3 Search Results for "Fernández-Baca, David"

Document
DOI: 10.4230/LIPIcs.WABI.2025.9
Dolphyin: A Combinatorial Algorithm for Identifying 1-Dollo Phylogenies in Cancer

Authors: Daniel W. Feng and Mohammed El-Kebir

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
Several recent cancer phylogeny inference methods have used the k-Dollo evolutionary model for single-nucleotide variants. Specifically, in this problem one is given an m × n binary matrix B and seeks a rooted tree T with m leaves that correspond to the m rows of B, and each node of T is labeled by a binary state for each of the n characters subject to the restriction that each character is gained at most once (0-to-1 transition) and subsequently lost at most k times (1-to-0 transitions). The 1-Dollo variant, also known as the persistent perfect phylogeny where one is restricted to at most k = 1 losses per character, has been studied extensively, but its hardness remains an open question. Here, we prove that the 1-Dollo Linear Phylogeny (1DLP) problem, where we additionally require the resulting 1-Dollo phylogeny T to be linear, is equivalent to verifying whether the input matrix B adheres to the Consecutive Ones Property (C1P), which can be solved in polynomial time. Due to the equivalence, several known NP-hardness results for relevant variants of C1P carry over to 1DLP, including the minimization of false negatives (0-to-1 modifications to the input matrix B) or the allowance of 2 gains and 2 losses. We furthermore show how we can recursively decompose any, not necessarily linear, 1-Dollo phylogeny T into several 1-Dollo linear phylogenies, connected by matching branching points. We extend this characterization to matrices B that admit 1-Dollo phylogenies, giving necessary and sufficient conditions for the existence of a novel decomposition of B into several submatrices and corresponding branching points. This decomposition forms the basis of Dolphyin, a new exponential-time algorithm for inferring 1-Dollo phylogenies that efficiently leverages the determination of linear 1-Dollo phylogenies as a subroutine. Dolphyin can also be applied to input matrices B with false negatives. We demonstrate that Dolphyin is runtime-competitive with a previous integer linear programming based algorithm SPhyR on simulated datasets. We additionally analyze simulated datasets with false negative errors and find that in the median case, Dolphyin infers 1-Dollo phylogenies with inferred error rates at or below the ground truth rate. Finally, we apply Dolphyin to 99 acute myeloid leukemia single-cell sequencing datasets, finding that the majority of the cancers can be explained by 1-Dollo phylogenies with false negative error rates in line with the used sequencing technology. Availability. Dolphyin is available at: https://github.com/elkebir-group/Dolphyin.
Cite as

Daniel W. Feng and Mohammed El-Kebir. Dolphyin: A Combinatorial Algorithm for Identifying 1-Dollo Phylogenies in Cancer. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 9:1-9:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{feng_et_al:LIPIcs.WABI.2025.9,
  author =	{Feng, Daniel W. and El-Kebir, Mohammed},
  title =	{{Dolphyin: A Combinatorial Algorithm for Identifying 1-Dollo Phylogenies in Cancer}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{9:1--9:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.9},
  URN =		{urn:nbn:de:0030-drops-239356},
  doi =		{10.4230/LIPIcs.WABI.2025.9},
  annote =	{Keywords: Intra-tumor heterogeneity, persistent perfect phylogeny, consecutive ones property, combinatorics}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2021.6
An Approximation Algorithm for the Matrix Tree Multiplication Problem

Authors: Mahmoud Abo-Khamis, Ryan Curtin, Sungjin Im, Benjamin Moseley, Hung Ngo, Kirk Pruhs, and Alireza Samadian

Published in: LIPIcs, Volume 202, 46th International Symposium on Mathematical Foundations of Computer Science (MFCS 2021)

Abstract
We consider the Matrix Tree Multiplication problem. This problem is a generalization of the classic Matrix Chain Multiplication problem covered in the dynamic programming chapter of many introductory algorithms textbooks. An instance of the Matrix Tree Multiplication problem consists of a rooted tree with a matrix associated with each edge. The output is, for each leaf in the tree, the product of the matrices on the chain/path from the root to that leaf. Matrix multiplications that are shared between various chains need only be computed once, potentially being shared between different root to leaf chains. Algorithms are evaluated by the number of scalar multiplications performed. Our main result is a linear time algorithm for which the number of scalar multiplications performed is at most 15 times the optimal number of scalar multiplications.
Cite as

Mahmoud Abo-Khamis, Ryan Curtin, Sungjin Im, Benjamin Moseley, Hung Ngo, Kirk Pruhs, and Alireza Samadian. An Approximation Algorithm for the Matrix Tree Multiplication Problem. In 46th International Symposium on Mathematical Foundations of Computer Science (MFCS 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 202, pp. 6:1-6:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{abokhamis_et_al:LIPIcs.MFCS.2021.6,
  author =	{Abo-Khamis, Mahmoud and Curtin, Ryan and Im, Sungjin and Moseley, Benjamin and Ngo, Hung and Pruhs, Kirk and Samadian, Alireza},
  title =	{{An Approximation Algorithm for the Matrix Tree Multiplication Problem}},
  booktitle =	{46th International Symposium on Mathematical Foundations of Computer Science (MFCS 2021)},
  pages =	{6:1--6:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-201-3},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{202},
  editor =	{Bonchi, Filippo and Puglisi, Simon J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2021.6},
  URN =		{urn:nbn:de:0030-drops-144464},
  doi =		{10.4230/LIPIcs.MFCS.2021.6},
  annote =	{Keywords: Matrix Multiplication, Approximation Algorithm}
}
Document
DOI: 10.4230/LIPIcs.CPM.2016.12
Fast Compatibility Testing for Rooted Phylogenetic Trees

Authors: Yun Deng and David Fernández-Baca

Published in: LIPIcs, Volume 54, 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)

Abstract
We consider the following basic problem in phylogenetic tree construction. Let $\mathcal P = {T_1, ..., T_k} be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks whether there is a tree T with the following property: for each i in {1, ..., k}, T_i can be obtained from the restriction of T to the species set of T_i by contracting zero or more edges. If such a tree T exists, we say that P is compatible. We give a ~O(M_P) algorithm for the tree compatibility problem, where M_P is the total number of nodes and edges in P. Unlike previous algorithms for this problem, the running time of our method does not depend on the degrees of the nodes in the input trees. Thus, it is equally fast on highly resolved and highly unresolved trees.
Cite as

Yun Deng and David Fernández-Baca. Fast Compatibility Testing for Rooted Phylogenetic Trees. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 12:1-12:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)

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@InProceedings{deng_et_al:LIPIcs.CPM.2016.12,
  author =	{Deng, Yun and Fern\'{a}ndez-Baca, David},
  title =	{{Fast Compatibility Testing for Rooted Phylogenetic Trees}},
  booktitle =	{27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)},
  pages =	{12:1--12:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-012-5},
  ISSN =	{1868-8969},
  year =	{2016},
  volume =	{54},
  editor =	{Grossi, Roberto and Lewenstein, Moshe},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.12},
  URN =		{urn:nbn:de:0030-drops-60884},
  doi =		{10.4230/LIPIcs.CPM.2016.12},
  annote =	{Keywords: Algorithms, computational biology, phylogenetics}
}
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