Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Article Citation - WoS: 26Citation - Scopus: 48Metabolic Imaging Based Sub-Classification of Lung Cancer(IEEE-Inst Electrical Electronics Engineers Inc, 2020) Bicakci, Mustafa; Ayyildiz, Oguzhan; Aydin, Zafer; Basturk, Alper; Karacavus, Seyhan; Yilmaz, BulentLung cancer is one of the deadliest cancer types whose 84% is non-small cell lung cancer (NSCLC). In this study, deep learning-based classification methods were investigated comprehensively to differentiate two subtypes of NSCLC, namely adenocarcinoma (ADC) and squamous cell carcinoma (SqCC). The study used 1457 F-18-FDG PET images/slices with tumor from 94 patients (88 men), 38 of which were ADC and the rest were SqCC. Three experiments were carried out to examine the contribution of peritumoral areas in PET images on subtype classification of tumors. We assessed multilayer perceptron (MLP) and three convolutional neural network (CNN) models such as SqueezeNet, VGG16 and VGG19 using three kinds of images in these experiments: 1) Whole slices without cropping or segmentation, 2) cropped image portions (square subimages) that include the tumor and 3) segmented image portions corresponding to tumors using random walk method. Several optimizers and regularization methods were used to optimize each model for the diagnostic classification. The classification models were trained and evaluated by performing stratified 10-fold cross validation, and F-score and area-under-curve (AUC) metrics were used to quantify the performance. According to our results, it is possible to say that inclusion of peritumoral regions/tissues both contributes to the success of models and makes segmentation effort unnecessary. To the best of our knowledge, deep learning-based models have not been applied to the subtype classification of NSCLC in PET imaging, therefore, this study is a significant cornerstone providing thorough comparisons and evaluations of several deep learning models on metabolic imaging for lung cancer. Even simpler deep learning models are found promising in this domain, indicating that any improvement in deep learning models in machine learning community can be reflected well in this domain as well.Article Citation - WoS: 24Citation - Scopus: 30Improved Classification of Colorectal Polyps on Histopathological Images With Ensemble Learning and Stain Normalization(Elsevier Ireland Ltd, 2023-04) Yengec-Tasdemir, Sena Busra; Aydin, Zafer; Akay, Ebru; Dogan, Serkan; Yilmaz, BulentBackground and Objective: Early detection of colon adenomatous polyps is critically important because correct detection of it significantly reduces the potential of developing colon cancers in the future. The key challenge in the detection of adenomatous polyps is differentiating it from its visually similar counterpart, non-adenomatous tissues. Currently, it solely depends on the experience of the pathologist. To assist the pathologists, the objective of this work is to provide a novel non-knowledge-based Clinical Decision Support System (CDSS) for improved detection of adenomatous polyps on colon histopathology images. Methods: The domain shift problem arises when the train and test data are coming from different distributions of diverse settings and unequal color levels. This problem, which can be tackled by stain normalization techniques, restricts the machine learning models to attain higher classification accuracies. In this work, the proposed method integrates stain normalization techniques with ensemble of competitively accurate, scalable and robust variants of CNNs, ConvNexts. The improvement is empirically analyzed for five widely employed stain normalization techniques. The classification performance of the proposed method is evaluated on three datasets comprising more than 10k colon histopathology images. Results: The comprehensive experiments demonstrate that the proposed method outperforms the stateof-the-art deep convolutional neural network based models by attaining 95% classification accuracy on the curated dataset, and 91.1% and 90% on EBHI and UniToPatho public datasets, respectively. Conclusions: These results show that the proposed method can accurately classify colon adenomatous polyps on histopathology images. It retains remarkable performance scores even for different datasets coming from different distributions. This indicates that the model has a notable generalization ability. (c) 2023 Elsevier B.V. All rights reserved.Article Citation - WoS: 8Citation - Scopus: 10Developing Structural Profile Matrices for Protein Secondary Structure and Solvent Accessibility Prediction(Oxford Univ Press, 2019-04-01) Aydin, Zafer; Azginoglu, Nuh; Bilgin, Halil Ibrahim; Celik, MeteMotivation: Predicting secondary structure and solvent accessibility of proteins are among the essential steps that preclude more elaborate 3D structure prediction tasks. Incorporating class label information contained in templates with known structures has the potential to improve the accuracy of prediction methods. Building a structural profile matrix is one such technique that provides a distribution for class labels at each amino acid position of the target. Results: In this paper, a new structural profiling technique is proposed that is based on deriving PFAM families and is combined with an existing approach. Cross-validation experiments on two benchmark datasets and at various similarity intervals demonstrate that the proposed profiling strategy performs significantly better than Homolpro, a state-of-the-art method for incorporating template information, as assessed by statistical hypothesis tests.Article Citation - Scopus: 43BAUM-2: A Multilingual Audio-Visual Affective Face Database(Kluwer Academic Publishers barbara.b.bertram@gsk.com, 2014-05-09) Erdem, Cigdem Eroglu; Turan, Çigdem; Aydin, Zafer; Eroglu Erdem, CigdemAccess to audio-visual databases, which contain enough variety and are richly annotated is essential to assess the performance of algorithms in affective computing applications, which require emotion recognition from face and/or speech data. Most databases available today have been recorded under tightly controlled environments, are mostly acted and do not contain speech data. We first present a semi-automatic method that can extract audio-visual facial video clips from movies and TV programs in any language. The method is based on automatic detection and tracking of faces in a movie until the face is occluded or a scene cut occurs. We also created a video-based database, named as BAUM-2, which consists of annotated audio-visual facial clips in several languages. The collected clips simulate real-world conditions by containing various head poses, illumination conditions, accessories, temporary occlusions and subjects with a wide range of ages. The proposed semi-automatic affective clip extraction method can easily be used to extend the database to contain clips in other languages. We also created an image based facial expression database from the peak frames of the video clips, which is named as BAUM-2i. Baseline image and video-based facial expression recognition results using state-of-the art features and classifiers indicate that facial expression recognition under tough and close-to-natural conditions is quite challenging. © 2017 Elsevier B.V., All rights reserved.Article Citation - Scopus: 15An Effective Colorectal Polyp Classification for Histopathological Images Based on Supervised Contrastive Learning(Elsevier Ltd, 2024-04) Yengec-Tasdemir, Sena Busra; Aydin, Zafer; Akay, Ebru; Doǧan, Serkan; Yilmaz, BulentEarly detection of colon adenomatous polyps is pivotal in reducing colon cancer risk. In this context, accurately distinguishing between adenomatous polyp subtypes, especially tubular and tubulovillous, from hyperplastic variants is crucial. This study introduces a cutting-edge computer-aided diagnosis system optimized for this task. Our system employs advanced Supervised Contrastive learning to ensure precise classification of colon histopathology images. Significantly, we have integrated the Big Transfer model, which has gained prominence for its exemplary adaptability to visual tasks in medical imaging. Our novel approach discerns between in-class and out-of-class images, thereby elevating its discriminatory power for polyp subtypes. We validated our system using two datasets: a specially curated one and the publicly accessible UniToPatho dataset. The results reveal that our model markedly surpasses traditional deep convolutional neural networks, registering classification accuracies of 87.1% and 70.3% for the custom and UniToPatho datasets, respectively. Such results emphasize the transformative potential of our model in polyp classification endeavors. © 2024 Elsevier B.V., All rights reserved.Article Citation - WoS: 15Citation - Scopus: 14A Review of Mammographic Region of Interest Classification(Wiley Periodicals, inc, 2020-02-18) Yengec Tasdemir, Sena B.; Tasdemir, Kasim; Aydin, ZaferEarly detection of breast cancer is important and highly valuable in clinical practice. X-ray mammography is broadly used for prescreening the breast and is also attractive due to its noninvasive nature. However, experts can misdiagnose a significant proportion of the cases, which may either cause redundant examinations or cancer. In order to reduce false positive and negative rates of mammography screening, computer-aided breast cancer detection has been studied for more than 30 years and many methods have been proposed by the researchers. In this review, region of interest (ROI) classification methods, which operate on a predefined or segmented ROIs with a focus on mass classification are surveyed. A total of 72 high quality journal and conference papers are selected from the Web of Science (WOS) database that meet several inclusion criteria. A comparative analysis is provided based on ROI extraction methods, data sets and machine learning techniques employed, the prediction accuracies, and usage frequency statistics. Based on the performances obtained on publicly available data sets, the ROI classification problem from mammogram images can be considered as approaching to be solved. Nonetheless, it can still be used as complementary information in breast cancer detection from the whole mammograms, which has room for improvement. This article is categorized under: Application Areas > Science and Technology Technologies > Machine Learning Technologies > ClassificationArticle Citation - WoS: 10Citation - Scopus: 13A Noise-Aware Feature Selection Approach for Classification(Springer, 2021-02-17) Sabzekar, Mostafa; Aydin, ZaferA noise-aware version of support vector machines is utilized for feature selection in this paper. Combining this method and sequential backward search (SBS), a new algorithm for removing irrelevant features is proposed. Although feature selection methods in the literature which utilize support vector machines have provided acceptable results, noisy samples and outliers may affect the performance of SVM and feature selections method, consequently. Recently, we have proposed relaxed constrains SVM (RSVM) which handles noisy data and outliers. Each training sample in RSVM is associated with a degree of importance utilizing the fuzzy c-means clustering