Mujdat Cetin

Canberk Ekmekci, Mujdat Cetin

Deep unrolling is an emerging deep learning-based image reconstruction methodology that bridges the gap between model-based and purely deep learning-based image reconstruction methods. Although deep unrolling methods achieve state-of-the-art performance for imaging problems and allow the incorporation of the observation model into the reconstruction process, they do not provide any uncertainty information about the reconstructed image, which severely limits their use in practice, especially for safety-critical imaging applications. In this paper, we propose a learning-based image reconstruction framework that incorporates the observation model into the reconstruction task and that is capable of quantifying epistemic and aleatoric uncertainties, based on deep unrolling and Bayesian neural networks. We demonstrate the uncertainty characterization capability of the proposed framework on magnetic resonance imaging and computed tomography reconstruction problems. We investigate the characteristics of the epistemic and aleatoric uncertainty information provided by the proposed framework to motivate future research on utilizing uncertainty information to develop more accurate, robust, trustworthy, uncertainty-aware, learning-based image reconstruction and analysis methods for imaging problems. We show that the proposed framework can provide uncertainty information while achieving comparable reconstruction performance to state-of-the-art deep unrolling methods.

Shadi Sartipi, Mastaneh Torkamani-Azar, Mujdat Cetin

Recently, physiological data such as electroencephalography (EEG) signals have attracted significant attention in affective computing. In this context, the main goal is to design an automated model that can assess emotional states. Lately, deep neural networks have shown promising performance in emotion recognition tasks. However, designing a deep architecture that can extract practical information from raw data is still a challenge. Here, we introduce a deep neural network that acquires interpretable physiological representations by a hybrid structure of spatio-temporal encoding and recurrent attention network blocks. Furthermore, a preprocessing step is applied to the raw data using graph signal processing tools to perform graph smoothing in the spatial domain. We demonstrate that our proposed architecture exceeds state-of-the-art results for emotion classification on the publicly available DEAP dataset. To explore the generality of the learned model, we also evaluate the performance of our architecture towards transfer learning (TL) by transferring the model parameters from a specific source to other target domains. Using DEAP as the source dataset, we demonstrate the effectiveness of our model in performing cross-modality TL and improving emotion classification accuracy on DREAMER and the Emotional English Word (EEWD) datasets, which involve EEG-based emotion classification tasks with different stimuli.

Hakki Motorcu, Mujdat Cetin

Spatially varying image deblurring remains a fundamentally ill-posed problem, especially when degradations arise from complex mixtures of motion and other forms of blur under significant noise. State-of-the-art learning-based approaches generally fall into two paradigms: model-based deep unrolling methods that enforce physical constraints by modeling the degradations, but often produce over-smoothed, artifact-laden textures, and generative models that achieve superior perceptual quality yet hallucinate details due to weak physical constraints. In this paper, we propose a novel framework that uniquely reconciles these paradigms by taming a powerful generative prior with explicit, dense physical constraints. Rather than oversimplifying the degradation field, we model it as a dense continuum of high-dimensional compressed kernels, ensuring that minute variations in motion and other degradation patterns are captured. We leverage this rich descriptor field to condition a ControlNet architecture, strongly guiding the diffusion sampling process. Extensive experiments demonstrate that our method effectively bridges the gap between physical accuracy and perceptual realism, outperforming state-of-the-art model-based methods as well as generative baselines in challenging, severely blurred scenarios.

Shadi Sartipi, Mujdat Cetin

Motor imagery (MI) classification based on electroencephalogram (EEG) is a widely-used technique in non-invasive brain-computer interface (BCI) systems. Since EEG recordings suffer from heterogeneity across subjects and labeled data insufficiency, designing a classifier that performs the MI independently from the subject with limited labeled samples would be desirable. To overcome these limitations, we propose a novel subject-independent semi-supervised deep architecture (SSDA). The proposed SSDA consists of two parts: an unsupervised and a supervised element. The training set contains both labeled and unlabeled data samples from multiple subjects. First, the unsupervised part, known as the columnar spatiotemporal auto-encoder (CST-AE), extracts latent features from all the training samples by maximizing the similarity between the original and reconstructed data. A dimensional scaling approach is employed to reduce the dimensionality of the representations while preserving their discriminability. Second, a supervised part learns a classifier based on the labeled training samples using the latent features acquired in the unsupervised part. Moreover, we employ center loss in the supervised part to minimize the embedding space distance of each point in a class to its center. The model optimizes both parts of the network in an end-to-end fashion. The performance of the proposed SSDA is evaluated on test subjects who were not seen by the model during the training phase. To assess the performance, we use two benchmark EEG-based MI task datasets. The results demonstrate that SSDA outperforms state-of-the-art methods and that a small number of labeled training samples can be sufficient for strong classification performance.

