6,519 research outputs found
Fitting the Continuum Component of A Composite SDSS Quasar Spectrum Using CMA-ES
Fitting the continuum component of a quasar spectrum in UV/optical band is
challenging due to contamination of numerous emission lines. Traditional
fitting algorithms such as the least-square fitting and the Levenberg-Marquardt
algorithm (LMA) are fast but are sensitive to initial values of fitting
parameters. They cannot guarantee to find global optimum solutions when the
object functions have multiple minima. In this work, we attempt to fit a
typical quasar spectrum using the Covariance Matrix Adaptation Evolution
Strategy (CMA-ES). The spectrum is generated by composing a number of real
quasar spectra from the Sloan Digital Sky Survey (SDSS) quasar catalog data
release 3 (DR3) so it has a higher signal-to-noise ratio. The CMA-ES algorithm
is an evolutionary algorithm that is designed to find the global rather than
the local minima. The algorithm we implemented achieves an improved fitting
result than the LMA and unlike the LMA, it is independent of initial parameter
values. We are looking forward to implementing this algorithm to real quasar
spectra in UV/optical band.Comment: 23 pages, 8 figures, 5 table
An Introduction to Programming for Bioscientists: A Python-based Primer
Computing has revolutionized the biological sciences over the past several
decades, such that virtually all contemporary research in the biosciences
utilizes computer programs. The computational advances have come on many
fronts, spurred by fundamental developments in hardware, software, and
algorithms. These advances have influenced, and even engendered, a phenomenal
array of bioscience fields, including molecular evolution and bioinformatics;
genome-, proteome-, transcriptome- and metabolome-wide experimental studies;
structural genomics; and atomistic simulations of cellular-scale molecular
assemblies as large as ribosomes and intact viruses. In short, much of
post-genomic biology is increasingly becoming a form of computational biology.
The ability to design and write computer programs is among the most
indispensable skills that a modern researcher can cultivate. Python has become
a popular programming language in the biosciences, largely because (i) its
straightforward semantics and clean syntax make it a readily accessible first
language; (ii) it is expressive and well-suited to object-oriented programming,
as well as other modern paradigms; and (iii) the many available libraries and
third-party toolkits extend the functionality of the core language into
virtually every biological domain (sequence and structure analyses,
phylogenomics, workflow management systems, etc.). This primer offers a basic
introduction to coding, via Python, and it includes concrete examples and
exercises to illustrate the language's usage and capabilities; the main text
culminates with a final project in structural bioinformatics. A suite of
Supplemental Chapters is also provided. Starting with basic concepts, such as
that of a 'variable', the Chapters methodically advance the reader to the point
of writing a graphical user interface to compute the Hamming distance between
two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables,
numerous exercises, and 19 pages of Supporting Information; currently in
press at PLOS Computational Biolog
An archiving model for a hierarchical information storage environment
Cataloged from PDF version of article.We consider an archiving model for a database consisting of secondary and tertiary storage devices in which the
query rate for a record declines as it ages. We propose a `dynamic' archiving policy based on the number of records and
the age of the records in the secondary device. We analyze the cases when the number of new records inserted in the
system over time are either constant or follow a Poisson process. For both scenarios, we characterize the properties of
the policy parameters and provide optimization results when the objective is to minimize the average record retrieval
times. Furthermore, we propose a simple heuristic method for obtaining near-optimal policies in large databases when
the record query rate declines exponentially with time. The e ectiveness of the heuristic is tested via a numerical experiment.
Finally, we examine the behavior of performance measures such as the average record retrieval time and the
hit rate as system parameters are varied. Ó 2000 Elsevier Science B.V. All rights reserved
Dynamic lot sizing for a warm/cold process: Heuristics and insights
Cataloged from PDF version of article.We consider the dynamic lot sizing problem for a warm/cold process where the process can be kept
warm at a unit variable cost for the next period if more than a prespecified quantity has been produced.
Exploiting the optimal production plan structures, we develop nine rule-based forward solution
heuristics. Proposed heuristics are modified counterparts of the heuristics developed previously for
the classical dynamic lot sizing problem. In a numerical study, we investigate the performance of the
proposed heuristics and identify operating environment characteristics where each particular heuristic
is the best or among the best. Moreover, for a warm/cold process setting, our numerical studies indicate
that, when used on a rolling horizon basis, a heuristic may also perform better costwise than a solution
obtained using a dynamic programming approach.
