Dong Hye Ye

David Helminiak, Hang Hu, Julia Laskin et al.

Mass Spectrometry Imaging (MSI), using traditional rectilinear scanning, takes hours to days for high spatial resolution acquisitions. Given that most pixels within a sample's field of view are often neither relevant to underlying biological structures nor chemically informative, MSI presents as a prime candidate for integration with sparse and dynamic sampling algorithms. During a scan, stochastic models determine which locations probabilistically contain information critical to the generation of low-error reconstructions. Decreasing the number of required physical measurements thereby minimizes overall acquisition times. A Deep Learning Approach for Dynamic Sampling (DLADS), utilizing a Convolutional Neural Network (CNN) and encapsulating molecular mass intensity distributions within a third dimension, demonstrates a simulated 70% throughput improvement for Nanospray Desorption Electrospray Ionization (nano-DESI) MSI tissues. Evaluations are conducted between DLADS and a Supervised Learning Approach for Dynamic Sampling, with Least-Squares regression (SLADS-LS) and a Multi-Layer Perceptron (MLP) network (SLADS-Net). When compared with SLADS-LS, limited to a single m/z channel, as well as multichannel SLADS-LS and SLADS-Net, DLADS respectively improves regression performance by 36.7%, 7.0%, and 6.2%, resulting in gains to reconstruction quality of 6.0%, 2.1%, and 3.4% for acquisition of targeted m/z.

Nagur Shareef Shaik, Teja Krishna Cherukuri, Dong Hye Ye

Automating medical reports for retinal images requires a sophisticated blend of visual pattern recognition and deep clinical knowledge. Current Large Vision-Language Models (LVLMs) often struggle in specialized medical fields where data is scarce, leading to models that overfit and miss subtle but critical pathologies. To address this, we introduce DREAM (Dynamic Retinal Enhancement with Adaptive Multi-modal Fusion), a novel framework for high-fidelity medical report generation that excels even with limited data. DREAM employs a unique two-stage fusion mechanism that intelligently integrates visual data with clinical keywords curated by ophthalmologists. First, the Abstractor module maps image and keyword features into a shared space, enhancing visual data with pathology-relevant insights. Next, the Adaptor performs adaptive multi-modal fusion, dynamically weighting the importance of each modality using learnable parameters to create a unified representation. To ensure the model's outputs are semantically grounded in clinical reality, a Contrastive Alignment module aligns these fused representations with ground-truth medical reports during training. By combining medical expertise with an efficient fusion strategy, DREAM sets a new state-of-the-art on the DeepEyeNet benchmark, achieving a BLEU-4 score of 0.241, and further demonstrates strong generalization to the ROCO dataset.

Nagur Shareef Shaik, Teja Krishna Cherukuri, Dong Hye Ye

Breast cancer diagnosis demands rapid and precise tools, yet traditional histopathological methods often fall short in intra-operative settings. Deep Ultraviolet (DUV) fluorescence imaging emerges as a transformative approach, offering high-contrast, label-free visualization of whole-slide images (WSIs) with unprecedented detail, surpassing conventional hematoxylin and eosin (H&E) staining in speed and resolution. However, existing deep learning methods for breast cancer classification, predominantly patch-based, fragment spatial context and incur significant preprocessing overhead, limiting their clinical utility. Moreover, standard attention mechanisms, such as Spatial, Squeeze-and-Excitation, Global Context and Guided Context Gating, fail to fully exploit the rich, multi-scale regional relationships inherent in DUV-WSI data, often prioritizing generic feature recalibration over diagnostic specificity. This study introduces a novel Region-Affinity Attention mechanism tailored for DUV-WSI breast cancer classification, processing entire slides without patching to preserve spatial integrity. By modeling local neighbor distances and constructing a full affinity matrix, our method dynamically highlights diagnostically relevant regions, augmented by a contrastive loss to enhance feature discriminability. Evaluated on a dataset of 136 DUV-WSI samples, our approach achieves an accuracy of 92.67 +/- 0.73% and an AUC of 95.97%, outperforming existing attention methods.

