arXiv subjects

Craig Jones

Publications and source records attributed to Craig Jones.

8 recordsLinked to original sources

arXiv2026

Topology-Driven Fusion of nnU-Net and MedNeXt for Accurate Brain Tumor Segmentation on Sub-Saharan Africa Dataset

Accurate automatic brain tumor segmentation in Low and Middle-Income (LMIC) countries is challenging due to the lack of defined national imaging protocols, diverse imaging data, extensive use of low-field Magnetic Resonance Imaging (MRI) scanners and limited health-care resources. As part of the Brain Tumor Segmentation (BraTS) Africa 2025 Challenge, we applied topology refinement to the state-of-the-art segmentation models like nnU-Net, MedNeXt, and a combination of both. Since the BraTS-Africa dataset has low MRI image quality, we incorporated the BraTS 2025 challenge data of pre-treatment adult glioma (Task 1) to pre-train the segmentation model and use it to fine-tune on the BraTS-Africa dataset. We added an extra topology refinement module to address the issue of deformation in prediction that arose due to topological error. With the introduction of this module, we achieved a better Normalized Surface Distance (NSD) of 0.810, 0.829, and 0.895 on Surrounding Non-Enhancing FLAIR Hyperintensity (SNFH) , Non-Enhancing Tumor Core (NETC) and Enhancing tumor (ET).

eess.IV↗

arXiv2025

OpenMAP-BrainAge: Generalizable and Interpretable Brain Age Predictor

Purpose: To develop an age prediction model which is interpretable and robust to demographic and technological variances in brain MRI scans. Materials and Methods: We propose a transformer-based architecture that leverages self-supervised pre-training on large-scale datasets. Our model processes pseudo-3D T1-weighted MRI scans from three anatomical views and incorporates brain volumetric information. By introducing a stem architecture, we reduce the conventional quadratic complexity of transformer models to linear complexity, enabling scalability for high-dimensional MRI data. We trained our model on ADNI2 $\&$ 3 (N=1348) and OASIS3 (N=716) datasets (age range: 42 - 95) from the North America, with an 8:1:1 split for train, validation and test. Then, we validated it on the AIBL dataset (N=768, age range: 60 - 92) from Australia. Results: We achieved an MAE of 3.65 years on ADNI2 $\&$ 3 and OASIS3 test set and a high generalizability of MAE of 3.54 years on AIBL. There was a notable increase in brain age gap (BAG) across cognitive groups, with mean of 0.15 years (95% CI: [-0.22, 0.51]) in CN, 2.55 years ([2.40, 2.70]) in MCI, 6.12 years ([5.82, 6.43]) in AD. Additionally, significant negative correlation between BAG and cognitive scores was observed, with correlation coefficient of -0.185 (p < 0.001) for MoCA and -0.231 (p < 0.001) for MMSE. Gradient-based feature attribution highlighted ventricles and white matter structures as key regions influenced by brain aging. Conclusion: Our model effectively fused information from different views and volumetric information to achieve state-of-the-art brain age prediction accuracy, improved generalizability and interpretability with association to neurodegenerative disorders.

cs.CV↗

arXiv2024

Predicting dark matter halo masses from simulated galaxy images and environments

Galaxies are theorized to form and co-evolve with their dark matter halos, such that their stellar masses and halo masses should be well-correlated. However, it is not known whether other observable galaxy features, such as their morphologies or large-scale environments, can be used to tighten the correlation between galaxy properties and halo masses. In this work, we train a baseline random forest model to predict halo mass using galaxy features from the Illustris TNG50 hydrodynamical simulation, and compare with convolutional neural networks (CNNs) and graph neural networks (GNNs) trained respectively using galaxy image cutouts and galaxy point clouds. The best baseline model has a root mean squared error (RMSE) of 0.310 and mean absolute error (MAE) of 0.220, compared to the CNN (RSME=0.359, MAE=0.238), GNN (RMSE=0.248, MAE=0.158), and a novel combined CNN+GNN (RMSE=0.248, MAE=0.144). The CNN is likely limited by our small data set, and we anticipate that the CNN and CNN+GNN would benefit from training on larger cosmological simulations. We conclude that deep learning models can leverage information from galaxy appearances and environment, beyond commonly used summary statistics, in order to better predict the halo mass.

astro-ph.CO↗

arXiv2024

RTA-Former: Reverse Transformer Attention for Polyp Segmentation

Polyp segmentation is a key aspect of colorectal cancer prevention, enabling early detection and guiding subsequent treatments. Intelligent diagnostic tools, including deep learning solutions, are widely explored to streamline and potentially automate this process. However, even with many powerful network architectures, there still comes the problem of producing accurate edge segmentation. In this paper, we introduce a novel network, namely RTA-Former, that employs a transformer model as the encoder backbone and innovatively adapts Reverse Attention (RA) with a transformer stage in the decoder for enhanced edge segmentation. The results of the experiments illustrate that RTA-Former achieves state-of-the-art (SOTA) performance in five polyp segmentation datasets. The strong capability of RTA-Former holds promise in improving the accuracy of Transformer-based polyp segmentation, potentially leading to better clinical decisions and patient outcomes. Our code is publicly available on GitHub.

eess.IV↗

arXiv2023

Evidential Uncertainty Quantification: A Variance-Based Perspective

Uncertainty quantification of deep neural networks has become an active field of research and plays a crucial role in various downstream tasks such as active learning. Recent advances in evidential deep learning shed light on the direct quantification of aleatoric and epistemic uncertainties with a single forward pass of the model. Most traditional approaches adopt an entropy-based method to derive evidential uncertainty in classification, quantifying uncertainty at the sample level. However, the variance-based method that has been widely applied in regression problems is seldom used in the classification setting. In this work, we adapt the variance-based approach from regression to classification, quantifying classification uncertainty at the class level. The variance decomposition technique in regression is extended to class covariance decomposition in classification based on the law of total covariance, and the class correlation is also derived from the covariance. Experiments on cross-domain datasets are conducted to illustrate that the variance-based approach not only results in similar accuracy as the entropy-based one in active domain adaptation but also brings information about class-wise uncertainties as well as between-class correlations. The code is available at https://github.com/KerryDRX/EvidentialADA. This alternative means of evidential uncertainty quantification will give researchers more options when class uncertainties and correlations are important in their applications.