Shadi Sartipi, Mujdat Cetin

Although deep learning-based algorithms have demonstrated excellent performance in automated emotion recognition via electroencephalogram (EEG) signals, variations across brain signal patterns of individuals can diminish the model's effectiveness when applied across different subjects. While transfer learning techniques have exhibited promising outcomes, they still encounter challenges related to inadequate feature representations and may overlook the fact that source subjects themselves can possess distinct characteristics. In this work, we propose a multi-source domain adaptation approach with a transformer-based feature generator (MSDA-TF) designed to leverage information from multiple sources. The proposed feature generator retains convolutional layers to capture shallow spatial, temporal, and spectral EEG data representations, while self-attention mechanisms extract global dependencies within these features. During the adaptation process, we group the source subjects based on correlation values and aim to align the moments of the target subject with each source as well as within the sources. MSDA-TF is validated on the SEED dataset and is shown to yield promising results.

Canberk Ekmekci, Tekin Bicer, Zichao Wendy Di et al.

Ptychography is a scanning coherent diffractive imaging technique that enables imaging nanometer-scale features in extended samples. One main challenge is that widely used iterative image reconstruction methods often require significant amount of overlap between adjacent scan locations, leading to large data volumes and prolonged acquisition times. To address this key limitation, this paper proposes a Bayesian inversion method for ptychography that performs effectively even with less overlap between neighboring scan locations. Furthermore, the proposed method can quantify the inherent uncertainty on the ptychographic object, which is created by the ill-posed nature of the ptychographic inverse problem. At a high level, the proposed method first utilizes a deep generative model to learn the prior distribution of the object and then generates samples from the posterior distribution of the object by using a Markov Chain Monte Carlo algorithm. Our results from simulated ptychography experiments show that the proposed framework can consistently outperform a widely used iterative reconstruction algorithm in cases of reduced overlap. Moreover, the proposed framework can provide uncertainty estimates that closely correlate with the true error, which is not available in practice. The project website is available here.

Canberk Ekmekci, Mujdat Cetin

Uncertainty quantification plays an important role in achieving trustworthy and reliable learning-based computational imaging. Recent advances in generative modeling and Bayesian neural networks have enabled the development of uncertainty-aware image reconstruction methods. Current generative model-based methods seek to quantify the inherent (aleatoric) uncertainty on the underlying image for given measurements by learning to sample from the posterior distribution of the underlying image. On the other hand, Bayesian neural network-based approaches aim to quantify the model (epistemic) uncertainty on the parameters of a deep neural network-based reconstruction method by approximating the posterior distribution of those parameters. Unfortunately, an ongoing need for an inversion method that can jointly quantify complex aleatoric uncertainty and epistemic uncertainty patterns still persists. In this paper, we present a scalable framework that can quantify both aleatoric and epistemic uncertainties. The proposed framework accepts an existing generative model-based posterior sampling method as an input and introduces an epistemic uncertainty quantification capability through Bayesian neural networks with latent variables and deep ensembling. Furthermore, by leveraging the conformal prediction methodology, the proposed framework can be easily calibrated to ensure rigorous uncertainty quantification. We evaluated the proposed framework on magnetic resonance imaging, computed tomography, and image inpainting problems and showed that the epistemic and aleatoric uncertainty estimates produced by the proposed framework display the characteristic features of true epistemic and aleatoric uncertainties. Furthermore, our results demonstrated that the use of conformal prediction on top of the proposed framework enables marginal coverage guarantees consistent with frequentist principles.

Shadi Sartipi, Mie Andersen, Natalie Hauglund et al.

Efficiently identifying sleep stages is crucial for unraveling the intricacies of sleep in both preclinical and clinical research. The labor-intensive nature of manual sleep scoring, demanding substantial expertise, has prompted a surge of interest in automated alternatives. Sleep studies in mice play a significant role in understanding sleep patterns and disorders and underscore the need for robust scoring methodologies. In response, this study introduces LG-Sleep, a novel subject-independent deep neural network architecture designed for mice sleep scoring through electroencephalogram (EEG) signals. LG-Sleep extracts local and global temporal transitions within EEG signals to categorize sleep data into three stages: wake, rapid eye movement (REM) sleep, and non-rapid eye movement (NREM) sleep. The model leverages local and global temporal information by employing time-distributed convolutional neural networks to discern local temporal transitions in EEG data. Subsequently, features derived from the convolutional filters traverse long short-term memory blocks, capturing global transitions over extended periods. Crucially, the model is optimized in an autoencoder-decoder fashion, facilitating generalization across distinct subjects and adapting to limited training samples. Experimental findings demonstrate superior performance of LG-Sleep compared to conventional deep neural networks. Moreover, the model exhibits good performance across different sleep stages even when tasked with scoring based on limited training samples.

