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Tushar Kataria

Publications and source records attributed to Tushar Kataria.

At least 19 recordsLinked to original sources

Lesion Overlap Ranks PET Segmentation Models but Does Not Certify Patient-Level Tumor Burden

Metabolic tumor volume (MTV) summarizes whole-body PET disease burden for prognostic stratification and treatment assessment. Automated MTV is useful only if its estimate is reliable for the individual patient, yet segmentation models are usually evaluated with overlap metrics such as Dice rather than burden error. We examined whether overlap metrics identify unreliable MTV estimates using 1,014 autoPET FDG PET/CT studies. We evaluated LesionTracer predictions held out from fine-tuning, compared five selected released models on 489 tumor-positive patients, and examined the findings in 597 PSMA studies. Across the five FDG models, ranking by higher mean Dice gave the same order as ranking by lower mean relative MTV error ($ρ=-1.00$, exact $p=0.017$). At the patient level, however, out-of-fold Dice tracked relative MTV error strongly ($ρ=-0.75$), yet 82 of 489 patients (16.8\%) fell on opposite sides of the Dice 0.80 and MTV-error 25\% thresholds. Within the training-exposed released models, correlations ranged from $-0.47$ to $-0.74$ over narrower, high-Dice ranges. Out of fold, opposing false-positive and false-negative volumes cancelled about one third of spatial error in net MTV. In 236 of 489 patients, each of the five models missed at least one lesion, though not necessarily the same lesion. Thus, agreement in average model rankings did not establish the reliability of individual MTV estimates or reveal shared lesion misses. PET segmentation benchmarks should report patient-level MTV error and missed-lesion counts alongside Dice and other overlap metrics.

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Anchored Slice Propagation with Boundary Transport for 3D CT Segmentation from Three Orthogonal Annotated Slices

Sli2Vol propagates a binary mask through affinities between adjacent slices, but an error can persist because each prediction becomes the input to the next step. Three orthogonal annotations reduce dependence on any one chain, yet they offer more than three starting masks: where a chain crosses another annotated plane, the correct label is already known. Those labels could correct drift during propagation and indicate how much to trust each chain at fusion. Between annotated planes, the information carried by the chain may matter as well. A binary mask records foreground membership but discards distance to the boundary, a cue that could help follow gradual shape changes between slices.We address these two sources of error with a fixed pretrained affinity backbone. We anchor each chain by correcting its prediction where it crosses another annotated plane, then use its agreement with those labels to weight fusion. We compare this anchored mask with two ways of transporting boundary geometry: a truncated signed-distance field (SDF) propagated by dense affinity averaging, and a contour whose vertices follow motion cues from the same affinity. The contour tracker starts from a hand-crafted rule and learns a motion correction from supervoxel pseudo-objects in 506 CT volumes, without manual organ labels. On 2,091 held-out structure instances from approximately 403 CT scans spanning 17 abdominal structures, anchoring raises mean Dice from 0.737 with orthogonal mask propagation to 0.769 and improves every structure. Beyond the anchored mask, learned contour tracking improves Dice by 5.7\% for the esophagus and 5.9\% for the postcava, while SDF transport improves right-adrenal Dice by 2.8\%. The anchored methods have similar mean Dice (0.769--0.772); contour tracking performs worse on the kidneys, stomach, and hepatic vessel tree.

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FLASHSWIN: Unlocking Large Windows and Dense Tokens in Swin Vision Transformers with Memory Efficient Attention

