WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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Article Citation - WoS: 10Citation - Scopus: 13On the Characterization of Cognitive Tasks Using Activity-Specific Short-Lived Synchronization Between Electroencephalography Channels(Elsevier, 2021) Olcay, B. Orkan; Olcay, Bilal Orkan; Karaçalı, Bilge; 01.01. Units Affiliated to the Rectorate; 03.05. Department of Electrical and Electronics Engineering; 01. Izmir Institute of Technology; 03. Faculty of EngineeringAccurate characterization of brain activity during a cognitive task is challenging due to the dynamically changing and the complex nature of the brain. The majority of the proposed approaches assume stationarity in brain activity and disregard the systematic timing organization among brain regions during cognitive tasks. In this study, we propose a novel cognitive activity recognition method that captures the activity-specific timing parameters from training data that elicits maximal average short-lived pairwise synchronization between electroencephalography signals. We evaluated the characterization power of the activity-specific timing parameter triplets in a motor imagery activity recognition framework. The activity-specific timing parameter triplets consist of latency of the maximally synchronized signal segments from activity onset Delta t, the time lag between maximally synchronized signal segments t, and the duration of the maximally synchronized signal segments w. We used cosine-based similarity, wavelet bi-coherence, phase-locking value, phase coherence value, linearized mutual information, and cross-correntropy to calculate the channel synchronizations at the specific timing parameters. Recognition performances as well as statistical analyses on both BCI Competition-III dataset IVa and PhysioNet Motor Movement/Imagery dataset, indicate that the interchannel short-lived synchronization calculated using activity-specific timing parameter triplets elicit significantly distinct synchronization profiles for different motor imagery tasks and can thus reliably be used for cognitive task recognition purposes. (C) 2021 Elsevier Ltd. All rights reserved.Conference Object Citation - WoS: 2Türk Makam Müziği Notaları için Otomatik Ezgi Bölütleme(Institute of Electrical and Electronics Engineers Inc., 2014) Bozkurt, Barış; Karaçalı, Bilge; Karaçalı, Bilge; Bozkurt, Barış; Karaosmanoğlu, M. Kemal; Ünal, Erdem; 03.05. Department of Electrical and Electronics Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyAutomatic 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 makant 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.Conference Object Citation - Scopus: 2Model-Free Expectation Maximization for Divisive Hierarchical Clustering of Multicolor Flow Cytometry Data(IEEE, 2014) Köktürk, Başak Esin; Karaçalı, Bilge; Karaçalı, Bilge; 03.05. Department of Electrical and Electronics Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyThis 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.Conference Object Citation - Scopus: 3Gri Seviye Birliktelik Matrisi Öznitelikleri ve Manifold Öğrenme Yardımıyla Histoloji Görüntülerinde Otomatik Doku Sınıflandırılması(Institute of Electrical and Electronics Engineers Inc., 2009) Önder, Devrim; Karaçalı, Bilge; Karaçalı, Bilge; 03.05. Department of Electrical and Electronics Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyThe aim of this work is to perform automated texture classification of histology slides using grayscale images and manifold learning method. Texture feature vectors were obtained using local gray scale co-occurrence matrices and the dimension of the feature vector space was lowered using Isomap dimension reduction. In a lower dimension feature space, k-means clustering operation was performed in order to provide separate texture clusters. In this work, experimental results were obtained using human kidney histology slides. Corresponding feature vectors and determined texture types were given as results.Article Citation - WoS: 14Citation - Scopus: 17Evaluation of Synchronization Measures for Capturing the Lagged Synchronization Between Eeg Channels: a Cognitive Task Recognition Approach(Elsevier, 2019) Olcay, Bilal Orkan; Olcay, Bilal Orkan; Karaçalı, Bilge; Karaçalı, Bilge; 01.01. Units Affiliated to the Rectorate; 03.05. Department of Electrical and Electronics Engineering; 01. Izmir Institute of Technology; 03. Faculty of EngineeringDuring cognitive, perceptual and sensory tasks, connectivity profile changes across different regions of the brain. Variations of such connectivity patterns between different cognitive tasks can be evaluated using pairwise synchronization measures applied to electrophysiological signals, such as electroencephalography (EEG). However, connectivity-based task recognition approaches achieving viable recognition performance have been lacking from the literature. By using several synchronization measures, we identify time lags between channel pairs during different cognitive tasks. We employed mutual information, cross correntropy, cross correlation, phase locking value, cosine similarity and nonlinear interdependence measures. In the training phase, for each type of cognitive task, we identify the time lags that maximize the average synchronization between channel pairs. These lags are used to calculate pairwise synchronization values with which we construct the train and test feature vectors for recognition of the cognitive task carried out using Fisher's linear discriminant (FLD) analysis. We tested our framework in a motor imagery activity recognition scenario on PhysioNet Motor Movement/Imagery and BCI Competition-III IVa datasets. For PhysioNet dataset, average performance results ranging between % 51 and % 61 across 