2014
Erdoğan, E; Muşta, MS; Güçlüoğlu, T Outage probability of a cooperative maximum ratio transmission Journal Article 2014 22nd Signal Processing and Communications Applications Conference (SIU …, 2014. @article{pop00062, title = {Outage probability of a cooperative maximum ratio transmission}, author = {E Erdoğan and MS Muşta and T Güçlüoğlu}, year = {2014}, date = {2014-01-01}, journal = {2014 22nd Signal Processing and Communications Applications Conference (SIU …}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Atakan, Barış; Atakan, Barış Passive Molecular Communication Through Absorbers Incollection Molecular Communications and Nanonetworks, 2014. @incollection{Atakan2014d, title = {Passive Molecular Communication Through Absorbers}, author = {Barış Atakan and Barış Atakan}, doi = {10.1007/978-1-4939-0739-7_2}, year = {2014}, date = {2014-01-01}, booktitle = {Molecular Communications and Nanonetworks}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
Atakan, Barış; Atakan, Barış Active Molecular Communication Incollection Molecular Communications and Nanonetworks, 2014. @incollection{Atakan2014c, title = {Active Molecular Communication}, author = {Barış Atakan and Barış Atakan}, doi = {10.1007/978-1-4939-0739-7_4}, year = {2014}, date = {2014-01-01}, booktitle = {Molecular Communications and Nanonetworks}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
Atakan, B; Galms, S Autonomous Communication and Coordination Inspired by Nature Book Springer Publishing Company, Incorporated, 2014. @book{pop00034bb, title = {Autonomous Communication and Coordination Inspired by Nature}, author = {B Atakan and S Galms}, year = {2014}, date = {2014-01-01}, publisher = {Springer Publishing Company, Incorporated}, keywords = {}, pubstate = {published}, tppubtype = {book} } |
Özbek, Berna; Ruyet, Didier Le Feedback strategies for wireless communication Book 2014, ISBN: 9781461477419. @book{Ozbek2014a, title = {Feedback strategies for wireless communication}, author = {Berna Özbek and Didier Le Ruyet}, doi = {10.1007/978-1-4614-7741-9}, isbn = {9781461477419}, year = {2014}, date = {2014-01-01}, booktitle = {Feedback Strategies for Wireless Communication}, keywords = {}, pubstate = {published}, tppubtype = {book} } |
Özbek, Berna; Ruyet, Didier Le Feedback strategies for wireless communication Book 2014, ISBN: 9781461477419. @book{Ozbek2014ab, title = {Feedback strategies for wireless communication}, author = {Berna Özbek and Didier Le Ruyet}, doi = {10.1007/978-1-4614-7741-9}, isbn = {9781461477419}, year = {2014}, date = {2014-01-01}, booktitle = {Feedback Strategies for Wireless Communication}, keywords = {}, pubstate = {published}, tppubtype = {book} } |
Yaman, Fatih; Weiland, Thomas Inhomogeneity reconstructions in tendon ducts via boundary integral equations Journal Article NDT and E International, 2014, ISSN: 09638695. @article{Yaman2014a, title = {Inhomogeneity reconstructions in tendon ducts via boundary integral equations}, author = {Fatih Yaman and Thomas Weiland}, doi = {10.1016/j.ndteint.2014.08.007}, issn = {09638695}, year = {2014}, date = {2014-01-01}, journal = {NDT and E International}, abstract = {In this study, as an alternative to the formerly presented investigations, Newton-type numerical algorithms are proposed to find location and shape of an air void inside of a tendon duct and to identify gathered metallic bars in a concrete column. The simulated structures are illuminated by four acoustic sources at a fixed frequency such that the scattered field is measured in a near-field region at 128 points. According to the nature of physical problems, the Dirichlet boundary condition is employed to model air-filled cavities and transmission conditions are assumed for metallic objects. Additionally, conductive boundary conditions are suggested for a more realistic representation of the inhomogeneities for the rusty metallic skin of the duct. Potential approaches are used to derive boundary integral equations. The proper treatment of the ill-conditioned equations is established via Tikhonov regularization. Applicability of the proposed inversion algorithms is tested with realistic parameters for different scenarios using noisy scattered field data and accurate numerical results are presented at 10 kHz for the unknown physical properties of the duct's skin.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this study, as an alternative to the formerly presented investigations, Newton-type numerical algorithms are proposed to find location and shape of an air void inside of a tendon duct and to identify gathered metallic bars in a concrete column. The simulated structures are illuminated by four acoustic sources at a fixed frequency such that the scattered field is measured in a near-field region at 128 points. According to the nature of physical problems, the Dirichlet boundary condition is employed to model air-filled cavities and transmission conditions are assumed for metallic objects. Additionally, conductive boundary conditions are suggested for a more realistic representation of the inhomogeneities for the rusty metallic skin of the duct. Potential approaches are used to derive boundary integral equations. The proper treatment of the ill-conditioned equations is established via Tikhonov regularization. Applicability of the proposed inversion algorithms is tested with realistic parameters for different scenarios using noisy scattered field data and accurate numerical results are presented at 10 kHz for the unknown physical properties of the duct's skin. |
Özbek, Berna; Ruyet, Didier Le Adaptive limited feedback links for cooperative multi-antenna multicell networks Journal Article Eurasip Journal on Wireless Communications and Networking, 2014, ISSN: 16871499. @article{Ozbek2014c, title = {Adaptive limited feedback links for cooperative multi-antenna multicell networks}, author = {Berna Özbek and Didier Le Ruyet}, doi = {10.1186/1687-1499-2014-193}, issn = {16871499}, year = {2014}, date = {2014-01-01}, journal = {Eurasip Journal on Wireless Communications and Networking}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Aycan, Esra; Özbek, Berna; Ruyet, Didier Le Hierarchical successive stream selection for heterogeneous network interference Inproceedings IEEE Wireless Communications and Networking Conference, WCNC, 2014, ISSN: 15253511. @inproceedings{Aycan2014, title = {Hierarchical successive stream selection for heterogeneous network interference}, author = {Esra Aycan and Berna Özbek and Didier Le Ruyet}, doi = {10.1109/WCNC.2014.6952290}, issn = {15253511}, year = {2014}, date = {2014-01-01}, booktitle = {IEEE Wireless Communications and Networking Conference, WCNC}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Özbek, Berna; Ruyet, Didier Le; Pischella, Mylene Adaptive reduced feedback links for distributed power allocation in multicell MISO-OFDMA networks Journal Article IEEE Wireless Communications Letters, 2014, ISSN: 21622345. @article{Ozbek2014d, title = {Adaptive reduced feedback links for distributed power allocation in multicell MISO-OFDMA networks}, author = {Berna Özbek and Didier Le Ruyet and Mylene Pischella}, doi = {10.1109/WCL.2013.120513.130743}, issn = {21622345}, year = {2014}, date = {2014-01-01}, journal = {IEEE Wireless Communications Letters}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ekren, ŞN; Apaydın, MS Incorporating triple resonance experiment data into NVR for NMR protein structure-based assignments Journal Article 2014 22nd Signal Processing and Communications Applications Conference (SIU …, 2014. @article{pop00007j, title = {Incorporating triple resonance experiment data into NVR for NMR protein structure-based assignments}, author = {ŞN Ekren and MS Apaydın}, year = {2014}, date = {2014-01-01}, journal = {2014 22nd Signal Processing and Communications Applications Conference (SIU …}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Basturk, Ilhan; Ozbek, Berna Effect Of mobile relays on the OFDMA-based cellular network performance Inproceedings 2014. @inproceedings{Basturk2014, title = {Effect Of mobile relays on the OFDMA-based cellular network performance}, author = {Ilhan Basturk and Berna Ozbek}, doi = {10.1109/siu.2014.6830234}, year = {2014}, date = {2014-01-01}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Özbek, Berna; Ruyet, Didier Le; Pischella, Mylene Sum capacity maximization in distributed multicell MISO-OFDMA systems with reduced feedback links Inproceedings 2014 11th International Symposium on Wireless Communications Systems, ISWCS 2014 - Proceedings, 2014, ISBN: 9781479958634. @inproceedings{Ozbek2014j, title = {Sum capacity maximization in distributed multicell MISO-OFDMA systems with reduced feedback links}, author = {Berna Özbek and Didier Le Ruyet and Mylene Pischella}, doi = {10.1109/ISWCS.2014.6933407}, isbn = {9781479958634}, year = {2014}, date = {2014-01-01}, booktitle = {2014 11th International Symposium on Wireless Communications Systems, ISWCS 2014 - Proceedings}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Ruyet, Didier Le; Zakaria, Rostom; Özbek, Berna On precoding MIMO-FBMC with imperfect channel state information at the transmitter Inproceedings 2014 11th International Symposium on Wireless Communications Systems, ISWCS 2014 - Proceedings, 2014, ISBN: 9781479958634. @inproceedings{LeRuyet2014, title = {On precoding MIMO-FBMC with imperfect channel state information at the transmitter}, author = {Didier Le Ruyet and Rostom Zakaria and Berna Özbek}, doi = {10.1109/ISWCS.2014.6933464}, isbn = {9781479958634}, year = {2014}, date = {2014-01-01}, booktitle = {2014 11th International Symposium on Wireless Communications Systems, ISWCS 2014 - Proceedings}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Pala, D Analysis and modelling of a novel approach for the interrogation unit of fiber Bragg grating sensors using optical frequency domain reflectometry techniques Journal Article İzmir Institute of Technology, 2014. @article{pop00040d, title = {Analysis and modelling of a novel approach for the interrogation unit of fiber Bragg grating sensors using optical frequency domain reflectometry techniques}, author = {D Pala}, year = {2014}, date = {2014-01-01}, journal = {İzmir Institute of Technology}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Özbek, Berna; Ruyet, Didier Le; Özbek, Berna; Ruyet, Didier Le Feedback in MIMO Wireless Communication Incollection Feedback Strategies for Wireless Communication, 2014. @incollection{Ozbek2014h, title = {Feedback in MIMO Wireless Communication}, author = {Berna Özbek and Didier Le Ruyet and Berna Özbek and Didier Le Ruyet}, doi = {10.1007/978-1-4614-7741-9_4}, year = {2014}, date = {2014-01-01}, booktitle = {Feedback Strategies for Wireless Communication}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
