Onat Dalmaz

Hasan Atakan Bedel, Irmak Şıvgın, Onat Dalmaz et al.

Deep-learning models have enabled performance leaps in analysis of high-dimensional functional MRI (fMRI) data. Yet, many previous methods are suboptimally sensitive for contextual representations across diverse time scales. Here, we present BolT, a blood-oxygen-level-dependent transformer model, for analyzing multi-variate fMRI time series. BolT leverages a cascade of transformer encoders equipped with a novel fused window attention mechanism. Encoding is performed on temporally-overlapped windows within the time series to capture local representations. To integrate information temporally, cross-window attention is computed between base tokens in each window and fringe tokens from neighboring windows. To gradually transition from local to global representations, the extent of window overlap and thereby number of fringe tokens are progressively increased across the cascade. Finally, a novel cross-window regularization is employed to align high-level classification features across the time series. Comprehensive experiments on large-scale public datasets demonstrate the superior performance of BolT against state-of-the-art methods. Furthermore, explanatory analyses to identify landmark time points and regions that contribute most significantly to model decisions corroborate prominent neuroscientific findings in the literature.

Onat Dalmaz, Usama Mirza, Gökberk Elmas et al.

Multi-institutional collaborations are key for learning generalizable MRI synthesis models that translate source- onto target-contrast images. To facilitate collaboration, federated learning (FL) adopts decentralized training and mitigates privacy concerns by avoiding sharing of imaging data. However, FL-trained synthesis models can be impaired by the inherent heterogeneity in the data distribution, with domain shifts evident when common or variable translation tasks are prescribed across sites. Here we introduce the first personalized FL method for MRI Synthesis (pFLSynth) to improve reliability against domain shifts. pFLSynth is based on an adversarial model that produces latents specific to individual sites and source-target contrasts, and leverages novel personalization blocks to adaptively tune the statistics and weighting of feature maps across the generator stages given latents. To further promote site specificity, partial model aggregation is employed over downstream layers of the generator while upstream layers are retained locally. As such, pFLSynth enables training of a unified synthesis model that can reliably generalize across multiple sites and translation tasks. Comprehensive experiments on multi-site datasets clearly demonstrate the enhanced performance of pFLSynth against prior federated methods in multi-contrast MRI synthesis.

Muzaffer Özbey, Onat Dalmaz, Salman UH Dar et al.

Imputation of missing images via source-to-target modality translation can improve diversity in medical imaging protocols. A pervasive approach for synthesizing target images involves one-shot mapping through generative adversarial networks (GAN). Yet, GAN models that implicitly characterize the image distribution can suffer from limited sample fidelity. Here, we propose a novel method based on adversarial diffusion modeling, SynDiff, for improved performance in medical image translation. To capture a direct correlate of the image distribution, SynDiff leverages a conditional diffusion process that progressively maps noise and source images onto the target image. For fast and accurate image sampling during inference, large diffusion steps are taken with adversarial projections in the reverse diffusion direction. To enable training on unpaired datasets, a cycle-consistent architecture is devised with coupled diffusive and non-diffusive modules that bilaterally translate between two modalities. Extensive assessments are reported on the utility of SynDiff against competing GAN and diffusion models in multi-contrast MRI and MRI-CT translation. Our demonstrations indicate that SynDiff offers quantitatively and qualitatively superior performance against competing baselines.

Idil Aytekin, Onat Dalmaz, Kaan Gonc et al.

Monitoring of prevalent airborne diseases such as COVID-19 characteristically involves respiratory assessments. While auscultation is a mainstream method for preliminary screening of disease symptoms, its utility is hampered by the need for dedicated hospital visits. Remote monitoring based on recordings of respiratory sounds on portable devices is a promising alternative, which can assist in early assessment of COVID-19 that primarily affects the lower respiratory tract. In this study, we introduce a novel deep learning approach to distinguish patients with COVID-19 from healthy controls given audio recordings of cough or breathing sounds. The proposed approach leverages a novel hierarchical spectrogram transformer (HST) on spectrogram representations of respiratory sounds. HST embodies self-attention mechanisms over local windows in spectrograms, and window size is progressively grown over model stages to capture local to global context. HST is compared against state-of-the-art conventional and deep-learning baselines. Demonstrations on crowd-sourced multi-national datasets indicate that HST outperforms competing methods, achieving over 83% area under the receiver operating characteristic curve (AUC) in detecting COVID-19 cases.

Can Koz, Onat Dalmaz, Mertay Dayanc

Optical Coherence Tomography Angiography (OCTA) is a non-invasive imaging technique that provides high-resolution cross-sectional images of the retina, which are useful for diagnosing and monitoring various retinal diseases. However, manual segmentation of OCTA images is a time-consuming and labor-intensive task, which motivates the development of automated segmentation methods. In this paper, we propose a novel multi-task learning method for OCTA segmentation, called OCTA-MTL, that leverages an image-to-DT (Distance Transform) branch and an adaptive loss combination strategy. The image-to-DT branch predicts the distance from each vessel voxel to the vessel surface, which can provide useful shape prior and boundary information for the segmentation task. The adaptive loss combination strategy dynamically adjusts the loss weights according to the inverse of the average loss values of each task, to balance the learning process and avoid the dominance of one task over the other. We evaluate our method on the ROSE-2 dataset its superiority in terms of segmentation performance against two baseline methods: a single-task segmentation method and a multi-task segmentation method with a fixed loss combination.

