Gerardo Hermosillo Valadez

Xiongchao Chen, Yoshihisa Shinagawa, Zhigang Peng et al.

Magnetic resonance imaging (MRI) is one of the most commonly applied tests in neurology and neurosurgery. However, the utility of MRI is largely limited by its long acquisition time, which might induce many problems including patient discomfort and motion artifacts. Acquiring fewer k-space sampling is a potential solution to reducing the total scanning time. However, it can lead to severe aliasing reconstruction artifacts and thus affect the clinical diagnosis. Nowadays, deep learning has provided new insights into the sparse reconstruction of MRI. In this paper, we present a new approach to this problem that iteratively fuses the information of k-space and MRI images using novel dual Squeeze-Excitation Networks and Cross-Iteration Residual Connections. This study included 720 clinical multi-coil brain MRI cases adopted from the open-source deidentified fastMRI Dataset. 8-folder downsampling rate was applied to generate the sparse k-space. Results showed that the average reconstruction error over 120 testing cases by our proposed method was 2.28%, which outperformed the existing image-domain prediction (6.03%, p<0.001), k-space synthesis (6.12%, p<0.001), and dual-domain feature fusion (4.05%, p<0.001).

Xiongchao Chen, Zhigang Peng, Gerardo Hermosillo Valadez

Magnetic resonance imaging (MRI) is widely employed for diagnostic tests in neurology. However, the utility of MRI is largely limited by its long acquisition time. Acquiring fewer k-space data in a sparse manner is a potential solution to reducing the acquisition time, but it can lead to severe aliasing reconstruction artifacts. In this paper, we present a novel Dual-Domain Cross-Iteration Squeeze and Excitation Network (DD-CISENet) for accelerated sparse MRI reconstruction. The information of k-spaces and MRI images can be iteratively fused and maintained using the Cross-Iteration Residual connection (CIR) structures. This study included 720 multi-coil brain MRI cases adopted from the open-source fastMRI Dataset. Results showed that the average reconstruction error by DD-CISENet was 2.28 $\pm$ 0.57%, which outperformed existing deep learning methods including image-domain prediction (6.03 $\pm$ 1.31, p < 0.001), k-space synthesis (6.12 $\pm$ 1.66, p < 0.001), and dual-domain feature fusion approaches (4.05 $\pm$ 0.88, p < 0.001).

Halid Ziya Yerebakan, Yoshihisa Shinagawa, Mahesh Ranganath et al.

We propose a method to match anatomical locations between pairs of medical images in longitudinal comparisons. The matching is made possible by computing a descriptor of the query point in a source image based on a hierarchical sparse sampling of image intensities that encode the location information. Then, a hierarchical search operation finds the corresponding point with the most similar descriptor in the target image. This simple yet powerful strategy reduces the computational time of mapping points to a millisecond scale on a single CPU. Thus, radiologists can compare similar anatomical locations in near real-time without requiring extra architectural costs for precomputing or storing deformation fields from registrations. Our algorithm does not require prior training, resampling, segmentation, or affine transformation steps. We have tested our algorithm on the recently published Deep Lesion Tracking dataset annotations. We observed more accurate matching compared to Deep Lesion Tracker while being 24 times faster than the most precise algorithm reported therein. We also investigated the matching accuracy on CT and MR modalities and compared the proposed algorithm's accuracy against ground truth consolidated from multiple radiologists.

Xueqi Guo, Halid Ziya Yerebakan, Yoshihisa Shinagawa et al.

Multi-organ segmentation of 3D medical images is fundamental with meaningful applications in various clinical automation pipelines. Although deep learning has achieved superior performance, the time and memory consumption of segmenting the entire 3D volume voxel by voxel using neural networks can be huge. Classifiers have been developed as an alternative in cases with certain points of interest, but the trade-off between speed and accuracy remains an issue. Thus, we propose a novel fast multi-organ segmentation framework with the usage of hierarchical sparse sampling and a Residual Transformer. Compared with whole-volume analysis, the hierarchical sparse sampling strategy could successfully reduce computation time while preserving a meaningful hierarchical context utilizing multiple resolution levels. The architecture of the Residual Transformer segmentation network could extract and combine information from different levels of information in the sparse descriptor while maintaining a low computational cost. In an internal data set containing 10,253 CT images and the public dataset TotalSegmentator, the proposed method successfully improved qualitative and quantitative segmentation performance compared to the current fast organ classifier, with fast speed at the level of ~2.24 seconds on CPU hardware. The potential of achieving real-time fine organ segmentation is suggested.

Halid Ziya Yerebakan, Gerardo Hermosillo Valadez

We propose a visualization technique that utilizes neural network embeddings and a generative network to reconstruct original data. This method allows for independent manipulation of individual image embeddings through its non-parametric structure, providing more flexibility than traditional autoencoder approaches. We have evaluated the effectiveness of this technique in data visualization and compared it to t-SNE and VAE methods. Furthermore, we have demonstrated the scalability of our method through visualizations on the ImageNet dataset. Our technique has potential applications in human-in-the-loop training, as it allows for independent editing of embedding locations without affecting the optimization process.