cs.LG↗

arXiv2023

Automated Artifact Detection in Ultra-widefield Fundus Photography of Patients with Sickle Cell Disease

Importance: Ultra-widefield fundus photography (UWF-FP) has shown utility in sickle cell retinopathy screening; however, image artifact may diminish quality and gradeability of images. Objective: To create an automated algorithm for UWF-FP artifact classification. Design: A neural network based automated artifact detection algorithm was designed to identify commonly encountered UWF-FP artifacts in a cross section of patient UWF-FP. A pre-trained ResNet-50 neural network was trained on a subset of the images and the classification accuracy, sensitivity, and specificity were quantified on the hold out test set. Setting: The study is based on patients from a tertiary care hospital site. Participants: There were 243 UWF-FP acquired from patients with sickle cell disease (SCD), and artifact labelling in the following categories was performed: Eyelash Present, Lower Eyelid Obstructing, Upper Eyelid Obstructing, Image Too Dark, Dark Artifact, and Image Not Centered. Results: Overall, the accuracy for each class was Eyelash Present at 83.7%, Lower Eyelid Obstructing at 83.7%, Upper Eyelid Obstructing at 98.0%, Image Too Dark at 77.6%, Dark Artifact at 93.9%, and Image Not Centered at 91.8%. Conclusions and Relevance: This automated algorithm shows promise in identifying common imaging artifacts on a subset of Optos UWF-FP in SCD patients. Further refinement is ongoing with the goal of improving efficiency of tele-retinal screening in sickle cell retinopathy (SCR) by providing a photographer real-time feedback as to the types of artifacts present, and the need for image re-acquisition. This algorithm also may have potential future applicability in other retinal diseases by improving quality and efficiency of image acquisition of UWF-FP.

cs.CV↗

arXiv2023

Active Learning in Brain Tumor Segmentation with Uncertainty Sampling, Annotation Redundancy Restriction, and Data Initialization

Deep learning models have demonstrated great potential in medical 3D imaging, but their development is limited by the expensive, large volume of annotated data required. Active learning (AL) addresses this by training a model on a subset of the most informative data samples without compromising performance. We compared different AL strategies and propose a framework that minimizes the amount of data needed for state-of-the-art performance. 638 multi-institutional brain tumor MRI images were used to train a 3D U-net model and compare AL strategies. We investigated uncertainty sampling, annotation redundancy restriction, and initial dataset selection techniques. Uncertainty estimation techniques including Bayesian estimation with dropout, bootstrapping, and margins sampling were compared to random query. Strategies to avoid annotation redundancy by removing similar images within the to-be-annotated subset were considered as well. We determined the minimum amount of data necessary to achieve similar performance to the model trained on the full dataset ({\alpha} = 0.1). A variance-based selection strategy using radiomics to identify the initial training dataset is also proposed. Bayesian approximation with dropout at training and testing showed similar results to that of the full data model with less than 20% of the training data (p=0.293) compared to random query achieving similar performance at 56.5% of the training data (p=0.814). Annotation redundancy restriction techniques achieved state-of-the-art performance at approximately 40%-50% of the training data. Radiomics dataset initialization had higher Dice with initial dataset sizes of 20 and 80 images, but improvements were not significant. In conclusion, we investigated various AL strategies with dropout uncertainty estimation achieving state-of-the-art performance with the least annotated data.

cs.CV↗

arXiv2021

Using Uncertainty in Deep Learning Reconstruction for Cone-Beam CT of the Brain

Contrast resolution beyond the limits of conventional cone-beam CT (CBCT) systems is essential to high-quality imaging of the brain. We present a deep learning reconstruction method (dubbed DL-Recon) that integrates physically principled reconstruction models with DL-based image synthesis based on the statistical uncertainty in the synthesis image. A synthesis network was developed to generate a synthesized CBCT image (DL-Synthesis) from an uncorrected filtered back-projection (FBP) image. To improve generalizability (including accurate representation of lesions not seen in training), voxel-wise epistemic uncertainty of DL-Synthesis was computed using a Bayesian inference technique (Monte-Carlo dropout). In regions of high uncertainty, the DL-Recon method incorporates information from a physics-based reconstruction model and artifact-corrected projection data. Two forms of the DL-Recon method are proposed: (i) image-domain fusion of DL-Synthesis and FBP (DL-FBP) weighted by DL uncertainty; and (ii) a model-based iterative image reconstruction (MBIR) optimization using DL-Synthesis to compute a spatially varying regularization term based on DL uncertainty (DL-MBIR). The error in DL-Synthesis images was correlated with the uncertainty in the synthesis estimate. Compared to FBP and PWLS, the DL-Recon methods (both DL-FBP and DL-MBIR) showed ~50% reduction in noise (at matched spatial resolution) and ~40-70% improvement in image uniformity. Conventional DL-Synthesis alone exhibited ~10-60% under-estimation of lesion contrast and ~5-40% reduction in lesion segmentation accuracy (Dice coefficient) in simulated and real brain lesions, suggesting a lack of reliability / generalizability for structures unseen in the training data. DL-FBP and DL-MBIR improved the accuracy of reconstruction by directly incorporating information from the measurements in regions of high uncertainty.

physics.med-ph↗