20 subjects. For BCI Competition-III dataset, we achieve an average recognition performance of % 76 which is above the minimum reliable communication rate (% 70). We achieved an average accuracy over the minimum reliable communication rate on the BCI Competition-III dataset. Performance levels were lower on the PhysioNet dataset. These results indicate that a viable task recognition system is achievable using pairwise synchronization measures evaluated at the proper task specific lags.Article Citation - WoS: 560Citation - Scopus: 607A Community Effort To Assess and Improve Drug Sensitivity Prediction Algorithms(Nature Publishing Group, 2014) Costello, James C.; Karaçalı, Bilge; 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; NCI-DREAM Community; Karaçalı, Bilge; Collins, James J.; Gallahan, Dan; Singer, Dinah; Saez-Rodriguez, Julio; Kaski, Samuel; Gray, Joe W.; Stolovitzky, Gustavo; 03.05. Department of Electrical and Electronics Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyPredicting 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.Article Citation - WoS: 240Citation - Scopus: 264A Community Computational Challenge To Predict the Activity of Pairs of Compounds(Nature Publishing Group, 2014) Bansal, Mukesh; Karaçalı, Bilge; 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; NCI-DREAM Community; Karaçalı, Bilge; Gallahan, Daniel; Singer, Dinah; Saez-Rodriguez, Julio; Xie, Yang; Stolovitzky, Gustavo; Califano, Andrea; 03.05. Department of Electrical and Electronics Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyRecent 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.Conference Object Citation - WoS: 1Citation - Scopus: 1Eeg Verisinde Kanallar-arası Zaman Uyumluluk Profilleri Kullanılarak Hayali Hareket Tanıma(Institute of Electrical and Electronics Engineers Inc., 2016) Olcay, Bilal Orkan; Özgören, Murat; Olcay, Bilal Orkan; Karaçalı, Bilge; 01.01. Units Affiliated to the Rectorate; 03.05. Department of Electrical and Electronics Engineering; 01. Izmir Institute of Technology; 03. Faculty of EngineeringBu çalışmada, elektrotlar arası zaman gecikmesi kullanılarak bir beyin-bilgisayar ara yüzü çalışması gerçekleştirilmiştir. Öznitelik olarak, seçilen referans kanalı ile geriye kalan tüm kanalların çapraz kovaryansının mutlak değerinin en yüksek olduğu zaman gecikmeleri hesaplanmıştır. Çalışmada kullanılan 5 kişi içinden 3 kişinin sınıflandırma performansının %100’e yakın olmasının yanında bu kişilerin eğitim veri seti sayısının diğer iki kişiye göre oldukça düşük olması ve literatürde buna benzer çalışmaların azlığı, önerilen yaklaşımın geliştirilmeye açık olduğunu göstermektedir.Article Citation - WoS: 19Citation - Scopus: 25Taste dysfunction in multiple sclerosis(D. Steinkopff-Verlag, 2016) Doty, Richard L.; Karaçalı, Bilge; Pham, Dzung L.; Cuzzocreo, Jennifer L.; Udupa, Jayaram K.; Karaçalı, Bilge; Beals, Evan; Fabius, Laura; Leon-Sarmiento, Fidias E.; Moonis, Gul; Kim, Taehoon; Mihama, Toru; Geckle, Rena J.; Yousem, David M.; 03.05. Department of Electrical and Electronics Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyEmpirical studies of taste function in multiple sclerosis (MS) are rare. Moreover, a detailed assessment of whether quantitative measures of taste function correlate with the punctate and patchy myelin-related lesions found throughout the CNS of MS patients has not been made. We administered a 96-trial test of sweet (sucrose), sour (citric acid), bitter (caffeine) and salty (NaCl) taste perception to the left and right anterior (CN VII) and posterior (CN IX) tongue regions of 73 MS patients and 73 matched controls. The number and volume of lesions were assessed using quantitative MRI in 52 brain regions of 63 of the MS patients. Taste identification scores were significantly lower in the MS patients for sucrose (p = 0.0002), citric acid (p = 0.0001), caffeine (p = 0.0372) and NaCl (p = 0.0004) and were present in both anterior and posterior tongue regions. The percent of MS patients with identification scores falling below the 5th percentile of controls was 15.07 % for caffeine, 21.9 % for citric acid, 24.66 % for sucrose, and 31.50 % for NaCl. Such scores were inversely correlated with lesion volumes in the temporal, medial frontal, and superior frontal lobes, and with the number of lesions in the left and right superior frontal lobes, right anterior cingulate gyrus, and left parietal operculum. Regardless of the subject group, women outperformed men on the taste measures. These findings indicate that a sizable number of MS patients exhibit taste deficits that are associated with MS-related lesions throughout the brain.Conference Object Citation - WoS: 1Citation - Scopus: 2Fisher's Linear Discriminant Analysis Based Prediction Using Transient Features of Seismic Events in Coal Mines(Institute of Electrical and Electronics Engineers Inc., 2016) Köktürk Güzel, Başak Esin; Karaçalı, Bilge; Karaçalı, Bilge; 03.05. Department of Electrical and Electronics Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyIdentification of seismic activity levels in coal mines is important to avoid accidents such as rockburst. Creating an early warning system that can save lives requires an automated way of predicting. This study proposes a prediction algorithm for the AAIA'16 Data Mining Challenge: Predicting Dangerous Seismic Events in Active Coal Mines that is based on transient activity features along with average indicators evaluated by a Fisher's linear discriminant analysis. Performance evaluation experiments on the training datasets revealed an accuracy level of around 0.9438 while the performance on the test dataset was at a level of 0.9297. These results suggest that the proposed approach achieves high accuracy in predicting danger seismic events while maintaining low complexity.