arXiv subjects

Harini Veeraraghavan

Publications and source records attributed to Harini Veeraraghavan.

At least 19 recordsLinked to original sources

arXiv2026

Parameter-Efficient pretrained-CT-to-MRI Transfer for Rectal Cancer Segmentation: Performance-Calibration Trade-offs

Accurate rectal cancer segmentation from magnetic resonance imaging (MRI) is essential for adaptive radiotherapy and tumor response assessment, but deployment also requires computational efficiency and informative, calibrated uncertainty estimates. We therefore introduce SWIFT, a SWin pretrained model wIth parameter-eFficient and Tumor-aware fine-tuning for rectal cancer segmentation. A Swin V2 encoder pretrained on 10,444 public 3D CT volumes using a DINOv2-style objective was adapted to T2-weighted MRI through four cumulative configurations: full fine-tuning (SWIFT), decoder compression (SWIFTe), low-rank adaptation (SWIFTe-LoRA), and a four-member LoRA-decoder ensemble (SWIFTe-LDE4). Geometric accuracy, tumor detection, radiomic agreement, and probability calibration were evaluated on a held-out 247-case test set from a single-institution cohort acquired using 1.5 or 3 Tesla GE scanners. Compared with SWIFT, SWIFTe reduced total parameters by 70.1% (from 72.8M to 21.8M) and increased tumor detection rate from 89.9% to 93.9%, while achieving a slightly lower median surface DSC (0.61 versus 0.62) and improved radiomic agreement. In a separate SWIFTe ablation, removing tumor-aware augmentation reduced detection from 93.9% to 89.9% but increased surface DSC from 0.61 to 0.64, demonstrating a detection-boundary-agreement trade-off. SWIFTe-LoRA used 14.6% of SWIFTe's trainable parameters while retaining similar segmentation performance. SWIFTe-LDE4 achieved the lowest calibration errors among the four configurations after temperature scaling (expected calibration error, 0.217; Brier score, 0.222), although the absolute expected calibration error indicates residual miscalibration. Similar efficiency-calibration patterns were observed using the public VoCo checkpoint, supporting robustness across pretrained initializations rather than external clinical generalizability.

cs.CV↗

arXiv2026

Tumor-aware augmentation with task-guided attention analysis improves rectal cancer segmentation from magnetic resonance images

Although self-supervised pretraining is expected to learn broadly transferable representations, its effectiveness across imaging modalities substantially different from the pretraining domain, and on complex tumor-segmentation tasks, remains understudied. Evaluating CT-pretrained transformers on MRI rectal cancer segmentation, we identified two interacting failure modes in CT-to-MRI transfer: (a) inefficient token usage caused by zero-padding to match pretrained input dimensions, and (b) ineffective feature adaptation. We investigated these vulnerabilities using two primary CT-pretrained hierarchical shifted-window transformer backbones, SMIT and Swin UNETR, together with VoCo as a large-scale-pretrained supporting benchmark; these models differ in pretraining objectives and datasets. Mechanistic analysis leveraged an attention dilution index (ADI), an entropy-based metric quantifying attention diverted toward uninformative padding tokens, and centered kernel alignment (CKA) to measure feature reuse during MRI adaptation. ADI increased with zero-padding, while high feature reuse did not necessarily translate to improved downstream accuracy. To mitigate these issues, we introduced two interventions: a tumor-aware augmentation strategy to expand tumor appearance heterogeneity coverage, and an anisotropic cropping strategy to restore token efficiency. Fine-tuning with these strategies on identical rectal MRI datasets yielded detection rates of 91.1% (225/247) and 88.7% (219/247) for the primary SMIT and Swin UNETR backbones, with the supporting VoCo benchmark reaching 90.3% (223/247), demonstrating significantly improved robustness under CT-to-MRI transfer. This study is among the first to examine when pretrained transformers fail to transfer across imaging modalities and demonstrates how targeted mitigation strategies can systematically overcome cross-modality transfer limitations.

eess.IV↗

arXiv2026

Tumor-anchored deep feature random forests for out-of-distribution detection in lung cancer segmentation