Nagur Shareef Shaik, Teja Krishna Cherukuri, Vince D. Calhoun et al.

Schizophrenia (SZ) is a severe brain disorder marked by diverse cognitive impairments, abnormalities in brain structure, function, and genetic factors. Its complex symptoms and overlap with other psychiatric conditions challenge traditional diagnostic methods, necessitating advanced systems to improve precision. Existing research studies have mostly focused on imaging data, such as structural and functional MRI, for SZ diagnosis. There has been less focus on the integration of genomic features despite their potential in identifying heritable SZ traits. In this study, we introduce a Multi-modal Imaging Genomics Transformer (MIGTrans), that attentively integrates genomics with structural and functional imaging data to capture SZ-related neuroanatomical and connectome abnormalities. MIGTrans demonstrated improved SZ classification performance with an accuracy of 86.05% (+/- 0.02), offering clear interpretations and identifying significant genomic locations and brain morphological/connectivity patterns associated with SZ.

Badhan Mazumder, Lei Wu, Sir-Lord Wiafe et al.

Exposure to psychoactive substances during pregnancy, such as cannabis, can disrupt neurodevelopment and alter large-scale brain networks, yet identifying their neural signatures remains challenging. We introduced KOCOBrain: KuramotO COupled Brain Graph Network; a unified graph neural network framework that integrates structural and functional connectomes via Kuramoto-based phase dynamics and cognition-aware attention. The Kuramoto layer models neural synchronization over anatomical connections, generating phase-informed embeddings that capture structure-function coupling, while cognitive scores modulate information routing in a subject-specific manner followed by a joint objective enhancing robustness under class imbalance scenario. Applied to the ABCD cohort, KOCOBrain improved prenatal drug exposure prediction over relevant baselines and revealed interpretable structure-function patterns that reflect disrupted brain network coordination associated with early exposure.

Nagur Shareef Shaik, Teja Krishna Cherukuri, Adnan Masood et al.

The integration of medical images with clinical context is essential for generating accurate and clinically interpretable radiology reports. However, current automated methods often rely on resource-heavy Large Language Models (LLMs) or static knowledge graphs and struggle with two fundamental challenges in real-world clinical data: (1) missing modalities, such as incomplete clinical context , and (2) feature entanglement, where mixed modality-specific and shared information leads to suboptimal fusion and clinically unfaithful hallucinated findings. To address these challenges, we propose the DiA-gnostic VLVAE, which achieves robust radiology reporting through Disentangled Alignment. Our framework is designed to be resilient to missing modalities by disentangling shared and modality-specific features using a Mixture-of-Experts (MoE) based Vision-Language Variational Autoencoder (VLVAE). A constrained optimization objective enforces orthogonality and alignment between these latent representations to prevent suboptimal fusion. A compact LLaMA-X decoder then uses these disentangled representations to generate reports efficiently. On the IU X-Ray and MIMIC-CXR datasets, DiA has achieved competetive BLEU@4 scores of 0.266 and 0.134, respectively. Experimental results show that the proposed method significantly outperforms state-of-the-art models.

Sepehr Salem Ghahfarokhi, Tyrell To, Julie Jorns et al.

Data limitation is a significant challenge in applying deep learning to medical images. Recently, the diffusion probabilistic model (DPM) has shown the potential to generate high-quality images by converting Gaussian random noise into realistic images. In this paper, we apply the DPM to augment the deep ultraviolet fluorescence (DUV) image dataset with an aim to improve breast cancer classification for intraoperative margin assessment. For classification, we divide the whole surface DUV image into small patches and extract convolutional features for each patch by utilizing the pre-trained ResNet. Then, we feed them into an XGBoost classifier for patch-level decisions and then fuse them with a regional importance map computed by Grad-CAM++ for whole surface-level prediction. Our experimental results show that augmenting the training dataset with the DPM significantly improves breast cancer detection performance in DUV images, increasing accuracy from 93% to 97%, compared to using Affine transformations and ProGAN.

Pouya Afshin, David Helminiak, Tianling Niu et al.