Özbek, Berna; Ruyet, Didier Le; Özbek, Berna; Ruyet, Didier Le Feedback in SISO Single User Wireless Communication Incollection Feedback Strategies for Wireless Communication, 2014. @incollection{Ozbek2014i, title = {Feedback in SISO Single User Wireless Communication}, author = {Berna Özbek and Didier Le Ruyet and Berna Özbek and Didier Le Ruyet}, doi = {10.1007/978-1-4614-7741-9_3}, year = {2014}, date = {2014-01-01}, booktitle = {Feedback Strategies for Wireless Communication}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
Özbek, Berna; Ruyet, Didier Le; Özbek, Berna; Ruyet, Didier Le Feedback Strategies in LTE Systems Incollection Feedback Strategies for Wireless Communication, 2014. @incollection{Ozbek2014e, title = {Feedback Strategies in LTE Systems}, author = {Berna Özbek and Didier Le Ruyet and Berna Özbek and Didier Le Ruyet}, doi = {10.1007/978-1-4614-7741-9_8}, year = {2014}, date = {2014-01-01}, booktitle = {Feedback Strategies for Wireless Communication}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
Özbek, Berna; Ruyet, Didier Le; Özbek, Berna; Ruyet, Didier Le Feedback Strategies for Multiantenna Multiuser Systems Incollection Feedback Strategies for Wireless Communication, 2014. @incollection{Ozbek2014f, title = {Feedback Strategies for Multiantenna Multiuser Systems}, author = {Berna Özbek and Didier Le Ruyet and Berna Özbek and Didier Le Ruyet}, doi = {10.1007/978-1-4614-7741-9_6}, year = {2014}, date = {2014-01-01}, booktitle = {Feedback Strategies for Wireless Communication}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
Özbek, B; Ruyet, Le D Feedback Strategies for Multiuser Systems Journal Article Feedback Strategies for Wireless Communication, pp. 165–190, 2014. @article{pop00089, title = {Feedback Strategies for Multiuser Systems}, author = {B Özbek and Le D Ruyet}, year = {2014}, date = {2014-01-01}, journal = {Feedback Strategies for Wireless Communication}, pages = {165--190}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Özbek, Berna; Ruyet, Didier Le; Özbek, Berna; Ruyet, Didier Le Background onWireless Communication Incollection Feedback Strategies for Wireless Communication, 2014. @incollection{Ozbek2014b, title = {Background onWireless Communication}, author = {Berna Özbek and Didier Le Ruyet and Berna Özbek and Didier Le Ruyet}, doi = {10.1007/978-1-4614-7741-9_2}, year = {2014}, date = {2014-01-01}, booktitle = {Feedback Strategies for Wireless Communication}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
Altınkaya, Mustafa A Benefits of averaging lateration estimates obtained using overlapped subgroups of sensor data Journal Article Digital Signal Processing: A Review Journal, 2014, ISSN: 10512004. @article{Altnkaya2014, title = {Benefits of averaging lateration estimates obtained using overlapped subgroups of sensor data}, author = {Mustafa A Altınkaya}, doi = {10.1016/j.dsp.2013.09.004}, issn = {10512004}, year = {2014}, date = {2014-01-01}, journal = {Digital Signal Processing: A Review Journal}, abstract = {In this paper, we suggest averaging lateration estimates obtained using overlapped subgroups of distance measurements as opposed to obtaining a single lateration estimate from all of the measurements directly if a redundant number of measurements are available. Least squares based closed form equations are used in the lateration. In the case of Gaussian measurement noise the performances are similar in general and for some subgroup sizes marginal gains are attained. Averaging laterations method becomes especially beneficial if the lateration estimates are classified as useful or not in the presence of outlier measurements whose distributions are modeled by a mixture of Gaussians (MOG) pdf. A new modified trimmed mean robust averager helps to regain the performance loss caused by the outliers. If the measurement noise is Gaussian, large subgroup sizes are preferable. On the contrary, in robust averaging small subgroup sizes are more effective for eliminating measurements highly contaminated with MOG noise. The effect of high-variance noise was almost totally eliminated when robust averaging of estimates is applied to QR decomposition based location estimator. The performance of this estimator is just 1 cm worse in root mean square error compared to the Cramér–Rao lower bound (CRLB) on the variance both for Gaussian and MOG noise cases. Theoretical CRLBs in the case of MOG noise are derived both for time of arrival and time difference of arrival measurement data.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this paper, we suggest averaging lateration estimates obtained using overlapped subgroups of distance measurements as opposed to obtaining a single lateration estimate from all of the measurements directly if a redundant number of measurements are available. Least squares based closed form equations are used in the lateration. In the case of Gaussian measurement noise the performances are similar in general and for some subgroup sizes marginal gains are attained. Averaging laterations method becomes especially beneficial if the lateration estimates are classified as useful or not in the presence of outlier measurements whose distributions are modeled by a mixture of Gaussians (MOG) pdf. A new modified trimmed mean robust averager helps to regain the performance loss caused by the outliers. If the measurement noise is Gaussian, large subgroup sizes are preferable. On the contrary, in robust averaging small subgroup sizes are more effective for eliminating measurements highly contaminated with MOG noise. The effect of high-variance noise was almost totally eliminated when robust averaging of estimates is applied to QR decomposition based location estimator. The performance of this estimator is just 1 cm worse in root mean square error compared to the Cramér–Rao lower bound (CRLB) on the variance both for Gaussian and MOG noise cases. Theoretical CRLBs in the case of MOG noise are derived both for time of arrival and time difference of arrival measurement data. |
Onder, Devrim; Sarioglu, Sulen; Karacali, Bilge Automated labeling of cancer textures in larynx histopathology slides using Quasi-supervised learning Journal Article Analytical and Quantitative Cytology and Histology, 2014, ISSN: 08846812. @article{Onder2014, title = {Automated labeling of cancer textures in larynx histopathology slides using Quasi-supervised learning}, author = {Devrim Onder and Sulen Sarioglu and Bilge Karacali}, issn = {08846812}, year = {2014}, date = {2014-01-01}, journal = {Analytical and Quantitative Cytology and Histology}, abstract = {Quasi-supervised learning is a statistical learning algorithm that contrasts two datasets by computing estimate for the posterior probability of each sample in either dataset. This method has not been applied to histopathological images before. The purpose of this study is to evaluate the performance of the method to identify colorectal tissues with or without adenocarcinoma. Light microscopic digital images from histopathological sections were obtained from 30 colorectal radical surgery materials including adenocarcinoma and non-neoplastic regions. The texture features were extracted by using local histograms and co-occurrence matrices. The quasi-supervised learning algorithm operates on two datasets, one containing samples of normal tissues labelled only indirectly, and the other containing an unlabeled collection of samples of both normal and cancer tissues. As such, the algorithm eliminates the need for manually labelled samples of normal and cancer tissues for conventional supervised learning and significantly reduces the expert intervention. Several texture feature vector datasets corresponding to different extraction parameters were tested within the proposed framework. The Independent Component Analysis dimensionality reduction approach was also identified as the one improving the labelling performance evaluated in this series. In this series, the proposed method was applied to the dataset of 22,080 vectors with reduced dimensionality 119 from 132. Regions containing cancer tissue could be identified accurately having false and true positive rates up to 19% and 88% respectively without using manually labelled ground-truth