Accurate segmentation of lung tumors from 3D computed tomography (CT) scans is essential for automated treatment planning and response assessment. Despite self-supervised pretraining on numerous datasets, state-of-the-art transformer backbones remain susceptible to out-of-distribution (OOD) inputs, often producing confidently incorrect segmentations with potential for risk in clinical deployment. Hence, we introduce RF-Deep, a lightweight post-hoc random forests-based framework that leverages deep features trained with limited outlier exposure, requiring as few as 40 labeled scans (20 in-distribution and 20 OOD), to improve scan-level OOD detection. RF-Deep repurposes the hierarchical features from the pretrained-then-finetuned segmentation backbones, aggregating features from multiple regions-of-interest anchored to predicted tumor regions to capture OOD likelihood. We evaluated RF-Deep on 2,232 CT volumes spanning near-OOD (pulmonary embolism, COVID-19 negative) and far-OOD (kidney cancer, healthy pancreas) datasets. RF-Deep achieved AUROC >~93 on the challenging near-OOD datasets, where it outperformed the next best method by 4--7 percentage points, and produced near-perfect detection (AUROC >~99) on far-OOD datasets. The approach also showed transferability to two blinded validation datasets under the ensemble configuration (COVID-19 positive and breast cancer; AUROC >~94). RF-Deep maintained consistent performance across backbones of different depths and pretraining strategies, demonstrating applicability of post-hoc detectors as a safety filter for clinical deployment of tumor segmentation pipelines.

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arXiv2026

Enhancing Prostate Cancer Segmentation for Multi-Domain Generalization using a novel Parallel-Route Coherent Mixup Regularization Training

MRI guided adaptive radiotherapy (MRgART) for prostate cancer (PCa) targets tumors while sparing organs from unnecessary radiation. Daily treatment adaptation requires accurate segmentation of tumors and organs. Manual delineation can be time and cost prohibitive. Deep learning segmentation methods have limited success applied to datasets distinct from training, hampering generalizability and adoption of MRgART. We develop a novel parallel route coherent mixup (PaRC-mix) training approach for single source to multi-domain generalization. PaRC-mix creates feature augmentations at multiple network layers through linear combination of features from different training samples in a batch. PaRC-mix training was implemented on two deep and residually connected networks, a multiple resolution residual network (MRRN) and UNet++ to segment PCa dominant intraprostatic lesions from apparent diffusion coefficient images. Models were trained on 2,029 samples from 3.0T GE MRI and tested on 1,547 PCa samples from 5 datasets acquired using 3T Siemens, 3T Philips, and 1.5T Elekta Unity MR-Linac scanners. PaRC-mix training led to significantly more accurate tumor detection and segmentation for both networks compared to training without mixup as well as input-mix training. PaRC-mix also achieved better recall to precision tradeoff than mixup applied only on the network backbone or input-mixup. Using a normalized composite DSC, HD95, and MSD score the accuracy gap between aggressive and non-aggressive lesions decreased from 21.1 and 19.5 for MRRN and UNet++ models trained without mixup to 5.2 and 7.9 with same models trained with PaRC-mix. This paper presents an easy to implement network agnostic approach to feature augmentation in multi-stream networks that enhances generalizability for the difficult problem of prostate cancer lesion segmentation.

eess.IV↗

arXiv2026

Dual Cross-Attention Siamese Transformer for Rectal Tumor Regrowth Assessment in Watch-and-Wait Endoscopy

