111,099 research outputs found
Computational Performance Evaluation of Two Integer Linear Programming Models for the Minimum Common String Partition Problem
In the minimum common string partition (MCSP) problem two related input
strings are given. "Related" refers to the property that both strings consist
of the same set of letters appearing the same number of times in each of the
two strings. The MCSP seeks a minimum cardinality partitioning of one string
into non-overlapping substrings that is also a valid partitioning for the
second string. This problem has applications in bioinformatics e.g. in
analyzing related DNA or protein sequences. For strings with lengths less than
about 1000 letters, a previously published integer linear programming (ILP)
formulation yields, when solved with a state-of-the-art solver such as CPLEX,
satisfactory results. In this work, we propose a new, alternative ILP model
that is compared to the former one. While a polyhedral study shows the linear
programming relaxations of the two models to be equally strong, a comprehensive
experimental comparison using real-world as well as artificially created
benchmark instances indicates substantial computational advantages of the new
formulation.Comment: arXiv admin note: text overlap with arXiv:1405.5646 This paper
version replaces the one submitted on January 10, 2015, due to detected error
in the calculation of the variables involved in the ILP model
Index to Library Trends Volume 38
published or submitted for publicatio
High-speed in vitro intensity diffraction tomography
We demonstrate a label-free, scan-free intensity diffraction tomography technique utilizing annular illumination (aIDT) to rapidly characterize large-volume three-dimensional (3-D) refractive index distributions in vitro. By optimally matching the illumination geometry to the microscope pupil, our technique reduces the data requirement by 60 times to achieve high-speed 10-Hz volume rates. Using eight intensity images, we recover volumes of ∼350 μm × 100 μm × 20 μm, with near diffraction-limited lateral resolution of ∼ 487 nm and axial resolution of ∼ 3.4 μm. The attained large volume rate and high-resolution enable 3-D quantitative phase imaging of complex living biological samples across multiple length scales. We demonstrate aIDT’s capabilities on unicellular diatom microalgae, epithelial buccal cell clusters with native bacteria, and live Caenorhabditis elegans specimens. Within these samples, we recover macroscale cellular structures, subcellular organelles, and dynamic micro-organism tissues with minimal motion artifacts. Quantifying such features has significant utility in oncology, immunology, and cellular pathophysiology, where these morphological features are evaluated for changes in the presence of disease, parasites, and new drug treatments. Finally, we simulate the aIDT system to highlight the accuracy and sensitivity of the proposed technique. aIDT shows promise as a powerful high-speed, label-free computational microscopy approach for applications where natural imaging is required to evaluate environmental effects on a sample in real time.https://arxiv.org/abs/1904.06004Accepted manuscrip
On computing fixpoints in well-structured regular model checking, with applications to lossy channel systems
We prove a general finite convergence theorem for "upward-guarded" fixpoint
expressions over a well-quasi-ordered set. This has immediate applications in
regular model checking of well-structured systems, where a main issue is the
eventual convergence of fixpoint computations. In particular, we are able to
directly obtain several new decidability results on lossy channel systems.Comment: 16 page
Kochen-Specker Sets and Generalized Orthoarguesian Equations
Every set (finite or infinite) of quantum vectors (states) satisfies
generalized orthoarguesian equations (OA). We consider two 3-dim
Kochen-Specker (KS) sets of vectors and show how each of them should be
represented by means of a Hasse diagram---a lattice, an algebra of subspaces of
a Hilbert space--that contains rays and planes determined by the vectors so as
to satisfy OA. That also shows why they cannot be represented by a special
kind of Hasse diagram called a Greechie diagram, as has been erroneously done
in the literature. One of the KS sets (Peres') is an example of a lattice in
which 6OA pass and 7OA fails, and that closes an open question of whether the
7oa class of lattices properly contains the 6oa class. This result is important
because it provides additional evidence that our previously given proof of noa
=< (n+1)oa can be extended to proper inclusion noa < (n+1)oa and that nOA form
an infinite sequence of successively stronger equations.Comment: 16 pages and 5 figure
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