1

December 2017
ACM Transactions on Computational Logic (TOCL): Volume 18 Issue 4, December 2017

**Publisher:** ACM

**Bibliometrics**:

Citation Count: 0

Downloads (6 Weeks): 3, Downloads (12 Months): 30, Downloads (Overall): 30

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We study the expressive power and succinctness of order-invariant sentences of first-order (FO) and monadic second-order (MSO) logic on structures of bounded tree-depth. Order-invariance is undecidable in general and, thus, one strives for logics with a decidable syntax that have the same expressive power as order-invariant sentences. We show that ...

**Keywords**:
first-order logic, order-invariance, tree-depth, monadic second-order logic, succinctness, Expressivity

2

October 2017
ACM Transactions on Computation Theory (TOCT): Volume 9 Issue 3, October 2017

**Publisher:** ACM

**Bibliometrics**:

Citation Count: 0

Downloads (6 Weeks): 1, Downloads (12 Months): 42, Downloads (Overall): 42

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Graph canonization is the problem of computing a unique representative, a canon, from the isomorphism class of a given graph. This implies that two graphs are isomorphic exactly if their canons are equal. We show that graphs of bounded tree width can be canonized by logarithmic-space (logspace) algorithms. This implies ...

**Keywords**:
Algorithmic graph theory, computational complexity, graph canonization, graph isomorphism, logspace algorithms, tree width

3

September 2016
ACM Transactions on Computational Logic (TOCL): Volume 17 Issue 4, November 2016

**Publisher:** ACM

**Bibliometrics**:

Citation Count: 1

Downloads (6 Weeks): 3, Downloads (12 Months): 30, Downloads (Overall): 162

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We study on which classes of graphs first-order logic ( fo ) and monadic second-order logic ( mso ) have the same expressive power. We show that for all classes C of graphs that are closed under taking subgraphs, fo and mso have the same expressive power on C if ...

**Keywords**:
First-order logic, graph classes, guarded second-order logic, monadic second-order logic, tree depth

4

July 2016
LICS '16: Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science

**Publisher:** ACM

**Bibliometrics**:

Citation Count: 0

Downloads (6 Weeks): 6, Downloads (12 Months): 24, Downloads (Overall): 24

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Order-invariant formulas access an ordering on a structure's universe, but the model relation is independent of the used ordering. They are frequently used for logic-based approaches in computer science. Order-invariant formulas capture unordered problems of complexity classes and they model the independence of the answer to a database query from ...

**Keywords**:
first-order logic, modulo-counting logic, monadic second-order logic, order-invariant logic, bounded tree width, finite model theory, planarity

5

February 2016
ACM SIGLOG News: Volume 3 Issue 1, January 2016

**Publisher:** ACM

**Bibliometrics**:

Citation Count: 0

Downloads (6 Weeks): 1, Downloads (12 Months): 5, Downloads (Overall): 33

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It is well known that monadic-second order logic (MSO) expresses many natural NP-complete problems. However, a famous theorem of Courcelle states that every problem expressible in MSO can be solved in linear time for input graphs whose tree width is bounded by a fixed constant [Courcelle 1990]. Courcelle's Theorem is ...

6

March 2015
Algorithmica: Volume 71 Issue 3, March 2015

**Publisher:** Springer-Verlag New York, Inc.

The parameterized complexity of a problem is generally considered "settled" once it has been shown to be fixed-parameter tractable or to be complete for a class in a parameterized hierarchy such as the weft hierarchy. Several natural parameterized problems have, however, resisted such a classification. In the present paper we ...

**Keywords**:
Associative generability problem, Completeness, Feedback vertex set problem, Longest common subsequence problem, Space complexity, Parameterized complexity

7

May 2014
STOC '14: Proceedings of the forty-sixth annual ACM symposium on Theory of computing

**Publisher:** ACM

**Bibliometrics**:

Citation Count: 2

Downloads (6 Weeks): 6, Downloads (12 Months): 23, Downloads (Overall): 153

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Graph embeddings of bounded Euler genus (that means, embeddings with bounded orientable or nonorientable genus) help to design time-efficient algorithms for many graph problems. Since linear-time algorithms are known to compute embeddings of any bounded Euler genus, one can always assume to work with embedded graphs and, thus, obtain fast ...

**Keywords**:
algorithmic graph theory, logspace, Euler genus, computational complexity theory, isomorphism, graph embedding

8

April 2013
Theoretical Computer Science: Volume 483, April, 2013

**Publisher:** Elsevier Science Publishers Ltd.

Graph orientation is a fundamental problem in graph theory that has recently arisen in the study of signaling-regulatory pathways in protein networks. Given a graph and a list of source-target vertex pairs, one wishes to assign directions to the edges so as to maximize the number of pairs that admit ...

**Keywords**:
Protein-protein interaction network, Approximation algorithm, Mixed graph, Graph orientation

9

September 2012
IPEC'12: Proceedings of the 7th international conference on Parameterized and Exact Computation

**Publisher:** Springer-Verlag

Parameterized complexity theory measures the complexity of computational problems predominantly in terms of their parameterized time complexity. The purpose of the present paper is to demonstrate that the study of parameterized space complexity can give new insights into the complexity of well-studied parameterized problems like the feedback vertex set problem. ...

**Keywords**:
feedback vertex set, logarithmic space, fixedparameter tractable problems, parameterized complexity theory, reachability problems.