Increasing evidence supports watch-and-wait (WW) surveillance for patients with rectal cancer who show clinical complete response (cCR) at restaging following total neoadjuvant treatment (TNT). However, accurate methods to early detect local regrowth (LR) from follow-up endoscopy images during WW are essential to manage care and prevent distant metastases. Hence, we developed a Siamese Swin Transformer with Dual Cross-Attention (SSDCA) to combine longitudinal endoscopic images at restaging and follow-up and distinguish cCR from LR. SSDCA leverages pretrained Swin Transformers to extract domain agnostic features and enhance robustness to imaging variations. Dual cross attention is implemented to emphasize features from the paired scans without requiring any spatial alignment to predict response. SSDCA as well as Swin-based baselines were trained using image pairs from 135 patients and evaluated on a held-out set of image pairs from 62 patients. SSDCA produced the best balanced accuracy (81.76% $\pm$ 0.04), sensitivity (90.07% $\pm$ 0.08), and specificity (72.86% $\pm$ 0.05). Robustness analysis showed stable performance irrespective of artifacts including blood, stool, telangiectasia, and poor image quality. UMAP clustering of extracted features showed maximal inter-cluster separation (1.45 $\pm$ 0.18) and minimal intra-cluster dispersion (1.07 $\pm$ 0.19) with SSDCA, confirming discriminative representation learning. Code and weights available at: https://github.com/Jotanator/SSDCA

cs.CV↗

arXiv2026

BrainDINO: A Brain MRI Foundation Model for Generalizable Clinical Representation Learning

Brain MRI underpins a wide range of neuroscientific and clinical applications, yet most learning-based methods remain task-specific and require substantial labeled data. Here we show that a single self-supervised representation can generalize across heterogeneous brain MRI endpoints. We trained BrainDINO, a self-distilled foundation model, on approximately 6.6 million unlabeled axial slices from 20 datasets encompassing broad variation in population, disease, and acquisition setting. Using a frozen encoder with lightweight task heads, BrainDINO supported transfer across tumor segmentation, neurodegenerative and neurodevelopmental conditions classification, brain age estimation, post-stroke temporal prediction, molecular status prediction, MRI sequence classification, and survival modeling. Across tasks and supervision regimes, BrainDINO consistently equaled or exceeded natural-image and MRI-specific self-supervised baselines, with particularly strong advantages under label scarcity. Representation analyses further showed anatomically organized and pathology-sensitive feature structure in the absence of task-specific supervision. Our findings indicate that large-scale slice-wise self-supervised learning can yield a unified brain MRI representation that supports diverse neuroimaging tasks without volumetric pretraining or full-network fine-tuning, establishing a scalable foundation for robust and data-efficient brain imaging analysis. Code is available at https://github.com/mclwu22/BrainDINO

cs.LG↗

arXiv2026

Benchmarking transferability of SSL pretraining to same and different modality segmentation tasks

Methods: Nine SSL methods spanning four pretext-task families were pretrained from scratch using the same 10{,}412 3D CT scans (1.89~M 2D axial slices) covering varied disease sites. The pretrained Swin Transformer encoder from each method was integrated into a SwinUNETR-style segmentation network (Swin encoder with a 3D CNN decoder and skip connections) and fine-tuned on nine public segmentation tasks of varying complexity, including large abdominal organs, head-and-neck structures, and tumors from CT and MRI. Performance was assessed using Dice similarity coefficient (DSC). Fine-tuning convergence speed, transferability across modalities (CT-to-MRI), and feature-reuse patterns between few- and many-shot fine tuning were further analyzed using centered kernel alignment. Results: Self-distilled masked image transformer (SMIT), which combines masked image modeling (MIM) with local and global self-distillation, achieved the highest overall segmentation accuracy across the nine tasks, the fastest fine-tuning convergence, and the smallest few-shot-to-many-shot performance gap, indicating the strongest data efficiency. SMIT also showed the most consistent feature-reuse patterns between few- and many-shot fine tuning. MIM-based SimMIM and self-distillation methods (DINO, iBOT) outperformed contrastive learning and rotation prediction, which rely on image-level global representations. Differences between SSL methods were largest in the few-shot setting and narrowed as the size of the labeled fine-tuning dataset increased, indicating that the choice of SSL pretraining matters most under limited annotation budgets.

