Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Article Vim-Polyp: Multimodal Colon Polyp Dataset with Video, Histopathology, and Protein Expression(Nature Portfolio, 2025-12-03) Dogan, Refika Sultan; Akay, Ebru; Dogan, Serkan; Yilmaz, BulentThe dataset in this study includes 202 videos with a total of 422 minutes, reaching Kayseri City Hospital's gastroenterology department as colonoscopy videos and 1903 microscopy images between 2019 and 2021. It includes 399 colonoscopy, microscopy images, and pathological diagnoses of polyps, as well as immunohistochemical staining results for proteins that play an important role in the assessment of cancerous cells, such as staining results for p53 (clone: bp53-11), Ki-67 (clone: 30-9), CD34 (clone: QBend/10), PD-L1 (clone: SP142), BRAF (clone: V600E) and VEGF (clone: SP125). By sharing the data openly, we aim to facilitate benchmarking, exploratory analysis and transfer-learning studies on colorectal polyps and cancer. In combination with external datasets or pretrained models, the resource can help advance data-driven detection and characterisation work. The diverse range of polyps assigned to cancer stages from 201 patients makes this tool valuable for researchers and clinicians in furthering diagnosis and treatment.Article Citation - WoS: 5Citation - Scopus: 6Transfer Learning for P300 Brain-Computer Interfaces by Joint Alignment of Feature Vectors(IEEE-Inst Electrical Electronics Engineers Inc, 2023-10) Altindis, Fatih; Banerjee, Antara; Phlypo, Ronald; Yilmaz, Bulent; Congedo, MarcoThis article presents a new transfer learning method named group learning, that jointly aligns multiple domains (many-to-many) and an extension named fast alignment that aligns any further domain to previously aligned group of domains (many-to-one). The proposed group alignment algorithm (GALIA) is evaluated on brain-computer interface (BCI) data and optimal hyper-parameter values of the algorithm are studied for classification performance and computational cost. Six publicly available P300 databases comprising 333 sessions from 177 subjects are used. As compared to the conventional subject-specific train/test pipeline, both group learning and fast alignment significantly improve the classification accuracy except for the database with clinical subjects (average improvement: 2.12 +/- 1.88%). GALIA utilizes cyclic approximate joint diagonalization (AJD) to find a set of linear transformations, one for each domain, jointly aligning the feature vectors of all domains. Group learning achieves a many-to-many transfer learning without compromising the classification performance on non-clinical BCI data. Fast alignment further extends the group learning for any unseen domains, allowing a many-to-one transfer learning with the same properties. The former method creates a single machine learning model using data from previous subjects and/or sessions, whereas the latter exploits the trained model for an unseen domain requiring no further training of the classifier.Article Citation - WoS: 27Citation - Scopus: 30Super Resolution Convolutional Neural Network Based Pre-Processing for Automatic Polyp Detection in Colonoscopy Images(Pergamon-Elsevier Science Ltd, 2021-03) Tas, Merve; Yilmaz, BulentColonoscopy is the most common methodology used to detect polyps on the colon surface. Increasing the image resolution has the potential to improve the automatic colonoscopy based diagnosis and polyp detection and localization. In this study, we proposed a pre-processing approach that uses convolutional neural network based super resolution method (SRCNN) to increase the resolution of the training colonoscopy images before the localization of polyps. We also investigated the use of CNN based models such as the Single Shot MultiBox Detector (SSD) and Faster Regional CNN (RCNN) for real-time polyp detection and localization. Our results showed that using SRCNN method before the training process provides better results in terms of accuracy in both models compared to the low-resolution cases. Furthermore, we reached an F2 score of 0.945 for the correct localization of colon polyps using Faster RCNN with ResNet-101 feature extractor.Article Citation - WoS: 7Citation - Scopus: 9Split-Attention Effects in Multimedia Learning Environments: Eye-Tracking and EEG Analysis(Springer, 2022-02-02) Mutlu-Bayraktar, Duygu; Ozel, Pinar; Altindis, Fatih; Yilmaz, BulentThis study aimed to evaluate the split-attention effect in multimedia learning environments via objective measurements as EEG and eye-tracking. Two different multimedia learning environments in a focused (integrated) and split-attention (separated) format were designed. The experimental design method was used. The participants consisted of 44 students divided into two groups for focused attention and split-attention. There were significant differences between the fixation, brain wave, and retention performance of the two groups. Fixations of the split-attention group were higher than the focused attention group. A significant difference was found in the focused attention group in the alpha brain wave in the frontal region for intra-group comparisons and in the split-attention group in the beta brain wave in the frontal area for the inter-group comparison. The retention performance of the focused attention group was higher than the split-attention group. Accordingly, more cognitive activity emerged in environments where the text was not integrated into the picture. Additionally, the narration of text instead of printed text is effective for focusing attention. To prevent the emergence of a split-attention effect, the text should be integrated into the picture in designs. Due to the split-attention effect, the eye-tracking and EEG data were different between the groups.Conference Object Citation - Scopus: 2Sliding Window and Filterbank Utilization on Riemannian Geometry(Institute of Electrical and Electronics Engineers Inc., 2022-08-08) Altindis, Fatih; Yilmaz, BulentRiemannian geometry-based signal processing approaches on EEG signals provides similar decoding performance compared to state-of-the-art methods. However, Riemannian geometry framework requires predefine EEG signal epoch that is to be used in the analysis. Sliding window approach that operates in Riemannian geometry proposed to enable use of EEG signals without constrained by the record length. Decoding performance of tangent space mapping was increased more than 6% in overall accuracy compared the previous study's results. Instead of using single band-pass filter, utilization of filterbank is proposed to increase decoding performance. Distance based Riemannian classifier's overall performance were increased