28 Search Results for "Chen, Yi"


Document
On the Power of Nonstandard Quantum Oracles

Authors: Roozbeh Bassirian, Bill Fefferman, and Kunal Marwaha

Published in: LIPIcs, Volume 266, 18th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2023)


Abstract
We study how the choices made when designing an oracle affect the complexity of quantum property testing problems defined relative to this oracle. We encode a regular graph of even degree as an invertible function f, and present f in different oracle models. We first give a one-query QMA protocol to test if a graph encoded in f has a small disconnected subset. We then use representation theory to show that no classical witness can help a quantum verifier efficiently decide this problem relative to an in-place oracle. Perhaps surprisingly, a simple modification to the standard oracle prevents a quantum verifier from efficiently deciding this problem, even with access to an unbounded witness.

Cite as

Roozbeh Bassirian, Bill Fefferman, and Kunal Marwaha. On the Power of Nonstandard Quantum Oracles. In 18th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 266, pp. 11:1-11:25, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)


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@InProceedings{bassirian_et_al:LIPIcs.TQC.2023.11,
  author =	{Bassirian, Roozbeh and Fefferman, Bill and Marwaha, Kunal},
  title =	{{On the Power of Nonstandard Quantum Oracles}},
  booktitle =	{18th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2023)},
  pages =	{11:1--11:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-283-9},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{266},
  editor =	{Fawzi, Omar and Walter, Michael},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TQC.2023.11},
  URN =		{urn:nbn:de:0030-drops-183215},
  doi =		{10.4230/LIPIcs.TQC.2023.11},
  annote =	{Keywords: quantum complexity, QCMA, expander graphs, representation theory}
}
Document
Track A: Algorithms, Complexity and Games
Quantum Algorithms and Lower Bounds for Linear Regression with Norm Constraints

Authors: Yanlin Chen and Ronald de Wolf

Published in: LIPIcs, Volume 261, 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)


Abstract
Lasso and Ridge are important minimization problems in machine learning and statistics. They are versions of linear regression with squared loss where the vector θ ∈ ℝ^d of coefficients is constrained in either 𝓁₁-norm (for Lasso) or in 𝓁₂-norm (for Ridge). We study the complexity of quantum algorithms for finding ε-minimizers for these minimization problems. We show that for Lasso we can get a quadratic quantum speedup in terms of d by speeding up the cost-per-iteration of the Frank-Wolfe algorithm, while for Ridge the best quantum algorithms are linear in d, as are the best classical algorithms. As a byproduct of our quantum lower bound for Lasso, we also prove the first classical lower bound for Lasso that is tight up to polylog-factors.

Cite as

Yanlin Chen and Ronald de Wolf. Quantum Algorithms and Lower Bounds for Linear Regression with Norm Constraints. In 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 261, pp. 38:1-38:21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)


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@InProceedings{chen_et_al:LIPIcs.ICALP.2023.38,
  author =	{Chen, Yanlin and de Wolf, Ronald},
  title =	{{Quantum Algorithms and Lower Bounds for Linear Regression with Norm Constraints}},
  booktitle =	{50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)},
  pages =	{38:1--38:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-278-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{261},
  editor =	{Etessami, Kousha and Feige, Uriel and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2023.38},
  URN =		{urn:nbn:de:0030-drops-180907},
  doi =		{10.4230/LIPIcs.ICALP.2023.38},
  annote =	{Keywords: Quantum algorithms, Regularized linear regression, Lasso, Ridge, Lower bounds}
}
Document
Track A: Algorithms, Complexity and Games
A Study of Weisfeiler-Leman Colorings on Planar Graphs

Authors: Sandra Kiefer and Daniel Neuen

Published in: LIPIcs, Volume 229, 49th International Colloquium on Automata, Languages, and Programming (ICALP 2022)