cs.CV↗

arXiv2026

Prediction of Rectal Cancer Regrowth from Longitudinal Endoscopy

Clinical trial studies indicate benefit of watch-and-wait (WW) surveillance for patients with rectal cancer showing a complete or near clinical response (CR) directly after treatment (restaging). However, there are no objectively accurate methods to early detect local tumor regrowth (LR) in patients undergoing WW from follow-up exams. Hence, we developed Temporal Rectal Endoscopy Cross-attention (TREX), a longitudinal deep learning approach that combines pairs of images acquired at restaging and follow-up to distinguish CR from LR. TREX uses pretrained Swin Transformers in a siamese setting to extract features from longitudinal images and dual cross-attention to combine the features without spatial co-registration between image pairs. TREX and Swin-based baselines were trained under two settings: (a) detecting LR or CR at the last available follow-up and (b) early detection of LR at 3--6, 6--12, and 12--24 months before clinical confirmation. TREX achieved the highest accuracy in detecting LR with a high sensitivity of 97% $\pm$ 6% and a balanced accuracy of 90% $\pm$ 3%, and outperformed all baselines in early detection at both 3--6 (74% $\pm$ 1%) and 6--12 months (62% $\pm$ 4%) prior to clinical detection. Clinical validation via a surgeon survey showed that TREX matched attending-level overall accuracy (TREX: 86.21% vs.\ Clinicians: 87.84% $\pm$ 1.28%). Finally, we explored TREX's ability to predict treatment response by combining pre-treatment (pre-TNT) and restaging endoscopies, achieving a balanced accuracy of 73% $\pm$ 12%. These results show that longitudinal deep learning analysis of endoscopy may improve surveillance and enable earlier identification of rectal cancer regrowth.

cs.CV↗

arXiv2026

Co-distilled attention guided masked image modeling with noisy teacher for self-supervised learning on medical images

Masked image modeling (MIM) is a highly effective self-supervised learning (SSL) approach to extract useful feature representations from unannotated data. Predominantly used random masking methods make SSL less effective for medical images due to the contextual similarity of neighboring patches, leading to information leakage and SSL simplification. Hierarchical shifted window (Swin) transformer, a highly effective approach for medical images cannot use advanced masking methods as it lacks a global [CLS] token. Hence, we introduced an attention guided masking mechanism for Swin within a co-distillation learning framework to selectively mask semantically co-occurring and discriminative patches, to reduce information leakage and increase the difficulty of SSL pretraining. However, attention guided masking inevitably reduces the diversity of attention heads, which negatively impacts downstream task performance. To address this, we for the first time, integrate a noisy teacher into the co-distillation framework (termed DAGMaN) that performs attentive masking while preserving high attention head diversity. We demonstrate the capability of DAGMaN on multiple tasks including full- and few-shot lung nodule classification, immunotherapy outcome prediction, tumor segmentation, and unsupervised organs clustering.

cs.CV↗

arXiv2026

Transformer-based cardiac substructure segmentation from contrast and non-contrast computed tomography for radiotherapy planning

Accurate segmentation of cardiac substructures on computed tomography (CT) scans is essential for radiotherapy planning but typically requires large annotated datasets and often generalizes poorly across imaging protocols and patient variations. This study evaluated whether pretrained transformers enable data-efficient training using a fixed architecture with balanced curriculum learning. A hybrid pretrained transformer-convolutional network (SMIT) was fine-tuned on lung cancer patients (Cohort I, N $=$ 180) imaged in the supine position and validated on 60 held-out Cohort I patients and 65 breast cancer patients (Cohort II) imaged in both supine and prone positions. Two configurations were evaluated: SMIT-Balanced (32 contrast-enhanced CTs and 32 non-contrast CTs) and SMIT-Oracle (180 CTs). Performance was compared with nnU-Net and TotalSegmentator. Segmentation accuracy was assessed primarily using the 95th percentile Hausdorff distance (HD95), with radiation dose and overlap-based metrics evaluated as secondary endpoints. SMIT-Balanced achieved accuracy comparable to SMIT-Oracle despite using 64$\%$ fewer training scans. On Cohort I, HD95 was 6.6 $\pm$ 4.3 mm versus 5.4 $\pm$ 2.6 mm, and on Cohort II, 10.0 $\pm$ 9.4 mm versus 9.4 $\pm$ 9.8 mm, respectively, demonstrating robustness to patient, imaging, and data variations. Radiation dose metrics derived from SMIT segmentations were equivalent to those from manual delineations. Although nnU-Net improved over the publicly trained TotalSegmentator, it showed reduced cross-domain robustness compared to SMIT. Balanced curriculum training reduced labeled data requirements without compromising accuracy relative to the oracle model and maintained robustness across patient and imaging variations. Pretraining reduced dependence on data domain and obviated the need for data-specific architectural reconfiguration required by nnU-Net.