High-resolution vision backbones have long been forced to trade away local token density to afford larger receptive fields. Hierarchical Swin transformers impose this compromise because standard windowed attention materializes an $M^2\times M^2$ score matrix per window, incurring $O(M^4)$ memory as windows or token grids grow. Furthermore, Swin adds a learned relative-position bias elementwise to attention scores, requiring full materialization of the score matrix and its gradient. This keeps Swin and SwinV2 trapped in a small-window($M=8,16$), coarse-token regime with patch size $4\times4$ ($p=4$), limiting performance for fine-grained tasks. We introduce FLASHSWIN, which replaces standard windowed attention with a FlashAttention implementation that computes exact softmax attention without materializing the score matrix, reducing per-window memory from $O(M^4)$ to $O(M^2)$. This enables higher token density and larger receptive fields without inflating memory overhead. Training memory is flat across window sizes: at a $32\times32$ window, FLASHSWIN-T requires only $12.4$\,GB, unchanged from $8\times8$, compared to $70/90$\,GB for SwinV2/V1-T. However, applying FlashAttention directly to Swin creates a trade-off: bypassing the score matrix precludes Swin's additive relative-position bias, forfeiting spatial information in exchange for memory efficiency. FLASHSWIN restores position information as window-local learnable 2D RoPE, making large windows and dense token grids both affordable and accurate. At matched scale, FLASHSWIN-T outperforms Swin variants. With dense tokens and wide windows ($p=2,M=32$), the same Tiny model reaches $84.1\%$ ImageNet-1K, $44.1$ COCO box AP, and $47.28$ ADE20K mIoU---gains of $+1.3$, $+5.1$, and $+1.82$ over SwinV2-T at $M=16$, respectively. At fixed $M=32$, halving the patch size yields roughly $3\times$ larger gains in boundary quality than in mIoU.

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BoundarySeg:Boundary-Aware Multi-Task Learning for Semi-Supervised 3D Medical Image Segmentation with Limited Unlabeled Data

Data scarcity is a primary bottleneck in 3D medical image segmentation: expert voxel-level annotations are expensive, and privacy regulations often severely restrict access to unannotated clinical volumes. While semi-supervised learning (SSL) aims to alleviate annotation burdens, existing paradigms implicitly rely on large pools of unlabeled data ($U$) relative to labeled data ($L$), assuming $U \gg L$ to filter noise and enforce consistency. When restricted to the data-constrained regime where unlabeled data are limited ($U \le L$), standard SSL methods suffer from severe pseudo-label degeneracy, performance degradation, and high seed-to-seed variance. In this work, we propose BoundarySeg, a unified multi-task semi-supervised framework specifically designed for the limited unlabeled data regime ($U \le L$). BoundarySeg formulates volumetric segmentation as a joint learning task that predicts whole-organ geometry alongside auxiliary organ boundaries. Rather than relying on large cohorts to average out pseudo-label noise, BoundarySeg employs the auxiliary boundary branch as an internal geometric anchor. Coupled with uncertainty-weighted mean-teacher consistency across both tasks alongside axis-flip equivariance and copy-paste regularization, this joint supervision stabilizes spatial representations and prevents segmentation collapse when $U \le L$. Across multiple 3D segmentation datasets, BoundarySeg maintains high performance stability as unlabeled pool size shrinks, consistently outperforming state-of-the-art semi-supervised frameworks in low-data settings. \href{https://github.com/tushaarkataria/BoundarySeg}{https://github.com/tushaarkataria/BoundarySeg}

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IMPLICITSTAINER: Resolution Agnostic Data-Efficient Virtual Staining Using Neural Implicit Functions

Hematoxylin and eosin (H&E)-stained slides are central to cancer diagnosis and monitoring, visualizing tissue architecture and cellular morphology. However, H&E lacks the molecular specificity needed to distinguish cell states and functional activation. Antibody-based stains, such as immunohistochemistry (IHC), are therefore required to identify specific phenotypes (e.g., CD3$^+$ T cells or HER2-positive tumor cells) but are costly, time-consuming, and not universally available. Deep learning-based image translation methods, often termed virtual staining, offer a complementary alternative by generating virtual immunostains directly from H&E images. Most existing virtual staining methods are patch-based and operate at fixed resolutions, often requiring large datasets and additional post-hoc super-resolution models to generate high-resolution images. Furthermore, GAN- and diffusion-based approaches introduce stochasticity into generated stains which, although beneficial for visual realism in natural images, can lead to hallucinations and structural distortions that affect the accuracy and reliability required for clinical use. We propose IMPLICITSTAINER, a deterministic framework that reformulates virtual staining as a continuous pixel-level translation problem. In contrast to existing patch-based approaches, IMPLICITSTAINER formulates image translation as a continuous spatial mapping using neural implicit deep learning models. Each target-domain (IHC) pixel is predicted from a high-dimensional embedding of the corresponding source-domain H&E pixel, its local spatial neighborhood, and explicit coordinate information. IMPLICITSTAINER enables resolution-agnostic inference, improves robustness in low-data regimes, and yields deterministic, reproducible outputs. Across more than twenty baselines, IMPLICITSTAINER achieves SOTA performance on virtual staining tasks, including IHC and mIF.