Onat Dalmaz, Arjun D. Desai, Reinhard Heckel et al.

Accelerated MRI reconstruction involves solving an ill-posed inverse problem where noise in acquired data propagates to the reconstructed images. Noise analyses are central to MRI reconstruction for providing an explicit measure of solution fidelity and for guiding the design and deployment of novel reconstruction methods. However, deep learning (DL)-based reconstruction methods have often overlooked noise propagation due to inherent analytical and computational challenges, despite its critical importance. This work proposes a theoretically grounded, memory-efficient technique to calculate voxel-wise variance for quantifying uncertainty due to acquisition noise in accelerated MRI reconstructions. Our approach approximates noise covariance using the DL network's Jacobian, which is intractable to calculate. To circumvent this, we derive an unbiased estimator for the diagonal of this covariance matrix (voxel-wise variance) and introduce a Jacobian sketching technique to efficiently implement it. We evaluate our method on knee and brain MRI datasets for both data- and physics-driven networks trained in supervised and unsupervised manners. Compared to empirical references obtained via Monte Carlo simulations, our technique achieves near-equivalent performance while reducing computational and memory demands by an order of magnitude or more. Furthermore, our method is robust across varying input noise levels, acceleration factors, and diverse undersampling schemes, highlighting its broad applicability. Our work reintroduces accurate and efficient noise analysis as a central tenet of reconstruction algorithms, holding promise to reshape how we evaluate and deploy DL-based MRI. Our code will be made publicly available upon acceptance.

Omer F. Atli, Bilal Kabas, Fuat Arslan et al.

Multi-modal medical image synthesis involves nonlinear transformation of tissue signals between source and target modalities, where tissues exhibit contextual interactions across diverse spatial distances. As such, the utility of a network architecture in synthesis depends on its ability to express the broad set of contextual features in medical images. Convolutional neural networks (CNNs) offer high local precision at the expense of poor sensitivity to long-range context. While transformers promise to alleviate this issue, they suffer from an unfavorable trade-off between sensitivity to long- versus short-range context due to the intrinsic complexity of attention filters. To effectively capture contextual features while avoiding the complexitydriven trade-offs, here we introduce a novel multi-modal synthesis method, I2I-Mamba, based on the state space modeling (SSM) framework. Focusing on high-level representations across a hybrid residual architecture, I2I-Mamba leverages novel dual-domain Mamba (ddMamba) blocks for complementary contextual modeling in image and Fourier domains, while maintaining spatial precision with convolutional layers. Diverting from conventional raster-scan trajectories, ddMamba leverages novel SSM operators based on a spiral-scan trajectory to learn context with enhanced angular isotropy and radial coverage, and a channel-mixing layer to aggregate context across the channel dimension. Comprehensive demonstrations on multi-contrast MRI and MRI-CT protocols indicate that I2I-Mamba outperforms state-of-the-art CNNs, transformers and SSMs.

Fuat Arslan, Bilal Kabas, Onat Dalmaz et al.

Denoising diffusion models (DDM) have gained recent traction in medical image translation given improved training stability over adversarial models. DDMs learn a multi-step denoising transformation to progressively map random Gaussian-noise images onto target-modality images, while receiving stationary guidance from source-modality images. As this denoising transformation diverges significantly from the task-relevant source-to-target transformation, DDMs can suffer from weak source-modality guidance. Here, we propose a novel self-consistent recursive diffusion bridge (SelfRDB) for improved performance in medical image translation. Unlike DDMs, SelfRDB employs a novel forward process with start- and end-points defined based on target and source images, respectively. Intermediate image samples across the process are expressed via a normal distribution with mean taken as a convex combination of start-end points, and variance from additive noise. Unlike regular diffusion bridges that prescribe zero variance at start-end points and high variance at mid-point of the process, we propose a novel noise scheduling with monotonically increasing variance towards the end-point in order to boost generalization performance and facilitate information transfer between the two modalities. To further enhance sampling accuracy in each reverse step, we propose a novel sampling procedure where the network recursively generates a transient-estimate of the target image until convergence onto a self-consistent solution. Comprehensive analyses in multi-contrast MRI and MRI-CT translation indicate that SelfRDB offers superior performance against competing methods.

Onat Dalmaz, Mahmut Yurt, Tolga Çukur

Generative adversarial models with convolutional neural network (CNN) backbones have recently been established as state-of-the-art in numerous medical image synthesis tasks. However, CNNs are designed to perform local processing with compact filters, and this inductive bias compromises learning of contextual features. Here, we propose a novel generative adversarial approach for medical image synthesis, ResViT, that leverages the contextual sensitivity of vision transformers along with the precision of convolution operators and realism of adversarial learning.} ResViT's generator employs a central bottleneck comprising novel aggregated residual transformer (ART) blocks that synergistically combine residual convolutional and transformer modules. Residual connections in ART blocks promote diversity in captured representations, while a channel compression module distills task-relevant information. A weight sharing strategy is introduced among ART blocks to mitigate computational burden. A unified implementation is introduced to avoid the need to rebuild separate synthesis models for varying source-target modality configurations. Comprehensive demonstrations are performed for synthesizing missing sequences in multi-contrast MRI, and CT images from MRI. Our results indicate superiority of ResViT against competing CNN- and transformer-based methods in terms of qualitative observations and quantitative metrics.