datasets in a quasi-supervised strategy. The resulting labelling performances were compared to that of a conventional powerful supervised classifier using manually labelled ground-truth data. The supervised classifier results were calculated as 3.5% and 95% for the same case. The results in this series in comparison with the benchmark classifier, suggest that quasi-supervised image texture labelling may be a useful method in the analysis and classification of pathological slides but further study is required to improve the results. textcopyright 2013 Elsevier Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Quasi-supervised learning is a statistical learning algorithm that contrasts two datasets by computing estimate for the posterior probability of each sample in either dataset. This method has not been applied to histopathological images before. The purpose of this study is to evaluate the performance of the method to identify colorectal tissues with or without adenocarcinoma. Light microscopic digital images from histopathological sections were obtained from 30 colorectal radical surgery materials including adenocarcinoma and non-neoplastic regions. The texture features were extracted by using local histograms and co-occurrence matrices. The quasi-supervised learning algorithm operates on two datasets, one containing samples of normal tissues labelled only indirectly, and the other containing an unlabeled collection of samples of both normal and cancer tissues. As such, the algorithm eliminates the need for manually labelled samples of normal and cancer tissues for conventional supervised learning and significantly reduces the expert intervention. Several texture feature vector datasets corresponding to different extraction parameters were tested within the proposed framework. The Independent Component Analysis dimensionality reduction approach was also identified as the one improving the labelling performance evaluated in this series. In this series, the proposed method was applied to the dataset of 22,080 vectors with reduced dimensionality 119 from 132. Regions containing cancer tissue could be identified accurately having false and true positive rates up to 19% and 88% respectively without using manually labelled ground-truth datasets in a quasi-supervised strategy. The resulting labelling performances were compared to that of a conventional powerful supervised classifier using manually labelled ground-truth data. The supervised classifier results were calculated as 3.5% and 95% for the same case. The results in this series in comparison with the benchmark classifier, suggest that quasi-supervised image texture labelling may be a useful method in the analysis and classification of pathological slides but further study is required to improve the results. textcopyright 2013 Elsevier Ltd. |
Altinkaya, Mustafa A New results in robust location estimation with trimmed averages Inproceedings 2014. @inproceedings{Altinkaya2014, title = {New results in robust location estimation with trimmed averages}, author = {Mustafa A Altinkaya}, doi = {10.1109/siu.2014.6830700}, year = {2014}, date = {2014-01-01}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Bozkurt, Barış; Karaosmanoğlu, Kemal M; Karacalı, Bilge; Ünal, Erdem Usul and Makam driven automatic melodic segmentation for Turkish music Journal Article Journal of New Music Research, 2014, ISSN: 17445027. @article{Bozkurt2014, title = {Usul and Makam driven automatic melodic segmentation for Turkish music}, author = {Barış Bozkurt and Kemal M Karaosmanoğlu and Bilge Karacalı and Erdem Ünal}, doi = {10.1080/09298215.2014.924535}, issn = {17445027}, year = {2014}, date = {2014-01-01}, journal = {Journal of New Music Research}, abstract = {textcopyright 2014, textcopyright 2014 Taylor & Francis. Automatic melodic segmentation is a topic studied extensively, aiming at developing systems that perform grouping of musical events. Here, we consider the problem of automatic segmentation via supervised learning from a dataset containing segmentation labels of an expert. We present a statistical classification-based segmentation system developed specifically for Turkish makam music. The proposed system uses two novel features, a makam-based and an usul-based feature, together with features commonly used in literature. The makam-based feature is defined as the probability of a note to appear at the phrase boundary, computed from the distributions of boundaries with respect to the piece's makam pitches. Likewise, the usul-based feature is computed from the distributions of boundaries with respect to beats in the rhythmic cycle, usul of the piece. Several experimental setups using different feature groups are designed to test the contribution of the proposed features on three datasets. The results show that the new features carry complementary information to existing features in the literature within the Turkish makam music segmentation context and that the inclusion of new features resulted in statistically significant performance improvement.}, keywords = {}, pubstate = {published}, tppubtype = {article} } textcopyright 2014, textcopyright 2014 Taylor & Francis. Automatic melodic segmentation is a topic studied extensively, aiming at developing systems that perform grouping of musical events. Here, we consider the problem of automatic segmentation via supervised learning from a dataset containing segmentation labels of an expert. We present a statistical classification-based segmentation system developed specifically for Turkish makam music. The proposed system uses two novel features, a makam-based and an usul-based feature, together with features commonly used in literature. The makam-based feature is defined as the probability of a note to appear at the phrase boundary, computed from the distributions of boundaries with respect to the piece's makam pitches. Likewise, the usul-based feature is computed from the distributions of boundaries with respect to beats in the rhythmic cycle, usul of the piece. Several experimental setups using different feature groups are designed to test the contribution of the proposed features on three datasets. The results show that the new features carry complementary information to existing features in the literature within the Turkish makam music segmentation context and that the inclusion of new features resulted in statistically significant performance improvement. |
Köktürk, Başak Esin; Karacali, Bilge Model-free expectation maximization for divisive hierarchical clustering of multicolor flow cytometry data Inproceedings Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014, 2014, ISBN: 9781479956692. @inproceedings{Kokturk2014, title = {Model-free expectation maximization for divisive hierarchical clustering of multicolor flow cytometry data}, author = {Başak Esin Köktürk and Bilge Karacali}, doi = {10.1109/BIBM.2014.6999166}, isbn = {9781479956692}, year = {2014}, date = {2014-01-01}, booktitle = {Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014}, abstract = {textcopyright 2014 IEEE.This paper proposes a new method for automated clustering of high dimensional datasets. The method is based on a recursive binary division strategy that successively divides an original dataset into distinct clusters. Each binary division is carried out using a model-free expectation maximization scheme that exploits the posterior probability computation capability of the quasi-supervised learning algorithm. The divisions are carried out until a division cost exceeds an adaptively determined limit. Experiment results on synthetic as well as real multi-color flow cytometry datasets showed that the proposed method can accurately capture the prominent clusters without requiring any knowledge on the number of clusters or their distribution models.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } textcopyright 2014 IEEE.This paper proposes a new method for automated clustering of high dimensional datasets. The method is based on a recursive binary division strategy that successively divides an original dataset into distinct clusters. Each binary division is carried out using a model-free expectation maximization scheme that exploits the posterior probability computation capability of the quasi-supervised learning algorithm. The divisions are carried out until a division cost exceeds an adaptively determined limit. Experiment results on synthetic as well as real multi-color flow cytometry datasets showed that the proposed method can accurately capture the prominent clusters without requiring any knowledge on the number of clusters or their distribution models. |