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Inference-Time Orthogonal Seeding Enables Geometry-Aligned 3D Organ Segmentation for Slice-Propagation Methods

Dense voxel-level annotation remains a major bottleneck in 3D medical image segmentation. Single-slice propagation methods such as Sli2Vol reduce this burden by propagating one annotated seed slice through a volume using label-free registration. However, axial-only propagation accumulates errors with distance from the seed, especially in surface-distance metrics, because it ignores coronal and sagittal evidence and therefore underuses the 3D information available in CT/MRI volumes. To better leverage volumetric geometry, we study how key training and inference choices affect slice-propagation models, including single-axis versus multi-axis label-free registration, single-seed versus multi-seed propagation, and orthogonal seed configurations. Instead of propagating from a single axial seed, we use three orthogonal seeds---one axial, one coronal, and one sagittal---and fuse their propagated labels with a simple label-free rule. Our results show that the training paradigm has limited impact: an axially trained network applied to off-axis seeds captures nearly all the improvement, while explicit three-axis training adds little. Instead, performance is driven by inference-time seed geometry, especially orthogonality rather than the number of annotated slices, as a budget-matched three-axial control provides no benefit and can even degrade performance. On a multi-organ CT cohort, orthogonal seeding with the axial Sli2Vol backbone improves Dice by 21.9%, Normalized Surface Dice by 25.5%, and reduces Average Hausdorff Distance by 53.5% over the single-axis baseline.

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On the Viability of Semi-Supervised Segmentation Methods for Statistical Shape Modeling

Statistical Shape Models (SSMs) excel at identifying population level anatomical variations, which is at the core of various clinical and biomedical applications, including morphology-based diagnostics and surgical planning. However, the effectiveness of SSMs is often constrained by the necessity for expert-driven manual segmentation, a time-intensive and expensive process that restricts their broader utility. While deep learning approaches offer a potential workaround by directly estimating SSMs from unsegmented images, they merely shift the burden. Although these models do not require segmentation during deployment, they still fail to address the challenge of acquiring the manual annotations needed for training, particularly in resource-limited settings. Semi-supervised models for anatomy segmentation present a logical solution to the annotation burden. However, the lack of established guidelines leaves end-users uncertain about the actual effectiveness of these approaches for the downstream task of constructing SSMs. In this study, we bridge this gap by systematically evaluating semi-supervised methods as viable alternatives to manual segmentation. By applying these methods under low-annotation settings and utilizing the predicted segmentations for SSM generation, we establish a comprehensive new performance benchmark. Our findings reveal a clear divide in performance: while certain methods yield noisy segmentations that degrade SSM quality, others accurately capture the population's modes of variation comparable to those obtained from manual-segmentation SSMs despite a 60-80% reduction in manual annotation requirements.

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MorphoFlow: Sparse-Supervised Generative Shape Modeling with Adaptive Latent Relevance

Statistical shape modeling (SSM) is central to population level analysis of anatomical variability, yet most existing approaches rely on densely annotated segmentations and fixed latent representations. These requirements limit scalability and reduce flexibility when modeling complex anatomical variation. We introduce MorphoFlow, a sparse supervised generative shape modeling framework that learns compact probabilistic shape representations directly from sparse surface annotations. MorphoFlow integrates neural implicit shape representations with an autodecoder formulation and autoregressive normalizing flows to learn an expressive probabilistic density over the latent shape space. The neural implicit representation enables resolution-agnostic modeling of 3D anatomy, while the autodecoder formulation supports direct optimization of per-instance latent codes under sparse supervision. The autoregressive flow captures the distribution of latent anatomical variability providing a tractable, likelihood-based generative model of shapes. To promote compact and structured latent representations, we incorporate adaptive latent relevance weighting through sparsity-inducing priors, enabling the model to regulate the contribution of individual latent dimensions according to their relevance to the underlying anatomical variation while preserving generative expressivity. The resulting latent space supports uncertainty quantification and anatomically plausible shape synthesis without manual latent dimensionality tuning. Evaluation on publicly available lumbar vertebrae and femur datasets demonstrates accurate high-resolution reconstruction from sparse inputs and recovery of structured modes of anatomical variation consistent with population level trends.