Abstract
The Weisfeiler-Leman (WL) algorithm is a combinatorial procedure that computes colorings on graphs, which can often be used to detect their (non-)isomorphism. Particularly the 1- and 2-dimensional versions 1-WL and 2-WL have received much attention, due to their numerous links to other areas of computer science. Knowing the expressive power of a certain dimension of the algorithm usually amounts to understanding the computed colorings. An increase in the dimension leads to finer computed colorings and, thus, more graphs can be distinguished. For example, on the class of planar graphs, 3-WL solves the isomorphism problem. However, the expressive power of 2-WL on the class is poorly understood (and, in particular, it may even well be that it decides isomorphism). In this paper, we investigate the colorings computed by 2-WL on planar graphs. Towards this end, we analyze the graphs induced by edge color classes in the graph. Based on the obtained classification, we show that for every 3-connected planar graph, it holds that: a) after coloring all pairs with their 2-WL color, the graph has fixing number 1 with respect to 1-WL, or b) there is a 2-WL-definable matching that can be used to transform the graph into a smaller one, or c) 2-WL detects a connected subgraph that is essentially the graph of a Platonic or Archimedean solid, a prism, a cycle, or a bipartite graph K_{2,𝓁}. In particular, the graphs from case (a) are identified by 2-WL.

Cite as

Sandra Kiefer and Daniel Neuen. A Study of Weisfeiler-Leman Colorings on Planar Graphs. In 49th International Colloquium on Automata, Languages, and Programming (ICALP 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 229, pp. 81:1-81:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)


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@InProceedings{kiefer_et_al:LIPIcs.ICALP.2022.81,
  author =	{Kiefer, Sandra and Neuen, Daniel},
  title =	{{A Study of Weisfeiler-Leman Colorings on Planar Graphs}},
  booktitle =	{49th International Colloquium on Automata, Languages, and Programming (ICALP 2022)},
  pages =	{81:1--81:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-235-8},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{229},
  editor =	{Boja\'{n}czyk, Miko{\l}aj and Merelli, Emanuela and Woodruff, David P.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2022.81},
  URN =		{urn:nbn:de:0030-drops-164228},
  doi =		{10.4230/LIPIcs.ICALP.2022.81},
  annote =	{Keywords: Weisfeiler-Leman algorithm, planar graphs, edge-transitive graphs, fixing number}
}
Document
RANDOM
The Product of Gaussian Matrices Is Close to Gaussian

Authors: Yi Li and David P. Woodruff

Published in: LIPIcs, Volume 207, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2021)


Abstract
We study the distribution of the matrix product G₁ G₂ ⋯ G_r of r independent Gaussian matrices of various sizes, where G_i is d_{i-1} × d_i, and we denote p = d₀, q = d_r, and require d₁ = d_{r-1}. Here the entries in each G_i are standard normal random variables with mean 0 and variance 1. Such products arise in the study of wireless communication, dynamical systems, and quantum transport, among other places. We show that, provided each d_i, i = 1, …, r, satisfies d_i ≥ C p ⋅ q, where C ≥ C₀ for a constant C₀ > 0 depending on r, then the matrix product G₁ G₂ ⋯ G_r has variation distance at most δ to a p × q matrix G of i.i.d. standard normal random variables with mean 0 and variance ∏_{i = 1}^{r-1} d_i. Here δ → 0 as C → ∞. Moreover, we show a converse for constant r that if d_i < C' max{p,q}^{1/2}min{p,q}^{3/2} for some i, then this total variation distance is at least δ', for an absolute constant δ' > 0 depending on C' and r. This converse is best possible when p = Θ(q).

