23,855 research outputs found
A survey on algorithmic aspects of modular decomposition
The modular decomposition is a technique that applies but is not restricted
to graphs. The notion of module naturally appears in the proofs of many graph
theoretical theorems. Computing the modular decomposition tree is an important
preprocessing step to solve a large number of combinatorial optimization
problems. Since the first polynomial time algorithm in the early 70's, the
algorithmic of the modular decomposition has known an important development.
This paper survey the ideas and techniques that arose from this line of
research
Fast Parallel Fixed-Parameter Algorithms via Color Coding
Fixed-parameter algorithms have been successfully applied to solve numerous
difficult problems within acceptable time bounds on large inputs. However, most
fixed-parameter algorithms are inherently \emph{sequential} and, thus, make no
use of the parallel hardware present in modern computers. We show that parallel
fixed-parameter algorithms do not only exist for numerous parameterized
problems from the literature -- including vertex cover, packing problems,
cluster editing, cutting vertices, finding embeddings, or finding matchings --
but that there are parallel algorithms working in \emph{constant} time or at
least in time \emph{depending only on the parameter} (and not on the size of
the input) for these problems. Phrased in terms of complexity classes, we place
numerous natural parameterized problems in parameterized versions of AC. On
a more technical level, we show how the \emph{color coding} method can be
implemented in constant time and apply it to embedding problems for graphs of
bounded tree-width or tree-depth and to model checking first-order formulas in
graphs of bounded degree
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Inference of single-cell phylogenies from lineage tracing data using Cassiopeia.
The pairing of CRISPR/Cas9-based gene editing with massively parallel single-cell readouts now enables large-scale lineage tracing. However, the rapid growth in complexity of data from these assays has outpaced our ability to accurately infer phylogenetic relationships. First, we introduce Cassiopeia-a suite of scalable maximum parsimony approaches for tree reconstruction. Second, we provide a simulation framework for evaluating algorithms and exploring lineage tracer design principles. Finally, we generate the most complex experimental lineage tracing dataset to date, 34,557 human cells continuously traced over 15 generations, and use it for benchmarking phylogenetic inference approaches. We show that Cassiopeia outperforms traditional methods by several metrics and under a wide variety of parameter regimes, and provide insight into the principles for the design of improved Cas9-enabled recorders. Together, these should broadly enable large-scale mammalian lineage tracing efforts. Cassiopeia and its benchmarking resources are publicly available at www.github.com/YosefLab/Cassiopeia
Finding approximate palindromes in strings
We introduce a novel definition of approximate palindromes in strings, and
provide an algorithm to find all maximal approximate palindromes in a string
with up to errors. Our definition is based on the usual edit operations of
approximate pattern matching, and the algorithm we give, for a string of size
on a fixed alphabet, runs in time. We also discuss two
implementation-related improvements to the algorithm, and demonstrate their
efficacy in practice by means of both experiments and an average-case analysis
Generating realistic scaled complex networks
Research on generative models is a central project in the emerging field of
network science, and it studies how statistical patterns found in real networks
could be generated by formal rules. Output from these generative models is then
the basis for designing and evaluating computational methods on networks, and
for verification and simulation studies. During the last two decades, a variety
of models has been proposed with an ultimate goal of achieving comprehensive
realism for the generated networks. In this study, we (a) introduce a new
generator, termed ReCoN; (b) explore how ReCoN and some existing models can be
fitted to an original network to produce a structurally similar replica, (c)
use ReCoN to produce networks much larger than the original exemplar, and
finally (d) discuss open problems and promising research directions. In a
comparative experimental study, we find that ReCoN is often superior to many
other state-of-the-art network generation methods. We argue that ReCoN is a
scalable and effective tool for modeling a given network while preserving
important properties at both micro- and macroscopic scales, and for scaling the
exemplar data by orders of magnitude in size.Comment: 26 pages, 13 figures, extended version, a preliminary version of the
paper was presented at the 5th International Workshop on Complex Networks and
their Application
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