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MedConcept: Unsupervised Concept Discovery for Interpretability in Medical VLMs

While medical Vision-Language models (VLMs) achieve strong performance on tasks such as tumor or organ segmentation and diagnosis prediction, their opaque latent representations limit clinical trust and the ability to explain predictions. Interpretability of these multimodal representations are therefore essential for the trustworthy clinical deployment of pretrained medical VLMs. However, current interpretability methods, such as gradient- or attention-based visualizations, are often limited to specific tasks such as classification. Moreover, they do not provide concept-level explanations derived from shared pretrained representations that can be reused across downstream tasks. We introduce MedConcept, a framework that uncovers latent medical concepts in a fully unsupervised manner and grounds them in clinically verifiable textual semantics. MedConcept identifies sparse neuron-level concept activations from pretrained VLM representations and translates them into pseudo-report-style summaries, enabling physician-level inspection of internal model reasoning. To address the lack of quantitative evaluation in concept-based interpretability, we introduce a quantitative semantic verification protocol that leverages an independent pretrained medical LLM as a frozen external evaluator to assess concept alignment with radiology reports. We define three concept scores, Aligned, Unaligned, and Uncertain, to quantify semantic support, contradiction, or ambiguity relative to radiology reports and use them exclusively for post hoc evaluation. These scores provide a quantitative baseline for assessing interpretability in medical VLMs. All codes, prompt and data to be released on acceptance. Ke

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MapVerse: A Benchmark for Geospatial Question Answering on Diverse Real-World Maps

Maps are powerful carriers of structured and contextual knowledge, encompassing geography, demographics, infrastructure, and environmental patterns. Reasoning over such knowledge requires models to integrate spatial relationships, visual cues, real-world context, and domain-specific expertise-capabilities that current large language models (LLMs) and vision-language models (VLMs) still struggle to exhibit consistently. Yet, datasets used to benchmark VLMs on map-based reasoning remain narrow in scope, restricted to specific domains, and heavily reliant on artificially generated content (outputs from LLMs or pipeline-based methods), offering limited depth for evaluating genuine geospatial reasoning. To address this gap, we present MapVerse, a large-scale benchmark built on real-world maps. It comprises 11,837 human-authored question-answer pairs across 1,025 maps, spanning ten diverse map categories and multiple question categories for each. The dataset provides a rich setting for evaluating map reading, interpretation, and multimodal reasoning. We evaluate ten state-of-the-art models against our benchmark to establish baselines and quantify reasoning gaps. Beyond overall performance, we conduct fine-grained categorical analyses to assess model inference across multiple dimensions and investigate the visual factors shaping reasoning outcomes. Our findings reveal that while current VLMs perform competitively on classification-style tasks, both open- and closed-source models fall short on advanced tasks requiring complex spatial reasoning.

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Building Trust in Virtual Immunohistochemistry: Automated Assessment of Image Quality

Deep learning models can generate virtual immunohistochemistry (IHC) stains from hematoxylin and eosin (H&E) images, offering a scalable and low-cost alternative to laboratory IHC. However, reliable evaluation of image quality remains a challenge as current texture- and distribution-based metrics quantify image fidelity rather than the accuracy of IHC staining. Here, we introduce an automated and accuracy grounded framework to determine image quality across sixteen paired or unpaired image translation models. Using color deconvolution, we generate masks of pixels stained brown (i.e., IHC-positive) as predicted by each virtual IHC model. We use the segmented masks of real and virtual IHC to compute stain accuracy metrics (Dice, IoU, Hausdorff distance) that directly quantify correct pixel - level labeling without needing expert manual annotations. Our results demonstrate that conventional image fidelity metrics, including Frechet Inception Distance (FID), peak signal-to-noise ratio (PSNR), and structural similarity (SSIM), correlate poorly with stain accuracy and pathologist assessment. Paired models such as PyramidPix2Pix and AdaptiveNCE achieve the highest stain accuracy, whereas unpaired diffusion- and GAN-based models are less reliable in providing accurate IHC positive pixel labels. Moreover, whole-slide images (WSI) reveal performance declines that are invisible in patch-based evaluations, emphasizing the need for WSI-level benchmarks. Together, this framework defines a reproducible approach for assessing the quality of virtual IHC models, a critical step to accelerate translation towards routine use by pathologists.

