5 Search Results for "Wang, Carol"


Document
Quantified Uncertainty of Flexible Protein-Protein Docking Algorithms

Authors: Nathan L. Clement

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


Abstract
The strength or weakness of an algorithm is ultimately governed by the confidence of its result. When the domain of the problem is large (e.g. traversal of a high-dimensional space), an exact solution often cannot be obtained, so approximations must be made. These approximations often lead to a reported quantity of interest (QOI) which varies between runs, decreasing the confidence of any single run. When the algorithm further computes this QOI based on uncertain or noisy data, the variability (or lack of confidence) of the QOI increases. Unbounded, these two sources of uncertainty (algorithmic approximations and uncertainty in input data) can result in a reported statistic that has low correlation with ground truth. In molecular biology applications, this is especially applicable, as the search space is generally large and observations are often noisy. This research applies uncertainty quantification techniques to the difficult protein-protein docking problem, where uncertainties arise from the explicit conversion from continuous to discrete space for protein representation (introducing some uncertainty in the input data), as well as discrete sampling of the conformations. It describes the variability that exists in existing software, and then provides a method for computing probabilistic certificates in the form of Chernoff-like bounds. Finally, this paper leverages these probabilistic certificates to accurately bound the uncertainty in docking from two docking algorithms, providing a QOI that is both robust and statistically meaningful.

Cite as

Nathan L. Clement. Quantified Uncertainty of Flexible Protein-Protein Docking Algorithms. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 3:1-3:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{clement:LIPIcs.WABI.2019.3,
  author =	{Clement, Nathan L.},
  title =	{{Quantified Uncertainty of Flexible Protein-Protein Docking Algorithms}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{3:1--3:12},
  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.2019.3},
  URN =		{urn:nbn:de:0030-drops-110335},
  doi =		{10.4230/LIPIcs.WABI.2019.3},
  annote =	{Keywords: protein-protein docking, uncertainty quantification, protein flexibility, low-discrepancy sampling, high-dimensional sampling}
}
Document
Deletion Codes in the High-noise and High-rate Regimes

Authors: Venkatesan Guruswami and Carol Wang

Published in: LIPIcs, Volume 40, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2015)


Abstract
The noise model of deletions poses significant challenges in coding theory, with basic questions like the capacity of the binary deletion channel still being open. In this paper, we study the harder model of worst-case deletions, with a focus on constructing efficiently encodable and decodable codes for the two extreme regimes of high-noise and high-rate. Specifically, we construct polynomial-time decodable codes with the following trade-offs (for any epsilon > 0): (1) Codes that can correct a fraction 1-epsilon of deletions with rate poly(eps) over an alphabet of size poly(1/epsilon); (2) Binary codes of rate 1-O~(sqrt(epsilon)) that can correct a fraction eps of deletions; and (3) Binary codes that can be list decoded from a fraction (1/2-epsilon) of deletions with rate poly(epsion) Our work is the first to achieve the qualitative goals of correcting a deletion fraction approaching 1 over bounded alphabets, and correcting a constant fraction of bit deletions with rate aproaching 1. The above results bring our understanding of deletion code constructions in these regimes to a similar level as worst-case errors.

Cite as

Venkatesan Guruswami and Carol Wang. Deletion Codes in the High-noise and High-rate Regimes. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2015). Leibniz International Proceedings in Informatics (LIPIcs), Volume 40, pp. 867-880, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2015)


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@InProceedings{guruswami_et_al:LIPIcs.APPROX-RANDOM.2015.867,
  author =	{Guruswami, Venkatesan and Wang, Carol},
  title =	{{Deletion Codes in the High-noise and High-rate Regimes}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2015)},
  pages =	{867--880},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-89-7},
  ISSN =	{1868-8969},
  year =	{2015},
  volume =	{40},
  editor =	{Garg, Naveen and Jansen, Klaus and Rao, Anup and Rolim, Jos\'{e} D. P.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX-RANDOM.2015.867},
  URN =		{urn:nbn:de:0030-drops-53417},
  doi =		{10.4230/LIPIcs.APPROX-RANDOM.2015.867},
  annote =	{Keywords: algorithmic coding theory, deletion codes, list decoding, probabilistic method, explicit constructions}
}
Document
Dimension Expanders via Rank Condensers

Authors: Michael A. Forbes and Venkatesan Guruswami

Published in: LIPIcs, Volume 40, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2015)


Abstract
An emerging theory of "linear algebraic pseudorandomness: aims to understand the linear algebraic analogs of fundamental Boolean pseudorandom objects where the rank of subspaces plays the role of the size of subsets. In this work, we study and highlight the interrelationships between several such algebraic objects such as subspace designs, dimension expanders, seeded rank condensers, two-source rank condensers, and rank-metric codes. In particular, with the recent construction of near-optimal subspace designs by Guruswami and Kopparty as a starting point, we construct good (seeded) rank condensers (both lossless and lossy versions), which are a small collection of linear maps F^n to F^t for t<<n such that for every subset of F^n of small rank, its rank is preserved (up to a constant factor in the lossy case) by at least one of the maps. We then compose a tensoring operation with our lossy rank condenser to construct constant-degree dimension expanders over polynomially large fields. That is, we give a constant number of explicit linear maps A_i from F^n to F^n such that for any subspace V of F^n of dimension at most n/2, the dimension of the span of the A_i(V) is at least (1+Omega(1)) times the dimension of V. Previous constructions of such constant-degree dimension expanders were based on Kazhdan's property T (for the case when F has characteristic zero) or monotone expanders (for every field F); in either case the construction was harder than that of usual vertex expanders. Our construction, on the other hand, is simpler. For two-source rank condensers, we observe that the lossless variant (where the output rank is the product of the ranks of the two sources) is equivalent to the notion of a linear rank-metric code. For the lossy case, using our seeded rank condensers, we give a reduction of the general problem to the case when the sources have high (n^Omega(1)) rank. When the sources have constant rank, combining this with an "inner condenser" found by brute-force leads to a two-source rank condenser with output length nearly matching the probabilistic constructions.

