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