2 Search Results for "Srinivasan, Rajgopal"


Document
Read Mapping on Genome Variation Graphs

Authors: Kavya Vaddadi, Rajgopal Srinivasan, and Naveen Sivadasan

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


Abstract
Genome variation graphs are natural candidates to represent a pangenome collection. In such graphs, common subsequences are encoded as vertices and the genomic variations are captured by introducing additional labeled vertices and directed edges. Unlike a linear reference, a reference graph allows a rich representation of the genomic diversities and avoids reference bias. We address the fundamental problem of mapping reads to genome variation graphs. We give a novel mapping algorithm V-MAP for efficient identification of small subgraph of the genome graph for optimal gapped alignment of the read. V-MAP creates space efficient index using locality sensitive minimizer signatures computed using a novel graph winnowing and graph embedding onto metric space for fast and accurate mapping. Experiments involving graph constructed from the 1000 Genomes data and using both real and simulated reads show that V-MAP is fast, memory efficient and can map short reads, as well as PacBio/Nanopore long reads with high accuracy. V-MAP performance was significantly better than the state-of-the-art, especially for long reads.

Cite as

Kavya Vaddadi, Rajgopal Srinivasan, and Naveen Sivadasan. Read Mapping on Genome Variation Graphs. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 7:1-7:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{vaddadi_et_al:LIPIcs.WABI.2019.7,
  author =	{Vaddadi, Kavya and Srinivasan, Rajgopal and Sivadasan, Naveen},
  title =	{{Read Mapping on Genome Variation Graphs}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{7:1--7:17},
  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.2019.7},
  URN =		{urn:nbn:de:0030-drops-110375},
  doi =		{10.4230/LIPIcs.WABI.2019.7},
  annote =	{Keywords: read mapping, pangenome, genome variation graphs, locality sensitive hashing}
}
Document
Deterministically Counting Satisfying Assignments for Constant-Depth Circuits with Parity Gates, with Implications for Lower Bounds

Authors: Ninad Rajgopal, Rahul Santhanam, and Srikanth Srinivasan

Published in: LIPIcs, Volume 117, 43rd International Symposium on Mathematical Foundations of Computer Science (MFCS 2018)


Abstract
We give a deterministic algorithm for counting the number of satisfying assignments of any AC^0[oplus] circuit C of size s and depth d over n variables in time 2^(n-f(n,s,d)), where f(n,s,d) = n/O(log(s))^(d-1), whenever s = 2^o(n^(1/d)). As a consequence, we get that for each d, there is a language in E^{NP} that does not have AC^0[oplus] circuits of size 2^o(n^(1/(d+1))). This is the first lower bound in E^{NP} against AC^0[oplus] circuits that beats the lower bound of 2^Omega(n^(1/2(d-1))) due to Razborov and Smolensky for large d. Both our algorithm and our lower bounds extend to AC^0[p] circuits for any prime p.

Cite as

Ninad Rajgopal, Rahul Santhanam, and Srikanth Srinivasan. Deterministically Counting Satisfying Assignments for Constant-Depth Circuits with Parity Gates, with Implications for Lower Bounds. In 43rd International Symposium on Mathematical Foundations of Computer Science (MFCS 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 117, pp. 78:1-78:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)


Copy BibTex To Clipboard

@InProceedings{rajgopal_et_al:LIPIcs.MFCS.2018.78,
  author =	{Rajgopal, Ninad and Santhanam, Rahul and Srinivasan, Srikanth},
  title =	{{Deterministically Counting Satisfying Assignments for Constant-Depth Circuits with Parity Gates, with Implications for Lower Bounds}},
  booktitle =	{43rd International Symposium on Mathematical Foundations of Computer Science (MFCS 2018)},
  pages =	{78:1--78:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-086-6},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{117},
  editor =	{Potapov, Igor and Spirakis, Paul and Worrell, James},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2018.78},
  URN =		{urn:nbn:de:0030-drops-96607},
  doi =		{10.4230/LIPIcs.MFCS.2018.78},
  annote =	{Keywords: circuit satisfiability, circuit lower bounds, polynomial method, derandomization}
}
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