5 Search Results for "De-Los-Santos, Alicia"


Document
Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem

Authors: Yutong Qiu, Cong Ma, Han Xie, and Carl Kingsford

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


Abstract
Transcriptomic structural variants (TSVs) - large-scale transcriptome sequence change due to structural variation - are common, especially in cancer. Detecting TSVs is a challenging computational problem. Sample heterogeneity (including differences between alleles in diploid organisms) is a critical confounding factor when identifying TSVs. To improve TSV detection in heterogeneous RNA-seq samples, we introduce the Multiple Compatible Arrangement Problem (MCAP), which seeks k genome rearrangements to maximize the number of reads that are concordant with at least one rearrangement. This directly models the situation of a heterogeneous or diploid sample. We prove that MCAP is NP-hard and provide a 1/4-approximation algorithm for k=1 and a 3/4-approximation algorithm for the diploid case (k=2) assuming an oracle for k=1. Combining these, we obtain a 3/16-approximation algorithm for MCAP when k=2 (without an oracle). We also present an integer linear programming formulation for general k. We characterize the graph structures that require k>1 to satisfy all edges and show such structures are prevalent in cancer samples. We evaluate our algorithms on 381 TCGA samples and 2 cancer cell lines and show improved performance compared to the state-of-the-art TSV-calling tool, SQUID.

Cite as

Yutong Qiu, Cong Ma, Han Xie, and Carl Kingsford. Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 18:1-18:5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{qiu_et_al:LIPIcs.WABI.2019.18,
  author =	{Qiu, Yutong and Ma, Cong and Xie, Han and Kingsford, Carl},
  title =	{{Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{18:1--18:5},
  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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.18},
  URN =		{urn:nbn:de:0030-drops-110483},
  doi =		{10.4230/LIPIcs.WABI.2019.18},
  annote =	{Keywords: transcriptomic structural variation, integer linear programming, heterogeneity}
}
Document
Alignment- and Reference-Free Phylogenomics with Colored de Bruijn Graphs

Authors: Roland Wittler

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


Abstract
We present a new whole-genome based approach to infer large-scale phylogenies that is alignment- and reference-free. In contrast to other methods, it does not rely on pairwise comparisons to determine distances to infer edges in a tree. Instead, a colored de Bruijn graph is constructed, and information on common subsequences is extracted to infer phylogenetic splits. Application to different datasets confirms robustness of the approach. A comparison to other state-of-the-art whole-genome based methods indicates comparable or higher accuracy and efficiency.

Cite as

Roland Wittler. Alignment- and Reference-Free Phylogenomics with Colored de Bruijn Graphs. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 2:1-2:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{wittler:LIPIcs.WABI.2019.2,
  author =	{Wittler, Roland},
  title =	{{Alignment- and Reference-Free Phylogenomics with Colored de Bruijn Graphs}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{2:1--2:14},
  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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.2},
  URN =		{urn:nbn:de:0030-drops-110325},
  doi =		{10.4230/LIPIcs.WABI.2019.2},
  annote =	{Keywords: Phylogenomics, phylogenetics, phylogenetic splits, colored de Bruijn graphs}
}
Document
Tracking the Flow of Ideas through the Programming Languages Literature

Authors: Michael Greenberg, Kathleen Fisher, and David Walker

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


Abstract
How have conferences like ICFP, OOPSLA, PLDI, and POPL evolved over the last 20 years? Did generalizing the Call for Papers for OOPSLA in 2007 or changing the name of the umbrella conference to SPLASH in 2010 have any effect on the kinds of papers published there? How do POPL and PLDI papers compare, topic-wise? Is there related work that I am missing? Have the ideas in O'Hearn's classic paper on separation logic shifted the kinds of papers that appear in POPL? Does a proposed program committee cover the range of submissions expected for the conference? If we had better tools for analyzing the programming language literature, we might be able to answer these questions and others like them in a data-driven way. In this paper, we explore how topic modeling, a branch of machine learning, might help the programming language community better understand our literature.