eess.IV↗

arXiv2026

Random forest-based out-of-distribution detection for robust lung cancer segmentation

Accurate detection and segmentation of cancerous lesions from computed tomography (CT) scans is essential for automated treatment planning and cancer treatment response assessment. Transformer-based models with self-supervised pretraining can produce reliably accurate segmentation from in-distribution (ID) data but degrade when applied to out-of-distribution (OOD) datasets. We address this challenge with RF-Deep, a random forest classifier that utilizes deep features from a pretrained transformer encoder of the segmentation model to detect OOD scans and enhance segmentation reliability. The segmentation model comprises a Swin Transformer encoder, pretrained with masked image modeling (SimMIM) on 10,432 unlabeled 3D CT scans covering cancerous and non-cancerous conditions, with a convolution decoder, trained to segment lung cancers in 317 3D scans. Independent testing was performed on 603 3D CT public datasets that included one ID dataset and four OOD datasets comprising chest CTs with pulmonary embolism (PE) and COVID-19, and abdominal CTs with kidney cancers and healthy volunteers. RF-Deep detected OOD cases with a FPR95 of 18.26%, 27.66%, and less than 0.1% on PE, COVID-19, and abdominal CTs, consistently outperforming established OOD approaches. The RF-Deep classifier provides a simple and effective approach to enhance reliability of cancer segmentation in ID and OOD scenarios.

eess.IV↗

arXiv2026

MHub.ai: A Simple, Standardized, and Reproducible Platform for AI Models in Medical Imaging

Artificial intelligence (AI) has the potential to transform medical imaging by automating image analysis and accelerating clinical research. However, research and clinical use are limited by the wide variety of AI implementations and architectures, inconsistent documentation, and reproducibility issues. Here, we introduce MHub$.$ai, an open-source, container-based platform that standardizes access to AI models with minimal configuration, promoting accessibility and reproducibility in medical imaging. MHub$.$ai packages models from peer-reviewed publications into standardized containers that support direct processing of DICOM and other formats, provide a unified application interface, and embed structured metadata. Each model is accompanied by publicly available reference data that can be used to confirm model operation. MHub$.$ai includes an initial set of state-of-the-art segmentation, prediction, and feature extraction models for different modalities. The modular framework enables adaptation of any model and supports community contributions. We demonstrate the utility of the platform in a clinical use case through comparative evaluation of lung segmentation models. To further strengthen transparency and reproducibility, we publicly release the generated segmentations and evaluation metrics and provide interactive dashboards that allow readers to inspect individual cases and reproduce or extend our analysis. By simplifying model use, MHub$.$ai enables side-by-side benchmarking with identical execution commands and standardized outputs, and lowers the barrier to clinical translation.

cs.AI↗

arXiv2025

brat: Aligned Multi-View Embeddings for Brain MRI Analysis

We present brat (brain report alignment transformer), a multi-view representation learning framework for brain magnetic resonance imaging (MRI) trained on MRIs paired with clinical reports. Brain MRIs present unique challenges due to the presence of numerous, highly varied, and often subtle abnormalities that are localized to a few slices within a 3D volume. To address these challenges, we introduce a brain MRI dataset $10\times$ larger than existing ones, containing approximately 80,000 3D scans with corresponding radiology reports, and propose a multi-view pre-training approach inspired by advances in document retrieval. We develop an implicit query-feature matching mechanism and adopt concepts from quality-diversity to obtain multi-view embeddings of MRIs that are aligned with the clinical features given by report sentences. We evaluate our approach across multiple vision-language and vision tasks, demonstrating substantial performance improvements. The brat foundation models are publicly released.

cs.CV↗

arXiv2025

Segmentation Regularized Training for Multi-Domain Deep Learning Registration applied to MR-Guided Prostate Cancer Radiotherapy

