Aneesh Rangnekar

Leonard Nürnberg, Dennis Bontempi, Suraj Pai et al.

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.

Aneesh Rangnekar, Christopher Kanan, Matthew Hoffman

Using deep learning, we now have the ability to create exceptionally good semantic segmentation systems; however, collecting the prerequisite pixel-wise annotations for training images remains expensive and time-consuming. Therefore, it would be ideal to minimize the number of human annotations needed when creating a new dataset. Here, we address this problem by proposing a novel algorithm that combines active learning and semi-supervised learning. Active learning is an approach for identifying the best unlabeled samples to annotate. While there has been work on active learning for segmentation, most methods require annotating all pixel objects in each image, rather than only the most informative regions. We argue that this is inefficient. Instead, our active learning approach aims to minimize the number of annotations per-image. Our method is enriched with semi-supervised learning, where we use pseudo labels generated with a teacher-student framework to identify image regions that help disambiguate confused classes. We also integrate mechanisms that enable better performance on imbalanced label distributions, which have not been studied previously for active learning in semantic segmentation. In experiments on the CamVid and CityScapes datasets, our method obtains over 95% of the network's performance on the full-training set using less than 17% of the training data, whereas the previous state of the art required 40% of the training data.

Aneesh Rangnekar, Christopher Kanan, Matthew Hoffman

Obtaining human per-pixel labels for semantic segmentation is incredibly laborious, often making labeled dataset construction prohibitively expensive. Here, we endeavor to overcome this problem with a novel algorithm that combines semi-supervised and active learning, resulting in the ability to train an effective semantic segmentation algorithm with significantly lesser labeled data. To do this, we extend the prior state-of-the-art S4AL algorithm by replacing its mean teacher approach for semi-supervised learning with a self-training approach that improves learning with noisy labels. We further boost the neural network's ability to query useful data by adding a contrastive learning head, which leads to better understanding of the objects in the scene, and hence, better queries for active learning. We evaluate our method on CamVid and CityScapes datasets, the de-facto standards for active learning for semantic segmentation. We achieve more than 95% of the network's performance on CamVid and CityScapes datasets, utilizing only 12.1% and 15.1% of the labeled data, respectively. We also benchmark our method across existing stand-alone semi-supervised learning methods on the CityScapes dataset and achieve superior performance without any bells or whistles.

Jue Jiang, Aneesh Rangnekar, Harini Veeraraghavan

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.

Jue Jiang, Aneesh Rangnekar, Chloe Min Seo Choi et al.

Pretraining vision transformers (ViT) with attention guided masked image modeling (MIM) has shown to increase downstream accuracy for natural image analysis. Hierarchical shifted window (Swin) transformer, often used in medical image analysis cannot use attention guided masking as it lacks an explicit [CLS] token, needed for computing attention maps for selective masking. We thus enhanced Swin with semantic class attention. We developed a co-distilled Swin transformer that combines a noisy momentum updated teacher to guide selective masking for MIM. Our approach called \textsc{s}e\textsc{m}antic \textsc{a}ttention guided co-distillation with noisy teacher \textsc{r}egularized Swin \textsc{T}rans\textsc{F}ormer (SMARTFormer) was applied for analyzing 3D computed tomography datasets with lung nodules and malignant lung cancers (LC). We also analyzed the impact of semantic attention and noisy teacher on pretraining and downstream accuracy. SMARTFormer classified lesions (malignant from benign) with a high accuracy of 0.895 of 1000 nodules, predicted LC treatment response with accuracy of 0.74, and achieved high accuracies even in limited data regimes. Pretraining with semantic attention and noisy teacher improved ability to distinguish semantically meaningful structures such as organs in a unsupervised clustering task and localize abnormal structures like tumors. Code, models will be made available through GitHub upon paper acceptance.