Cite as

Yi Li and David P. Woodruff. The Product of Gaussian Matrices Is Close to Gaussian. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 207, pp. 35:1-35:22, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2021)


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@InProceedings{li_et_al:LIPIcs.APPROX/RANDOM.2021.35,
  author =	{Li, Yi and Woodruff, David P.},
  title =	{{The Product of Gaussian Matrices Is Close to Gaussian}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2021)},
  pages =	{35:1--35:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-207-5},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{207},
  editor =	{Wootters, Mary and Sanit\`{a}, Laura},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2021.35},
  URN =		{urn:nbn:de:0030-drops-147281},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2021.35},
  annote =	{Keywords: random matrix theory, total variation distance, matrix product}
}
Document
K-LLVM: A Relatively Complete Semantics of LLVM IR

Authors: Liyi Li and Elsa L. Gunter

Published in: LIPIcs, Volume 166, 34th European Conference on Object-Oriented Programming (ECOOP 2020)


Abstract
LLVM [Lattner and Adve, 2004] is designed for the compile-time, link-time and run-time optimization of programs written in various programming languages. The language supported by LLVM targeted by modern compilers is LLVM IR [llvm.org, 2018]. In this paper we define K-LLVM, a reference semantics for LLVM IR. To the best of our knowledge, K-LLVM is the most complete formal LLVM IR semantics to date, including all LLVM IR instructions, intrinsic functions in the LLVM documentation and Standard-C library functions that are necessary to execute many LLVM IR programs. Additionally, K-LLVM formulates an abstract machine that executes all LLVM IR instructions. The machine allows to describe our formal semantics in terms of simulating a conceptual virtual machine that runs LLVM IR programs, including non-deterministic programs. Even though the K-LLVM memory model in this paper is assumed to be a sequentially consistent memory model and does not include all LLVM concurrency memory behaviors, the design of K-LLVM’s data layout allows the K-LLVM abstract machine to execute some LLVM IR programs that previous semantics did not cover, such as the full range of LLVM IR behaviors for the interaction among LLVM IR casting, pointer arithmetic, memory operations and some memory flags (e.g. readonly) of function headers. Additionally, the memory model is modularized in a manner that supports investigating other memory models. To validate K-LLVM, we have implemented it in 𝕂 [Roşu, 2016], which generated an interpreter for LLVM IR. Using this, we ran tests including 1,385 unit test programs and around 3,000 concrete LLVM IR programs, and K-LLVM passed all of them.

Cite as

Liyi Li and Elsa L. Gunter. K-LLVM: A Relatively Complete Semantics of LLVM IR. In 34th European Conference on Object-Oriented Programming (ECOOP 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 166, pp. 7:1-7:29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)


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@InProceedings{li_et_al:LIPIcs.ECOOP.2020.7,
  author =	{Li, Liyi and Gunter, Elsa L.},
  title =	{{K-LLVM: A Relatively Complete Semantics of LLVM IR}},
  booktitle =	{34th European Conference on Object-Oriented Programming (ECOOP 2020)},
  pages =	{7:1--7:29},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-154-2},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{166},
  editor =	{Hirschfeld, Robert and Pape, Tobias},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2020.7},
  URN =		{urn:nbn:de:0030-drops-131649},
  doi =		{10.4230/LIPIcs.ECOOP.2020.7},
  annote =	{Keywords: LLVM, formal semantics, K framework, memory model, abstract machine}
}
Document
Random Sampling and Size Estimation Over Cyclic Joins

Authors: Yu Chen and Ke Yi

Published in: LIPIcs, Volume 155, 23rd International Conference on Database Theory (ICDT 2020)


Abstract
Computing joins is expensive, and often unnecessary when the output size is large. In 1999, Chaudhuri et al. [Surajit Chaudhuri et al., 1999] posed the problem of random sampling over joins as a potentially effective approach to avoiding computing the join in full, while obtaining important statistical information about the join results. Unfortunately, no significant progress has been made in the last 20 years, except for the case of acyclic joins. In this paper, we present the first non-trivial result on sampling over cyclic joins. We show that after a linear-time preprocessing step, a join result can be drawn uniformly at random in expected time O(IN^ρ/OUT), where IN^ρ is known as the AGM bound of the join and OUT is its output size. This result holds for all joins on binary relations, as well as certain joins on relations of higher arity. We further show how this algorithm immediately leads to a join size estimation algorithm with the same running time.

