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Yayın Implicit theories and self-efficacy in an introductory programming course(Institute of Electrical and Electronics Engineers Inc, 2018-08) Tek, Faik Boray; Benli, Kristin Surpuhi; Deveci, EzgiContribution: This paper examined student effort and performance in an introductory programming course with respect to student-held implicit theories and self-efficacy. Background: Implicit theories and self-efficacy help in understanding academic success, which must be considered when developing effective learning strategies for programming.Research Questions: Are implicit theories of intelligence and programming, and programming-efficacy, related to each other and to student success in programming? Is it possible to predict student performance in a course using these constructs? Methodology: Two consecutive surveys ({N}=100 and {N}=81) were administered to non-CS engineering students in Işik University, Turkey. Findings: Implicit theories of programming-aptitude and programming-efficacy are interrelated and positively correlated with effort, performance, and previous failures in the course. Although it was not possible to predict student course grade the data confirms that students who believe in improvable programming aptitude have significantly higher programming efficacy, report more effort, and get higher course grades. In addition, failed students tend to associate the failure with fixed programming aptitude; repeating students favor fixed programming aptitude theory and have lower programming-efficacy, which increases the possibility of further failure.Yayın Assessment of algorithms for mitosis detection in breast cancer histopathology images(Elsevier Science BV, 2015-02) Veta, Mitko; Van Diest, Paul J.; Willems, Stefan Martin; Wang, Haibo; Madabhushi, Anant; Cruz-Roa, Angel; Gonzalez, Fabio; Larsen, Anders Boesen Lindbo; Vestergaard, Jacob Schack Chack; Dahl, Anders Bjorholm; Cireşan, Dan Claudiu; Schmidhuber, Jürgen U.; Giusti, Alessandro; Gambardella, Luca M.; Tek, Faik Boray; Walter, Thomas C.; Wang, Chingwei; Kondo, Satoshi; Matuszewski, Bogdan J.; Precioso, Frédéric; Snell, Violet; Kittler, Josef; De Campos, Teofilo E.; Khan, Adnan M.; Rajpoot, Nasir Mahmood; Arkoumani, Evdokia; Lacle, Miangela M.; Viergever, Max A.; Pluim, Josien P WThe proliferative activity of breast tumors, which is routinely estimated by counting of mitotic figures in hematoxylin and eosin stained histology sections, is considered to be one of the most important prognostic markers. However, mitosis counting is laborious, subjective and may suffer from low inter-observer agreement. With the wider acceptance of whole slide images in pathology labs, automatic image analysis has been proposed as a potential solution for these issues.In this paper, the results from the Assessment of Mitosis Detection Algorithms 2013 (AMIDA13) challenge are described. The challenge was based on a data set consisting of 12 training and 11 testing subjects, with more than one thousand annotated mitotic figures by multiple observers. Short descriptions and results from the evaluation of eleven methods are presented. The top performing method has an error rate that is comparable to the inter-observer agreement among pathologists.Yayın Adaptive convolution kernel for artificial neural networks(Academic Press Inc., 2021-02) Tek, Faik Boray; Çam, İlker; Karlı, DenizMany deep neural networks are built by using stacked convolutional layers of fixed and single size (often 3 × 3) kernels. This paper describes a method for learning the size of convolutional kernels to provide varying size kernels in a single layer. The method utilizes a differentiable, and therefore backpropagation-trainable Gaussian envelope which can grow or shrink in a base grid. Our experiments compared the proposed adaptive layers to ordinary convolution layers in a simple two-layer network, a deeper residual network, and a U-Net architecture. The results in the popular image classification datasets such as MNIST, MNIST-CLUTTERED, CIFAR-10, Fashion, and ‘‘Faces in the Wild’’ showed that the adaptive kernels can provide statistically significant improvements on ordinary convolution kernels. A segmentation experiment in the Oxford-Pets dataset demonstrated that replacing ordinary convolution layers in a U-shaped network with 7 × 7 adaptive layers can improve its learning performance and ability to generalize.Yayın Robust localization and identification of African clawed frogs in digital images(Elsevier Science BV, 2014-09) Tek, Faik Boray; Cannavo, Flavio; Nunnari, Giuseppe; Kale, İzzetWe study the automatic localization and identification of African clawed frogs (Xenopus laevis sp.) in digital images taken in a laboratory environment. We propose a novel and stable frog body localization and skin pattern window extraction algorithm. We show that it compensates scale and rotation changes very well. Moreover, it is able to localize and extract highly overlapping regions (pattern windows) even in the cases of intense affine transformations, blurring, Gaussian noise, and intensity transformations. The frog skin pattern (i.e. texture) provides a unique feature for the identification of individual frogs. We investigate the suitability of five different feature descriptors (Gabor filters, area granulometry, HoG,(1) dense SIFT,(2) and raw pixel values) to represent frog skin patterns. We compare the robustness of the features based on their identification performance using a nearest neighbor classifier. Our experiments show that among five features that we tested, the best performing feature against rotation, scale, and blurring modifications was the raw pixel