Breast-Conserving Surgery (BCS) requires precise intraoperative margin assessment to preserve healthy tissue. Deep Ultraviolet Fluorescence Scanning Microscopy (DUV-FSM) offers rapid, high-resolution surface imaging for this purpose; however, the scarcity of annotated DUV data hinders the training of robust deep learning models. To address this, we propose an Self-Supervised Learning (SSL)-guided Latent Diffusion Model (LDM) to generate high-quality synthetic training patches. By guiding the LDM with embeddings from a fine-tuned DINO teacher, we inject rich semantic details of cellular structures into the synthetic data. We combine real and synthetic patches to fine-tune a Vision Transformer (ViT), utilizing patch prediction aggregation for WSI-level classification. Experiments using 5-fold cross-validation demonstrate that our method achieves 96.47 % accuracy and reduces the FID score to 45.72, significantly outperforming class-conditioned baselines.

Badhan Mazumder, Ayush Kanyal, Lei Wu et al.

Clinical studies reveal disruptions in brain structural connectivity (SC) and functional connectivity (FC) in neuropsychiatric disorders such as schizophrenia (SZ). Traditional approaches might rely solely on SC due to limited functional data availability, hindering comprehension of cognitive and behavioral impairments in individuals with SZ by neglecting the intricate SC-FC interrelationship. To tackle the challenge, we propose a novel physics-guided deep learning framework that leverages a neural oscillation model to describe the dynamics of a collection of interconnected neural oscillators, which operate via nerve fibers dispersed across the brain's structure. Our proposed framework utilizes SC to simultaneously generate FC by learning SC-FC coupling from a system dynamics perspective. Additionally, it employs a novel multi-view graph neural network (GNN) with a joint loss to perform correlation-based SC-FC fusion and classification of individuals with SZ. Experiments conducted on a clinical dataset exhibited improved performance, demonstrating the robustness of our proposed approach.

Teja Krishna Cherukuri, Nagur Shareef Shaik, Jyostna Devi Bodapati et al.

Retinal image analysis is crucial for diagnosing and treating eye diseases, yet generating accurate medical reports from images remains challenging due to variability in image quality and pathology, especially with limited labeled data. Previous Transformer-based models struggled to integrate visual and textual information under limited supervision. In response, we propose a novel vision-language model for retinal image captioning that combines visual and textual features through a guided context self-attention mechanism. This approach captures both intricate details and the global clinical context, even in data-scarce scenarios. Extensive experiments on the DeepEyeNet dataset demonstrate a 0.023 BLEU@4 improvement, along with significant qualitative advancements, highlighting the effectiveness of our model in generating comprehensive medical captions.

Badhan Mazumder, Sir-Lord Wiafe, Vince D. Calhoun et al.

Early identification of adolescents at risk for substance use initiation (SUI) is vital yet difficult, as most predictors treat connectivity as static or cross-sectional and miss how brain networks change over time and with behavior. We proposed NeuroBRIDGE (Behavior conditioned RIemannian Koopman Dynamics on lonGitudinal connEctomes), a novel graph neural network-based framework that aligns longitudinal functional connectome in a Riemannian tangent space and couples dual-time attention with behavioral-conditioned Koopman dynamics to capture temporal change. Evaluated on ABCD, NeuroBRIDGE improved future SUI prediction over relevant baselines while offering interpretable insights into neural pathways, refining our understanding of neurodevelopmental risk and informing targeted prevention.

Badhan Mazumder, Sir-Lord Wiafe, Aline Kotoski et al.

Understanding how brain structure and function interact is key to explaining intelligence yet modeling them jointly is challenging as the structural and functional connectome capture complementary aspects of organization. We introduced Multi-scale Adaptive Graph Network (MAGNet), a Transformer-style graph neural network framework that adaptively learns structure-function interactions. MAGNet leverages source-based morphometry from structural MRI to extract inter-regional morphological features and fuses them with functional network connectivity from resting-state fMRI. A hybrid graph integrates direct and indirect pathways, while local-global attention refines connectivity importance and a joint loss simultaneously enforces cross-modal coherence and optimizes the prediction objective end-to-end. On the ABCD dataset, MAGNet outperformed relevant baselines, demonstrating effective multimodal integration for advancing our understanding of cognitive function.