method. Therefore, a less importance degree is assigned to noisy data and outliers. Moreover, RSVM has more relaxed constraints that can reduce the effect of noisy samples. Feature selection increases the accuracy of different machine learning applications by eliminating noisy and irrelevant features. In the proposed RSVM-SBS feature selection algorithm, noisy data have small effect on eliminating irrelevant features. Experimental results using real-world data verify that RSVM-SBS has better results in comparison with other feature selection approaches utilizing support vector machines.Article Citation - WoS: 17Citation - Scopus: 19A Deep Ensemble Approach for Long-Term Traffic Flow Prediction(Springer Heidelberg, 2024-01-27) Cini, Nevin; Aydin, ZaferIn the last 50 years, with the growth of cities and increase in the number of vehicles and mobility, traffic has become troublesome. As a result, traffic flow prediction started to attract attention as an important research area. However, despite the extensive literature, traffic flow prediction still remains as an open research problem, specifically for long-term traffic flow prediction. Compared to the models developed for short-term traffic flow prediction, the number of models developed for long-term traffic flow prediction is very few. Based on this shortcoming, in this study, we focus on long-term traffic flow prediction and propose a novel deep ensemble model (DEM). In order to build this ensemble model, first, we developed a convolutional neural network (CNN), a long short-term memory (LSTM) network and a gated recurrent unit (GRU) network as deep learning models, which formed the base learners. In the next step, we combine the output of these models according to their individual forecasting success. We use another deep learning model to determine the success of the individual models. Our proposed model is a flexible ensemble prediction model that can be updated based on traffic data. To evaluate the performance of the proposed model, we use a publicly available dataset. Experimental results show that the developed DEM model has a mean square error of 0.06 and a mean absolute error of 0.15 for single-step prediction; it shows that achieves a mean square error of 0.25 and a mean absolute error of 0.32 for multi-step prediction. We compared our proposed model with many models in different categories; individual deep learning models (i.e., LSTM, CNN, GRU), selected traditional machine learning models (i.e., linear regression, decision tree regression, k-nearest-neighbors regression) and other ensemble models such as random-forest regression. These results also support the claim that ensemble learning models perform better than individual models.Article Citation - WoS: 13Citation - Scopus: 13A Continuously Benchmarked and Crowdsourced Challenge for Rapid Development and Evaluation of Models to Predict COVID-19 Diagnosis and Hospitalization(Amer Medical Assoc, 2021-10-11) Yan, Yao; Schaffter, Thomas; Bergquist, Timothy; Yu, Thomas; Prosser, Justin; Aydin, Zafer; Mooney, SeanIMPORTANCE Machine learning could be used to predict the likelihood of diagnosis and severity of illness. Lack of COVID-19 patient data has hindered the data science community in developing models to aid in the response to the pandemic. OBJECTIVES To describe the rapid development and evaluation of clinical algorithms to predict COVID-19 diagnosis and hospitalization using patient data by citizen scientists, provide an unbiased assessment of model performance, and benchmark model performance on subgroups. DESIGN, SETTING, AND PARTICIPANTS This diagnostic and prognostic study operated a continuous, crowdsourced challenge using a model-to-data approach to securely enable the use of regularly updated COVID-19 patient data from the University of Washington by participants from May 6 to December 23, 2020. A postchallenge analysis was conducted from December 24, 2020, to April 7, 2021, to assess the generalizability of models on the cumulative data set as well as subgroups stratified by age, sex, race, and time of COVID-19 test. By December 23, 2020, this challenge engaged 482 participants from 90 teams and 7 countries. MAIN OUTCOMES AND MEASURES Machine learning algorithms used patient data and output a score that represented the probability of patients receiving a positive COVID-19 test result or being hospitalized within 21 days after receiving a positive COVID-19 test result. Algorithms were evaluated using area under the receiver operating characteristic curve (AUROC) and area under the precision recall curve (AUPRC) scores. Ensemble models aggregating models from the top challenge teams were developed and evaluated. RESULTS In the analysis using the cumulative data set, the best performance for COVID-19 diagnosis prediction was an AUROC of 0.776 (95% CI, 0.775-0.777) and an AUPRC of 0.297, and for hospitalization prediction, an AUROC of 0.796 (95% CI, 0.794-0.798) and an AUPRC of 0.188. Analysis on top models submitting to the challenge showed consistently better model performance on the female group than the male group. Among all age groups, the best performance was obtained for the 25- to 49-year age group, and the worst performance was obtained for the group aged 17 years or younger. CONCLUSIONS AND RELEVANCE In this diagnostic and prognostic study, models submitted by citizen scientists achieved high performance for the prediction of COVID-19 testing and hospitalization outcomes. Evaluation of challenge models on demographic subgroups and prospective data revealed performance discrepancies, providing insights into the potential bias and limitations in the models.