David Fuentes

Kai Huang, Prajnan Das, Adenike M. Olanrewaju et al.

To develop an automated workflow for rectal cancer three-dimensional conformal radiotherapy treatment planning that combines deep-learning(DL) aperture predictions and forward-planning algorithms. We designed an algorithm to automate the clinical workflow for planning with field-in-field. DL models were trained, validated, and tested on 555 patients to automatically generate aperture shapes for primary and boost fields. Network inputs were digitally reconstructed radiography, gross tumor volume(GTV), and nodal GTV. A physician scored each aperture for 20 patients on a 5-point scale(>3 acceptable). A planning algorithm was then developed to create a homogeneous dose using a combination of wedges and subfields. The algorithm iteratively identifies a hotspot volume, creates a subfield, and optimizes beam weight all without user intervention. The algorithm was tested on 20 patients using clinical apertures with different settings, and the resulting plans(4 plans/patient) were scored by a physician. The end-to-end workflow was tested and scored by a physician on 39 patients using DL-generated apertures and planning algorithms. The predicted apertures had Dice scores of 0.95, 0.94, and 0.90 for posterior-anterior, laterals, and boost fields, respectively. 100%, 95%, and 87.5% of the posterior-anterior, laterals, and boost apertures were scored as clinically acceptable, respectively. Wedged and non-wedged plans were clinically acceptable for 85% and 50% of patients, respectively. The final plans hotspot dose percentage was reduced from 121%($\pm$ 14%) to 109%($\pm$ 5%) of prescription dose. The integrated end-to-end workflow of automatically generated apertures and optimized field-in-field planning gave clinically acceptable plans for 38/39(97%) of patients. We have successfully automated the clinical workflow for generating radiotherapy plans for rectal cancer for our institution.

Adrian Celaya, Beatrice Riviere, David Fuentes

Within medical imaging segmentation, the Dice coefficient and Hausdorff-based metrics are standard measures of success for deep learning models. However, modern loss functions for medical image segmentation often only consider the Dice coefficient or similar region-based metrics during training. As a result, segmentation architectures trained over such loss functions run the risk of achieving high accuracy for the Dice coefficient but low accuracy for Hausdorff-based metrics. Low accuracy on Hausdorff-based metrics can be problematic for applications such as tumor segmentation, where such benchmarks are crucial. For example, high Dice scores accompanied by significant Hausdorff errors could indicate that the predictions fail to detect small tumors. We propose the Generalized Surface Loss function, a novel loss function to minimize Hausdorff-based metrics with more desirable numerical properties than current methods and with weighting terms for class imbalance. Our loss function outperforms other losses when tested on the LiTS and BraTS datasets using the state-of-the-art nnUNet architecture. These results suggest we can improve medical imaging segmentation accuracy with our novel loss function.

Adrian Celaya, Beatrice Riviere, David Fuentes

Accurate medical imaging segmentation is critical for precise and effective medical interventions. However, despite the success of convolutional neural networks (CNNs) in medical image segmentation, they still face challenges in handling fine-scale features and variations in image scales. These challenges are particularly evident in complex and challenging segmentation tasks, such as the BraTS multi-label brain tumor segmentation challenge. In this task, accurately segmenting the various tumor sub-components, which vary significantly in size and shape, remains a significant challenge, with even state-of-the-art methods producing substantial errors. Therefore, we propose two architectures, FMG-Net and W-Net, that incorporate the principles of geometric multigrid methods for solving linear systems of equations into CNNs to address these challenges. Our experiments on the BraTS 2020 dataset demonstrate that both FMG-Net and W-Net outperform the widely used U-Net architecture regarding tumor subcomponent segmentation accuracy and training efficiency. These findings highlight the potential of incorporating the principles of multigrid methods into CNNs to improve the accuracy and efficiency of medical imaging segmentation.

Adrian Celaya, Evan Lim, Rachel Glenn et al.

Medical imaging segmentation is a highly active area of research, with deep learning-based methods achieving state-of-the-art results in several benchmarks. However, the lack of standardized tools for training, testing, and evaluating new methods makes the comparison of methods difficult. To address this, we introduce the Medical Imaging Segmentation Toolkit (MIST), a simple, modular, and end-to-end medical imaging segmentation framework designed to facilitate consistent training, testing, and evaluation of deep learning-based medical imaging segmentation methods. MIST standardizes data analysis, preprocessing, and evaluation pipelines, accommodating multiple architectures and loss functions. This standardization ensures reproducible and fair comparisons across different methods. We detail MIST's data format requirements, pipelines, and auxiliary features and demonstrate its efficacy using the BraTS Adult Glioma Post-Treatment Challenge dataset. Our results highlight MIST's ability to produce accurate segmentation masks and its scalability across multiple GPUs, showcasing its potential as a powerful tool for future medical imaging research and development.

Wolfgang Stefan, David Fuentes, Erol Yeniaras et al.

