Browsing by Subject "algorithm"

Now showing 1 - 10 of 10

Open Access
A branch-and-price algorithm for the vehicle routing problem with roaming delivery locations
(Elsevier Ltd, 2017) Ozbaygin G.; Ekin Karasan O.; Savelsbergh M.; Yaman, H.
We study the vehicle routing problem with roaming delivery locations in which the goal is to find a least-cost set of delivery routes for a fleet of capacitated vehicles and in which a customer order has to be delivered to the trunk of the customer's car during the time that the car is parked at one of the locations in the (known) customer's travel itinerary. We formulate the problem as a set-covering problem and develop a branch-and-price algorithm for its solution. The algorithm can also be used for solving a more general variant in which a hybrid delivery strategy is considered that allows a delivery to either a customer's home or to the trunk of the customer's car. We evaluate the effectiveness of the many algorithmic features incorporated in the algorithm in an extensive computational study and analyze the benefits of these innovative delivery strategies. The computational results show that employing the hybrid delivery strategy results in average cost savings of nearly 20% for the instances in our test set. © 2017 Elsevier Ltd
Open Access
Classification of closed-and open-shell pistachio nuts using voice-recognition technology
(American Society of Agricultural and Biological Engineers, 2004) Çetin, A. Enis; Pearson, T. C.; Tewfik, A. H.
An algorithm using speech recognition technology was developed to distinguish pistachio nuts with closed shells from those with open shells. It was observed that upon impact with a steel plate, nuts with closed shells emit different sounds than nuts with open shells. Features extracted from the sound signals consisted of mel-cepstrum coefficients and eigenvalues obtained from the principle component analysis (PCA) of the autocorrelation matrix of the sound signals. Classification of a sound signal was performed by linearly combining the mel-cepstrum and PCA feature vectors. An important property of the algorithm is that it is easily trainable, as are most speech-recognition algorithms. During the training phase, sounds of nuts with closed shells and with open shells were used to obtain a representative vector of each class. During the recognition phase, the feature vector from the sample under question was compared with representative vectors. The classification accuracy of closed-shell nuts was more than 99% on the validation set, which did not include the training set.
Open Access
Detecting secondary structure and surface orientation of helical peptide monolayers from resonant hybridization signals
(Nature Publishing Group, 2013) Alici, K. B.; Gallardo I.F.
Hybridization of dominant vibrational modes with meta-surface resonance allows detection of both structural changes and surface orientations of bound helical peptides. Depending on the resonance frequency of meta-molecules, a red- or blue- shift in peptide Amide-I frequency is observed. The underlying coupling mechanism is described by using a temporal coupled mode theory that is in very good agreement with the experimental results. This hybridization phenomenon constitutes the basis of many nanophotonic systems such as tunable coupled mode bio-sensors and dynamic peptide systems driven by infrared signals.
Open Access
Diagnosis of gastric carcinoma by classification on feature projections
(Elsevier, 2004) Güvenir, H. A.; Emeksiz, N.; İkizler, N.; Örmeci, N.
A new classification algorithm, called benefit maximizing classifier on feature projections (BCFP), is developed and applied to the problem of diagnosis of gastric carcinoma. The domain contains records of patients with known diagnosis through gastroscopy results. Given a training set of such records, the BCFP classifier learns how to differentiate a new case in the domain. BCFP represents a concept in the form of feature projections on each feature dimension separately. Classification in the BCFP algorithm is based on a voting among the individual predictions made on each feature. In the gastric carcinoma domain, a lesion can be an indicator of one of nine different levels of gastric carcinoma, from early to late stages. The benefit of correct classification of early levels is much more than that of late cases. Also, the costs of wrong classifications are not symmetric. In the training phase, the BCFP algorithm learns classification rules that maximize the benefit of classification. In the querying phase, using these rules, the BCFP algorithm tries to make a prediction maximizing the benefit. A genetic algorithm is applied to select the relevant features. The performance of the BCFP algorithm is evaluated in terms of accuracy and running time. The rules induced are verified by experts of the domain. © 2004 Elsevier B.V. All rights reserved.
Open Access
Div-blast: Diversification of sequence search results
(Public Library of Science, 2014) Eser, E.; Can, T.; Ferhatosmanoglu H.
Sequence similarity tools, such as BLAST, seek sequences most similar to a query from a database of sequences. They return results significantly similar to the query sequence and that are typically highly similar to each other. Most sequence analysis tasks in bioinformatics require an exploratory approach, where the initial results guide the user to new searches. However, diversity has not yet been considered an integral component of sequence search tools for this discipline. Some redundancy can be avoided by introducing non-redundancy during database construction, but it is not feasible to dynamically set a level of non-redundancy tailored to a query sequence. We introduce the problem of diverse search and browsing in sequence databases that produce non-redundant results optimized for any given query. We define diversity measures for sequences and propose methods to obtain diverse results extracted from current sequence similarity search tools. We also propose a new measure to evaluate the diversity of a set of sequences that is returned as a result of a sequence similarity query. We evaluate the effectiveness of the proposed methods in post-processing BLAST and PSIBLAST results. We also assess the functional diversity of the returned results based on available Gene Ontology annotations. Additionally, we include a comparison with a current redundancy elimination tool, CD-HIT. Our experiments show that the proposed methods are able to achieve more diverse yet significant result sets compared to static non-redundancy approaches. In both sequencebased and functional diversity evaluation, the proposed diversification methods significantly outperform original BLAST results and other baselines. A web based tool implementing the proposed methods, Div-BLAST, can be accessed at cedar.cs.bilkent.edu.tr/Div-BLAST © 2014 Eser et al.