Aneesh Rangnekar, Harini Veeraraghavan

Accurate segmentation of cancerous lesions from 3D computed tomography (CT) scans is essential for automated treatment planning and response assessment. However, even state-of-the-art models combining self-supervised learning (SSL) pretrained transformers with convolutional decoders are susceptible to out-of-distribution (OOD) inputs, generating confidently incorrect tumor segmentations, posing risks for safe clinical deployment. Existing logit-based methods suffer from task-specific model biases, while architectural enhancements to explicitly detect OOD increase parameters and computational costs. Hence, we introduce a plug-and-play and lightweight post-hoc random forests-based OOD detection framework called RF-Deep that leverages deep features with limited outlier exposure. RF-Deep enhances generalization to imaging variations by repurposing the hierarchical features from the pretrained-then-finetuned backbone encoder, providing task-relevant OOD detection by extracting the features from multiple regions of interest anchored to the predicted tumor segmentations. Hence, it scales to images of varying fields-of-view. We compared RF-Deep against existing OOD detection methods using 1,916 CT scans across near-OOD (pulmonary embolism, negative COVID-19) and far-OOD (kidney cancer, healthy pancreas) datasets. RF-Deep achieved AUROC > 93.50 for the challenging near-OOD datasets and near-perfect detection (AUROC > 99.00) for the far-OOD datasets, substantially outperforming logit-based and radiomics approaches. RF-Deep maintained similar performance consistency across networks of different depths and pretraining strategies, demonstrating its effectiveness as a lightweight, architecture-agnostic approach to enhance the reliability of tumor segmentation from CT volumes.

Jorge Tapias Gomez, Despoina Kanata, Aneesh Rangnekar et al.

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, objectively 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 two scans without requiring any spatial alignment of images 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.

Maxime Kayser, Maksim Gridnev, Wanting Wang et al.

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.

Jorge Tapias Gomez, Despoina Kanata, Aneesh Rangnekar et al.

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.

Aneesh Rangnekar, Nilay Mokashi, Emmett Ientilucci et al.

We investigate applying convolutional neural network (CNN) architecture to facilitate aerial hyperspectral scene understanding and present a new hyperspectral dataset-AeroRIT-that is large enough for CNN training. To date the majority of hyperspectral airborne have been confined to various sub-categories of vegetation and roads and this scene introduces two new categories: buildings and cars. To the best of our knowledge, this is the first comprehensive large-scale hyperspectral scene with nearly seven million pixel annotations for identifying cars, roads, and buildings. We compare the performance of three popular architectures - SegNet, U-Net, and Res-U-Net, for scene understanding and object identification via the task of dense semantic segmentation to establish a benchmark for the scene. To further strengthen the network, we add squeeze and excitation blocks for better channel interactions and use self-supervised learning for better encoder initialization. Aerial hyperspectral image analysis has been restricted to small datasets with limited train/test splits capabilities and we believe that AeroRIT will help advance the research in the field with a more complex object distribution to perform well on. The full dataset, with flight lines in radiance and reflectance domain, is available for download at https://github.com/aneesh3108/AeroRIT. This dataset is the first step towards developing robust algorithms for hyperspectral airborne sensing that can robustly perform advanced tasks like vehicle tracking and occlusion handling.

Aneesh Rangnekar, Joao Miranda, Natally Horvat et al.

Pretraining on large-scale datasets has been shown to improve transformer generalizability, even for out-of-domain (OOD) modalities and tasks. However, two common assumptions often fail under OOD transfer: that downstream datasets can be adapted to the fixed input geometry of pretrained models and that pretrained representations transfer effectively across imaging modalities. We show that these assumptions break down through two interacting failure modes in CT-to-MRI transfer: inefficient token usage caused by zero-padding to match pretrained input dimensions and ineffective feature adaptation. These failures led to accuracy degradation despite extensive fine-tuning. We investigated these failure modes using two CT-pretrained hierarchical shifted-window transformer backbones, SMIT and Swin UNETR, pretrained with different objectives and datasets. Mechanistic analysis introduced 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 in MRI tasks. ADI increased with zero-padding, while high feature reuse did not necessarily correspond to improved accuracy. To mitigate these issues, we introduced two interventions: a tumor-aware augmentation strategy to improve tumor appearance heterogeneity coverage and an anisotropic cropping strategy to restore token efficiency. Fine-tuning on identical rectal MRI datasets improved detection rates to 224/247 (90.7%) for SMIT and 219/247 (88.7%) for Swin UNETR, demonstrating improved robustness under CT-to-MRI transfer. This study is among the first to examine when pretrained transformers fail to transfer effectively across imaging modalities and how simple mitigation strategies, motivated by mechanistic analysis of datasets, can reduce transfer limitations while improving robustness and MRI detection.

Aneesh Rangnekar, Harini Veeraraghavan

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.