Cite as

Yu Chen and Ke Yi. Random Sampling and Size Estimation Over Cyclic Joins. In 23rd International Conference on Database Theory (ICDT 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 155, pp. 7:1-7:18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)


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@InProceedings{chen_et_al:LIPIcs.ICDT.2020.7,
  author =	{Chen, Yu and Yi, Ke},
  title =	{{Random Sampling and Size Estimation Over Cyclic Joins}},
  booktitle =	{23rd International Conference on Database Theory (ICDT 2020)},
  pages =	{7:1--7:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-139-9},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{155},
  editor =	{Lutz, Carsten and Jung, Jean Christoph},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICDT.2020.7},
  URN =		{urn:nbn:de:0030-drops-119315},
  doi =		{10.4230/LIPIcs.ICDT.2020.7},
  annote =	{Keywords: Random sampling, joins, join size estimation}
}
Document
Invited Paper
Matching mu-Logic: Foundation of K Framework (Invited Paper)

Authors: Xiaohong Chen and Grigore Roşu

Published in: LIPIcs, Volume 139, 8th Conference on Algebra and Coalgebra in Computer Science (CALCO 2019)


Abstract
K framework is an effort in realizing the ideal language framework where programming languages must have formal semantics and all languages tools are automatically generated from the formal semantics in a correct-by-construction manner at no additional costs. In this extended abstract, we present matching mu-logic as the foundation of K and discuss some of its applications in defining constructors, transition systems, modal mu-logic and temporal logic variants, and reachability logic.

Cite as

Xiaohong Chen and Grigore Roşu. Matching mu-Logic: Foundation of K Framework (Invited Paper). In 8th Conference on Algebra and Coalgebra in Computer Science (CALCO 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 139, pp. 1:1-1:4, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{chen_et_al:LIPIcs.CALCO.2019.1,
  author =	{Chen, Xiaohong and Ro\c{s}u, Grigore},
  title =	{{Matching mu-Logic: Foundation of K Framework}},
  booktitle =	{8th Conference on Algebra and Coalgebra in Computer Science (CALCO 2019)},
  pages =	{1:1--1:4},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-120-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{139},
  editor =	{Roggenbach, Markus and Sokolova, Ana},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CALCO.2019.1},
  URN =		{urn:nbn:de:0030-drops-114296},
  doi =		{10.4230/LIPIcs.CALCO.2019.1},
  annote =	{Keywords: Matching mu-logic, Program verification, Reachability logic}
}
Document
Characteristic Formulae for Liveness Properties of Non-Terminating CakeML Programs

Authors: Johannes Åman Pohjola, Henrik Rostedt, and Magnus O. Myreen

Published in: LIPIcs, Volume 141, 10th International Conference on Interactive Theorem Proving (ITP 2019)


Abstract
There are useful programs that do not terminate, and yet standard Hoare logics are not able to prove liveness properties about non-terminating programs. This paper shows how a Hoare-like programming logic framework (characteristic formulae) can be extended to enable reasoning about the I/O behaviour of programs that do not terminate. The approach is inspired by transfinite induction rather than coinduction, and does not require non-terminating loops to be productive. This work has been developed in the HOL4 theorem prover and has been integrated into the ecosystem of proof tools surrounding the CakeML programming language.

Cite as

Johannes Åman Pohjola, Henrik Rostedt, and Magnus O. Myreen. Characteristic Formulae for Liveness Properties of Non-Terminating CakeML Programs. In 10th International Conference on Interactive Theorem Proving (ITP 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 141, pp. 32:1-32:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{amanpohjola_et_al:LIPIcs.ITP.2019.32,
  author =	{\r{A}man Pohjola, Johannes and Rostedt, Henrik and Myreen, Magnus O.},
  title =	{{Characteristic Formulae for Liveness Properties of Non-Terminating CakeML Programs}},
  booktitle =	{10th International Conference on Interactive Theorem Proving (ITP 2019)},
  pages =	{32:1--32:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-122-1},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{141},
  editor =	{Harrison, John and O'Leary, John and Tolmach, Andrew},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITP.2019.32},
  URN =		{urn:nbn:de:0030-drops-110872},
  doi =		{10.4230/LIPIcs.ITP.2019.32},
  annote =	{Keywords: Program verification, non-termination, liveness, Hoare logic}
}
Document
Topological Data Analysis Reveals Principles of Chromosome Structure in Cellular Differentiation