Erickson, David; O'Dell, Dakota; Jiang, Li; Oncescu, Vlad; Gumus, Abdurrahman; Lee, Seoho; Mancuso, Matthew; Mehta, Saurabh Smartphone technology can be transformative to the deployment of lab-on-chip diagnostics Journal Article Lab on a Chip, 2014, ISSN: 14730189. @article{Erickson2014, title = {Smartphone technology can be transformative to the deployment of lab-on-chip diagnostics}, author = {David Erickson and Dakota O'Dell and Li Jiang and Vlad Oncescu and Abdurrahman Gumus and Seoho Lee and Matthew Mancuso and Saurabh Mehta}, doi = {10.1039/c4lc00142g}, issn = {14730189}, year = {2014}, date = {2014-01-01}, journal = {Lab on a Chip}, abstract = {The rapid expansion of mobile technology is transforming the biomedical landscape.The rapid expansion of mobile technology is transforming the biomedical landscape. By 2016 there will be 260 M active smartphones in the US and millions of health accessories and software “apps” running off them. In parallel with this have come major technical achievements in lab-on-a-chip technology leading to incredible new biochemical sensors and molecular diagnostic devices. Despite these advancements, the uptake of lab-on-a-chip technologies at the consumer level has been somewhat limited. We believe that the widespread availability of smartphone technology and the capabilities they offer in terms of computation, communication, social networking, and imaging will be transformative to the deployment of lab-on-a-chip type technology both in the developed and developing world. In this paper we outline why we believe this is the case, the new business models that may emerge, and detail some specific application areas in which this synergy will have long term impact, namely: nutrition monitoring and disease diagnostics in limited resource settings.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The rapid expansion of mobile technology is transforming the biomedical landscape.The rapid expansion of mobile technology is transforming the biomedical landscape. By 2016 there will be 260 M active smartphones in the US and millions of health accessories and software “apps” running off them. In parallel with this have come major technical achievements in lab-on-a-chip technology leading to incredible new biochemical sensors and molecular diagnostic devices. Despite these advancements, the uptake of lab-on-a-chip technologies at the consumer level has been somewhat limited. We believe that the widespread availability of smartphone technology and the capabilities they offer in terms of computation, communication, social networking, and imaging will be transformative to the deployment of lab-on-a-chip type technology both in the developed and developing world. In this paper we outline why we believe this is the case, the new business models that may emerge, and detail some specific application areas in which this synergy will have long term impact, namely: nutrition monitoring and disease diagnostics in limited resource settings. |
Bozkurt, Baris; Karaosmanoglu, Kemal M; Karacali, Bilge; Unal, Erdem Automatic melodic segmentation of Turkish makam music scores Inproceedings 2014. @inproceedings{Bozkurt2014a, title = {Automatic melodic segmentation of Turkish makam music scores}, author = {Baris Bozkurt and Kemal M Karaosmanoglu and Bilge Karacali and Erdem Unal}, doi = {10.1109/siu.2014.6830262}, year = {2014}, date = {2014-01-01}, abstract = {Automatic melodic segmentation is one of the important steps in computational analysis of melodic content from symbolic data. This widely studied research problem has been very rarely considered for Turkish makam music. In this paper we first present test results for state-of-the-art techniques from literature on Turkish makam music data. Then, we present a statistical classification-based segmentation system that exploits the link between makam melodies and usul and makam scale hierarchies together with the well-known features in literature. We show through tests on a large dataset that the proposed system has a higher accuracy. textcopyright 2014 IEEE.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } Automatic melodic segmentation is one of the important steps in computational analysis of melodic content from symbolic data. This widely studied research problem has been very rarely considered for Turkish makam music. In this paper we first present test results for state-of-the-art techniques from literature on Turkish makam music data. Then, we present a statistical classification-based segmentation system that exploits the link between makam melodies and usul and makam scale hierarchies together with the well-known features in literature. We show through tests on a large dataset that the proposed system has a higher accuracy. textcopyright 2014 IEEE. |
Bozkurt, Baris; Karaosmanoglu, Kemal M; Karacali, Bilge; Unal, Erdem Türk makam müziǧi notalari icin otomatik ezgi bölütleme Inproceedings 2014 22nd Signal Processing and Communications Applications Conference, SIU 2014 - Proceedings, 2014, ISBN: 9781479948741. @inproceedings{Bozkurt2014b, title = {Türk makam müziǧi notalari icin otomatik ezgi bölütleme}, author = {Baris Bozkurt and Kemal M Karaosmanoglu and Bilge Karacali and Erdem Unal}, doi = {10.1109/SIU.2014.6830262}, isbn = {9781479948741}, year = {2014}, date = {2014-01-01}, booktitle = {2014 22nd Signal Processing and Communications Applications Conference, SIU 2014 - Proceedings}, abstract = {Automatic melodic segmentation is one of the important steps in computational analysis of melodic content from symbolic data. This widely studied research problem has been very rarely considered for Turkish makam music. In this paper we first present test results for state-of-the-art techniques from literature on Turkish makam music data. Then, we present a statistical classification-based segmentation system that exploits the link between makam melodies and usul and makam scale hierarchies together with the well-known features in literature. We show through tests on a large dataset that the proposed system has a higher accuracy.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } Automatic melodic segmentation is one of the important steps in computational analysis of melodic content from symbolic data. This widely studied research problem has been very rarely considered for Turkish makam music. In this paper we first present test results for state-of-the-art techniques from literature on Turkish makam music data. Then, we present a statistical classification-based segmentation system that exploits the link between makam melodies and usul and makam scale hierarchies together with the well-known features in literature. We show through tests on a large dataset that the proposed system has a higher accuracy. |
Gumus, A; Lee, S; Karlsson, K; Gabrielson, R; Winkler, DW; Erickson, D Real-time in vivo uric acid biosensor system for biophysical monitoring of birds Journal Article Analyst, 139 (4), pp. 742–748, 2014. @article{pop00008f, title = {Real-time in vivo uric acid biosensor system for biophysical monitoring of birds}, author = {A Gumus and S Lee and K Karlsson and R Gabrielson and DW Winkler and D Erickson}, year = {2014}, date = {2014-01-01}, journal = {Analyst}, volume = {139}, number = {4}, pages = {742--748}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bozkurt, Barış; Karaosmanoğlu, Kemal M; Karacalı, Bilge; Ünal, Erdem Türk makam müziği notaları icin otomatik ezgi bölütleme Inproceedings IEEE 22. Sinyal İşleme ve İletişim Uygulamaları Kurultayı (SIU), 2014, ISBN: 9781479948741. @inproceedings{Bozkurt2014c, title = {Türk makam müziği notaları icin otomatik ezgi bölütleme}, author = {Barış Bozkurt and Kemal M Karaosmanoğlu and Bilge Karacalı and Erdem Ünal}, isbn = {9781479948741}, year = {2014}, date = {2014-01-01}, booktitle = {IEEE 22. Sinyal İşleme ve İletişim Uygulamaları Kurultayı (SIU)}, abstract = {Automatic melodic segmentation is one of the important steps in computational analysis of melodic content from symbolic data. This widely studied research problem has been very rarely considered for Turkish makam music. In this paper we first present test results for state-of-the-art techniques from literature on Turkish makam music data. Then, we present a statistical classification-based segmentation system that exploits the link between makam melodies and usul and makam scale hierarchies together with the well-known features in literature. We show through tests on a large dataset that the proposed system has a higher accuracy.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } Automatic melodic segmentation is one of the important steps in computational analysis of melodic content from symbolic data. This widely studied research problem has been very rarely considered for Turkish makam music. In this paper we first present test results for state-of-the-art techniques from literature on Turkish makam music data. Then, we present a statistical classification-based segmentation system that exploits the link between makam melodies and usul and makam scale hierarchies together with the well-known features in literature. We show through tests on a large dataset that the proposed system has a higher accuracy. |
