1,034 research outputs found
Modifications of the Limited Memory BFGS Algorithm for Large-scale Nonlinear Optimization
In this paper we present two new numerical methods for unconstrained large-scale optimization. These methods apply update formulae, which are derived by considering different techniques of approximating the objective function. Theoretical analysis is given to show the advantages of using these update formulae. It is observed that these update formulae can be employed within the framework of limited memory strategy with only a modest increase in the linear algebra cost. Comparative results with limited memory BFGS (L-BFGS) method are presented.</p
Second order adjoints for solving PDE-constrained optimization problems
Inverse problems are of utmost importance in many fields of science and engineering. In the
variational approach inverse problems are formulated as PDE-constrained optimization problems,
where the optimal estimate of the uncertain parameters is the minimizer of a certain cost
functional subject to the constraints posed by the model equations. The numerical solution
of such optimization problems requires the computation of derivatives of the model output
with respect to model parameters. The first order derivatives of a cost functional (defined
on the model output) with respect to a large number of model parameters can be calculated
efficiently through first order adjoint sensitivity analysis. Second order adjoint models
give second derivative information in the form of matrix-vector products between the Hessian
of the cost functional and user defined vectors. Traditionally, the construction of second
order derivatives for large scale models has been considered too costly. Consequently, data
assimilation applications employ optimization algorithms that use only first order derivative
information, like nonlinear conjugate gradients and quasi-Newton methods.
In this paper we discuss the mathematical foundations of second order adjoint sensitivity
analysis and show that it provides an efficient approach to obtain Hessian-vector products. We
study the benefits of using of second order information in the numerical optimization process
for data assimilation applications. The numerical studies are performed in a twin experiment
setting with a two-dimensional shallow water model. Different scenarios are considered with
different discretization approaches, observation sets, and noise levels. Optimization algorithms
that employ second order derivatives are tested against widely used methods that require
only first order derivatives. Conclusions are drawn regarding the potential benefits and the
limitations of using high-order information in large scale data assimilation problems
The LBFGS Quasi-Newtonian Method for Molecular Modeling Prion AGAAAAGA Amyloid Fibrils
Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance)
spectroscopy, dual polarization interferometry, etc are indeed very powerful
tools to determine the 3-Dimensional structure of a protein (including the
membrane protein); theoretical mathematical and physical computational
approaches can also allow us to obtain a description of the protein 3D
structure at a submicroscopic level for some unstable, noncrystalline and
insoluble proteins. X-ray crystallography finds the X-ray final structure of a
protein, which usually need refinements using theoretical protocols in order to
produce a better structure. This means theoretical methods are also important
in determinations of protein structures. Optimization is always needed in the
computer-aided drug design, structure-based drug design, molecular dynamics,
and quantum and molecular mechanics. This paper introduces some optimization
algorithms used in these research fields and presents a new theoretical
computational method - an improved LBFGS Quasi-Newtonian mathematical
optimization method - to produce 3D structures of Prion AGAAAAGA amyloid
fibrils (which are unstable, noncrystalline and insoluble), from the potential
energy minimization point of view. Because the NMR or X-ray structure of the
hydrophobic region AGAAAAGA of prion proteins has not yet been determined, the
model constructed by this paper can be used as a reference for experimental
studies on this region, and may be useful in furthering the goals of medicinal
chemistry in this field
Optimization Methods for Inverse Problems
Optimization plays an important role in solving many inverse problems.
Indeed, the task of inversion often either involves or is fully cast as a
solution of an optimization problem. In this light, the mere non-linear,
non-convex, and large-scale nature of many of these inversions gives rise to
some very challenging optimization problems. The inverse problem community has
long been developing various techniques for solving such optimization tasks.
However, other, seemingly disjoint communities, such as that of machine
learning, have developed, almost in parallel, interesting alternative methods
which might have stayed under the radar of the inverse problem community. In
this survey, we aim to change that. In doing so, we first discuss current
state-of-the-art optimization methods widely used in inverse problems. We then
survey recent related advances in addressing similar challenges in problems
faced by the machine learning community, and discuss their potential advantages
for solving inverse problems. By highlighting the similarities among the
optimization challenges faced by the inverse problem and the machine learning
communities, we hope that this survey can serve as a bridge in bringing
together these two communities and encourage cross fertilization of ideas.Comment: 13 page
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