Shadi Sartipi, Mujdat Cetin

Automated emotion recognition using electroencephalogram (EEG) signals has gained substantial attention. Although deep learning approaches exhibit strong performance, they often suffer from vulnerabilities to various perturbations, like environmental noise and adversarial attacks. In this paper, we propose an Inception feature generator and two-sided perturbation (INC-TSP) approach to enhance emotion recognition in brain-computer interfaces. INC-TSP integrates the Inception module for EEG data analysis and employs two-sided perturbation (TSP) as a defensive mechanism against input perturbations. TSP introduces worst-case perturbations to the model's weights and inputs, reinforcing the model's elasticity against adversarial attacks. The proposed approach addresses the challenge of maintaining accurate emotion recognition in the presence of input uncertainties. We validate INC-TSP in a subject-independent three-class emotion recognition scenario, demonstrating robust performance.

Seyed Saman Saboksayr, Gonzalo Mateos, Mujdat Cetin

The growing success of graph signal processing (GSP) approaches relies heavily on prior identification of a graph over which network data admit certain regularity. However, adaptation to increasingly dynamic environments as well as demands for real-time processing of streaming data pose major challenges to this end. In this context, we develop novel algorithms for online network topology inference given streaming observations assumed to be smooth on the sought graph. Unlike existing batch algorithms, our goal is to track the (possibly) time-varying network topology while maintaining the memory and computational costs in check by processing graph signals sequentially-in-time. To recover the graph in an online fashion, we leverage proximal gradient (PG) methods to solve a judicious smoothness-regularized, time-varying optimization problem. Under mild technical conditions, we establish that the online graph learning algorithm converges to within a neighborhood of (i.e., it tracks) the optimal time-varying batch solution. Computer simulations using both synthetic and real financial market data illustrate the effectiveness of the proposed algorithm in adapting to streaming signals to track slowly-varying network connectivity.

Mastaneh Torkamani-Azar, Sumeyra Demir Kanik, Serap Aydin et al.

Resting-state brain networks represent the intrinsic state of the brain during the majority of cognitive and sensorimotor tasks. However, no study has yet presented concise predictors of task-induced vigilance variability from spectrospatial features of the pre-task, resting-state electroencephalograms (EEG). We asked ten healthy volunteers (6 females, 4 males) to participate in 105-minute fixed-sequence-varying-duration sessions of sustained attention to response task (SART). A novel and adaptive vigilance scoring scheme was designed based on the performance and response time in consecutive trials, and demonstrated large inter-participant variability in terms of maintaining consistent tonic performance. Multiple linear regression using feature relevance analysis obtained significant predictors of the mean cumulative vigilance score (CVS), mean response time, and variabilities of these scores from the resting-state, band-power ratios of EEG signals, p<0.05. Single-layer neural networks trained with cross-validation also captured different associations for the beta sub-bands. Increase in the gamma (28-48 Hz) and upper beta ratios from the left central and temporal regions predicted slower reactions and more inconsistent vigilance as explained by the increased activation of default mode network (DMN) and differences between the high- and low-attention networks at temporal regions. Higher ratios of parietal alpha from the Brodmann's areas 18, 19, and 37 during the eyes-open states predicted slower responses but more consistent CVS and reactions associated with the superior ability in vigilance maintenance. The proposed framework and these findings on the most stable and significant attention predictors from the intrinsic EEG power ratios can be used to model attention variations during the calibration sessions of BCI applications and vigilance monitoring systems.

Ertunc Erdil, Ali Ozgur Argunsah, Tolga Tasdizen et al.

