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Documents authored by Li, Yue

Found 2 Possible Name Variants:

Li, Yue

Document
DOI: 10.4230/LIPIcs.ECOOP.2016.15
Program Tailoring: Slicing by Sequential Criteria

Authors: Yue Li, Tian Tan, Yifei Zhang, and Jingling Xue

Published in: LIPIcs, Volume 56, 30th European Conference on Object-Oriented Programming (ECOOP 2016)

Abstract
Protocol and typestate analyses often report some sequences of statements ending at a program point P that needs to be scrutinized, since P may be erroneous or imprecisely analyzed. Program slicing focuses only on the behavior at P by computing a slice of the program affecting the values at P. In this paper, we propose to restrict our attention to the subset of that behavior at P affected by one or several statement sequences, called a sequential criterion (SC). By leveraging the ordering information in a SC, e.g., the temporal order in a few valid/invalid API method invocation sequences, we introduce a new technique, program tailoring, to compute a tailored program that comprises the statements in all possible execution paths passing through at least one sequence in SC in the given order. With a prototyping implementation, Tailor, we show why tailoring is practically useful by conducting two case studies on seven large real-world Java applications. For program debugging and understanding, Tailor can complement program slicing by removing SC-irrelevant statements. For program analysis, Tailor can enable a pointer analysis, which is unscalable to a program, to perform a more focused and therefore potentially scalable analysis to its specific parts containing hard language features such as reflection.
Cite as

Yue Li, Tian Tan, Yifei Zhang, and Jingling Xue. Program Tailoring: Slicing by Sequential Criteria. In 30th European Conference on Object-Oriented Programming (ECOOP 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 56, pp. 15:1-15:27, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)

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@InProceedings{li_et_al:LIPIcs.ECOOP.2016.15,
  author =	{Li, Yue and Tan, Tian and Zhang, Yifei and Xue, Jingling},
  title =	{{Program Tailoring: Slicing by Sequential Criteria}},
  booktitle =	{30th European Conference on Object-Oriented Programming (ECOOP 2016)},
  pages =	{15:1--15:27},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-014-9},
  ISSN =	{1868-8969},
  year =	{2016},
  volume =	{56},
  editor =	{Krishnamurthi, Shriram and Lerner, Benjamin S.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2016.15},
  URN =		{urn:nbn:de:0030-drops-61092},
  doi =		{10.4230/LIPIcs.ECOOP.2016.15},
  annote =	{Keywords: Program Slicing, Program Analysis, API Protocol Analysis}
}
Document
DOI: 10.4230/DARTS.2.1.8
Program Tailoring: Slicing by Sequential Criteria (Artifact)

Authors: Tian Tan, Yue Li, Yifei Zhang, and Jingling Xue

Published in: DARTS, Volume 2, Issue 1, Special Issue of the 30th European Conference on Object-Oriented Programming (ECOOP 2016)

Abstract
Protocol and typestate analyses often report some sequences of statements ending at a program point P that needs to be scrutinized, since P may be erroneous or imprecisely analyzed. Program slicing focuses only on the behavior at P by computing a slice of the program affecting the values at P. In our companion paper "Program Tailoring: Slicing by Sequential Criteria", we propose to focus on the subset of that behavior at P affected by one or several statement sequences, called a sequential criterion (SC). By leveraging the ordering information in a SC, e.g., the temporal order in a few valid/invalid API method invocation sequences, we introduce a new technique, program tailoring, to compute a tailored program that comprises the statements in all possible execution paths passing through at least one sequence in SC in the given order. This artifact is based on TAILOR, a prototyping implementation of program tailoring, to evaluate the usefulness of TAILOR in practice. The provided package is designed to support repeatability of all the experiments of our companion paper. Specifically, it allows users to reproduce the results for all the three research questions addressed in the evaluation section of our companion paper. In addition, an extensive set of extra results, which are not described in the companion paper, are also included, in order to help users better understand this work.
Cite as

Tian Tan, Yue Li, Yifei Zhang, and Jingling Xue. Program Tailoring: Slicing by Sequential Criteria (Artifact). In Special Issue of the 30th European Conference on Object-Oriented Programming (ECOOP 2016). Dagstuhl Artifacts Series (DARTS), Volume 2, Issue 1, pp. 8:1-8:3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)

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@Article{tan_et_al:DARTS.2.1.8,
  author =	{Tan, Tian and Li, Yue and Zhang, Yifei and Xue, Jingling},
  title =	{{Program Tailoring: Slicing by Sequential Criteria (Artifact)}},
  pages =	{8:1--8:3},
  journal =	{Dagstuhl Artifacts Series},
  ISSN =	{2509-8195},
  year =	{2016},
  volume =	{2},
  number =	{1},
  editor =	{Tan, Tian and Li, Yue and Zhang, Yifei and Xue, Jingling},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DARTS.2.1.8},
  URN =		{urn:nbn:de:0030-drops-61298},
  doi =		{10.4230/DARTS.2.1.8},
  annote =	{Keywords: Program Slicing, Program Analysis, API Protocol Specification}
}

Yue, William

Document
DOI: 10.4230/LIPIcs.WABI.2021.19
Efficient Haplotype Block Matching in Bi-Directional PBWT

Authors: Ardalan Naseri, William Yue, Shaojie Zhang, and Degui Zhi

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

Abstract
Efficient haplotype matching search is of great interest when large genotyped cohorts are becoming available. Positional Burrows-Wheeler Transform (PBWT) enables efficient searching for blocks of haplotype matches. However, existing efficient PBWT algorithms sweep across the haplotype panel from left to right, capturing all exact matches. As a result, PBWT does not account for mismatches. It is also not easy to investigate the patterns of changes between the matching blocks. Here, we present an extension to PBWT, called bi-directional PBWT that allows the information about the blocks of matches to be present at both sides of each site. We also present a set of algorithms to efficiently merge the matching blocks or examine the patterns of changes on both sides of each site. The time complexity of the algorithms to find and merge matching blocks using bi-directional PBWT is linear to the input size. Using real data from the UK Biobank, we demonstrate the run time and memory efficiency of our algorithms. More importantly, our algorithms can identify more blocks by enabling tolerance of mismatches. Moreover, by using mutual information (MI) between the forward and the reverse PBWT matching block sets as a measure of haplotype consistency, we found the MI derived from European samples in the 1000 Genomes Project is highly correlated (Spearman correlation r=0.87) with the deCODE recombination map.
Cite as

Ardalan Naseri, William Yue, Shaojie Zhang, and Degui Zhi. Efficient Haplotype Block Matching in Bi-Directional PBWT. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 19:1-19:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{naseri_et_al:LIPIcs.WABI.2021.19,
  author =	{Naseri, Ardalan and Yue, William and Zhang, Shaojie and Zhi, Degui},
  title =	{{Efficient Haplotype Block Matching in Bi-Directional PBWT}},
  booktitle =	{21st International Workshop on Algorithms in Bioinformatics (WABI 2021)},
  pages =	{19:1--19:13},
  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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.19},
  URN =		{urn:nbn:de:0030-drops-143729},
  doi =		{10.4230/LIPIcs.WABI.2021.19},
  annote =	{Keywords: PBWT, Bi-directional, Haplotype Matching}
}
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