# Weakly Supervised AI for Efficient Analysis of 3D Pathology Samples

arXiv: https://arxiv.org/abs/2307.14907 · HTML: https://mlsanity.com/paper/2307.14907/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Mamba for medical image analysis, one of 10 directions in State-space sequence models (S4, Mamba).
- Builds on 14 of its 61 references that are in the map.
- First posted on arXiv 27 Jul 2023.

## Placed in

- State-space sequence models (S4, Mamba) / [Mamba for medical image analysis](https://mlsanity.com/ssm/mamba-for-medical-image-analysis/)

## Builds on (most cited first, 14 of 14)

- [Axiomatic Attribution for Deep Networks](https://mlsanity.com/paper/1703.01365/) (2017)
- [Quo Vadis, Action Recognition? A New Model and the Kinetics Dataset](https://mlsanity.com/paper/1705.07750/) (2017)
- [A Closer Look at Spatiotemporal Convolutions for Action Recognition](https://mlsanity.com/paper/1711.11248/) (2017)
- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [Video Swin Transformer](https://mlsanity.com/paper/2106.13230/) (2021)
- [Data Efficient and Weakly Supervised Computational Pathology on Whole Slide Images](https://mlsanity.com/paper/2004.09666/) (2020)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [Efficient Multi-Scale 3D CNN with Fully Connected CRF for Accurate Brain Lesion Segmentation](https://mlsanity.com/paper/1603.05959/) (2016)
- [3D Self-Supervised Methods for Medical Imaging](https://mlsanity.com/paper/2006.03829/) (2020)
- [Deep Learning-based Computational Pathology Predicts Origins for Cancers of Unknown Primary](https://mlsanity.com/paper/2006.13932/) (2020)
- [Automated Gleason Grading of Prostate Biopsies using Deep Learning](https://mlsanity.com/paper/1907.07980/) (2019)
- [Video Transformers: A Survey](https://mlsanity.com/paper/2201.05991/) (2022)
- [X-CAL: Explicit Calibration for Survival Analysis](https://mlsanity.com/paper/2101.05346/) (2021)
- [Robust breast cancer detection in mammography and digital breast tomosynthesis using annotation-efficient deep learning approach](https://mlsanity.com/paper/1912.11027/) (2019)

## Abstract (arXiv)

Human tissue and its constituent cells form a microenvironment that is fundamentally three-dimensional (3D). However, the standard-of-care in pathologic diagnosis involves selecting a few two-dimensional (2D) sections for microscopic evaluation, risking sampling bias and misdiagnosis. Diverse methods for capturing 3D tissue morphologies have been developed, but they have yet had little translation to clinical practice; manual and computational evaluations of such large 3D data have so far been impractical and/or unable to provide patient-level clinical insights. Here we present Modality-Agnostic Multiple instance learning for volumetric Block Analysis (MAMBA), a deep-learning-based platform for processing 3D tissue images from diverse imaging modalities and predicting patient outcomes. Archived prostate cancer specimens were imaged with open-top light-sheet microscopy or microcomputed tomography and the resulting 3D datasets were used to train risk-stratification networks based on 5-year biochemical recurrence outcomes via MAMBA. With the 3D block-based approach, MAMBA achieves an area under the receiver operating characteristic curve (AUC) of 0.86 and 0.74, superior to 2D traditional single-slice-based prognostication (AUC of 0.79 and 0.57), suggesting superior prognostication with 3D morphological features. Further analyses reveal that the incorporation of greater tissue volume improves prognostic performance and mitigates risk prediction variability from sampling bias, suggesting the value of capturing larger extents of heterogeneous 3D morphology. With the rapid growth and adoption of 3D spatial biology and pathology techniques by researchers and clinicians, MAMBA provides a general and efficient framework for 3D weakly supervised learning for clinical decision support and can help to reveal novel 3D morphological biomarkers for prognosis and therapeutic response.