Authors: Natalie Sauerwald, Yihang Shen, and Carl Kingsford

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


Abstract
Topological data analysis (TDA) is a mathematically well-founded set of methods to derive robust information about the structure and topology of data. It has been applied successfully in several biological contexts. Derived primarily from algebraic topology, TDA rigorously identifies persistent features in complex data, making it well-suited to better understand the key features of three-dimensional chromosome structure. Chromosome structure has a significant influence in many diverse genomic processes and has recently been shown to relate to cellular differentiation. While there exist many methods to study specific substructures of chromosomes, we are still missing a global view of all geometric features of chromosomes. By applying TDA to the study of chromosome structure through differentiation across three cell lines, we provide insight into principles of chromosome folding and looping. We identify persistent connected components and one-dimensional topological features of chromosomes and characterize them across cell types and stages of differentiation. Availability: Scripts to reproduce the results from this study can be found at https://github.com/Kingsford-Group/hictda

Cite as

Natalie Sauerwald, Yihang Shen, and Carl Kingsford. Topological Data Analysis Reveals Principles of Chromosome Structure in Cellular Differentiation. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 23:1-23:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{sauerwald_et_al:LIPIcs.WABI.2019.23,
  author =	{Sauerwald, Natalie and Shen, Yihang and Kingsford, Carl},
  title =	{{Topological Data Analysis Reveals Principles of Chromosome Structure in Cellular Differentiation}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{23:1--23:16},
  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.2019.23},
  URN =		{urn:nbn:de:0030-drops-110537},
  doi =		{10.4230/LIPIcs.WABI.2019.23},
  annote =	{Keywords: topological data analysis, chromosome structure, Hi-C, topologically associating domains}
}
Document
Jointly Embedding Multiple Single-Cell Omics Measurements

Authors: Jie Liu, Yuanhao Huang, Ritambhara Singh, Jean-Philippe Vert, and William Stafford Noble

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


Abstract
Many single-cell sequencing technologies are now available, but it is still difficult to apply multiple sequencing technologies to the same single cell. In this paper, we propose an unsupervised manifold alignment algorithm, MMD-MA, for integrating multiple measurements carried out on disjoint aliquots of a given population of cells. Effectively, MMD-MA performs an in silico co-assay by embedding cells measured in different ways into a learned latent space. In the MMD-MA algorithm, single-cell data points from multiple domains are aligned by optimizing an objective function with three components: (1) a maximum mean discrepancy (MMD) term to encourage the differently measured points to have similar distributions in the latent space, (2) a distortion term to preserve the structure of the data between the input space and the latent space, and (3) a penalty term to avoid collapse to a trivial solution. Notably, MMD-MA does not require any correspondence information across data modalities, either between the cells or between the features. Furthermore, MMD-MA’s weak distributional requirements for the domains to be aligned allow the algorithm to integrate heterogeneous types of single cell measures, such as gene expression, DNA accessibility, chromatin organization, methylation, and imaging data. We demonstrate the utility of MMD-MA in simulation experiments and using a real data set involving single-cell gene expression and methylation data.