Akin, O; Dinleyici, MS Demonstration of pulse controlled all-optical switch/modulator Journal Article Optics letters, 39 (6), pp. 1469–1472, 2014. @article{pop00007d, title = {Demonstration of pulse controlled all-optical switch/modulator}, author = {O Akin and MS Dinleyici}, year = {2014}, date = {2014-01-01}, journal = {Optics letters}, volume = {39}, number = {6}, pages = {1469--1472}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bansal, Mukesh; Yang, Jichen; Karan, Charles; Menden, Michael P; Costello, James C; Tang, Hao; Xiao, Guanghua; Li, Yajuan; Allen, Jeffrey; Zhong, Rui; Chen, Beibei; Kim, Minsoo; Wang, Tao; Heiser, Laura M; Realubit, Ronald; Mattioli, Michela; Alvarez, Mariano J; Shen, Yao; Gallahan, Daniel; Singer, Dinah; Saez-Rodriguez, Julio; Xie, Yang; Stolovitzky, Gustavo; Califano, Andrea; Abbuehl, Jean Paul; Altman, Russ B; Balcome, Shawn; Bell, Ana; Bender, Andreas; Berger, Bonnie; Bernard, Jonathan; Bieberich, Andrew A; Borboudakis, Giorgos; Chan, Christina; Chen, Ting Huei; Choi, Jaejoon; Coelho, Luis Pedro; Creighton, Chad J; Dampier, Will; Davisson, Jo V; Deshpande, Raamesh; Diao, Lixia; Camillo, Barbara Di; Dundar, Murat; Ertel, Adam; Goswami, Chirayu P; Gottlieb, Assaf; Gould, Michael N; Goya, Jonathan; Grau, Michael; Gray, Joe W; Hejase, Hussein A; Hoffmann, Michael F; Homicsko, Krisztian; Homilius, Max; Hwang, Woochang; Ijzerman, Adriaan P; Kallioniemi, Olli; Karacali, Bilge; Kaski, Samuel; Kim, Junho; Krishnan, Arjun; Lee, Junehawk; Lee, Young Suk; Lenselink, Eelke B; Lenz, Peter; Li, Lang; Li, Jun; Liang, Han; Mpindi, John Patrick; Myers, Chad L; Newton, Michael A; Overington, John P; Parkkinen, Juuso; Prill, Robert J; Peng, Jian; Pestell, Richard; Qiu, Peng; Rajwa, Bartek; Sadanandam, Anguraj; Sambo, Francesco; Sridhar, Arvind; Sun, Wei; Toffolo, Gianna M; Tozeren, Aydin; Troyanskaya, Olga G; Tsamardinos, Ioannis; Vlijmen, Herman Van W T; Wang, Wen; Wegner, Joerg K; Wennerberg, Krister; Westen, Gerard Van J P; Xia, Tian; Yang, Yang; Yao, Victoria; Yuan, Yuan; Zeng, Haoyang; Zhang, Shihua; Zhao, Junfei; Zhou, Jian A community computational challenge to predict the activity of pairs of compounds Journal Article Nature Biotechnology, 2014, ISSN: 15461696. @article{Bansal2014, title = {A community computational challenge to predict the activity of pairs of compounds}, author = {Mukesh Bansal and Jichen Yang and Charles Karan and Michael P Menden and James C Costello and Hao Tang and Guanghua Xiao and Yajuan Li and Jeffrey Allen and Rui Zhong and Beibei Chen and Minsoo Kim and Tao Wang and Laura M Heiser and Ronald Realubit and Michela Mattioli and Mariano J Alvarez and Yao Shen and Daniel Gallahan and Dinah Singer and Julio Saez-Rodriguez and Yang Xie and Gustavo Stolovitzky and Andrea Califano and Jean Paul Abbuehl and Russ B Altman and Shawn Balcome and Ana Bell and Andreas Bender and Bonnie Berger and Jonathan Bernard and Andrew A Bieberich and Giorgos Borboudakis and Christina Chan and Ting Huei Chen and Jaejoon Choi and Luis Pedro Coelho and Chad J Creighton and Will Dampier and Jo V Davisson and Raamesh Deshpande and Lixia Diao and Barbara Di Camillo and Murat Dundar and Adam Ertel and Chirayu P Goswami and Assaf Gottlieb and Michael N Gould and Jonathan Goya and Michael Grau and Joe W Gray and Hussein A Hejase and Michael F Hoffmann and Krisztian Homicsko and Max Homilius and Woochang Hwang and Adriaan P Ijzerman and Olli Kallioniemi and Bilge Karacali and Samuel Kaski and Junho Kim and Arjun Krishnan and Junehawk Lee and Young Suk Lee and Eelke B Lenselink and Peter Lenz and Lang Li and Jun Li and Han Liang and John Patrick Mpindi and Chad L Myers and Michael A Newton and John P Overington and Juuso Parkkinen and Robert J Prill and Jian Peng and Richard Pestell and Peng Qiu and Bartek Rajwa and Anguraj Sadanandam and Francesco Sambo and Arvind Sridhar and Wei Sun and Gianna M Toffolo and Aydin Tozeren and Olga G Troyanskaya and Ioannis Tsamardinos and Herman Van W T Vlijmen and Wen Wang and Joerg K Wegner and Krister Wennerberg and Gerard Van J P Westen and Tian Xia and Yang Yang and Victoria Yao and Yuan Yuan and Haoyang Zeng and Shihua Zhang and Junfei Zhao and Jian Zhou}, doi = {10.1038/nbt.3052}, issn = {15461696}, year = {2014}, date = {2014-01-01}, journal = {Nature Biotechnology}, abstract = {Recent therapeutic successes have renewed interest in drug combinations, but experimental screening approaches are costly and often identify only small numbers of synergistic combinations. The DREAM consortium launched an open challenge to foster the development of in silico methods to computationally rank 91 compound pairs, from the most synergistic to the most antagonistic, based on gene-expression profiles of human B cells treated with individual compounds at multiple time points and concentrations. Using scoring metrics based on experimental dose-response curves, we assessed 32 methods (31 community-generated approaches and SynGen), four of which performed significantly better than random guessing. We highlight similarities between the methods. Although the accuracy of predictions was not optimal, we find that computational prediction of compound-pair activity is possible, and that community challenges can be useful to advance the field of in silico compound-synergy prediction. Recent success in the study of synergistic combinations, such as the use of CHK1 inhibitors in combination with several DNA damaging agents 1 or of the PARP inhibitor olaparib in combination with the PI3K inhibitor BKM120 (ref. 2), have generated significant interest in the systematic screening of compound pairs to identify synergistic pairs for combination therapy. Compound synergy can be measured by multiple endpoints, including reducing or delaying the devel-opment of resistance to treatment 3 (for instance by abrogating the emergence of resistant clones 4–6), improving overall survival 7,8 or lowering toxicity by decreasing individual compound dose 9 . Similarly, at the molecular level, synergistic interactions can be implemented by several distinct mechanisms. For instance, a compound may sensitize cells to another compound by regulating its absorption and distribution, modulating the cell's growth prop-erties 10 , inhibiting compound degradation 11 , inhibiting pathways that induce resistance 6 or reducing the other compound's toxicity 12 . When used in combination, two compounds may elicit one of three distinct responses: (i) additive, when the combined effect is equivalent to the sum of the independent effects; (ii) synergistic, when the combined effect is greater than additive; and (iii) antago-nistic, when the combined effect is smaller than additive. The goal of combination therapy is thus to attain a synergistic or at least an additive yet complementary effect. Most approaches to identify synergistic compound pairs are still exploratory 13,14 . In cancer research, synergy assays are usually performed by treating cell lines in vitro with all possible compound combinations from a diverse library or with candidate combinations selected on the basis of mechanistic principles. Unfortunately, such experimental screens impose severe limits on the practical size of compound diversity libraries. Computational methods to predict compound synergy can potentially complement high-throughput synergy screens, but the few that have been published lack rigorous experimental validation or are appropriate only for compounds that modulate well-studied molecular pathways 15 or that are equivalent to previously established combinations 16 . Current algorithms are not generalizable to arbitrary compound combinations unless molecular profile data following compound-pair treatment are available 17 , which is clearly impractical. Thus, there is a need for new methods to predict compound synergy from molecular profiles of single compound activity, as well as for assays designed to objectively and systematically evaluate the accuracy and specificity of such predictions. To address this issue, the DREAM Challenges initiative (an effort run by a community of researchers that poses fundamental ques-tions in systems biology and translational science in the form of a community computational challenge to predict the activity of pairs of compounds}, keywords = {}, pubstate = {published}, tppubtype = {article} } Recent therapeutic successes have renewed interest in drug combinations, but experimental screening approaches are costly and often identify only small numbers of synergistic combinations. The DREAM consortium launched an open challenge to foster the development of in silico methods to computationally rank 91 compound pairs, from the most synergistic to the most antagonistic, based on gene-expression profiles of human B cells treated with individual compounds at multiple time points and concentrations. Using scoring metrics based on experimental dose-response curves, we assessed 32 methods (31 community-generated approaches and SynGen), four of which performed significantly better than random guessing. We highlight similarities between the methods. Although the accuracy of predictions was not optimal, we find that computational prediction of compound-pair activity is possible, and that community challenges can be useful to advance the field of in silico compound-synergy prediction. Recent success in the study of synergistic combinations, such as the use of CHK1 inhibitors in combination with several DNA damaging agents 1 or of the PARP inhibitor olaparib in combination with the PI3K inhibitor BKM120 (ref. 2), have generated significant interest in the systematic screening of compound pairs to identify synergistic pairs for combination therapy. Compound synergy can be measured by multiple endpoints, including reducing or delaying the devel-opment of resistance to treatment 3 (for instance by abrogating the emergence of resistant clones 4–6), improving overall survival 7,8 or lowering toxicity by decreasing individual compound dose 9 . Similarly, at the molecular level, synergistic interactions can be implemented by several distinct mechanisms. For instance, a compound may sensitize cells to another compound by regulating its absorption and distribution, modulating the cell's growth prop-erties 10 , inhibiting compound degradation 11 , inhibiting pathways that induce resistance 6 or reducing the other compound's toxicity 12 . When used in combination, two compounds may elicit one of three distinct responses: (i) additive, when the combined effect is equivalent to the sum of the independent effects; (ii) synergistic, when the combined effect is greater than additive; and (iii) antago-nistic, when the combined effect is smaller than additive. The goal of combination therapy is thus