feature, whereas the SIFT feature was the best performing one against affine and intensity modifications.Yayın An adaptive locally connected neuron model: Focusing neuron(Elsevier B.V., 2021-01-02) Tek, Faik BorayThis paper presents a new artificial neuron model capable of learning its receptive field in the topological domain of inputs. The experiments include tests of focusing neuron networks of one or two hidden layers on synthetic and well-known image recognition data sets. The results demonstrated that the focusing neurons can move their receptive fields towards more informative inputs. In the simple two-hidden layer networks, the focusing layers outperformed the dense layers in the classification of the 2D spatial data sets. Moreover, the focusing networks performed better than the dense networks even when 70% of the weights were pruned. The tests on convolutional networks revealed that using focusing layers instead of dense layers for the classification of convolutional features may work better in some data sets.Yayın Mitosis detection using generic features and an ensemble of cascade adaboosts(Elsevier, 2013-05-30) Tek, Faik BorayContext: Mitosis count is one of the factors that pathologists use to assess the risk of metastasis and survival of the patients, which are affected by the breast cancer. Aims: We investigate an application of a set of generic features and an ensemble of cascade adaboosts to the automated mitosis detection. Calculation of the features rely minimally on object -level descriptions and thus require minimal segmentation. Materials and Methods: The proposed work was developed and tested on International Conference on Pattern Recognition (ICPR) 2012 mitosis detection contest data. Statistical Analysis Used: We plotted receiver operating characteristics curves of true positive versus false positive rates; calculated recall, precision, F -measure, and region overlap ratio measures. Results: We tested our features with two different classifier configurations: 1)An ensemble of single adaboosts, 2) an ensemble of cascade adaboosts. On the ICPR 2012 mitosis detection contest evaluation, the cascade ensemble scored 54, 62.7, and 58, whereas the non -cascade version scored 68, 28.1, and 39.7 for the recall, precision, and F -measure measures, respectively. Mostly used features in the adaboost classifier rules were a shape?based feature, which counted granularity and a color-based feature, which relied on Red, Green, and Blue channel statistics. Conclusions: The features, which express the granular structure and color variations, are found useful for mitosis detection. The ensemble of adaboosts performs better than the individual adaboost classifiers. Moreover, the ensemble of cascaded adaboosts was better than the ensemble of single adaboosts for mitosis detection.Yayın Automated diagnosis of Alzheimer’s Disease using OCT and OCTA: a systematic review(Institute of Electrical and Electronics Engineers Inc., 2024-08-06) Turkan, Yasemin; Tek, Faik Boray; Arpacı, Fatih; Arslan, Ozan; Toslak, Devrim; Bulut, Mehmet; Yaman, AylinRetinal optical coherence tomography (OCT) and optical coherence tomography angiography (OCTA) have emerged as promising, non-invasive, and cost-effective modalities for the early diagnosis of Alzheimer's disease (AD). However, a comprehensive review of automated deep learning techniques for diagnosing AD or mild cognitive impairment (MCI) using OCT/OCTA data is lacking. We addressed this gap by conducting a systematic review using the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) guidelines. We systematically searched databases, including Scopus, PubMed, and Web of Science, and identified 16 important studies from an initial set of 4006 references. We then analyzed these studies through a structured framework, focusing on the key aspects of deep learning workflows for AD/MCI diagnosis using OCT-OCTA. This included dataset curation, model training, and validation methodologies. Our findings indicate a shift towards employing end-to-end deep learning models to directly analyze OCT/OCTA images in diagnosing AD/MCI, moving away from traditional machine learning approaches. However, we identified inconsistencies in the data collection methods across studies, leading to varied outcomes. We emphasize the need for longitudinal studies on early AD and MCI diagnosis, along with further research on interpretability tools to enhance model accuracy and reliability for clinical translation.Yayın Text-to-SQL: a methodical review of challenges and models(TÜBİTAK, 2024-05-20) Kanburoğlu, Ali Buğra; Tek, Faik BorayThis survey focuses on Text-to-SQL, automated translation of natural language queries into SQL queries. Initially, we describe the problem and its main challenges. Then, by following the PRISMA systematic review methodology, we survey the existing Text-to-SQL review papers in the literature. We apply the same method to extract proposed Text-to-SQL models and classify them with respect to used evaluation metrics and benchmarks. We highlight the accuracies achieved by various models on Text-to-SQL datasets and discuss execution-guided evaluation strategies. We present insights into model training times and implementations of different models. We also explore the availability of Text-to-SQL datasets in non-English languages. Additionally, we focus on large language model (LLM) based approaches for the Text-to-SQL task, where we examine LLM-based studies in the literature and subsequently evaluate the LLMs on the cross-domain Spider dataset. Finally, we conclude with a discussion of future directions for Text-to-SQL research, identifying potential areas of improvement and advancements in this field.