10

June 2012
LICS '12: Proceedings of the 2012 27th Annual IEEE/ACM Symposium on Logic in Computer Science

**Publisher:** IEEE Computer Society

**Bibliometrics**:

Citation Count: 4

Downloads (6 Weeks): 0, Downloads (12 Months): 7, Downloads (Overall): 62

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We study on which classes of graphs first-order logic (FO) and monadic second-order logic (MSO) have the same expressive power. We show that for each class of graphs that is closed under taking subgraphs, FO and MSO have the same expressive power on the class if, and only if, it ...

**Keywords**:
first-order logic, monadic second-order logic, guarded second-order logic, tree depth, graph classes

11

May 2012
Theoretical Computer Science: Volume 432, May, 2012

**Publisher:** Elsevier Science Publishers Ltd.

Haplotyping, also known as haplotype phase prediction, is the problem of predicting likely haplotypes based on genotype data. One fast haplotyping method is based on an evolutionary model in which a perfect phylogenetic tree is sought that explains the observed data. Unfortunately, when data entries are missing, which is often ...

**Keywords**:
Fixed-parameter algorithms, Phylogenies, Computational biology, Computational complexity, Haplotyping

12

April 2012
Information and Computation: Volume 213, April, 2012

**Publisher:** Academic Press, Inc.

Haplotyping, also known as haplotype phase prediction, is the problem of predicting likely haplotypes based on genotype data. One fast computational haplotyping method is based on an evolutionary model where a perfect phylogenetic tree is sought that explains the observed data. An extension of this approach tries to incorporate prior ...

**Keywords**:
Fixed-parameter algorithms, Perfect phylogeny, Polynomial-time algorithms, Maximum parsimony, Haplotype inference

13

June 2011
CPM'11: Proceedings of the 22nd annual conference on Combinatorial pattern matching

**Publisher:** Springer-Verlag

Graph orientation is a fundamental problem in graph theory that has recently arisen in the study of signaling-regulatory pathways in protein networks. Given a graph and a list of ordered source-target vertex pairs, it calls for assigning directions to the edges of the graph so as to maximize the number ...

**Keywords**:
graph orientation, mixed graph, approximation algorithm, protein-protein interaction network

14

March 2011
RECOMB'11: Proceedings of the 15th Annual international conference on Research in computational molecular biology

**Publisher:** Springer-Verlag

In a network orientation problem one is given a mixed graph, consisting of directed and undirected edges, and a set of source-target vertex pairs. The goal is to orient the undirected edges so that a maximum number of pairs admit a directed path from the source to the target. This ...

**Keywords**:
network orientation, protein-protein interaction, integer linear program, mixed graph, proteindna interaction

15

February 2011
Theoretical Computer Science: Volume 412 Issue 6, February, 2011

**Publisher:** Elsevier Science Publishers Ltd.

A string-based negative selection algorithm is an immune-inspired classifier that infers a partitioning of a string space @S^@? into ''normal'' and ''anomalous'' partitions from a training set S containing only samples from the ''normal'' partition. The algorithm generates a set of patterns, called ''detectors'', to cover regions of the string ...

**Keywords**:
Artificial immune systems, Negative selection, Anomaly detection, r-contiguous detectors, r-chunk detectors

16

October 2010
FOCS '10: Proceedings of the 2010 IEEE 51st Annual Symposium on Foundations of Computer Science

**Publisher:** IEEE Computer Society

Bodlaender's Theorem states that for every k there is a linear-time algorithm that decides whether an input graph has tree width k and, if so, computes a width-k tree composition. Courcelle's Theorem builds on Bodlaender's Theorem and states that for every monadic second-order formula φ and for every k there ...

**Keywords**:
deterministic logarithmic space, tree width, partial k-trees, monadic second-order logic

17

June 2010
CPM'10: Proceedings of the 21st annual conference on Combinatorial pattern matching

**Publisher:** Springer-Verlag

Haplotyping, also known as haplotype phase prediction, is the problem of predicting likely haplotypes based on genotype data. One fast computational haplotyping method is based on an evolutionary model where a perfect phylogenetic tree is sought that explains the observed data. In their CPM 2009 paper, Fellows et al. studied ...

18

August 2009
ICARIS '09: Proceedings of the 8th International Conference on Artificial Immune Systems

**Publisher:** Springer-Verlag

String-based negative selection is an immune-inspired classification scheme: Given a self-set <em>S</em> of strings, generate a set <em>D</em> of detectors that do not match any element of <em>S</em> . Then, use these detectors to partition a monitor set <em>M</em> into self and non-self elements. Implementations of this scheme are often ...

19

May 2009
TAMC '09: Proceedings of the 6th Annual Conference on Theory and Applications of Models of Computation

**Publisher:** Springer-Verlag

Haplotyping, also known as haplotype phase prediction, is the problem of predicting likely haplotypes from genotype data. One fast haplotyping method is based on an evolutionary model where a perfect phylogenetic tree is sought that explains the observed data. Unfortunately, when data entries are missing as is often the case ...

20

August 2008
MFCS '08: Proceedings of the 33rd international symposium on Mathematical Foundations of Computer Science

**Publisher:** Springer-Verlag

Haplotyping, also known as haplotype phase prediction, is the problem of predicting likely haplotypes based on genotype data. This problem, which has strong practical applications, can be approached using both statistical as well as combinatorial methods. While the most direct combinatorial approach, maximum parsimony, leads to NP-complete problems, the perfect ...

**Keywords**:
haplotyping, circuit classes, bioinformatics, computational complexity, perfect phylogenies