179,454 research outputs found
Linear-Time Algorithms for Finding Tucker Submatrices and Lekkerkerker-Boland Subgraphs
Lekkerkerker and Boland characterized the minimal forbidden induced subgraphs
for the class of interval graphs. We give a linear-time algorithm to find one
in any graph that is not an interval graph. Tucker characterized the minimal
forbidden submatrices of binary matrices that do not have the consecutive-ones
property. We give a linear-time algorithm to find one in any binary matrix that
does not have the consecutive-ones property.Comment: A preliminary version of this work appeared in WG13: 39th
International Workshop on Graph-Theoretic Concepts in Computer Scienc
PQ TREES, CONSECUTIVE ONES PROBLEM AND APPLICATIONS
A PQ tree is an advanced tree–based data structure, which represents a family of permutations on a set of elements. In this research article, we considered the significance of PQ trees and the Consecutive ones Problem to Computer Science and bioinformatics and their various applications.
We also went further to demonstrate the operations of the characteristics of the Consecutive ones property by simulation, using high level programming languages. Attempt was also made at developing a PQ tree–Consecutive Ones analyzer, which could be instrumental not only as an
educative tool to inquisitive students, but also serve as an important tool in developing clustering software in the field of bioinformatics and other application domains, with respect to solving real life problems
Isomorphism of graph classes related to the circular-ones property
We give a linear-time algorithm that checks for isomorphism between two 0-1
matrices that obey the circular-ones property. This algorithm leads to
linear-time isomorphism algorithms for related graph classes, including Helly
circular-arc graphs, \Gamma-circular-arc graphs, proper circular-arc graphs and
convex-round graphs.Comment: 25 pages, 9 figure
Subclasses of Normal Helly Circular-Arc Graphs
A Helly circular-arc model M = (C,A) is a circle C together with a Helly
family \A of arcs of C. If no arc is contained in any other, then M is a proper
Helly circular-arc model, if every arc has the same length, then M is a unit
Helly circular-arc model, and if there are no two arcs covering the circle,
then M is a normal Helly circular-arc model. A Helly (resp. proper Helly, unit
Helly, normal Helly) circular-arc graph is the intersection graph of the arcs
of a Helly (resp. proper Helly, unit Helly, normal Helly) circular-arc model.
In this article we study these subclasses of Helly circular-arc graphs. We show
natural generalizations of several properties of (proper) interval graphs that
hold for some of these Helly circular-arc subclasses. Next, we describe
characterizations for the subclasses of Helly circular-arc graphs, including
forbidden induced subgraphs characterizations. These characterizations lead to
efficient algorithms for recognizing graphs within these classes. Finally, we
show how do these classes of graphs relate with straight and round digraphs.Comment: 39 pages, 13 figures. A previous version of the paper (entitled
Proper Helly Circular-Arc Graphs) appeared at WG'0
Minimal Conflicting Sets for the Consecutive Ones Property in ancestral genome reconstruction
A binary matrix has the Consecutive Ones Property (C1P) if its columns can be
ordered in such a way that all 1's on each row are consecutive. A Minimal
Conflicting Set is a set of rows that does not have the C1P, but every proper
subset has the C1P. Such submatrices have been considered in comparative
genomics applications, but very little is known about their combinatorial
structure and efficient algorithms to compute them. We first describe an
algorithm that detects rows that belong to Minimal Conflicting Sets. This
algorithm has a polynomial time complexity when the number of 1's in each row
of the considered matrix is bounded by a constant. Next, we show that the
problem of computing all Minimal Conflicting Sets can be reduced to the joint
generation of all minimal true clauses and maximal false clauses for some
monotone boolean function. We use these methods on simulated data related to
ancestral genome reconstruction to show that computing Minimal Conflicting Set
is useful in discriminating between true positive and false positive ancestral
syntenies. We also study a dataset of yeast genomes and address the reliability
of an ancestral genome proposal of the Saccahromycetaceae yeasts.Comment: 20 pages, 3 figure
Mol-CycleGAN - a generative model for molecular optimization
Designing a molecule with desired properties is one of the biggest challenges
in drug development, as it requires optimization of chemical compound
structures with respect to many complex properties. To augment the compound
design process we introduce Mol-CycleGAN - a CycleGAN-based model that
generates optimized compounds with high structural similarity to the original
ones. Namely, given a molecule our model generates a structurally similar one
with an optimized value of the considered property. We evaluate the performance
of the model on selected optimization objectives related to structural
properties (presence of halogen groups, number of aromatic rings) and to a
physicochemical property (penalized logP). In the task of optimization of
penalized logP of drug-like molecules our model significantly outperforms
previous results
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