Background: Accurate deformable image registration (DIR) is required for contour propagation and dose accumulation in MR-guided adaptive radiotherapy (MRgART). This study trained and evaluated a deep learning DIR method for domain invariant MR-MR registration. Methods: A progressively refined registration and segmentation (ProRSeg) method was trained with 262 pairs of 3T MR simulation scans from prostate cancer patients using weighted segmentation consistency loss. ProRSeg was tested on same- (58 pairs), cross- (72 1.5T MR Linac pairs), and mixed-domain (42 MRSim-MRL pairs) datasets for contour propagation accuracy of clinical target volume (CTV), bladder, and rectum. Dose accumulation was performed for 42 patients undergoing 5-fraction MRgART. Results: ProRSeg demonstrated generalization for bladder with similar Dice Similarity Coefficients across domains (0.88, 0.87, 0.86). For rectum and CTV, performance was domain-dependent with higher accuracy on cross-domain MRL dataset (DSCs 0.89) versus same-domain data. The model's strong cross-domain performance prompted us to study the feasibility of using it for dose accumulation. Dose accumulation showed 83.3% of patients met CTV coverage (D95 >= 40.0 Gy) and bladder sparing (D50 <= 20.0 Gy) constraints. All patients achieved minimum mean target dose (>40.4 Gy), but only 9.5% remained under upper limit (<42.0 Gy). Conclusions: ProRSeg showed reasonable multi-domain MR-MR registration performance for prostate cancer patients with preliminary feasibility for evaluating treatment compliance to clinical constraints.

cs.CV↗

arXiv2025

Modality-agnostic, patient-specific digital twins modeling temporally varying digestive motion

Objective: Clinical implementation of deformable image registration (DIR) requires voxel-based spatial accuracy metrics such as manually identified landmarks, which are challenging to implement for highly mobile gastrointestinal (GI) organs. To address this, patient-specific digital twins (DT) modeling temporally varying motion were created to assess the accuracy of DIR methods. Approach: 21 motion phases simulating digestive GI motion as 4D sequences were generated from static 3D patient scans using published analytical GI motion models through a semi-automated pipeline. Eleven datasets, including six T2w FSE MRI (T2w MRI), two T1w 4D golden-angle stack-of-stars, and three contrast-enhanced CT scans. The motion amplitudes of the DTs were assessed against real patient stomach motion amplitudes extracted from independent 4D MRI datasets. The generated DTs were then used to assess six different DIR methods using target registration error, Dice similarity coefficient, and the 95th percentile Hausdorff distance using summary metrics and voxel-level granular visualizations. Finally, for a subset of T2w MRI scans from patients treated with MR-guided radiation therapy, dose distributions were warped and accumulated to assess dose warping errors, including evaluations of DIR performance in both low- and high-dose regions for patient-specific error estimation. Main results: Our proposed pipeline synthesized DTs modeling realistic GI motion, achieving mean and maximum motion amplitudes and a mean log Jacobian determinant within 0.8 mm and 0.01, respectively, similar to published real-patient gastric motion data. It also enables the extraction of detailed quantitative DIR performance metrics and rigorous validation of dose mapping accuracy. Significance: The pipeline enables rigorously testing DIR tools for dynamic, anatomically complex regions enabling granular spatial and dosimetric accuracies.

cs.CV↗

arXiv2025

Quantifying uncertainty in lung cancer segmentation with foundation models applied to mixed-domain datasets