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StainDiffuser: MultiTask Dual Diffusion Model for Virtual Staining

Hematoxylin and Eosin (H&E) staining is widely regarded as the standard in pathology for diagnosing diseases and tracking tumor recurrence. While H&E staining shows tissue structures, it lacks the ability to reveal specific proteins that are associated with disease severity and treatment response. Immunohistochemical (IHC) stains use antibodies to highlight the expression of these proteins on their respective cell types, improving diagnostic accuracy, and assisting with drug selection for treatment. Despite their value, IHC stains require additional time and resources, limiting their utilization in some clinical settings. Recent advances in deep learning have positioned Image-to-Image (I2I) translation as a computational, cost-effective alternative for IHC. I2I generates high fidelity stain transformations digitally, potentially replacing manual staining in IHC. Diffusion models, the current state of the art in image generation and conditional tasks, are particularly well suited for virtual IHC due to their ability to produce high quality images and resilience to mode collapse. However, these models require extensive and diverse datasets (often millions of samples) to achieve a robust performance, a challenge in virtual staining applications where only thousands of samples are typically available. Inspired by the success of multitask deep learning models in scenarios with limited data, we introduce STAINDIFFUSER, a novel multitask diffusion architecture tailored to virtual staining that achieves convergence with smaller datasets. STAINDIFFUSER simultaneously trains two diffusion processes: (a) generating cell specific IHC stains from H&E images and (b) performing H&E based cell segmentation, utilizing coarse segmentation labels exclusively during training. STAINDIFFUSER generates high-quality virtual stains for two markers, outperforming over twenty I2I baselines.

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Leveraging LLM For Synchronizing Information Across Multilingual Tables

The vast amount of online information today poses challenges for non-English speakers, as much of it is concentrated in high-resource languages such as English and French. Wikipedia reflects this imbalance, with content in low-resource languages frequently outdated or incomplete. Recent research has sought to improve cross-language synchronization of Wikipedia tables using rule-based methods. These approaches can be effective, but they struggle with complexity and generalization. This paper explores large language models (LLMs) for multilingual information synchronization, using zero-shot prompting as a scalable solution. We introduce the Information Updation dataset, simulating the real-world process of updating outdated Wikipedia tables, and evaluate LLM performance. Our findings reveal that single-prompt approaches often produce suboptimal results, prompting us to introduce a task decomposition strategy that enhances coherence and accuracy. Our proposed method outperforms existing baselines, particularly in Information Updation (1.79%) and Information Addition (20.58%), highlighting the model strength in dynamically updating and enriching data across architectures.

cs.CL↗

TransientTables: Evaluating LLMs' Reasoning on Temporally Evolving Semi-structured Tables

Humans continuously make new discoveries, and understanding temporal sequence of events leading to these breakthroughs is essential for advancing science and society. This ability to reason over time allows us to identify future steps and understand the effects of financial and political decisions on our lives. However, large language models (LLMs) are typically trained on static datasets, limiting their ability to perform effective temporal reasoning. To assess the temporal reasoning capabilities of LLMs, we present the TRANSIENTTABLES dataset, which comprises 3,971 questions derived from over 14,000 tables, spanning 1,238 entities across multiple time periods. We introduce a template-based question-generation pipeline that harnesses LLMs to refine both templates and questions. Additionally, we establish baseline results using state-of-the-art LLMs to create a benchmark. We also introduce novel modeling strategies centered around task decomposition, enhancing LLM performance.