to attain a synergistic or at least an additive yet complementary effect. Most approaches to identify synergistic compound pairs are still exploratory 13,14 . In cancer research, synergy assays are usually performed by treating cell lines in vitro with all possible compound combinations from a diverse library or with candidate combinations selected on the basis of mechanistic principles. Unfortunately, such experimental screens impose severe limits on the practical size of compound diversity libraries. Computational methods to predict compound synergy can potentially complement high-throughput synergy screens, but the few that have been published lack rigorous experimental validation or are appropriate only for compounds that modulate well-studied molecular pathways 15 or that are equivalent to previously established combinations 16 . Current algorithms are not generalizable to arbitrary compound combinations unless molecular profile data following compound-pair treatment are available 17 , which is clearly impractical. Thus, there is a need for new methods to predict compound synergy from molecular profiles of single compound activity, as well as for assays designed to objectively and systematically evaluate the accuracy and specificity of such predictions. To address this issue, the DREAM Challenges initiative (an effort run by a community of researchers that poses fundamental ques-tions in systems biology and translational science in the form of a community computational challenge to predict the activity of pairs of compounds |
Costello, James C; Heiser, Laura M; Georgii, Elisabeth; Gönen, Mehmet; Menden, Michael P; Wang, Nicholas J; Bansal, Mukesh; Ammad-Ud-Din, Muhammad; Hintsanen, Petteri; Khan, Suleiman A; Mpindi, John Patrick; Kallioniemi, Olli; Honkela, Antti; Aittokallio, Tero; Wennerberg, Krister; Collins, James J; Gallahan, Dan; Singer, Dinah; Saez-Rodriguez, Julio; Kaski, Samuel; Gray, Joe W; Stolovitzky, Gustavo; Abbuehl, Jean Paul; Allen, Jeffrey; Altman, Russ B; Balcome, Shawn; Battle, Alexis; Bender, Andreas; Berger, Bonnie; Bernard, Jonathan; Bhattacharjee, Madhuchhanda; Bhuvaneshwar, Krithika; Bieberich, Andrew A; Boehm, Fred; Califano, Andrea; Chan, Christina; Chen, Beibei; Chen, Ting Huei; Choi, Jaejoon; Coelho, Luis Pedro; Cokelaer, Thomas; Collins, James C; Creighton, Chad J; Cui, Jike; Dampier, Will; Davisson, Jo V; Baets, Bernard De; Deshpande, Raamesh; DiCamillo, Barbara; Dundar, Murat; Duren, Zhana; Ertel, Adam; Fan, Haoyang; Fang, Hongbin; Gauba, Robinder; Gottlieb, Assaf; Grau, Michael; Gusev, Yuriy; Ha, Min Jin; Han, Leng; Harris, Michael; Henderson, Nicholas; Hejase, Hussein A; Homicsko, Krisztian; Hou, Jack P; Hwang, Woochang; IJzerman, Adriaan P; Karacali, Bilge; Keles, Sunduz; Kendziorski, Christina; Kim, Junho; Kim, Min; Kim, Youngchul; Knowles, David A; Koller, Daphne; Lee, Junehawk; Lee, Jae K; Lenselink, Eelke B; Li, Biao; Li, Bin; Li, Jun; Liang, Han; Ma, Jian; Madhavan, Subha; Mooney, Sean; Myers, Chad L; Newton, Michael A; Overington, John P; Pal, Ranadip; Peng, Jian; Pestell, Richard; Prill, Robert J; Qiu, Peng; Rajwa, Bartek; Sadanandam, Anguraj; Sambo, Francesco; Shin, Hyunjin; Song, Jiuzhou; Song, Lei; Sridhar, Arvind; Stock, Michiel; Sun, Wei; Ta, Tram; Tadesse, Mahlet; Tan, Ming; Tang, Hao; Theodorescu, Dan; Toffolo, Gianna Maria; Tozeren, Aydin; Trepicchio, William; Varoquaux, Nelle; Vert, Jean Philippe; Waegeman, Willem; Walter, Thomas; Wan, Qian; Wang, Difei; Wang, Wen; Wang, Yong; Wang, Zhishi; Wegner, Joerg K; Wu, Tongtong; Xia, Tian; Xiao, Guanghua; Xie, Yang; Xu, Yanxun; Yang, Jichen; Yuan, Yuan; Zhang, Shihua; Zhang, Xiang Sun; Zhao, Junfei; Zuo, Chandler; Vlijmen, Herman Van W T; Westen, Gerard Van J P A community effort to assess and improve drug sensitivity prediction algorithms Journal Article Nature Biotechnology, 2014, ISSN: 15461696. @article{Costello2014, title = {A community effort to assess and improve drug sensitivity prediction algorithms}, author = {James C Costello and Laura M Heiser and Elisabeth Georgii and Mehmet Gönen and Michael P Menden and Nicholas J Wang and Mukesh Bansal and Muhammad Ammad-Ud-Din and Petteri Hintsanen and Suleiman A Khan and John Patrick Mpindi and Olli Kallioniemi and Antti Honkela and Tero Aittokallio and Krister Wennerberg and James J Collins and Dan Gallahan and Dinah Singer and Julio Saez-Rodriguez and Samuel Kaski and Joe W Gray and Gustavo Stolovitzky and Jean Paul Abbuehl and Jeffrey Allen and Russ B Altman and Shawn Balcome and Alexis Battle and Andreas Bender and Bonnie Berger and Jonathan Bernard and Madhuchhanda Bhattacharjee and Krithika Bhuvaneshwar and Andrew A Bieberich and Fred Boehm and Andrea Califano and Christina Chan and Beibei Chen and Ting Huei Chen and Jaejoon Choi and Luis Pedro Coelho and Thomas Cokelaer and James C Collins and Chad J Creighton and Jike Cui and Will Dampier and Jo V Davisson and Bernard De Baets and Raamesh Deshpande and Barbara DiCamillo and Murat Dundar and Zhana Duren and Adam Ertel and Haoyang Fan and Hongbin Fang and Robinder Gauba and Assaf Gottlieb and Michael Grau and Yuriy Gusev and Min Jin Ha and Leng Han and Michael Harris and Nicholas Henderson and Hussein A Hejase and Krisztian Homicsko and Jack P Hou and Woochang Hwang and Adriaan P IJzerman and Bilge Karacali and Sunduz Keles and Christina Kendziorski and Junho Kim and Min Kim and Youngchul Kim and David A Knowles and Daphne Koller and Junehawk Lee and Jae K Lee and Eelke B Lenselink and Biao Li and Bin Li and Jun Li and Han Liang and Jian Ma and Subha Madhavan and Sean Mooney and Chad L Myers and Michael A Newton and John P Overington and Ranadip Pal and Jian Peng and Richard Pestell and Robert J Prill and Peng Qiu and Bartek Rajwa and Anguraj Sadanandam and Francesco Sambo and Hyunjin Shin and Jiuzhou Song and Lei Song and Arvind Sridhar and Michiel Stock and Wei Sun and Tram Ta and Mahlet Tadesse and Ming Tan and Hao Tang and Dan Theodorescu and Gianna Maria Toffolo and Aydin Tozeren and William Trepicchio and Nelle Varoquaux and Jean Philippe Vert and Willem Waegeman and Thomas Walter and Qian Wan and Difei Wang and Wen Wang and Yong Wang and Zhishi Wang and Joerg K Wegner and Tongtong Wu and Tian Xia and Guanghua Xiao and Yang Xie and Yanxun Xu and Jichen Yang and Yuan Yuan and Shihua Zhang and Xiang Sun Zhang and Junfei Zhao and Chandler Zuo and Herman Van W T Vlijmen and Gerard Van J P Westen}, doi = {10.1038/nbt.2877}, issn = {15461696}, year = {2014}, date = {2014-01-01}, journal = {Nature Biotechnology}, abstract = {Predicting the best treatment strategy from genomic information is a core goal of precision medicine. Here we focus on predicting drug response based on a cohort of genomic, epigenomic and proteomic profiling data sets measured in human breast cancer cell lines. Through a collaborative effort between the National Cancer Institute (NCI) and the Dialogue on Reverse Engineering Assessment and Methods (DREAM) project, we analyzed a total of 44 drug sensitivity prediction algorithms. The top-performing approaches modeled nonlinear relationships and incorporated biological pathway information. We found that gene expression microarrays consistently provided the best predictive power of the individual profiling data sets; however, performance was increased by including multiple, independent data sets. We discuss the innovations underlying the top-performing methodology, Bayesian multitask MKL, and we provide detailed descriptions of all methods. This study establishes benchmarks for drug sensitivity prediction and identifies approaches that can be leveraged for the development of new methods.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Predicting the best treatment strategy from genomic information is a core goal of precision medicine. Here we focus on predicting drug response based on a cohort of genomic, epigenomic and proteomic profiling data sets measured in human breast cancer cell lines. Through a collaborative effort between the National Cancer Institute (NCI) and the Dialogue on Reverse Engineering Assessment and Methods (DREAM) project, we analyzed a total of 44 drug sensitivity prediction algorithms. The top-performing approaches modeled nonlinear relationships and incorporated biological pathway information. We found that gene expression microarrays consistently provided the best predictive power of the individual profiling data sets; however, performance was increased by including multiple, independent data sets. We discuss the innovations underlying the top-performing methodology, Bayesian multitask MKL, and we provide detailed descriptions of all methods. This study establishes benchmarks for drug sensitivity prediction and identifies approaches that can be leveraged for the development of new methods. |