Nagur Shareef Shaik, Teja Krishna Cherukuri, Adnan Masood et al.

Diabetic retinopathy grading is inherently ordinal and long-tailed, with minority stages being scarce, heterogeneous, and clinically critical to detect accurately. Conventional methods often rely on isotropic Gaussian priors and symmetric loss functions, misaligning latent representations with the task's asymmetric nature. We propose the Constrained Asymmetric Prior Wasserstein Autoencoder (CAP-WAE), a novel framework that addresses these challenges through three key innovations. Our approach employs a Wasserstein Autoencoder (WAE) that aligns its aggregate posterior with a asymmetric prior, preserving the heavy-tailed and skewed structure of minority classes. The latent space is further structured by a Margin-Aware Orthogonality and Compactness (MAOC) loss to ensure grade-ordered separability. At the supervision level, we introduce a direction-aware ordinal loss, where a lightweight head predicts asymmetric dispersions to generate soft labels that reflect clinical priorities by penalizing under-grading more severely. Stabilized by an adaptive multi-task weighting scheme, our end-to-end model requires minimal tuning. Across public DR benchmarks, CAP-WAE consistently achieves state-of-the-art Quadratic Weighted Kappa, accuracy, and macro-F1, surpassing both ordinal classification and latent generative baselines. t-SNE visualizations further reveal that our method reshapes the latent manifold into compact, grade-ordered clusters with reduced overlap.

Badhan Mazumder, Aline Kotoski, Vince D. Calhoun et al.

Understanding how prenatal exposure to psychoactive substances such as cannabis shapes adolescent brain organization remains a critical challenge, complicated by the complexity of multimodal neuroimaging data and the limitations of conventional analytic methods. Existing approaches often fail to fully capture the complementary features embedded within structural and functional connectomes, constraining both biological insight and predictive performance. To address this, we introduced NeuroKoop, a novel graph neural network-based framework that integrates structural and functional brain networks utilizing neural Koopman operator-driven latent space fusion. By leveraging Koopman theory, NeuroKoop unifies node embeddings derived from source-based morphometry (SBM) and functional network connectivity (FNC) based brain graphs, resulting in enhanced representation learning and more robust classification of prenatal drug exposure (PDE) status. Applied to a large adolescent cohort from the ABCD dataset, NeuroKoop outperformed relevant baselines and revealed salient structural-functional connections, advancing our understanding of the neurodevelopmental impact of PDE.

Badhan Mazumder, Lei Wu, Vince D. Calhoun et al.

Gaining insights into the structural and functional mechanisms of the brain has been a longstanding focus in neuroscience research, particularly in the context of understanding and treating neuropsychiatric disorders such as Schizophrenia (SZ). Nevertheless, most of the traditional multimodal deep learning approaches fail to fully leverage the complementary characteristics of structural and functional connectomics data to enhance diagnostic performance. To address this issue, we proposed ConneX, a multimodal fusion method that integrates cross-attention mechanism and multilayer perceptron (MLP)-Mixer for refined feature fusion. Modality-specific backbone graph neural networks (GNNs) were firstly employed to obtain feature representation for each modality. A unified cross-modal attention network was then introduced to fuse these embeddings by capturing intra- and inter-modal interactions, while MLP-Mixer layers refined global and local features, leveraging higher-order dependencies for end-to-end classification with a multi-head joint loss. Extensive evaluations demonstrated improved performance on two distinct clinical datasets, highlighting the robustness of our proposed framework.

Pouya Afshin, David Helminiak, Tongtong Lu et al.