Cite as

Jie Liu, Yuanhao Huang, Ritambhara Singh, Jean-Philippe Vert, and William Stafford Noble. Jointly Embedding Multiple Single-Cell Omics Measurements. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 10:1-10:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{liu_et_al:LIPIcs.WABI.2019.10,
  author =	{Liu, Jie and Huang, Yuanhao and Singh, Ritambhara and Vert, Jean-Philippe and Noble, William Stafford},
  title =	{{Jointly Embedding Multiple Single-Cell Omics Measurements}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{10:1--10:13},
  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.2019.10},
  URN =		{urn:nbn:de:0030-drops-110401},
  doi =		{10.4230/LIPIcs.WABI.2019.10},
  annote =	{Keywords: Manifold alignment, single-cell sequencing}
}
Document
Approximate Counting CSP Seen from the Other Side

Authors: Andrei A. Bulatov and Stanislav Živný

Published in: LIPIcs, Volume 138, 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)


Abstract
In this paper we study the complexity of counting Constraint Satisfaction Problems (CSPs) of the form #CSP(C,-), in which the goal is, given a relational structure A from a class C of structures and an arbitrary structure B, to find the number of homomorphisms from A to B. Flum and Grohe showed that #CSP(C,-) is solvable in polynomial time if C has bounded treewidth [FOCS'02]. Building on the work of Grohe [JACM'07] on decision CSPs, Dalmau and Jonsson then showed that, if C is a recursively enumerable class of relational structures of bounded arity, then assuming FPT != #W[1], there are no other cases of #CSP(C,-) solvable exactly in polynomial time (or even fixed-parameter time) [TCS'04]. We show that, assuming FPT != W[1] (under randomised parametrised reductions) and for C satisfying certain general conditions, #CSP(C,-) is not solvable even approximately for C of unbounded treewidth; that is, there is no fixed parameter tractable (and thus also not fully polynomial) randomised approximation scheme for #CSP(C,-). In particular, our condition generalises the case when C is closed under taking minors.

Cite as

Andrei A. Bulatov and Stanislav Živný. Approximate Counting CSP Seen from the Other Side. In 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 138, pp. 60:1-60:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{bulatov_et_al:LIPIcs.MFCS.2019.60,
  author =	{Bulatov, Andrei A. and \v{Z}ivn\'{y}, Stanislav},
  title =	{{Approximate Counting CSP Seen from the Other Side}},
  booktitle =	{44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)},
  pages =	{60:1--60:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-117-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{138},
  editor =	{Rossmanith, Peter and Heggernes, Pinar and Katoen, Joost-Pieter},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2019.60},
  URN =		{urn:nbn:de:0030-drops-110041},
  doi =		{10.4230/LIPIcs.MFCS.2019.60},
  annote =	{Keywords: constraint satisfaction, approximate counting, homomorphisms}
}
Document
RLE Edit Distance in Near Optimal Time

Authors: Raphaël Clifford, Paweł Gawrychowski, Tomasz Kociumaka, Daniel P. Martin, and Przemysław Uznański

Published in: LIPIcs, Volume 138, 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)


Abstract
We show that the edit distance between two run-length encoded strings of compressed lengths m and n respectively, can be computed in O(mn log(mn)) time. This improves the previous record by a factor of O(n/log(mn)). The running time of our algorithm is within subpolynomial factors of being optimal, subject to the standard SETH-hardness assumption. This effectively closes a line of algorithmic research first started in 1993.

Cite as

Raphaël Clifford, Paweł Gawrychowski, Tomasz Kociumaka, Daniel P. Martin, and Przemysław Uznański. RLE Edit Distance in Near Optimal Time. In 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 138, pp. 66:1-66:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{clifford_et_al:LIPIcs.MFCS.2019.66,
  author =	{Clifford, Rapha\"{e}l and Gawrychowski, Pawe{\l} and Kociumaka, Tomasz and Martin, Daniel P. and Uzna\'{n}ski, Przemys{\l}aw},
  title =	{{RLE Edit Distance in Near Optimal Time}},
  booktitle =	{44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)},
  pages =	{66:1--66:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-117-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{138},
  editor =	{Rossmanith, Peter and Heggernes, Pinar and Katoen, Joost-Pieter},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2019.66},
  URN =		{urn:nbn:de:0030-drops-110109},
  doi =		{10.4230/LIPIcs.MFCS.2019.66},
  annote =	{Keywords: String algorithms, Compression, Pattern matching, Run-length encoding}
}
Document
The Power of the Weisfeiler-Leman Algorithm to Decompose Graphs