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NTSEBENCH: Cognitive Reasoning Benchmark for Vision Language Models

Cognitive textual and visual reasoning tasks, including puzzles, series, and analogies, demand the ability to quickly reason, decipher, and evaluate patterns both textually and spatially. Due to extensive training on vast amounts of human-curated data, LLMs and VLMs excel in common-sense reasoning tasks, however still struggle with more complex reasoning that demands deeper cognitive understanding. We introduce NTSEBench, a new dataset designed to evaluate cognitive multi-modal reasoning and problem-solving skills of large models. The dataset contains 2728 multiple-choice questions, accompanied by a total of 4,642 images, categorized into 26 different types. These questions are drawn from the nationwide NTSE examination in India and feature a mix of visual and textual general aptitude challenges, designed to assess intelligence and critical thinking skills beyond mere rote learning. We establish baselines on the dataset using state-of-the-art LLMs and VLMs. To facilitate a comparison between open source and propriety models, we propose four distinct modeling strategies to handle different modalities -- text and images -- in the dataset instances.

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Evaluating Concurrent Robustness of Language Models Across Diverse Challenge Sets

Language models, characterized by their black-box nature, often hallucinate and display sensitivity to input perturbations, causing concerns about trust. To enhance trust, it is imperative to gain a comprehensive understanding of the model's failure modes and develop effective strategies to improve their performance. In this study, we introduce a methodology designed to examine how input perturbations affect language models across various scales, including pre-trained models and large language models (LLMs). Utilizing fine-tuning, we enhance the model's robustness to input perturbations. Additionally, we investigate whether exposure to one perturbation enhances or diminishes the model's performance with respect to other perturbations. To address robustness against multiple perturbations, we present three distinct fine-tuning strategies. Furthermore, we broaden the scope of our methodology to encompass large language models (LLMs) by leveraging a chain of thought (CoT) prompting approach augmented with exemplars. We employ the Tabular-NLI task to showcase how our proposed strategies adeptly train a robust model, enabling it to address diverse perturbations while maintaining accuracy on the original dataset. https://msin-infotabs.github.io/

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EfficientMorph: Parameter-Efficient Transformer-Based Architecture for 3D Image Registration

Transformers have emerged as the state-of-the-art architecture in medical image registration, outperforming convolutional neural networks (CNNs) by addressing their limited receptive fields and overcoming gradient instability in deeper models. Despite their success, transformer-based models require substantial resources for training, including data, memory, and computational power, which may restrict their applicability for end users with limited resources. In particular, existing transformer-based 3D image registration architectures face two critical gaps that challenge their efficiency and effectiveness. Firstly, although window-based attention mechanisms reduce the quadratic complexity of full attention by focusing on local regions, they often struggle to effectively integrate both local and global information. Secondly, the granularity of tokenization, a crucial factor in registration accuracy, presents a performance trade-off: smaller voxel-size tokens enhance detail capture but come with increased computational complexity, higher memory usage, and a greater risk of overfitting. We present \name, a transformer-based architecture for unsupervised 3D image registration that balances local and global attention in 3D volumes through a plane-based attention mechanism and employs a Hi-Res tokenization strategy with merging operations, thus capturing finer details without compromising computational efficiency. Notably, \name sets a new benchmark for performance on the OASIS dataset with 16-27x fewer parameters. https://github.com/MedVIC-Lab/Efficient_Morph_Registration

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Estimation and Analysis of Slice Propagation Uncertainty in 3D Anatomy Segmentation

Supervised methods for 3D anatomy segmentation demonstrate superior performance but are often limited by the availability of annotated data. This limitation has led to a growing interest in self-supervised approaches in tandem with the abundance of available un-annotated data. Slice propagation has emerged as an self-supervised approach that leverages slice registration as a self-supervised task to achieve full anatomy segmentation with minimal supervision. This approach significantly reduces the need for domain expertise, time, and the cost associated with building fully annotated datasets required for training segmentation networks. However, this shift toward reduced supervision via deterministic networks raises concerns about the trustworthiness and reliability of predictions, especially when compared with more accurate supervised approaches. To address this concern, we propose the integration of calibrated uncertainty quantification (UQ) into slice propagation methods, providing insights into the model's predictive reliability and confidence levels. Incorporating uncertainty measures enhances user confidence in self-supervised approaches, thereby improving their practical applicability. We conducted experiments on three datasets for 3D abdominal segmentation using five UQ methods. The results illustrate that incorporating UQ improves not only model trustworthiness, but also segmentation accuracy. Furthermore, our analysis reveals various failure modes of slice propagation methods that might not be immediately apparent to end-users. This study opens up new research avenues to improve the accuracy and trustworthiness of slice propagation methods.

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