by 5% compared to standard Riemannian geometry approach. © 2022 Elsevier B.V., All rights reserved.Article Citation - Scopus: 1Robust Controller Electromyogram Prosthetic Hand With Artificial Neural Network Control and Position(Indian Journal of Forensic Medicine and Toxicology ijfmt@hotmail.com, 2020) Ahmed, Saygin Siddiq; Ahmed, Aydin S.; Yilmaz, Bulent; Doǧru, NuranIn this study, we proposed and designed a new control method for an electromyographically (EMG) controlled prosthetic hand. The objective is to increase the control efficiency of the human–machine interface and afford greater control of the prosthetic hand. The process works as follows: EMG biomedical signals acquired from Myoware sensors positioned on the relevant muscles are sent to the robot that consist of hand, Arduino and MATLAB program, which computes and controls the hand position in free space along with hand grasping operations. The Myoware device acquires muscle signals and sends them to the Arduino. The Arduino analyzes the received signals, based on which it controls the motor movement. In this design, the muscle signals are read and saved in a MATLAB system file. After program processing on the industrial hand which is applied by MATLAB simulation, the corresponding movement is transferred to the hand, enabling movements, such as, hand opening and closing according to the signal stored in the MATLAB system. In this study, hand and fingerprints were designed using a three-dimensional printer by separate recording finger and thumb signals. The muscle signals were then analyzed in order to obtain peak signal points and convert them into data. These results indicate the effectiveness of the proposed method and demonstrate the superiority of the method for amputees because of the improved controllability and perceptibility afforded by the design. © 2020 Elsevier B.V., All rights reserved.Article Citation - WoS: 14Citation - Scopus: 15Relationship Between Objective and Subjective Cognitive Load Measurements in Multimedia Learning(Routledge Journals, Taylor & Francis Ltd, 2020-11-15) Mutlu-Bayraktar, Duygu; Ozel, Pinar; Altindis, Fatih; Yilmaz, BulentThe aim of this study is to compare subjective and objective cognitive load measurements in a multimedia learning environment. For this purpose, 20 university students studied in multimedia environments designed by researchers during which eye movements and multichannel electroencephalography (EEG) signals were recorded. Self-report ratings were obtained at the end of the experiment, and retention performances of the students were measured. After the data were collected, Pearson Correlation analysis was applied. According to the results, significant relationship between the number of fixations and EEG frequency band powers was found. In addition, there was a negative relationship between retention performance and number of fixations. Moreover, a negative relationship was found between retention performance and self-reported measurements.Article Citation - WoS: 18Citation - Scopus: 21Parameter Investigation of Topological Data Analysis for EEG Signals(Elsevier Sci Ltd, 2021-01) Altindis, Fatih; Yilmaz, Bulent; Borisenok, Sergey; Icoz, KutayTopological data analysis (TDA) methods have become appealing in EEG signal processing, because they may help the scientists explore new features of complex and large amount of data by simplifying the process from a geometrical perspective. Time delay embedding is a common approach to embed EEG signals into the state space. Parameters of this embedding method are variable and the structure of the state space can be entirely different depending on their selection. Additionally, extracted persistent homologies of the state spaces depend on filtration level and the number of points used. In this study, we showed how to adapt false nearest neighbor (FNN) test to find out the suitable/optimal time embedding parameters (i.e., time delay and embedding dimension) for EEG signals, and compared their effects on different types of artefacts and motor intention waves that are commonly used in brain-computer interfaces. We extracted and compared persistent homologies of state spaces that were reconstructed with four different sets of parameters. Later, the effect of filtration level on extracted persistent homologies was compared, and statistical significance levels were computed between leftand right-hand movement imaginations. Finally, computational cost of the discussed methods was found, and the adaptability of this method to a real-time application was evaluated. We demonstrated that the discussed parameters of the TDA approach were highly crucial to extract true topological features of the EEG signals, and the adapted testing approaches depicted the applicability of this approach on real-time analysis of EEG signals.Article Citation - WoS: 3Citation - Scopus: 3Object Weight Perception in Motor Imagery Using Fourier-Based Synchrosqueezing Transform and Regularized Common Spatial Patterns(IEEE-Inst Electrical Electronics Engineers Inc, 2024) Karakullukcu, Nedime; Altindis, Fatih; Yilmaz, BulentThis study addresses the challenge faced by individuals with upper-limb prostheses in regulating grip force and adapting movements to different object weights. Despite limited exploration, this research pioneers the use of EEG to estimate object weight perception in the context of upper-limb prostheses. Investigating neural correlates in this population provides valuable insights and aids the development of neurofeedback-based strategies for weight perception. Our objective is to identify EEG features predicting the weight perception of held objects. Employing Fourier-based synchrosqueezing transform (FSST) and regularized Common Spatial Patterns (CSP) features, we classify motor imagery waves representing three weight categories (light, medium, heavy). Subjects perform actual motor tasks before imagery sessions, and our approach integrates EEG features of both movements to train subject-specific machine learning models. Results reveal that FSST- singular value decomposition (SVD) features for medium and heavy objects are most distinctive. Achieving up to 90% accuracy, spatial features demonstrate effective classification of motor imagery for different weights. Unlike weight prediction studies, our focus is on visual perception and imagination of object weights, enhancing prosthetic hand system preconditioning. Binary classification surpasses 70% accuracy in predicting object weights, uniquely utilizing actual movement data for CSP algorithm regularization coefficient estimation.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.
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