Medical image foundation models have shown the ability to segment organs and tumors with minimal fine-tuning. These models are typically evaluated on task-specific in-distribution (ID) datasets. However, reliable performance on ID datasets does not guarantee robust generalization on out-of-distribution (OOD) datasets. Importantly, once deployed for clinical use, it is impractical to have `ground truth' delineations to assess ongoing performance drifts, especially when images fall into the OOD category due to different imaging protocols. Hence, we introduced a comprehensive set of computationally fast metrics to evaluate the performance of multiple foundation models (Swin UNETR, SimMIM, iBOT, SMIT) trained with self-supervised learning (SSL). All models were fine-tuned on identical datasets for lung tumor segmentation from computed tomography (CT) scans. The evaluation was performed on two public lung cancer datasets (LRAD: n = 140, 5Rater: n = 21) with different image acquisitions and tumor stages compared to training data (n = 317 public resource with stage III-IV lung cancers) and a public non-cancer dataset containing volumetric CT scans of patients with pulmonary embolism (n = 120). All models produced similarly accurate tumor segmentation on the lung cancer testing datasets. SMIT produced the highest F1-score (LRAD: 0.60, 5Rater: 0.64) and lowest entropy (LRAD: 0.06, 5Rater: 0.12), indicating higher tumor detection rate and confident segmentations. In the OOD dataset, SMIT misdetected the least number of tumors, marked by a median volume occupancy of 5.67 cc compared to the best method SimMIM of 9.97 cc. Our analysis shows that additional metrics such as entropy and volume occupancy may help better understand model performance on mixed domain datasets.

eess.IV↗

arXiv2025

Swin transformers are robust to distribution and concept drift in endoscopy-based longitudinal rectal cancer assessment

Endoscopic images are used at various stages of rectal cancer treatment starting from cancer screening, diagnosis, during treatment to assess response and toxicity from treatments such as colitis, and at follow up to detect new tumor or local regrowth (LR). However, subjective assessment is highly variable and can underestimate the degree of response in some patients, subjecting them to unnecessary surgery, or overestimate response that places patients at risk of disease spread. Advances in deep learning has shown the ability to produce consistent and objective response assessment for endoscopic images. However, methods for detecting cancers, regrowth, and monitoring response during the entire course of patient treatment and follow-up are lacking. This is because, automated diagnosis and rectal cancer response assessment requires methods that are robust to inherent imaging illumination variations and confounding conditions (blood, scope, blurring) present in endoscopy images as well as changes to the normal lumen and tumor during treatment. Hence, a hierarchical shifted window (Swin) transformer was trained to distinguish rectal cancer from normal lumen using endoscopy images. Swin as well as two convolutional (ResNet-50, WideResNet-50), and vision transformer (ViT) models were trained and evaluated on follow-up longitudinal images to detect LR on private dataset as well as on out-of-distribution (OOD) public colonoscopy datasets to detect pre/non-cancerous polyps. Color shifts were applied using optimal transport to simulate distribution shifts. Swin and ResNet models were similarly accurate in the in-distribution dataset. Swin was more accurate than other methods (follow-up: 0.84, OOD: 0.83) even when subject to color shifts (follow-up: 0.83, OOD: 0.87), indicating capability to provide robust performance for longitudinal cancer assessment.

eess.IV↗

arXiv2024

Improving ovarian cancer segmentation accuracy with transformers through AI-guided labeling

Transformer models have demonstrated the capability to produce highly accurate segmentation of organs and tumors. However, model training requires high-quality curated datasets to ensure robust generalization to unseen datasets. Hence, we developed an artificial intelligence (AI) guided approach to assist with radiologist tumor delineation of partially segmented computed tomography datasets containing primary (adnexa) tumors and metastatic (omental) implants. AI guidance was implemented by training a 2D multiple resolution residual network trained with a dataset of 245 contrast-enhanced CTs with partially segmented examples. The same dataset curated through AI guidance was then used to refine two pretrained transformer models called SMIT and Swin UNETR. The models were independently tested on 71 publicly available multi-institutional 3D CT datasets. Segmentation accuracy was computed using the Dice similarity coefficient metric (DSC), average symmetric surface distance (ASSD), and the relative volume difference (RVD) metrics. Radiomic features reproducibility was assessed using the concordance correlation coefficient (CCC). Training with AI-guided segmentations significantly improved the accuracy of both SMIT (p = 6.2e-5) and Swin UNETR (p = 2e-4) models compared with using a partially delineated training dataset. Furthermore, SMIT-generated segmentations resulted in more reproducible features compared to Swin UNETR under multiple feature categories. Our results show that AI-guided data curation provides a more efficient approach to train AI models and that AI-generated segmentations can provide reproducible radiomics features.

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