Authors: Sandra Kiefer and Daniel Neuen

Published in: LIPIcs, Volume 138, 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)


Abstract
The Weisfeiler-Leman procedure is a widely-used approach for graph isomorphism testing that works by iteratively computing an isomorphism-invariant coloring of vertex tuples. Meanwhile, a fundamental tool in structural graph theory, which is often exploited in approaches to tackle the graph isomorphism problem, is the decomposition into bi- and triconnected components. We prove that the 2-dimensional Weisfeiler-Leman algorithm implicitly computes the decomposition of a graph into its triconnected components. Thus, the dimension of the algorithm needed to distinguish two given graphs is at most the dimension required to distinguish the corresponding decompositions into 3-connected components (assuming dimension at least 2). This result implies that for k >= 2, the k-dimensional algorithm distinguishes k-separators, i.e., k-tuples of vertices that separate the graph, from other vertex k-tuples. As a byproduct, we also obtain insights about the connectivity of constituent graphs of association schemes. In an application of the results, we show the new upper bound of k on the Weisfeiler-Leman dimension of graphs of treewidth at most k. Using a construction by Cai, Fürer, and Immerman, we also provide a new lower bound that is asymptotically tight up to a factor of 2.

Cite as

Sandra Kiefer and Daniel Neuen. The Power of the Weisfeiler-Leman Algorithm to Decompose Graphs. In 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 138, pp. 45:1-45:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{kiefer_et_al:LIPIcs.MFCS.2019.45,
  author =	{Kiefer, Sandra and Neuen, Daniel},
  title =	{{The Power of the Weisfeiler-Leman Algorithm to Decompose Graphs}},
  booktitle =	{44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)},
  pages =	{45:1--45:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-117-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{138},
  editor =	{Rossmanith, Peter and Heggernes, Pinar and Katoen, Joost-Pieter},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2019.45},
  URN =		{urn:nbn:de:0030-drops-109893},
  doi =		{10.4230/LIPIcs.MFCS.2019.45},
  annote =	{Keywords: Weisfeiler-Leman, separators, first-order logic, counting quantifiers}
}
Document
Counting Homomorphisms Modulo a Prime Number

Authors: Amirhossein Kazeminia and Andrei A. Bulatov

Published in: LIPIcs, Volume 138, 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)


Abstract
Counting problems in general and counting graph homomorphisms in particular have numerous applications in combinatorics, computer science, statistical physics, and elsewhere. One of the most well studied problems in this area is #GraphHom(H) - the problem of finding the number of homomorphisms from a given graph G to the graph H. Not only the complexity of this basic problem is known, but also of its many variants for digraphs, more general relational structures, graphs with weights, and others. In this paper we consider a modification of #GraphHom(H), the #_{p}GraphHom(H) problem, p a prime number: Given a graph G, find the number of homomorphisms from G to H modulo p. In a series of papers Faben and Jerrum, and Göbel et al. determined the complexity of #_{2}GraphHom(H) in the case H (or, in fact, a certain graph derived from H) is square-free, that is, does not contain a 4-cycle. Also, Göbel et al. found the complexity of #_{p}GraphHom(H) when H is a tree for an arbitrary prime p. Here we extend the above result to show that the #_{p}GraphHom(H) problem is #_{p}P-hard whenever the derived graph associated with H is square-free and is not a star, which completely classifies the complexity of #_{p}GraphHom(H) for square-free graphs H.

