIPIcs.WABI.2020.15
Advancing Divide-And-Conquer Phylogeny Estimation Using Robinson-Foulds Supertrees

Authors: Xilin Yu, Thien Le, Sarah Christensen, Erin K. Molloy, and Tandy Warnow

Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)

Abstract
One of the Grand Challenges in Science is the construction of the Tree of Life, an evolutionary tree containing several million species, spanning all life on earth. However, the construction of the Tree of Life is enormously computationally challenging, as all the current most accurate methods are either heuristics for NP-hard optimization problems or Bayesian MCMC methods that sample from tree space. One of the most promising approaches for improving scalability and accuracy for phylogeny estimation uses divide-and-conquer: a set of species is divided into overlapping subsets, trees are constructed on the subsets, and then merged together using a "supertree method". Here, we present Exact-RFS-2, the first polynomial-time algorithm to find an optimal supertree of two trees, using the Robinson-Foulds Supertree (RFS) criterion (a major approach in supertree estimation that is related to maximum likelihood supertrees), and we prove that finding the RFS of three input trees is NP-hard. We also present GreedyRFS (a greedy heuristic that operates by repeatedly using Exact-RFS-2 on pairs of trees, until all the trees are merged into a single supertree). We evaluate Exact-RFS-2 and GreedyRFS, and show that they have better accuracy than the current leading heuristic for RFS.
Cite as

Xilin Yu, Thien Le, Sarah Christensen, Erin K. Molloy, and Tandy Warnow. Advancing Divide-And-Conquer Phylogeny Estimation Using Robinson-Foulds Supertrees. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 15:1-15:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{yu_et_al:LIPIcs.WABI.2020.15,
  author =	{Yu, Xilin and Le, Thien and Christensen, Sarah and Molloy, Erin K. and Warnow, Tandy},
  title =	{{Advancing Divide-And-Conquer Phylogeny Estimation Using Robinson-Foulds Supertrees}},
  booktitle =	{20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
  pages =	{15:1--15:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-161-0},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{172},
  editor =	{Kingsford, Carl and Pisanti, Nadia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.15},
  URN =		{urn:nbn:de:0030-drops-128048},
  doi =		{10.4230/LIPIcs.WABI.2020.15},
  annote =	{Keywords: supertrees, divide-and-conquer, phylogeny estimation}
}
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