Peiyu Duan, Xueqi Guo, Sepehr Farhand et al.

Accurate 3D brain MRI subtype classification benefits from both localized anatomical cues and long-range contextual reasoning. We present AGA3DNet, a report-grounded framework that incorporates brief anatomical phrases extracted from radiology reports as a soft anatomical prior channel and fuses it with a lightweight 3D CNN and multi-view xLSTM aggregation. Specifically, extracted anatomical phrases are mapped to atlas-defined regions and converted into smooth spatial priors using a signed-distance transform followed by Gaussian weighting, providing interpretable, anatomy-grounded guidance without requiring dense voxel annotations. We evaluate AGA3DNet on a retrospective institutional brain MRI cohort for abnormal subtype discrimination and compare against reproducible 3D classification baselines. AGA3DNet achieves improved overall balance across performance metrics and supports clinically interpretable localization through the prior channel. We discuss limitations related to single-cohort evaluation and the lack of large-scale public brain MRI datasets paired with radiology reports under broadly usable terms.

Halid Ziya Yerebakan, Yoshihisa Shinagawa, Gerardo Hermosillo Valadez

Organ segmentation is a fundamental task in medical imaging since it is useful for many clinical automation pipelines. However, some tasks do not require full segmentation. Instead, a classifier can identify the selected organ without segmenting the entire volume. In this study, we demonstrate a classifier based method to obtain organ labels in real time by using a large context size with a sparse data sampling strategy. Although our method operates as an independent classifier at query locations, it can generate full segmentations by querying grid locations at any resolution, offering faster performance than segmentation algorithms. We compared our method with existing segmentation techniques, demonstrating its superior runtime potential for practical applications in medical imaging.

Halid Ziya Yerebakan, Gerardo Hermosillo Valadez

This study demonstrates that incorporating a consistency heuristic into the point-matching algorithm \cite{yerebakan2023hierarchical} improves robustness in matching anatomical locations across pairs of medical images. We validated our approach on diverse longitudinal internal and public datasets spanning CT and MRI modalities. Notably, it surpasses state-of-the-art results on the Deep Lesion Tracking dataset. Additionally, we show that the method effectively addresses landmark localization. The algorithm operates efficiently on standard CPU hardware and allows configurable trade-offs between speed and robustness. The method enables high-precision navigation between medical images without requiring a machine learning model or training data.

Halid Ziya Yerebakan, Kritika Iyer, Xueqi Guo et al.

We introduce a new type of foundational model for parsing human anatomy in medical images that works for different modalities. It supports supervised or unsupervised training and can perform matching, registration, classification, or segmentation with or without user interaction. We achieve this by training a neural network estimator that maps query locations to atlas coordinates via regression. Efficiency is improved by sparsely sampling the input, enabling response times of less than 1 ms without additional accelerator hardware. We demonstrate the utility of the algorithm in both CT and MRI modalities.

Mohamad Abdi, Gerardo Hermosillo Valadez, Halid Ziya Yerebakan

Anatomical landmarks are vital in medical imaging for navigation and anomaly detection. Modern large language models (LLMs), like Llama-2, offer promise for automating the mapping of these landmarks in free-text radiology reports to corresponding positions in image data. Recent studies propose LLMs may develop coherent representations of generative processes. Motivated by these insights, we investigated whether LLMs accurately represent the spatial positions of anatomical landmarks. Through experiments with Llama-2 models, we found that they can linearly represent anatomical landmarks in space with considerable robustness to different prompts. These results underscore the potential of LLMs to enhance the efficiency and accuracy of medical imaging workflows.

Orhan Akal, Zhigang Peng, Gerardo Hermosillo Valadez

3D segmentation with deep learning if trained with full resolution is the ideal way of achieving the best accuracy. Unlike in 2D, 3D segmentation generally does not have sparse outliers, prevents leakage to surrounding soft tissues, at the very least it is generally more consistent than 2D segmentation. However, GPU memory is generally the bottleneck for such an application. Thus, most of the 3D segmentation applications handle sub-sampled input instead of full resolution, which comes with the cost of losing precision at the boundary. In order to maintain precision at the boundary and prevent sparse outliers and leakage, we designed ComboNet. ComboNet is designed in an end to end fashion with three sub-network structures. The first two are parallel: 2D UNet with full resolution and 3D UNet with four times sub-sampled input. The last stage is the concatenation of 2D and 3D outputs along with a full-resolution input image which is followed by two convolution layers either with 2D or 3D convolutions. With ComboNet we have achieved $92.1\%$ dice accuracy for aorta segmentation. With Combonet, we have observed up to $2.3\%$ improvement of dice accuracy as opposed to 2D UNet with the full-resolution input image.