Breast-conserving surgery (BCS) aims to completely remove malignant lesions while maximizing healthy tissue preservation. Intraoperative margin assessment is essential to achieve a balance between thorough cancer resection and tissue conservation. A deep ultraviolet fluorescence scanning microscope (DUV-FSM) enables rapid acquisition of whole surface images (WSIs) for excised tissue, providing contrast between malignant and normal tissues. However, breast cancer classification with DUV WSIs is challenged by high resolutions and complex histopathological features. This study introduces a DUV WSI classification framework using a patch-level vision transformer (ViT) model, capturing local and global features. Grad-CAM++ saliency weighting highlights relevant spatial regions, enhances result interpretability, and improves diagnostic accuracy for benign and malignant tissue classification. A comprehensive 5-fold cross-validation demonstrates the proposed approach significantly outperforms conventional deep learning methods, achieving a classification accuracy of 98.33%.

Teja Krishna Cherukuri, Nagur Shareef Shaik, Sribhuvan Reddy Yellu et al.

Colorectal polyps are key indicators for early detection of colorectal cancer. However, traditional endoscopic imaging often struggles with accurate polyp localization and lacks comprehensive contextual awareness, which can limit the explainability of diagnoses. To address these issues, we propose the Dynamic Contextual Attention Network (DCAN). This novel approach transforms spatial representations into adaptive contextual insights, using an attention mechanism that enhances focus on critical polyp regions without explicit localization modules. By integrating contextual awareness into the classification process, DCAN improves decision interpretability and overall diagnostic performance. This advancement in imaging could lead to more reliable colorectal cancer detection, enabling better patient outcomes.

Nagur Shareef Shaik, Teja Krishna Cherukuri, Dong Hye Ye

Automated retinal image medical description generation is crucial for streamlining medical diagnosis and treatment planning. Existing challenges include the reliance on learned retinal image representations, difficulties in handling multiple imaging modalities, and the lack of clinical context in visual representations. Addressing these issues, we propose the Multi-Modal Medical Transformer (M3T), a novel deep learning architecture that integrates visual representations with diagnostic keywords. Unlike previous studies focusing on specific aspects, our approach efficiently learns contextual information and semantics from both modalities, enabling the generation of precise and coherent medical descriptions for retinal images. Experimental studies on the DeepEyeNet dataset validate the success of M3T in meeting ophthalmologists' standards, demonstrating a substantial 13.5% improvement in BLEU@4 over the best-performing baseline model.

Teja Krishna Cherukuri, Nagur Shareef Shaik, Dong Hye Ye

Effectively representing medical images, especially retinal images, presents a considerable challenge due to variations in appearance, size, and contextual information of pathological signs called lesions. Precise discrimination of these lesions is crucial for diagnosing vision-threatening issues such as diabetic retinopathy. While visual attention-based neural networks have been introduced to learn spatial context and channel correlations from retinal images, they often fall short in capturing localized lesion context. Addressing this limitation, we propose a novel attention mechanism called Guided Context Gating, an unique approach that integrates Context Formulation, Channel Correlation, and Guided Gating to learn global context, spatial correlations, and localized lesion context. Our qualitative evaluation against existing attention mechanisms emphasize the superiority of Guided Context Gating in terms of explainability. Notably, experiments on the Zenodo-DR-7 dataset reveal a substantial 2.63% accuracy boost over advanced attention mechanisms & an impressive 6.53% improvement over the state-of-the-art Vision Transformer for assessing the severity grade of retinopathy, even with imbalanced and limited training samples for each class.

Nagur Shareef Shaik, Teja Krishna Cherukuri, Vince Calhoun et al.

Schizophrenia is a debilitating, chronic mental disorder that significantly impacts an individual's cognitive abilities, behavior, and social interactions. It is characterized by subtle morphological changes in the brain, particularly in the gray matter. These changes are often imperceptible through manual observation, demanding an automated approach to diagnosis. This study introduces a deep learning methodology for the classification of individuals with Schizophrenia. We achieve this by implementing a diversified attention mechanism known as Spatial Sequence Attention (SSA) which is designed to extract and emphasize significant feature representations from structural MRI (sMRI). Initially, we employ the transfer learning paradigm by leveraging pre-trained DenseNet to extract initial feature maps from the final convolutional block which contains morphological alterations associated with Schizophrenia. These features are further processed by the proposed SSA to capture and emphasize intricate spatial interactions and relationships across volumes within the brain. Our experimental studies conducted on a clinical dataset have revealed that the proposed attention mechanism outperforms the existing Squeeze & Excitation Network for Schizophrenia classification.