Jue Jiang, Aneesh Rangnekar, Harini Veeraraghavan

Self-supervised learning (SSL) is an approach to extract useful feature representations from unlabeled data, and enable fine-tuning on downstream tasks with limited labeled examples. Self-pretraining is a SSL approach that uses the curated task dataset for both pretraining the networks and fine-tuning them. Availability of large, diverse, and uncurated public medical image sets provides the opportunity to apply SSL in the "wild" and potentially extract features robust to imaging variations. However, the benefit of wild- vs self-pretraining has not been studied for medical image analysis. In this paper, we compare robustness of wild versus self-pretrained transformer (vision transformer [ViT] and hierarchical shifted window [Swin]) models to computed tomography (CT) imaging differences for non-small cell lung cancer (NSCLC) segmentation. Wild-pretrained Swin models outperformed self-pretrained Swin for the various imaging acquisitions. ViT resulted in similar accuracy for both wild- and self-pretrained models. Masked image prediction pretext task that forces networks to learn the local structure resulted in higher accuracy compared to contrastive task that models global image information. Wild-pretrained models resulted in higher feature reuse at the lower level layers and feature differentiation close to output layer after fine-tuning. Hence, we conclude: Wild-pretrained networks were more robust to analyzed CT imaging differences for lung tumor segmentation than self-pretrained methods. Swin architecture benefited from such pretraining more than ViT.

Jorge Tapias Gomez, Aneesh Rangnekar, Hannah Williams et al.

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.

Aneesh Rangnekar, Nishant Nadkarni, Jue Jiang et al.

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.

Aneesh Rangnekar, Nilay Mokashi, Emmett Ientilucci et al.

Inferring spectral signatures from ground based natural images has acquired a lot of interest in applied deep learning. In contrast to the spectra of ground based images, aerial spectral images have low spatial resolution and suffer from higher noise interference. In this paper, we train a conditional adversarial network to learn an inverse mapping from a trichromatic space to 31 spectral bands within 400 to 700 nm. The network is trained on AeroCampus, a first of its kind aerial hyperspectral dataset. AeroCampus consists of high spatial resolution color images and low spatial resolution hyperspectral images (HSI). Color images synthesized from 31 spectral bands are used to train our network. With a baseline root mean square error of 2.48 on the synthesized RGB test data, we show that it is possible to generate spectral signatures in aerial imagery.

Burak Uzkent, Aneesh Rangnekar, Matthew J. Hoffman

Hyperspectral imaging holds enormous potential to improve the state-of-the-art in aerial vehicle tracking with low spatial and temporal resolutions. Recently, adaptive multi-modal hyperspectral sensors have attracted growing interest due to their ability to record extended data quickly from aerial platforms. In this study, we apply popular concepts from traditional object tracking, namely (1) Kernelized Correlation Filters (KCF) and (2) Deep Convolutional Neural Network (CNN) features to aerial tracking in hyperspectral domain. We propose the Deep Hyperspectral Kernelized Correlation Filter based tracker (DeepHKCF) to efficiently track aerial vehicles using an adaptive multi-modal hyperspectral sensor. We address low temporal resolution by designing a single KCF-in-multiple Regions-of-Interest (ROIs) approach to cover a reasonably large area. To increase the speed of deep convolutional features extraction from multiple ROIs, we design an effective ROI mapping strategy. The proposed tracker also provides flexibility to couple with the more advanced correlation filter trackers. The DeepHKCF tracker performs exceptionally well with deep features set up in a synthetic hyperspectral video generated by the Digital Imaging and Remote Sensing Image Generation (DIRSIG) software. Additionally, we generate a large, synthetic, single-channel dataset using DIRSIG to perform vehicle classification in the Wide Area Motion Imagery (WAMI) platform. This way, the high-fidelity of the DIRSIG software is proved and a large scale aerial vehicle classification dataset is released to support studies on vehicle detection and tracking in the WAMI platform.

Burak Uzkent, Aneesh Rangnekar, M. J. Hoffman

Hyperspectral cameras can provide unique spectral signatures for consistently distinguishing materials that can be used to solve surveillance tasks. In this paper, we propose a novel real-time hyperspectral likelihood maps-aided tracking method (HLT) inspired by an adaptive hyperspectral sensor. A moving object tracking system generally consists of registration, object detection, and tracking modules. We focus on the target detection part and remove the necessity to build any offline classifiers and tune a large amount of hyperparameters, instead learning a generative target model in an online manner for hyperspectral channels ranging from visible to infrared wavelengths. The key idea is that, our adaptive fusion method can combine likelihood maps from multiple bands of hyperspectral imagery into one single more distinctive representation increasing the margin between mean value of foreground and background pixels in the fused map. Experimental results show that the HLT not only outperforms all established fusion methods but is on par with the current state-of-the-art hyperspectral target tracking frameworks.