Cite as

Michael A. Forbes and Venkatesan Guruswami. Dimension Expanders via Rank Condensers. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2015). Leibniz International Proceedings in Informatics (LIPIcs), Volume 40, pp. 800-814, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2015)


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@InProceedings{forbes_et_al:LIPIcs.APPROX-RANDOM.2015.800,
  author =	{Forbes, Michael A. and Guruswami, Venkatesan},
  title =	{{Dimension Expanders via Rank Condensers}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2015)},
  pages =	{800--814},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-89-7},
  ISSN =	{1868-8969},
  year =	{2015},
  volume =	{40},
  editor =	{Garg, Naveen and Jansen, Klaus and Rao, Anup and Rolim, Jos\'{e} D. P.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX-RANDOM.2015.800},
  URN =		{urn:nbn:de:0030-drops-53379},
  doi =		{10.4230/LIPIcs.APPROX-RANDOM.2015.800},
  annote =	{Keywords: dimension expanders, rank condensers, rank-metric codes, subspace designs, Wronskians}
}
Document
List Decoding Group Homomorphisms Between Supersolvable Groups

Authors: Alan Guo and Madhu Sudan

Published in: LIPIcs, Volume 28, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2014)


Abstract
We show that the set of homomorphisms between two supersolvable groups can be locally list decoded up to the minimum distance of the code, extending the results of Dinur et al. (Proc. STOC 2008) who studied the case where the groups are abelian. Moreover, when specialized to the abelian case, our proof is more streamlined and gives a better constant in the exponent of the list size. The constant is improved from about 3.5 million to 105.

Cite as

Alan Guo and Madhu Sudan. List Decoding Group Homomorphisms Between Supersolvable Groups. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2014). Leibniz International Proceedings in Informatics (LIPIcs), Volume 28, pp. 737-747, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2014)


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@InProceedings{guo_et_al:LIPIcs.APPROX-RANDOM.2014.737,
  author =	{Guo, Alan and Sudan, Madhu},
  title =	{{List Decoding Group Homomorphisms Between Supersolvable Groups}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2014)},
  pages =	{737--747},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-74-3},
  ISSN =	{1868-8969},
  year =	{2014},
  volume =	{28},
  editor =	{Jansen, Klaus and Rolim, Jos\'{e} and Devanur, Nikhil R. and Moore, Cristopher},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX-RANDOM.2014.737},
  URN =		{urn:nbn:de:0030-drops-47359},
  doi =		{10.4230/LIPIcs.APPROX-RANDOM.2014.737},
  annote =	{Keywords: Group theory, error-correcting codes, locally decodable codes}
}
Document
Evading Subspaces Over Large Fields and Explicit List-decodable Rank-metric Codes

Authors: Venkatesan Guruswami and Carol Wang

Published in: LIPIcs, Volume 28, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2014)


Abstract
We construct an explicit family of linear rank-metric codes over any field F that enables efficient list decoding up to a fraction rho of errors in the rank metric with a rate of 1-rho-eps, for any desired rho in (0,1) and eps > 0. Previously, a Monte Carlo construction of such codes was known, but this is in fact the first explicit construction of positive rate rank-metric codes for list decoding beyond the unique decoding radius. Our codes are explicit subcodes of the well-known Gabidulin codes, which encode linearized polynomials of low degree via their values at a collection of linearly independent points. The subcode is picked by restricting the message polynomials to an F-subspace that evades certain structured subspaces over an extension field of F. These structured spaces arise from the linear-algebraic list decoder for Gabidulin codes due to Guruswami and Xing (STOC'13). Our construction is obtained by combining subspace designs constructed by Guruswami and Kopparty (FOCS'13) with subspace-evasive varieties due to Dvir and Lovett (STOC'12). We establish a similar result for subspace codes, which are a collection of subspaces, every pair of which have low-dimensional intersection, and which have received much attention recently in the context of network coding. We also give explicit subcodes of folded Reed-Solomon (RS) codes with small folding order that are list-decodable (in the Hamming metric) with optimal redundancy, motivated by the fact that list decoding RS codes reduces to list decoding such folded RS codes. However, as we only list decode a subcode of these codes, the Johnson radius continues to be the best known error fraction for list decoding RS codes.

Cite as

Venkatesan Guruswami and Carol Wang. Evading Subspaces Over Large Fields and Explicit List-decodable Rank-metric Codes. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2014). Leibniz International Proceedings in Informatics (LIPIcs), Volume 28, pp. 748-761, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2014)


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@InProceedings{guruswami_et_al:LIPIcs.APPROX-RANDOM.2014.748,
  author =	{Guruswami, Venkatesan and Wang, Carol},
  title =	{{Evading Subspaces Over Large Fields and Explicit List-decodable Rank-metric Codes}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2014)},
  pages =	{748--761},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-74-3},
  ISSN =	{1868-8969},
  year =	{2014},
  volume =	{28},
  editor =	{Jansen, Klaus and Rolim, Jos\'{e} and Devanur, Nikhil R. and Moore, Cristopher},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX-RANDOM.2014.748},
  URN =		{urn:nbn:de:0030-drops-47361},
  doi =		{10.4230/LIPIcs.APPROX-RANDOM.2014.748},
  annote =	{Keywords: list-decoding, pseudorandomness, algebraic coding, explicit constructions}
}
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