# Towards Whole-Study Screening for Congenital Heart Disease in Fetal Ultrasound Using Multiple Instance Learning

arXiv: https://arxiv.org/abs/2609.31376 · HTML: https://mlsanity.com/paper/2609.31376/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 29 of its 68 references that are in the map.
- First posted on arXiv 25 Sep 2026.

## Builds on (most cited first, 29 of 29)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [SGDR: Stochastic Gradient Descent with Warm Restarts](https://mlsanity.com/paper/1608.03983/) (2016)
- [On Calibration of Modern Neural Networks](https://mlsanity.com/paper/1706.04599/) (2017)
- [Gaussian Error Linear Units (GELUs)](https://mlsanity.com/paper/1606.08415/) (2016)
- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [Unsupervised Domain Adaptation by Backpropagation](https://mlsanity.com/paper/1409.7495/) (2014)
- [Deep CORAL: Correlation Alignment for Deep Domain Adaptation](https://mlsanity.com/paper/1607.01719/) (2016)
- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [Data Efficient and Weakly Supervised Computational Pathology on Whole Slide Images](https://mlsanity.com/paper/2004.09666/) (2020)
- [TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classification](https://mlsanity.com/paper/2106.00908/) (2021)
- [Dual-stream Multiple Instance Learning Network for Whole Slide Image Classification with Self-supervised Contrastive Learning](https://mlsanity.com/paper/2011.08939/) (2020)
- [Revisiting Multiple Instance Neural Networks](https://mlsanity.com/paper/1610.02501/) (2016)
- [SonoNet: Real-Time Detection and Localisation of Fetal Standard Scan Planes in Freehand Ultrasound](https://mlsanity.com/paper/1612.05601/) (2016)
- [Additive MIL: Intrinsically Interpretable Multiple Instance Learning for Pathology](https://mlsanity.com/paper/2206.01794/) (2022)
- [DGMIL: Distribution Guided Multiple Instance Learning for Whole Slide Image Classification](https://mlsanity.com/paper/2206.08861/) (2022)
- [A Review on Deep-Learning Algorithms for Fetal Ultrasound-Image Analysis](https://mlsanity.com/paper/2201.12260/) (2022)
- [FetalCLIP: A Visual-Language Foundation Model for Fetal Ultrasound Image Analysis](https://mlsanity.com/paper/2502.14807/) (2025)
- [A novel multiple instance learning framework for COVID-19 severity assessment via data augmentation and self-supervised learning](https://mlsanity.com/paper/2102.03837/) (2021)
- [Shortcut Learning in Medical Image Segmentation](https://mlsanity.com/paper/2403.06748/) (2024)
- [Generalisability of fetal ultrasound deep learning models to low-resource imaging settings in five African countries](https://mlsanity.com/paper/2209.09610/) (2022)
- [Ordinal Multiple-instance Learning for Ulcerative Colitis Severity Estimation with Selective Aggregated Transformer](https://mlsanity.com/paper/2411.14750/) (2024)
- [Automated Detection of Congenital Heart Disease in Fetal Ultrasound Screening](https://mlsanity.com/paper/2008.06966/) (2020)
- [Semi-Supervised Multimodal Multi-Instance Learning for Aortic Stenosis Diagnosis](https://mlsanity.com/paper/2403.06024/) (2024)
- [Medical-Knowledge Driven Multiple Instance Learning for Classifying Severe Abdominal Anomalies on Prenatal Ultrasound](https://mlsanity.com/paper/2507.01401/) (2025)
- [A multi-centre, multi-device benchmark dataset for landmark-based comprehensive fetal biometry](https://mlsanity.com/paper/2512.16710/) (2025)
- [CARDIUM: Congenital Anomaly Recognition with Diagnostic Images and Unified Medical records](https://mlsanity.com/paper/2510.15208/) (2025)
- [QG-MIL: A Gated Transformer Aggregator for Domain-Agnostic Multiple Instance Learning in Medical Imaging](https://mlsanity.com/paper/2606.20027/) (2026)

## Abstract (arXiv)

Congenital heart disease (CHD) is the most common birth defect, yet a large fraction of cases remain undetected on prenatal ultrasound, in part because current artificial-intelligence methods assume that the key diagnostic frames have already been isolated from a study, by a clinician or by a view classifier. We remove that assumption and address CHD screening directly at the level of the whole ultrasound study. We propose a two-stage framework that first learns transferable frame representations by self-supervised masked-autoencoder pre-training on unlabeled fetal ultrasound, then identifies cardiac frames with a disease-robust module and aggregates them with a transformer-based multiple instance learning (MIL) model that produces a case-level diagnosis from study-level labels alone. The model further returns its highest-scoring frames for clinician review, and a hierarchical head separates critical from non-critical CHD. On the internal test set of our multi-source development cohort (FUSE), the proposed cardiac-gated MIL model reaches an area under the curve (AUC) of 0.985 with a specificity of 0.990, outperforming the reproduced NATMED ensemble (AUC 0.861, specificity 0.600) and the FetalCLIP foundation model (AUC 0.867, specificity 0.710). On an independent external cohort, all models initially perform near chance, but label-free CORAL adaptation raises the proposed model from an AUC of 0.513 to 0.944, whereas whole-study and view-dependent baselines do not recover. These results indicate that whole-study MIL with disease-robust cardiac-frame identification is an accurate and deployable route to prenatal CHD screening.