# Conformal Lesion Segmentation for 3D Medical Images

arXiv: https://arxiv.org/abs/2510.17897 · HTML: https://mlsanity.com/paper/2510.17897/

## Key facts

- Cited by 5 papers in the map (data through 14 Oct 2026).
- Builds on 15 of its 38 references that are in the map.
- First posted on arXiv 19 Oct 2025.

## Builds on (most cited first, 15 of 15)

- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [The Liver Tumor Segmentation Benchmark (LiTS)](https://mlsanity.com/paper/1901.04056/) (2019)
- [Med3D: Transfer Learning for 3D Medical Image Analysis](https://mlsanity.com/paper/1904.00625/) (2019)
- [Distribution-Free, Risk-Controlling Prediction Sets](https://mlsanity.com/paper/2101.02703/) (2021)
- [SAM-Med3D: Towards General-purpose Segmentation Models for Volumetric Medical Images](https://mlsanity.com/paper/2310.15161/) (2023)
- [The KiTS21 Challenge: Automatic segmentation of kidneys, renal tumors, and renal cysts in corticomedullary-phase CT](https://mlsanity.com/paper/2307.01984/) (2023)
- [ConU: Conformal Uncertainty in Large Language Models with Correctness Coverage Guarantees](https://mlsanity.com/paper/2407.00499/) (2024)
- [VISTA3D: A Unified Segmentation Foundation Model For 3D Medical Imaging](https://mlsanity.com/paper/2406.05285/) (2024)
- [A New 2.5D Representation for Lymph Node Detection using Random Sets of Deep Convolutional Neural Network Observations](https://mlsanity.com/paper/1406.2639/) (2014)
- [A survey on deep learning in medical image registration: new technologies, uncertainty, evaluation metrics, and beyond](https://mlsanity.com/paper/2307.15615/) (2023)
- [BrainSegFounder: Towards 3D Foundation Models for Neuroimage Segmentation](https://mlsanity.com/paper/2406.10395/) (2024)
- [The ULS23 Challenge: a Baseline Model and Benchmark Dataset for 3D Universal Lesion Segmentation in Computed Tomography](https://mlsanity.com/paper/2406.05231/) (2024)
- [COIN: Uncertainty-Guarding Selective Question Answering for Foundation Models with Provable Risk Guarantees](https://mlsanity.com/paper/2506.20178/) (2025)
- [Seeing and Reasoning with Confidence: Supercharging Multimodal LLMs with an Uncertainty-Aware Agentic Framework](https://mlsanity.com/paper/2503.08308/) (2025)
- [Deep Learning for Pancreas Segmentation: a Systematic Review](https://mlsanity.com/paper/2407.16313/) (2024)

## Built on by (most cited first, 5 of 5)

- [LEC: Linear Expectation Constraints for Selection-Conditioned Risk Control in Selective Prediction and Routing Systems](https://mlsanity.com/paper/2512.01556/) (2025)
- [Set-Valued Prediction for Large Language Models with Feasibility-Aware Coverage Guarantees](https://mlsanity.com/paper/2603.22966/) (2026)
- [MiRD: Reliable Set-Valued Prediction for Open-Ended Question Answering via Miscoverage Risk Decomposition](https://mlsanity.com/paper/2605.27091/) (2026)
- [Hierarchical Spatio-Temporal Attention Network with Adaptive Risk-Aware Decision for Forward Collision Warning in Complex Scenarios](https://mlsanity.com/paper/2511.19952/) (2025)
- [Asymptotic Risk Calibration for Selective Question Answering](https://mlsanity.com/paper/2608.12008/) (2026)

## Abstract (arXiv)

Medical image segmentation serves as a critical component of precision medicine, enabling accurate localization and delineation of pathological regions, such as lesions. However, existing models empirically apply fixed thresholds (e.g., 0.5) to differentiate lesions from the background, offering no statistical guarantees on key metrics such as the false negative rate (FNR). This lack of principled risk control undermines their reliable deployment in high-stakes clinical applications, especially in challenging scenarios like 3D lesion segmentation (3D-LS). To address this issue, we propose a risk-constrained framework, termed Conformal Lesion Segmentation (CLS), that calibrates data-driven thresholds via conformalization to ensure the test-time FNR remains below a target tolerance varepsilon under desired risk levels. CLS begins by holding out a calibration set to analyze the threshold setting for each sample under the FNR tolerance, drawing on the idea of conformal prediction. We define an FNR-specific loss function and identify the critical threshold at which each calibration data point just satisfies the target tolerance. Given a user-specified risk level α, we then determine the approximate 1-α quantile of all the critical thresholds in the calibration set as the test-time confidence threshold. By conformalizing such critical thresholds, CLS generalizes the statistical regularities observed in the calibration set to new test data, providing rigorous FNR constraint while yielding more precise and reliable segmentations. We validate the statistical soundness and predictive performance of CLS on six 3D-LS datasets across five backbone models, and conclude with actionable insights for deploying risk-aware segmentation in clinical practice.