Data driven segmentation is an important initial step of shape prior-based segmentation methods since it is assumed that the data term brings a curve to a plausible level so that shape and data terms can then work together to produce better segmentations. When purely data driven segmentation produces poor results, the final segmentation is generally affected adversely. One challenge faced by many existing data terms is due to the fact that they consider only pixel intensities to decide whether to assign a pixel to the foreground or to the background region. When the distributions of the foreground and background pixel intensities have significant overlap, such data terms become ineffective, as they produce uncertain results for many pixels in a test image. In such cases, using prior information about the spatial context of the object to be segmented together with the data term can bring a curve to a plausible stage, which would then serve as a good initial point to launch shape-based segmentation. In this paper, we propose a new segmentation approach that combines nonparametric context priors with a learned-intensity-based data term and nonparametric shape priors. We perform experiments for dendritic spine segmentation in both 2D and 3D 2-photon microscopy images. The experimental results demonstrate that using spatial context priors leads to significant improvements.

Ertunc Erdil, Sinan Yildirim, Tolga Tasdizen et al.

In this paper, we propose an efficient pseudo-marginal Markov chain Monte Carlo (MCMC) sampling approach to draw samples from posterior shape distributions for image segmentation. The computation time of the proposed approach is independent from the size of the training set used to learn the shape prior distribution nonparametrically. Therefore, it scales well for very large data sets. Our approach is able to characterize the posterior probability density in the space of shapes through its samples, and to return multiple solutions, potentially from different modes of a multimodal probability density, which would be encountered, e.g., in segmenting objects from multiple shape classes. Experimental results demonstrate the potential of the proposed approach.

Jaime Fernando Delgado Saa, Mujdat Cetin

A brain-computer interface (BCI) is a system that aims for establishing a non-muscular communication path for subjects who had suffer from a neurodegenerative disease. Many BCI systems make use of the phenomena of event-related synchronization and de-synchronization of brain waves as a main feature for classification of different cognitive tasks. However, the temporal dynamics of the electroencephalographic (EEG) signals contain additional information that can be incorporated into the inference engine in order to improve the performance of the BCIs. This information about the dynamics of the signals have been exploited previously in BCIs by means of generative and discriminative methods. In particular, hidden Markov models (HMMs) have been used in previous works. These methods have the disadvantage that the model parameters such as the number of hidden states and the number of Gaussian mixtures need to be fix "a priori". In this work, we propose a Bayesian nonparametric model for brain signal classification that does not require "a priori" selection of the number of hidden states and the number of Gaussian mixtures of a HMM. The results show that the proposed model outperform other methods based on HMM as well as the winner algorithm of the BCI competition IV.

Muhammad Usman Ghani, Ertunc Erdil, Sumeyra Demir Kanik et al.

Functional properties of neurons are strongly coupled with their morphology. Changes in neuronal activity alter morphological characteristics of dendritic spines. First step towards understanding the structure-function relationship is to group spines into main spine classes reported in the literature. Shape analysis of dendritic spines can help neuroscientists understand the underlying relationships. Due to unavailability of reliable automated tools, this analysis is currently performed manually which is a time-intensive and subjective task. Several studies on spine shape classification have been reported in the literature, however, there is an on-going debate on whether distinct spine shape classes exist or whether spines should be modeled through a continuum of shape variations. Another challenge is the subjectivity and bias that is introduced due to the supervised nature of classification approaches. In this paper, we aim to address these issues by presenting a clustering perspective. In this context, clustering may serve both confirmation of known patterns and discovery of new ones. We perform cluster analysis on two-photon microscopic images of spines using morphological, shape, and appearance based features and gain insights into the spine shape analysis problem. We use histogram of oriented gradients (HOG), disjunctive normal shape models (DNSM), morphological features, and intensity profile based features for cluster analysis. We use x-means to perform cluster analysis that selects the number of clusters automatically using the Bayesian information criterion (BIC). For all features, this analysis produces 4 clusters and we observe the formation of at least one cluster consisting of spines which are difficult to be assigned to a known class. This observation supports the argument of intermediate shape types.

Fitsum Mesadi, Mujdat Cetin, Tolga Tasdizen

Level set methods are widely used for image segmentation because of their capability to handle topological changes. In this paper, we propose a novel parametric level set method called Disjunctive Normal Level Set (DNLS), and apply it to both two phase (single object) and multiphase (multi-object) image segmentations. The DNLS is formed by union of polytopes which themselves are formed by intersections of half-spaces. The proposed level set framework has the following major advantages compared to other level set methods available in the literature. First, segmentation using DNLS converges much faster. Second, the DNLS level set function remains regular throughout its evolution. Third, the proposed multiphase version of the DNLS is less sensitive to initialization, and its computational cost and memory requirement remains almost constant as the number of objects to be simultaneously segmented grows. The experimental results show the potential of the proposed method.