Oncescu, V; Lee, S; Gumus, A; Karlsson, K; Erickson, D Autonomous Device for Application in Late-Phase Hemorrhagic Shock Prevention Journal Article PloS one, 9 (2), pp. 89903, 2014. @article{pop00019b, title = {Autonomous Device for Application in Late-Phase Hemorrhagic Shock Prevention}, author = {V Oncescu and S Lee and A Gumus and K Karlsson and D Erickson}, year = {2014}, date = {2014-01-01}, journal = {PloS one}, volume = {9}, number = {2}, pages = {89903}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ozan, Ş; Gümüştekin, Ş Calibration of double stripe 3D laser scanner systems using planarity and orthogonality constraints Journal Article Digital Signal Processing, 24 , pp. 231–243, 2014. @article{pop00003fb, title = {Calibration of double stripe 3D laser scanner systems using planarity and orthogonality constraints}, author = {Ş Ozan and Ş Gümüştekin}, year = {2014}, date = {2014-01-01}, journal = {Digital Signal Processing}, volume = {24}, pages = {231--243}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bidikli, Baris; Tatlicioglu, Enver; Zergeroglu, Erkan A self tuning RISE controller formulation Inproceedings Proceedings of the American Control Conference, 2014, ISSN: 07431619. @inproceedings{Bidikli2014b, title = {A self tuning RISE controller formulation}, author = {Baris Bidikli and Enver Tatlicioglu and Erkan Zergeroglu}, doi = {10.1109/ACC.2014.6859217}, issn = {07431619}, year = {2014}, date = {2014-01-01}, booktitle = {Proceedings of the American Control Conference}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Ozan, Ş; Gümüştekin, Ş Enhancing multiview 3d reconstruction using polarization imaging Journal Article 2014 22nd Signal Processing and Communications Applications Conference (SIU …, 2014. @article{pop00017d, title = {Enhancing multiview 3d reconstruction using polarization imaging}, author = {Ş Ozan and Ş Gümüştekin}, year = {2014}, date = {2014-01-01}, journal = {2014 22nd Signal Processing and Communications Applications Conference (SIU …}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bidikli, Baris; Tatlicioglu, Enver; Zergeroglu, Erkan A robust tracking controller for dynamically positioned surface vessels with added mass Inproceedings Proceedings of the IEEE Conference on Decision and Control, 2014, ISSN: 07431546. @inproceedings{Bidikli2014a, title = {A robust tracking controller for dynamically positioned surface vessels with added mass}, author = {Baris Bidikli and Enver Tatlicioglu and Erkan Zergeroglu}, doi = {10.1109/CDC.2014.7040073}, issn = {07431546}, year = {2014}, date = {2014-01-01}, booktitle = {Proceedings of the IEEE Conference on Decision and Control}, abstract = {— This work concentrates on tracking control of dynamically positioned surface vessels with asymmetric added mass terms affecting the system model at the acceleration level. Specifically, we propose a novel continuous robust controller for surface vessels that, in addition to asymmetric added mass in its inertia matrix, contains unstructured uncertainties in all its system matrices. The proposed controller compensates the overall system uncertainties and ensures asymptotic tracking, while requiring only the knowledge of the sign of the leading principle minors of the input gain matrix. Lyapunov based approaches are applied in order to prove the stability of the closed–loop system and asymptotic convergence of the tracking error signal.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } — This work concentrates on tracking control of dynamically positioned surface vessels with asymmetric added mass terms affecting the system model at the acceleration level. Specifically, we propose a novel continuous robust controller for surface vessels that, in addition to asymmetric added mass in its inertia matrix, contains unstructured uncertainties in all its system matrices. The proposed controller compensates the overall system uncertainties and ensures asymptotic tracking, while requiring only the knowledge of the sign of the leading principle minors of the input gain matrix. Lyapunov based approaches are applied in order to prove the stability of the closed–loop system and asymptotic convergence of the tracking error signal. |
Bidikli, Baris; Tatlicioglu, Enver; Zergeroglu, Erkan Observer based output feedback tracking control of dynamically positioned surface vessels Inproceedings 2014. @inproceedings{Bidikli2014c, title = {Observer based output feedback tracking control of dynamically positioned surface vessels}, author = {Baris Bidikli and Enver Tatlicioglu and Erkan Zergeroglu}, doi = {10.1109/acc.2013.6579895}, year = {2014}, date = {2014-01-01}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Ozsahin, I; Unlu, MZ Modeling and simulation of Positron Emission Mammography (PEM) based on double-sided CdTe strip detectors Journal Article Journal of Instrumentation 9 (03), C, 3055 , 2014. @article{pop00010g, title = {Modeling and simulation of Positron Emission Mammography (PEM) based on double-sided CdTe strip detectors}, author = {I Ozsahin and MZ Unlu}, year = {2014}, date = {2014-01-01}, journal = {Journal of Instrumentation 9 (03), C}, volume = {3055}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Savaci, FA; Göknar, IC Electrical and Electronics Engineering Faculty Istanbul Technical University Journal Article System Structure and Control, 1992 , pp. 352–352, 2014. @article{pop00046b, title = {Electrical and Electronics Engineering Faculty Istanbul Technical University}, author = {FA Savaci and IC Göknar}, year = {2014}, date = {2014-01-01}, journal = {System Structure and Control}, volume = {1992}, pages = {352--352}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Okur, Beytullah; Zergeroglu, Erkan; Tatlicioglu, Enver; Aksoy, Orhan Nonlinear adaptive partial state feedback trajectory tracking control of tendon driven robot manipulators Inproceedings 2014 IEEE Conference on Control Applications, CCA 2014, 2014, ISBN: 9781479974092. @inproceedings{Okur2014, title = {Nonlinear adaptive partial state feedback trajectory tracking control of tendon driven robot manipulators}, author = {Beytullah Okur and Erkan Zergeroglu and Enver Tatlicioglu and Orhan Aksoy}, doi = {10.1109/CCA.2014.6981356}, isbn = {9781479974092}, year = {2014}, date = {2014-01-01}, booktitle = {2014 IEEE Conference on Control Applications, CCA 2014}, abstract = {textcopyright 2014 IEEE. In this work, the link position tracking control problem of a tendon driven robotic system is studied in the presence of parametric uncertainty and lack of velocity measurements both of links and actuators. A partial state feedback nonlinear adaptive controller is proposed to deal with the unmeasurable states and uncertain dynamical system parameters. A backstepping approach has been utilized to develop the control strategy. The proposed nonlinear tracking controller utilizes online update laws to adapt for parametric uncertainties, and requires only link and actuator position measurements and tendon tension measurements. Need for link velocity measurements are eliminated by using a nonlinear filter, and a set of linear filters is designed to estimate the actuator velocities. Lyapunov based arguments have been applied to prove the stability of the closed-loop system and semi-global asymptotic link position tracking is achieved.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } textcopyright 2014 IEEE. In this work, the link position tracking control problem of a tendon driven robotic system is studied in the presence of parametric uncertainty and lack of velocity measurements both of links and actuators. A partial state feedback nonlinear adaptive controller is proposed to deal with the unmeasurable states and uncertain dynamical system parameters. A backstepping approach has been utilized to develop the control strategy. The proposed nonlinear tracking controller utilizes online update laws to adapt for parametric uncertainties, and requires only link and actuator position measurements and tendon tension measurements. Need for link velocity measurements are eliminated by using a nonlinear filter, and a set of linear filters is designed to estimate the actuator velocities. Lyapunov based arguments have been applied to prove the stability of the closed-loop system and semi-global asymptotic link position tracking is achieved. |
Okur, B; Zergeroglu, E; Seker, M; Taticioglu, E Nonlinear robust control of 3 phase inverter with output LC filter Journal Article IFAC Proceedings Volumes, 47 (3), pp. 529–533, 2014. @article{pop00058b, title = {Nonlinear robust control of 3 phase inverter with output LC filter}, author = {B Okur and E Zergeroglu and M Seker and E Taticioglu}, year = {2014}, date = {2014-01-01}, journal = {IFAC Proceedings Volumes}, volume = {47}, number = {3}, pages = {529--533}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Hilavin, Sezgin; Kustepeli, Alp Design and implementation of a TEM stripline for EMC testing Journal Article IEEE Transactions on Electromagnetic Compatibility, 2014, ISSN: 00189375. @article{Hilavin2014, title = {Design and implementation of a TEM stripline for EMC testing}, author = {Sezgin Hilavin and Alp Kustepeli}, doi = {10.1109/TEMC.2013.2271834}, issn = {00189375}, year = {2014}, date = {2014-01-01}, journal = {IEEE Transactions on Electromagnetic Compatibility}, abstract = {—In this paper, a stripline for radiated field immunity testing of audio/video products is designed, constructed, calibrated, and verified. Since the canonical one is only suitable for testing equipments with height less than 70 cm, there is a need of a new device which is also in compliance with EN 55020 standard for testing new large sets, like 47 thin-film transistor liquid crys-tal display (TFT LCD) television sets, in the frequency range of 150 kHz–150 MHz. Increasing the height and width of testing area causes important problems in terms of field uniformity regarding the higher order modes, characteristic impedance, and reflections in addition to the room resonances and field interference sources like corners at the edges of stripline. Comprehensive numerical study is performed to overcome these problems and obtain the op-timum design before the construction. Measured data show that the new stripline is in very good agreement with the specifications determined by the standards and therefore it can be used for the electromagnetic compatibility (EMC) testing. Index Terms—Electromagnetic compatibility (EMC), immunity, susceptibility, stripline, EN 55020, EN 61000-4–20.