Open Access
Is the largest Lyapunov exponent preserved in embedded dynamics?
(2000) Dechert W.Davis, Gençay, R.
The method of reconstruction for an n-dimensional system from observations is to form vectors of m consecutive observations, which for m > 2n, is generically an embedding. This is Takens' result. Our analytical examples show that it is possible to obtain spurious Lyapunov exponents that are even larger than the largest Lyapunov exponent of the original system. Therefore, we present examples where the largest Lyapunov exponent may not be preserved under Takens' embedding theorem. (C) 2000 Elsevier Science B.V.
Open Access
Leg motion classification with artificial neural networks using wavelet-based features of gyroscope signals
(2011) Ayrulu-Erdem, B.; Barshan, B.
We extract the informative features of gyroscope signals using the discrete wavelet transform (DWT) decomposition and provide them as input to multi-layer feed-forward artificial neural networks (ANNs) for leg motion classification. Since the DWT is based on correlating the analyzed signal with a prototype wavelet function, selection of the wavelet type can influence the performance of wavelet-based applications significantly. We also investigate the effect of selecting different wavelet families on classification accuracy and ANN complexity and provide a comparison between them. The maximum classification accuracy of 97.7% is achieved with the Daubechies wavelet of order 16 and the reverse bi-orthogonal (RBO) wavelet of order 3.1, both with similar ANN complexity. However, the RBO 3.1 wavelet is preferable because of its lower computational complexity in the DWT decomposition and reconstruction. © 2011 by the authors; licensee MDPI, Basel, Switzerland.
Open Access
Reduced field-of-view DWI with robust fat suppression and unrestricted slice coverage using tilted 2D RF excitation
(John Wiley and Sons Inc., 2016) Banerjee, S.; Nishimura, D. G.; Shankaranarayanan, A.; Saritas, E. U.
Purpose: Reduced field-of-view (rFOV) diffusion-weighted imaging (DWI) using 2D echo-planar radiofrequency (2DRF) excitation has been widely and successfully applied in clinical settings. The purpose of this work is to further improve its clinical utility by overcoming slice coverage limitations without any scan time penalty while providing robust fat suppression. Theory and Methods: During multislice imaging with 2DRF pulses, periodic sidelobes in the slice direction cause partial saturation, limiting the slice coverage. In this work, a tilting of the excitation plane is proposed to push the sidelobes out of the imaging section while preserving robust fat suppression. The 2DRF pulse is designed using Shinnar-Le Roux algorithm on a rotated excitation k-space. The performance of the method is validated via simulations, phantom experiments, and high in-plane resolution in vivo DWI of the spinal cord. Results: Results show that rFOV DWI using the tilted 2DRF pulse provides increased signal-to-noise ratio, extended coverage, and robust fat suppression, without any scan time penalty. Conclusion: Using a tilted 2DRF excitation, a high-resolution rFOV DWI method with robust fat suppression and unrestricted slice coverage is presented. This method will be beneficial in clinical applications needing large slice coverage, for example, axial imaging of the spine, prostate, or breast. Magn Reson Med 76:1668–1676, 2016. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine
Open Access
SBGNViz: A tool for visualization and complexity management of SBGN process description maps
(Public Library of Science, 2015) Sari, M.; Bahceci I.; Dogrusoz, U.; Sumer, S.O.; Aksoy, B.A.; Babur O.; Demir, E.
Background Information about cellular processes and pathways is becoming increasingly available in detailed, computable standard formats such as BioPAX and SBGN. Effective visualization of this information is a key recurring requirement for biological data analysis, especially for -omic data. Biological data analysis is rapidly migrating to web based platforms; thus there is a substantial need for sophisticated web based pathway viewers that support these platforms and other use cases. Results Towards this goal, we developed a web based viewer named SBGNViz for process description maps in SBGN (SBGN-PD). SBGNViz can visualize both BioPAX and SBGN formats. Unique features of SBGNViz include the ability to nest nodes to arbitrary depths to represent molecular complexes and cellular locations, automatic pathway layout, editing and highlighting facilities to enable focus on sub-maps, and the ability to inspect pathway members for detailed information from EntrezGene. SBGNViz can be used within a web browser without any installation and can be readily embedded into web pages. SBGNViz has two editions built with ActionScript and JavaScript. The JavaScript edition, which also works on touch enabled devices, introduces novel methods for managing and reducing complexity of large SBGN-PD maps for more effective analysis. Conclusion SBGNViz fills an important gap by making the large and fast-growing corpus of rich pathway information accessible to web based platforms. SBGNViz can be used in a variety of contexts and in multiple scenarios ranging from visualization of the results of a single study in a web page to building data analysis platforms. © 2015 Sari et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Open Access
Unidirectional transmission in photonic-crystal gratings at beam-type illumination
(Optical Society of American (OSA), 2010) Cakmak, A.O.; Colak, E.; Serebryannikov, A.E.; Özbay, Ekmel
Unidirectional transmission is studied theoretically and experimentally for the gratings with one-side corrugations (non-symmetric gratings), which are based on two-dimensional photonic crystals composed of alumina rods. The unidirectional transmission appears at a fixed angle of incidence as a combined effect of the peculiar dispersion features of the photonic crystal and the properly designed corrugations. It is shown that the basic unidirectional transmission characteristics, which are observed at a plane-wave illumination, are preserved at Gaussian-beam and horn antenna illuminations. The main attention is paid to the single-beam unidirectional regime, which is associated with the strong directional selectivity arising due to the first negative diffraction order. An additional degree of freedom for controlling the transmission of the electromagnetic waves is obtained by making use of the asymmetric corrugations at the photonic crystal interface. © 2010 Optical Society of America.