Chi Nok Enoch Kan, Najibakram Maheenaboobacker, Dong Hye Ye

Deep learning is a popular and powerful tool in computed tomography (CT) image processing such as organ segmentation, but its requirement of large training datasets remains a challenge. Even though there is a large anatomical variability for children during their growth, the training datasets for pediatric CT scans are especially hard to obtain due to risks of radiation to children. In this paper, we propose a method to conditionally synthesize realistic pediatric CT images using a new auxiliary classifier generative adversarial network (ACGAN) architecture by taking age information into account. The proposed network generated age-conditioned high-resolution CT images to enrich pediatric training datasets.

Dong Hye Ye, Gregery T. Buzzard, Max Ruby et al.

Filtered back projection (FBP) is a classical method for image reconstruction from sinogram CT data. FBP is computationally efficient but produces lower quality reconstructions than more sophisticated iterative methods, particularly when the number of views is lower than the number required by the Nyquist rate. In this paper, we use a deep convolutional neural network (CNN) to produce high-quality reconstructions directly from sinogram data. A primary novelty of our approach is that we first back project each view separately to form a stack of back projections and then feed this stack as input into the convolutional neural network. These single-view back projections convert the encoding of sinogram data into the appropriate spatial location, which can then be leveraged by the spatial invariance of the CNN to learn the reconstruction effectively. We demonstrate the benefit of our CNN based back projection on simulated sparse-view CT data over classical FBP.

G. M. Dilshan P. Godaliyadda, Dong Hye Ye, Michael D. Uchic et al.

Sparse sampling schemes have the potential to dramatically reduce image acquisition time while simultaneously reducing radiation damage to samples. However, for a sparse sampling scheme to be useful it is important that we are able to reconstruct the underlying object with sufficient clarity using the sparse measurements. In dynamic sampling, each new measurement location is selected based on information obtained from previous measurements. Therefore, dynamic sampling schemes have the potential to dramatically reduce the number of measurements needed for high fidelity reconstructions. However, most existing dynamic sampling methods for point-wise measurement acquisition tend to be computationally expensive and are therefore too slow for practical applications. In this paper, we present a framework for dynamic sampling based on machine learning techniques, which we call a supervised learning approach for dynamic sampling (SLADS). In each step of SLADS, the objective is to find the pixel that maximizes the expected reduction in distortion (ERD) given previous measurements. SLADS is fast because we use a simple regression function to compute the ERD, and it is accurate because the regression function is trained using data sets that are representative of the specific application. In addition, we introduce a method to terminate dynamic sampling at a desired level of distortion, and we extended the SLADS methodology to sample groups of pixels at each step. Finally, we present results on computationally-generated synthetic data and experimentally-collected data to demonstrate a dramatic improvement over state-of-the-art static sampling methods.

Ruoqiao Zhang, Dong Hye Ye, Debashish Pal et al.

Markov random fields (MRFs) have been widely used as prior models in various inverse problems such as tomographic reconstruction. While MRFs provide a simple and often effective way to model the spatial dependencies in images, they suffer from the fact that parameter estimation is difficult. In practice, this means that MRFs typically have very simple structure that cannot completely capture the subtle characteristics of complex images. In this paper, we present a novel Gaussian mixture Markov random field model (GM-MRF) that can be used as a very expressive prior model for inverse problems such as denoising and reconstruction. The GM-MRF forms a global image model by merging together individual Gaussian-mixture models (GMMs) for image patches. In addition, we present a novel analytical framework for computing MAP estimates using the GM-MRF prior model through the construction of surrogate functions that result in a sequence of quadratic optimizations. We also introduce a simple but effective method to adjust the GM-MRF so as to control the sharpness in low- and high-contrast regions of the reconstruction separately. We demonstrate the value of the model with experiments including image denoising and low-dose CT reconstruction.