& 2012 Elsevier B.V. All rights reserved
On-board processing for future satellite communications systems: Satellite-Routed FDMA
A frequency division multiple access (FDMA) 30/20 GHz satellite communications architecture without on-board baseband processing is investigated. Conceptual system designs are suggested for domestic traffic models totaling 4 Gb/s of customer premises service (CPS) traffic and 6 Gb/s of trunking traffic. Emphasis is given to the CPS portion of the system which includes thousands of earth terminals with digital traffic ranging from a single 64 kb/s voice channel to hundreds of channels of voice, data, and video with an aggregate data rate of 33 Mb/s. A unique regional design concept that effectively smooths the non-uniform traffic distribution and greatly simplifies the satellite design is employed. The satellite antenna system forms thirty-two 0.33 deg beam on both the uplinks and the downlinks in one design. In another design matched to a traffic model with more dispersed users, there are twenty-four 0.33 deg beams and twenty-one 0.7 deg beams. Detailed system design techniques show that a single satellite producing approximately 5 kW of dc power is capable of handling at least 75% of the postulated traffic. A detailed cost model of the ground segment and estimated system costs based on current information from manufacturers are presented
On pricing of perishable assets with menu costs
Cataloged from PDF version of article.We consider dynamic pricing of perishable assets in the presence of price-sensitive
renewal demand processes. Unlike the existing works in the literature, we explicitly
incorporate non-negligible price change costs which reflects the revenue management
practice more realistically. These costs are also known as menu costs in the economic
literature. The objective is to maximize the discounted expected profit for an initial
inventory of Q items by determining the selling prices dynamically. We employ a
dynamic programming approach and formulate a model that captures the price–
demand relationship. We establish some theoretical results on the properties of the
problem at hand. Specifically, we establish the sufficient conditions under which the
within-period profit is concave in the selling price and in the remaining shelf life and,
furthermore, show the structure of the myopically and asymptotically optimal pricing
policy. In a numerical study, we investigate the impact of various system parameters
and, in particular, the existence of menu costs, on pricing decisions. We observe that
ignoring menu costs may be significantly misleading for the implementation of revenue
management. We also propose four implementable policy heuristics and examine their
performances. Our findings support some results previously obtained in settings with
continuous pricing and negligible price change costs; and, contradict some others.
& 2009 Published by Elsevier B.V
Centralized and decentralized management of groundwater with multiple users
Cataloged from PDF version of article.In this work, we investigate two groundwater inventory management schemes with multiple users in a
dynamic game-theoretic structure: (i) under the centralized management scheme, users are allowed to
pump water from a common aquifer with the supervision of a social planner, and (ii) under the decentralized
management scheme, each user is allowed to pump water from a common aquifer making usage
decisions individually in a non-cooperative fashion. This work is motivated by the work of Saak and Peterson
[14], which considers a model with two identical users sharing a common aquifer over a two-period
planning horizon. In our work, the model and results of Saak and Peterson [14] are generalized in
several directions. We first build on and extend their work to the case of n non-identical users distributed
over a common aquifer region. Furthermore, we consider two different geometric configurations overlying
the aquifer, namely, the strip and the ring configurations. In each configuration, general analytical
results of the optimal groundwater usage are obtained and numerical examples are discussed for both
centralized and decentralized problems.
2011 Elsevier B.V. All rights reserved
A Continuous Review Replenishment-Disposal Policy for an Inventory System with autonomous supply and fixed disposal costs
Cataloged from PDF version of article.In this study, we analyze an inventory system facing stochastic external demands and an autonomous supply (independent return flow) in the presence of fixed disposal costs and positive lead times under a continuous review replenishment-disposal policy. We derive the analytical expressions of the operating characteristics of the system; and, construct the objective function to minimize the total expected costs of ordering, holding, purchasing and disposal per unit time subject to a fill rate constraint. An extensive numerical analysis is conducted to study the sensitivity of the policy parameters and the benefit of employing a policy which allows for disposal of excess stock in this setting. We model the net demand process as the superposition of normally distributed external demand and inflows, which is expressed as a Brownian motion process. Our findings indicate that the disposal option results in considerable savings even (i) in the presence of non-zero fixed disposal costs, (ii) large actual demand rates with high return ratios (resulting in small net demands) and (iii) for moderate return ratios with high demand variability. (C) 2007 Elsevier B.V. All rights reserved
Single Item Lot Sizing Problem for a Warm/Cold Process with Immediate Lost Sales
Cataloged from PDF version of article.We consider the dynamic lot-sizing problem with finite capacity and possible lost sales for a process that could be kept
warm at a unit variable cost for the next period t + 1 only if more than a threshold value Qt has been produced and would
be cold, otherwise. Production with a cold process incurs a fixed positive setup cost, Kt and setup time, St, which may be
positive. Setup costs and times for a warm process are negligible. We develop a dynamic programming formulation of the
problem, establish theoretical results on the structure of the optimal production plan in the presence of zero and positive
setup times with Wagner–Whitin-type cost structures. We also show that the solution to the dynamic lot-sizing problem
with lost sales are generated from the full commitment production series improved via lost sales decisions in the presence of
a warm/cold process.
2006 Elsevier B.V. All rights reserved
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