Cite as

Michael Greenberg, Kathleen Fisher, and David Walker. Tracking the Flow of Ideas through the Programming Languages Literature. In 1st Summit on Advances in Programming Languages (SNAPL 2015). Leibniz International Proceedings in Informatics (LIPIcs), Volume 32, pp. 140-155, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2015)


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@InProceedings{greenberg_et_al:LIPIcs.SNAPL.2015.140,
  author =	{Greenberg, Michael and Fisher, Kathleen and Walker, David},
  title =	{{Tracking the Flow of Ideas through the Programming Languages Literature}},
  booktitle =	{1st Summit on Advances in Programming Languages (SNAPL 2015)},
  pages =	{140--155},
  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.2015.140},
  URN =		{urn:nbn:de:0030-drops-50232},
  doi =		{10.4230/LIPIcs.SNAPL.2015.140},
  annote =	{Keywords: programming languages literature, topic models, irony}
}
Document
Simultaneous frequency and capacity setting for rapid transit systems with a competing mode and capacity constraints

Authors: Alicia De-Los-Santos, Gilbert Laporte, Juan A. Mesa, and Federico Perea

Published in: OASIcs, Volume 42, 14th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (2014)


Abstract
The railway planning problem consists of several consecutive phases: network design, line planning, timetabling, personnel assignment and rolling stocks planning. In this paper we will focus on the line planning process. Traditionally, the line planning problem consists of determining a set of lines and their frequencies optimizing a certain objective. In this work we will focus on the line planning problem context taking into account aspects related to rolling stock and crew operating costs. We assume that the number of possible vehicles is limited, that is, the problem that we are considering is a capacitated problem and the line network can be a crowding network. The main novelty in this paper is the consideration of the size of vehicles and frequencies as variables as well as the inclusion of a congestion function measuring the level of in-vehicle crowding. Concretely, we present the problem and an algorithm to solve it, which are tested via a computational experience.

Cite as

Alicia De-Los-Santos, Gilbert Laporte, Juan A. Mesa, and Federico Perea. Simultaneous frequency and capacity setting for rapid transit systems with a competing mode and capacity constraints. In 14th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems. Open Access Series in Informatics (OASIcs), Volume 42, pp. 107-121, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2014)


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@InProceedings{delossantos_et_al:OASIcs.ATMOS.2014.107,
  author =	{De-Los-Santos, Alicia and Laporte, Gilbert and Mesa, Juan A. and Perea, Federico},
  title =	{{Simultaneous frequency and capacity setting for rapid transit systems with a competing mode and capacity constraints}},
  booktitle =	{14th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems},
  pages =	{107--121},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-75-0},
  ISSN =	{2190-6807},
  year =	{2014},
  volume =	{42},
  editor =	{Funke, Stefan and Mihal\'{a}k, Mat\'{u}s},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.ATMOS.2014.107},
  URN =		{urn:nbn:de:0030-drops-47563},
  doi =		{10.4230/OASIcs.ATMOS.2014.107},
  annote =	{Keywords: Line planning, railway, capacity, frequency, congestion}
}
Document
The additional difficulties for the automatic synthesis of specifications posed by logic features in functional-logic languages

Authors: Giovanni Bacci, Marco Comini, Marco A. Feliú, and Alicia Villanueva

Published in: LIPIcs, Volume 17, Technical Communications of the 28th International Conference on Logic Programming (ICLP'12) (2012)


Abstract
This paper discusses on the additional issues for the automatic inference of algebraic property-oriented specifications which arises because of interaction between laziness and logical variables in lazy functional logic languages. We present an inference technique that overcomes these issues for the first-order fragment of the lazy functional logic language Curry. Our technique statically infers from the source code of a Curry program a specification which consists of a set of equations relating (nested) operation calls that have the same behavior. Our proposal is a (glass-box) semantics-based inference method which can guarantee, to some extent, the correctness of the inferred specification, differently from other (black-box) approaches based on testing techniques.

Cite as

Giovanni Bacci, Marco Comini, Marco A. Feliú, and Alicia Villanueva. The additional difficulties for the automatic synthesis of specifications posed by logic features in functional-logic languages. In Technical Communications of the 28th International Conference on Logic Programming (ICLP'12). Leibniz International Proceedings in Informatics (LIPIcs), Volume 17, pp. 144-153, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2012)


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@InProceedings{bacci_et_al:LIPIcs.ICLP.2012.144,
  author =	{Bacci, Giovanni and Comini, Marco and A. Feli\'{u}, Marco and Villanueva, Alicia},
  title =	{{The additional difficulties for the automatic synthesis of specifications posed by logic features in functional-logic languages}},
  booktitle =	{Technical Communications of the 28th International Conference on Logic Programming (ICLP'12)},
  pages =	{144--153},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-43-9},
  ISSN =	{1868-8969},
  year =	{2012},
  volume =	{17},
  editor =	{Dovier, Agostino and Santos Costa, V{\'\i}tor},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICLP.2012.144},
  URN =		{urn:nbn:de:0030-drops-36174},
  doi =		{10.4230/LIPIcs.ICLP.2012.144},
  annote =	{Keywords: Curry, property-oriented specifications, semantics-based inference methods}
}
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