MR images have a magnitude and a phase, but in almost all clinical applications only the magnitude images are used, because the phase images have a smooth but strong background signal that masks useful information. The phase contains information such as the temperature during thermal ablation, and the iron content of brain tissue. We describe a novel method to suppress the background that is based on higher order edge detection and sparse image representation.

David Fuentes, Diana McSpadden, Sodiq Adewole

In this paper, we propose a distributed Generative Adversarial Networks (discGANs) to generate synthetic tabular data specific to the healthcare domain. While using GANs to generate images has been well studied, little to no attention has been given to generation of tabular data. Modeling distributions of discrete and continuous tabular data is a non-trivial task with high utility. We applied discGAN to model non-Gaussian multi-modal healthcare data. We generated 249,000 synthetic records from original 2,027 eICU dataset. We evaluated the performance of the model using machine learning efficacy, the Kolmogorov-Smirnov (KS) test for continuous variables and chi-squared test for discrete variables. Our results show that discGAN was able to generate data with distributions similar to the real data.

Adrian Celaya, Keegan Kirk, David Fuentes et al.

In recent years, there has been a growing interest in leveraging deep learning and neural networks to address scientific problems, particularly in solving partial differential equations (PDEs). However, many neural network-based methods like PINNs rely on auto differentiation and sampling collocation points, leading to a lack of interpretability and lower accuracy than traditional numerical methods. As a result, we propose a fully unsupervised approach, requiring no training data, to estimate finite difference solutions for PDEs directly via small linear convolutional neural networks. Our proposed approach uses substantially fewer parameters than similar finite difference-based approaches while also demonstrating comparable accuracy to the true solution for several selected elliptic and parabolic problems compared to the finite difference method.

Adrian Celaya, Tucker Netherton, Dawid Schellingerhout et al.

Medical image segmentation continues to advance rapidly, yet rigorous comparison between methods remains challenging due to a lack of standardized and customizable tooling. In this work, we present the current state of the Medical Imaging Segmentation Toolkit (MIST), with a particular focus on its flexible and modular postprocessing framework designed for the BraTS 2025 pre- and post-treatment glioma segmentation challenge. Since its debut in the 2024 BraTS adult glioma post-treatment segmentation challenge, MIST's postprocessing module has been significantly extended to support a wide range of transforms, including removal or replacement of small objects, extraction of the largest connected components, and morphological operations such as hole filling and closing. These transforms can be composed into user-defined strategies, enabling fine-grained control over the final segmentation output. We evaluate three such strategies - ranging from simple small-object removal to more complex, class-specific pipelines - and rank their performance using the BraTS ranking protocol. Our results highlight how MIST facilitates rapid experimentation and targeted refinement, ultimately producing high-quality segmentations for the BraTS 2025 challenge. MIST remains open source and extensible, supporting reproducible and scalable research in medical image segmentation.

Awj Twam, Adrian E. Celaya, Megan C. Jacobsen et al.

Cervical cancer remains the fourth most common malignancy amongst women worldwide.1 Concurrent chemoradiotherapy (CRT) serves as the mainstay definitive treatment regimen for locally advanced cervical cancers and includes external beam radiation followed by brachytherapy.2 Integral to radiotherapy treatment planning is the routine contouring of both the target tumor at the level of the cervix, associated gynecologic anatomy and the adjacent organs at risk (OARs). However, manual contouring of these structures is both time and labor intensive and associated with known interobserver variability that can impact treatment outcomes. While multiple tools have been developed to automatically segment OARs and the high-risk clinical tumor volume (HR-CTV) using computed tomography (CT) images,3,4,5,6 the development of deep learning-based tumor segmentation tools using routine T2-weighted (T2w) magnetic resonance imaging (MRI) addresses an unmet clinical need to improve the routine contouring of both anatomical structures and cervical cancers, thereby increasing quality and consistency of radiotherapy planning. This work applied a novel deep-learning model (PocketNet) to segment the cervix, vagina, uterus, and tumor(s) on T2w MRI. The performance of the PocketNet architecture was evaluated, when trained on data via five-fold cross validation. PocketNet achieved a mean Dice-Sorensen similarity coefficient (DSC) exceeding 70% for tumor segmentation and 80% for organ segmentation. Validation on a publicly available dataset from The Cancer Imaging Archive (TCIA) demonstrated the models robustness, achieving DSC scores of 67.3% for tumor segmentation and 80.8% for organ segmentation. These results suggest that PocketNet is robust to variations in contrast protocols, providing reliable segmentation of the regions of interest.

Cito Balsells, Beatrice Riviere, David Fuentes

We formulate truncated singular value decompositions of entire convolutional neural networks. We demonstrate the computed left and right singular vectors are useful in identifying which images the convolutional neural network is likely to perform poorly on. To create this diagnostic tool, we define two metrics: the Right Projection Ratio and the Left Projection Ratio. The Right (Left) Projection Ratio evaluates the fidelity of the projection of an image (label) onto the computed right (left) singular vectors. We observe that both ratios are able to identify the presence of class imbalance for an image classification problem. Additionally, the Right Projection Ratio, which only requires unlabeled data, is found to be correlated to the model's performance when applied to image segmentation. This suggests the Right Projection Ratio could be a useful metric to estimate how likely the model is to perform well on a sample.