}, keywords = {}, pubstate = {published}, tppubtype = {article} } —In this paper, a stripline for radiated field immunity testing of audio/video products is designed, constructed, calibrated, and verified. Since the canonical one is only suitable for testing equipments with height less than 70 cm, there is a need of a new device which is also in compliance with EN 55020 standard for testing new large sets, like 47 thin-film transistor liquid crys-tal display (TFT LCD) television sets, in the frequency range of 150 kHz–150 MHz. Increasing the height and width of testing area causes important problems in terms of field uniformity regarding the higher order modes, characteristic impedance, and reflections in addition to the room resonances and field interference sources like corners at the edges of stripline. Comprehensive numerical study is performed to overcome these problems and obtain the op-timum design before the construction. Measured data show that the new stripline is in very good agreement with the specifications determined by the standards and therefore it can be used for the electromagnetic compatibility (EMC) testing. Index Terms—Electromagnetic compatibility (EMC), immunity, susceptibility, stripline, EN 55020, EN 61000-4–20. |
Tanyer, Ilker; Tatlicioglu, Enver; Zergeroglu, Erkan A robust adaptive tracking controller for an aircraft with uncertain dynamical terms Inproceedings IFAC Proceedings Volumes (IFAC-PapersOnline), 2014, ISSN: 14746670. @inproceedings{Tanyer2014, title = {A robust adaptive tracking controller for an aircraft with uncertain dynamical terms}, author = {Ilker Tanyer and Enver Tatlicioglu and Erkan Zergeroglu}, issn = {14746670}, year = {2014}, date = {2014-01-01}, booktitle = {IFAC Proceedings Volumes (IFAC-PapersOnline)}, abstract = {Abstract This work presents, the design and the corresponding analysis of a nonlinear controller for an aircraft system subject to uncertainties in the dynamics and additive state–dependent nonlinear disturbance–like terms. Specifically; dynamic inversion technique in conjunction with a robust integral of the signum of the error feedback and an adaptive term is utilized in the overall controller design. Lyapunov based stability analysis techniques are then utilized to prove global asymptotic convergence of the tracking error.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } Abstract This work presents, the design and the corresponding analysis of a nonlinear controller for an aircraft system subject to uncertainties in the dynamics and additive state–dependent nonlinear disturbance–like terms. Specifically; dynamic inversion technique in conjunction with a robust integral of the signum of the error feedback and an adaptive term is utilized in the overall controller design. Lyapunov based stability analysis techniques are then utilized to prove global asymptotic convergence of the tracking error. |
Atakan, Barış Molecular communications and nanonetworks: From nature to practical systems Book 2014, ISBN: 9781493907397. @book{Atakan2014cb, title = {Molecular communications and nanonetworks: From nature to practical systems}, author = {Barış Atakan}, doi = {10.1007/978-1-4939-0739-7}, isbn = {9781493907397}, year = {2014}, date = {2014-01-01}, booktitle = {Molecular Communications and Nanonetworks: From Nature to Practical Systems}, keywords = {}, pubstate = {published}, tppubtype = {book} } |
Bidikli, Baris; Tatlicioglu, Enver; Zergeroglu, Erkan A self tuning RISE controller formulation Inproceedings Proceedings of the American Control Conference, 2014, ISSN: 07431619. @inproceedings{Bidikli2014bb, title = {A self tuning RISE controller formulation}, author = {Baris Bidikli and Enver Tatlicioglu and Erkan Zergeroglu}, doi = {10.1109/ACC.2014.6859217}, issn = {07431619}, year = {2014}, date = {2014-01-01}, booktitle = {Proceedings of the American Control Conference}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Bidikli, Baris; Tatlicioglu, Enver; Zergeroglu, Erkan A robust tracking controller for dynamically positioned surface vessels with added mass Inproceedings Proceedings of the IEEE Conference on Decision and Control, 2014, ISSN: 07431546. @inproceedings{Bidikli2014ab, title = {A robust tracking controller for dynamically positioned surface vessels with added mass}, author = {Baris Bidikli and Enver Tatlicioglu and Erkan Zergeroglu}, doi = {10.1109/CDC.2014.7040073}, issn = {07431546}, year = {2014}, date = {2014-01-01}, booktitle = {Proceedings of the IEEE Conference on Decision and Control}, abstract = {— This work concentrates on tracking control of dynamically positioned surface vessels with asymmetric added mass terms affecting the system model at the acceleration level. Specifically, we propose a novel continuous robust controller for surface vessels that, in addition to asymmetric added mass in its inertia matrix, contains unstructured uncertainties in all its system matrices. The proposed controller compensates the overall system uncertainties and ensures asymptotic tracking, while requiring only the knowledge of the sign of the leading principle minors of the input gain matrix. Lyapunov based approaches are applied in order to prove the stability of the closed–loop system and asymptotic convergence of the tracking error signal.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } — This work concentrates on tracking control of dynamically positioned surface vessels with asymmetric added mass terms affecting the system model at the acceleration level. Specifically, we propose a novel continuous robust controller for surface vessels that, in addition to asymmetric added mass in its inertia matrix, contains unstructured uncertainties in all its system matrices. The proposed controller compensates the overall system uncertainties and ensures asymptotic tracking, while requiring only the knowledge of the sign of the leading principle minors of the input gain matrix. Lyapunov based approaches are applied in order to prove the stability of the closed–loop system and asymptotic convergence of the tracking error signal. |
Atakan, B Molecular communication among nanomachines Journal Article Molecular Communications and Nanonetworks, pp. 1–24, 2014. @article{pop00022c, title = {Molecular communication among nanomachines}, author = {B Atakan}, year = {2014}, date = {2014-01-01}, journal = {Molecular Communications and Nanonetworks}, pages = {1--24}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bidikli, Baris; Tatlicioglu, Enver; Zergeroglu, Erkan Observer based output feedback tracking control of dynamically positioned surface vessels Inproceedings 2014. @inproceedings{Bidikli2014f, title = {Observer based output feedback tracking control of dynamically positioned surface vessels}, author = {Baris Bidikli and Enver Tatlicioglu and Erkan Zergeroglu}, doi = {10.1109/acc.2013.6579895}, year = {2014}, date = {2014-01-01}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Atakan, B Passive molecular communication through ligand–receptor binding Journal Article Molecular Communications and Nanonetworks, pp. 105–143, 2014. @article{pop00025b, title = {Passive molecular communication through ligand–receptor binding}, author = {B Atakan}, year = {2014}, date = {2014-01-01}, journal = {Molecular Communications and Nanonetworks}, pages = {105--143}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Atakan, Baris On exploiting sampling Jitter in vehicular sensor networks Journal Article IEEE Transactions on Vehicular Technology, 2014, ISSN: 00189545. @article{Atakan2014b, title = {On exploiting sampling Jitter in vehicular sensor networks}, author = {Baris Atakan}, doi = {10.1109/TVT.2013.2271359}, issn = {00189545}, year = {2014}, date = {2014-01-01}, journal = {IEEE Transactions on Vehicular Technology}, abstract = {Vehicular sensor networks (VSNs) are composed of vehicular sensor nodes that collaboratively sample, communicate, and reconstruct the event signal at the sink node. Samples of event signals are subjected to jitter based on the propagation speed of signal and locations of vehicular sensors. In this paper, a theoretical analysis is presented to understand the effects and how to exploit the jitter in the sensed event signal for energy-efficient and reliable communication in VSNs. Results reveal that sampling jitter can be advantageous and can be exploited in developing adaptive communication techniques, which can provide significant energy conservation while maintaining reliability in VSNs. [ABSTRACT FROM PUBLISHER]}, keywords = {}, pubstate = {published}, tppubtype = {article} } Vehicular sensor networks (VSNs) are composed of vehicular sensor nodes that collaboratively sample, communicate, and reconstruct the event signal at the sink node. Samples of event signals are subjected to jitter based on the propagation speed of signal and locations of vehicular sensors. In this paper, a theoretical analysis is presented to understand the effects and how to exploit the jitter in the sensed event signal for energy-efficient and reliable communication in VSNs. Results reveal that sampling jitter can be advantageous and can be exploited in developing adaptive communication techniques, which can provide significant energy conservation while maintaining reliability in VSNs. [ABSTRACT FROM PUBLISHER] |