Cite as

Amirhossein Kazeminia and Andrei A. Bulatov. Counting Homomorphisms Modulo a Prime Number. In 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 138, pp. 59:1-59:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{kazeminia_et_al:LIPIcs.MFCS.2019.59,
  author =	{Kazeminia, Amirhossein and Bulatov, Andrei A.},
  title =	{{Counting Homomorphisms Modulo a Prime Number}},
  booktitle =	{44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)},
  pages =	{59:1--59:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-117-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{138},
  editor =	{Rossmanith, Peter and Heggernes, Pinar and Katoen, Joost-Pieter},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2019.59},
  URN =		{urn:nbn:de:0030-drops-110032},
  doi =		{10.4230/LIPIcs.MFCS.2019.59},
  annote =	{Keywords: graph homomorphism, modular counting, computational hardness}
}
Document
Relations and Equivalences Between Circuit Lower Bounds and Karp-Lipton Theorems

Authors: Lijie Chen, Dylan M. McKay, Cody D. Murray, and R. Ryan Williams

Published in: LIPIcs, Volume 137, 34th Computational Complexity Conference (CCC 2019)


Abstract
A frontier open problem in circuit complexity is to prove P^{NP} is not in SIZE[n^k] for all k; this is a necessary intermediate step towards NP is not in P_{/poly}. Previously, for several classes containing P^{NP}, including NP^{NP}, ZPP^{NP}, and S_2 P, such lower bounds have been proved via Karp-Lipton-style Theorems: to prove C is not in SIZE[n^k] for all k, we show that C subset P_{/poly} implies a "collapse" D = C for some larger class D, where we already know D is not in SIZE[n^k] for all k. It seems obvious that one could take a different approach to prove circuit lower bounds for P^{NP} that does not require proving any Karp-Lipton-style theorems along the way. We show this intuition is wrong: (weak) Karp-Lipton-style theorems for P^{NP} are equivalent to fixed-polynomial size circuit lower bounds for P^{NP}. That is, P^{NP} is not in SIZE[n^k] for all k if and only if (NP subset P_{/poly} implies PH subset i.o.- P^{NP}_{/n}). Next, we present new consequences of the assumption NP subset P_{/poly}, towards proving similar results for NP circuit lower bounds. We show that under the assumption, fixed-polynomial circuit lower bounds for NP, nondeterministic polynomial-time derandomizations, and various fixed-polynomial time simulations of NP are all equivalent. Applying this equivalence, we show that circuit lower bounds for NP imply better Karp-Lipton collapses. That is, if NP is not in SIZE[n^k] for all k, then for all C in {Parity-P, PP, PSPACE, EXP}, C subset P_{/poly} implies C subset i.o.-NP_{/n^epsilon} for all epsilon > 0. Note that unconditionally, the collapses are only to MA and not NP. We also explore consequences of circuit lower bounds for a sparse language in NP. Among other results, we show if a polynomially-sparse NP language does not have n^{1+epsilon}-size circuits, then MA subset i.o.-NP_{/O(log n)}, MA subset i.o.-P^{NP[O(log n)]}, and NEXP is not in SIZE[2^{o(m)}]. Finally, we observe connections between these results and the "hardness magnification" phenomena described in recent works.

Cite as

Lijie Chen, Dylan M. McKay, Cody D. Murray, and R. Ryan Williams. Relations and Equivalences Between Circuit Lower Bounds and Karp-Lipton Theorems. In 34th Computational Complexity Conference (CCC 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 137, pp. 30:1-30:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{chen_et_al:LIPIcs.CCC.2019.30,
  author =	{Chen, Lijie and McKay, Dylan M. and Murray, Cody D. and Williams, R. Ryan},
  title =	{{Relations and Equivalences Between Circuit Lower Bounds and Karp-Lipton Theorems}},
  booktitle =	{34th Computational Complexity Conference (CCC 2019)},
  pages =	{30:1--30:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-116-0},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{137},
  editor =	{Shpilka, Amir},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2019.30},
  URN =		{urn:nbn:de:0030-drops-108525},
  doi =		{10.4230/LIPIcs.CCC.2019.30},
  annote =	{Keywords: Karp-Lipton Theorems, Circuit Lower Bounds, Derandomization, Hardness Magnification}
}
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