Adrian Celaya, Yimo Wang, David Fuentes et al.

In recent years, there has been an increasing interest in using deep learning and neural networks to tackle scientific problems, particularly in solving partial differential equations (PDEs). However, many neural network-based methods, such as physics-informed neural networks, depend on automatic differentiation and the sampling of collocation points, which can result in a lack of interpretability and lower accuracy compared to traditional numerical methods. To address this issue, we propose two approaches for learning discontinuous Galerkin solutions to PDEs using small linear convolutional neural networks. Our first approach is supervised and depends on labeled data, while our second approach is unsupervised and does not rely on any training data. In both cases, our methods use substantially fewer parameters than similar numerics-based neural networks while also demonstrating comparable accuracy to the true and DG solutions for elliptic problems.

Adrian Celaya, David Fuentes, Beatrice Riviere

Physics-informed neural networks (PINNs) have gained significant attention for solving forward and inverse problems related to partial differential equations (PDEs). While advancements in loss functions and network architectures have improved PINN accuracy, the impact of collocation point sampling on their performance remains underexplored. Fixed sampling methods, such as uniform random sampling and equispaced grids, can fail to capture critical regions with high solution gradients, limiting their effectiveness for complex PDEs. Adaptive methods, inspired by adaptive mesh refinement from traditional numerical methods, address this by dynamically updating collocation points during training but may overlook residual dynamics between updates, potentially losing valuable information. To overcome this limitation, we propose two adaptive collocation point selection strategies utilizing the QR Discrete Empirical Interpolation Method (QR-DEIM), a reduced-order modeling technique for efficiently approximating nonlinear functions. Our results on benchmark PDEs demonstrate that our QR-DEIM-based approaches improve PINN accuracy compared to existing methods, offering a promising direction for adaptive collocation point strategies.

Rajarajeswari Muthusivarajan, Adrian Celaya, Joshua P. Yung et al.

Deep neural networks with multilevel connections process input data in complex ways to learn the information.A networks learning efficiency depends not only on the complex neural network architecture but also on the input training images.Medical image segmentation with deep neural networks for skull stripping or tumor segmentation from magnetic resonance images enables learning both global and local features of the images.Though medical images are collected in a controlled environment,there may be artifacts or equipment based variance that cause inherent bias in the input set.In this study, we investigated the correlation between the image quality metrics of MR images with the neural network segmentation accuracy.For that we have used the 3D DenseNet architecture and let the network trained on the same input but applying different methodologies to select the training data set based on the IQM values.The difference in the segmentation accuracy between models based on the random training inputs with IQM based training inputs shed light on the role of image quality metrics on segmentation accuracy.By running the image quality metrics to choose the training inputs,further we may tune the learning efficiency of the network and the segmentation accuracy.

Adrian Celaya, Jonas A. Actor, Rajarajeswari Muthusivarajan et al.

Medical imaging deep learning models are often large and complex, requiring specialized hardware to train and evaluate these models. To address such issues, we propose the PocketNet paradigm to reduce the size of deep learning models by throttling the growth of the number of channels in convolutional neural networks. We demonstrate that, for a range of segmentation and classification tasks, PocketNet architectures produce results comparable to that of conventional neural networks while reducing the number of parameters by multiple orders of magnitude, using up to 90% less GPU memory, and speeding up training times by up to 40%, thereby allowing such models to be trained and deployed in resource-constrained settings.

Spyridon Bakas, Mauricio Reyes, Andras Jakab et al.

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset.

Reza Madankan, Wolfgang Stefan, Samuel Fahrenholtz et al.

An accelerated model-based information theoretic approach is presented to perform the task of Magnetic Resonance (MR) thermal image reconstruction from a limited number of observed samples on k-space. The key idea of the proposed approach is to utilize information theoretic techniques to optimally detect samples of k-space that are information rich with respect to a model of the thermal data acquisition. These highly informative k-space samples are then used to refine the mathematical model and reconstruct the image. The information theoretic reconstruction is demonstrated retrospectively in data acquired during MR guided Laser Induced Thermal Therapy (MRgLITT) procedures. The approach demonstrates that locations of high-information content with respect to a model based reconstruction of MR thermometry may be quantitatively identified. The predicted locations of high-information content are sorted and retrospectively extracted from the fully sampled k-space measurements data set. The effect of interactively increasing the predicted number of data points used in the subsampled reconstruction is quantified using the L2-norm of the distance between the subsampled and fully sampled reconstruction. Performance of the proposed approach is also compared with clinically available subsampling techniques (rectilinear subsampling and variable-density Poisson disk undersampling). It is shown that the proposed subsampling scheme results in accurate reconstructions using small fraction of k-space points and suggest that the reconstruction technique may be useful in improving the efficiency of the thermometry data temporal resolution.