5,958 research outputs found
If the Current Clique Algorithms are Optimal, so is Valiant's Parser
The CFG recognition problem is: given a context-free grammar
and a string of length , decide if can be obtained from
. This is the most basic parsing question and is a core computer
science problem. Valiant's parser from 1975 solves the problem in
time, where is the matrix multiplication
exponent. Dozens of parsing algorithms have been proposed over the years, yet
Valiant's upper bound remains unbeaten. The best combinatorial algorithms have
mildly subcubic complexity.
Lee (JACM'01) provided evidence that fast matrix multiplication is needed for
CFG parsing, and that very efficient and practical algorithms might be hard or
even impossible to obtain. Lee showed that any algorithm for a more general
parsing problem with running time can
be converted into a surprising subcubic algorithm for Boolean Matrix
Multiplication. Unfortunately, Lee's hardness result required that the grammar
size be . Nothing was known for the more relevant
case of constant size grammars.
In this work, we prove that any improvement on Valiant's algorithm, even for
constant size grammars, either in terms of runtime or by avoiding the
inefficiencies of fast matrix multiplication, would imply a breakthrough
algorithm for the -Clique problem: given a graph on nodes, decide if
there are that form a clique.
Besides classifying the complexity of a fundamental problem, our reduction
has led us to similar lower bounds for more modern and well-studied cubic time
problems for which faster algorithms are highly desirable in practice: RNA
Folding, a central problem in computational biology, and Dyck Language Edit
Distance, answering an open question of Saha (FOCS'14)
Landscape statistics of the low autocorrelated binary string problem
The statistical properties of the energy landscape of the low autocorrelated
binary string problem (LABSP) are studied numerically and compared with those
of several classic disordered models. Using two global measures of landscape
structure which have been introduced in the Simulated Annealing literature,
namely, depth and difficulty, we find that the landscape of LABSP, except
perhaps for a very large degeneracy of the local minima energies, is
qualitatively similar to some well-known landscapes such as that of the
mean-field 2-spin glass model. Furthermore, we consider a mean-field
approximation to the pure model proposed by Bouchaud and Mezard (1994, J.
Physique I France 4 1109) and show both analytically and numerically that it
describes extremely well the statistical properties of LABSP
The interval ordering problem
For a given set of intervals on the real line, we consider the problem of
ordering the intervals with the goal of minimizing an objective function that
depends on the exposed interval pieces (that is, the pieces that are not
covered by earlier intervals in the ordering). This problem is motivated by an
application in molecular biology that concerns the determination of the
structure of the backbone of a protein.
We present polynomial-time algorithms for several natural special cases of
the problem that cover the situation where the interval boundaries are
agreeably ordered and the situation where the interval set is laminar. Also the
bottleneck variant of the problem is shown to be solvable in polynomial time.
Finally we prove that the general problem is NP-hard, and that the existence of
a constant-factor-approximation algorithm is unlikely
Computational complexity of the landscape I
We study the computational complexity of the physical problem of finding
vacua of string theory which agree with data, such as the cosmological
constant, and show that such problems are typically NP hard. In particular, we
prove that in the Bousso-Polchinski model, the problem is NP complete. We
discuss the issues this raises and the possibility that, even if we were to
find compelling evidence that some vacuum of string theory describes our
universe, we might never be able to find that vacuum explicitly.
In a companion paper, we apply this point of view to the question of how
early cosmology might select a vacuum.Comment: JHEP3 Latex, 53 pp, 2 .eps figure
A Seeded Genetic Algorithm for RNA Secondary Structural Prediction with Pseudoknots
This work explores a new approach in using genetic algorithm to predict RNA secondary structures with pseudoknots. Since only a small portion of most RNA structures is comprised of pseudoknots, the majority of structural elements from an optimal pseudoknot-free structure are likely to be part of the true structure. Thus seeding the genetic algorithm with optimal pseudoknot-free structures will more likely lead it to the true structure than a randomly generated population. The genetic algorithm uses the known energy models with an additional augmentation to allow complex pseudoknots. The nearest-neighbor energy model is used in conjunction with Turner’s thermodynamic parameters for pseudoknot-free structures, and the H-type pseudoknot energy estimation for simple pseudoknots. Testing with known pseudoknot sequences from PseudoBase shows that it out performs some of the current popular algorithms
Lecture Notes of Tensor Network Contractions
Tensor network (TN), a young mathematical tool of high vitality and great
potential, has been undergoing extremely rapid developments in the last two
decades, gaining tremendous success in condensed matter physics, atomic
physics, quantum information science, statistical physics, and so on. In this
lecture notes, we focus on the contraction algorithms of TN as well as some of
the applications to the simulations of quantum many-body systems. Starting from
basic concepts and definitions, we first explain the relations between TN and
physical problems, including the TN representations of classical partition
functions, quantum many-body states (by matrix product state, tree TN, and
projected entangled pair state), time evolution simulations, etc. These
problems, which are challenging to solve, can be transformed to TN contraction
problems. We present then several paradigm algorithms based on the ideas of the
numerical renormalization group and/or boundary states, including density
matrix renormalization group, time-evolving block decimation,
coarse-graining/corner tensor renormalization group, and several distinguished
variational algorithms. Finally, we revisit the TN approaches from the
perspective of multi-linear algebra (also known as tensor algebra or tensor
decompositions) and quantum simulation. Despite the apparent differences in the
ideas and strategies of different TN algorithms, we aim at revealing the
underlying relations and resemblances in order to present a systematic picture
to understand the TN contraction approaches.Comment: 134 pages, 68 figures. In this version, the manuscript has been
changed into the format of book; new sections about tensor network and
quantum circuits have been adde
Forward Flux Sampling for rare event simulations
Rare events are ubiquitous in many different fields, yet they are notoriously
difficult to simulate because few, if any, events are observed in a conventiona
l simulation run. Over the past several decades, specialised simulation methods
have been developed to overcome this problem. We review one recently-developed
class of such methods, known as Forward Flux Sampling. Forward Flux Sampling
uses a series of interfaces between the initial and final states to calculate
rate constants and generate transition paths, for rare events in equilibrium or
nonequilibrium systems with stochastic dynamics. This review draws together a
number of recent advances, summarizes several applications of the method and
highlights challenges that remain to be overcome.Comment: minor typos in the manuscript. J.Phys.:Condensed Matter (accepted for
publication
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