Tian Xia

Pedro Sanchez, Jeremy P. Voisey, Tian Xia et al.

Causal machine learning (CML) has experienced increasing popularity in healthcare. Beyond the inherent capabilities of adding domain knowledge into learning systems, CML provides a complete toolset for investigating how a system would react to an intervention (e.g.\ outcome given a treatment). Quantifying effects of interventions allows actionable decisions to be made whilst maintaining robustness in the presence of confounders. Here, we explore how causal inference can be incorporated into different aspects of clinical decision support (CDS) systems by using recent advances in machine learning. Throughout this paper, we use Alzheimer's disease (AD) to create examples for illustrating how CML can be advantageous in clinical scenarios. Furthermore, we discuss important challenges present in healthcare applications such as processing high-dimensional and unstructured data, generalisation to out-of-distribution samples, and temporal relationships, that despite the great effort from the research community remain to be solved. Finally, we review lines of research within causal representation learning, causal discovery and causal reasoning which offer the potential towards addressing the aforementioned challenges.

Tian Xia, Pedro Sanchez, Chen Qin et al.

Due to the limited availability of medical data, deep learning approaches for medical image analysis tend to generalise poorly to unseen data. Augmenting data during training with random transformations has been shown to help and became a ubiquitous technique for training neural networks. Here, we propose a novel adversarial counterfactual augmentation scheme that aims at finding the most \textit{effective} synthesised images to improve downstream tasks, given a pre-trained generative model. Specifically, we construct an adversarial game where we update the input \textit{conditional factor} of the generator and the downstream \textit{classifier} with gradient backpropagation alternatively and iteratively. This can be viewed as finding the `\textit{weakness}' of the classifier and purposely forcing it to \textit{overcome} its weakness via the generative model. To demonstrate the effectiveness of the proposed approach, we validate the method with the classification of Alzheimer's Disease (AD) as a downstream task. The pre-trained generative model synthesises brain images using age as conditional factor. Extensive experiments and ablation studies have been performed to show that the proposed approach improves classification performance and has potential to alleviate spurious correlations and catastrophic forgetting. Code will be released upon acceptance.

Wei Peng, Tian Xia, Fabio De Sousa Ribeiro et al.

The number of samples in structural brain MRI studies is often too small to properly train deep learning models. Generative models show promise in addressing this issue by effectively learning the data distribution and generating high-fidelity MRI. However, they struggle to produce diverse, high-quality data outside the distribution defined by the training data. One way to address this issue is to use causal models developed for 3D volume counterfactuals. However, accurately modeling causality in high-dimensional spaces is challenging, so these models generally generate 3D brain MRIs of lower quality. To address these challenges, we propose a two-stage method that constructs a Structural Causal Model (SCM) within the latent space. In the first stage, we employ a VQ-VAE to learn a compact embedding of the MRI volume. Subsequently, we integrate our causal model into this latent space and execute a three-step counterfactual procedure using a closed-form Generalized Linear Model (GLM). Our experiments conducted on real-world high-resolution MRI data (1 mm) provided by the Alzheimer's Disease Neuroimaging Initiative (ADNI) and the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA) demonstrate that our method can generate high-quality 3D MRI counterfactuals.

Ke Ma, Yizhou Fang, Jean-Baptiste Weibel et al.

Estimating the geometric and volumetric properties of transparent deformable liquids is challenging due to optical complexities and dynamic surface deformations induced by container movements. Autonomous robots performing precise liquid manipulation tasks, such as dispensing, aspiration, and mixing, must handle containers in ways that inevitably induce these deformations, complicating accurate liquid state assessment. Current datasets lack comprehensive physics-informed simulation data representing realistic liquid behaviors under diverse dynamic scenarios. To bridge this gap, we introduce Phys-Liquid, a physics-informed dataset comprising 97,200 simulation images and corresponding 3D meshes, capturing liquid dynamics across multiple laboratory scenes, lighting conditions, liquid colors, and container rotations. To validate the realism and effectiveness of Phys-Liquid, we propose a four-stage reconstruction and estimation pipeline involving liquid segmentation, multi-view mask generation, 3D mesh reconstruction, and real-world scaling. Experimental results demonstrate improved accuracy and consistency in reconstructing liquid geometry and volume, outperforming existing benchmarks. The dataset and associated validation methods facilitate future advancements in transparent liquid perception tasks. The dataset and code are available at https://dualtransparency.github.io/Phys-Liquid/.

Tian Xia, Matthew Sinclair, Andreas Schuh et al.

Counterfactual image generation is a powerful tool for augmenting training data, de-biasing datasets, and modeling disease. Current approaches rely on external classifiers or regressors to increase the effectiveness of subject-level interventions (e.g., changing the patient's age). For structure-specific interventions (e.g., changing the area of the left lung in a chest radiograph), we show that this is insufficient, and can result in undesirable global effects across the image domain. Previous work used pixel-level label maps as guidance, requiring a user to provide hypothetical segmentations which are tedious and difficult to obtain. We propose Segmentor-guided Counterfactual Fine-Tuning (Seg-CFT), which preserves the simplicity of intervening on scalar-valued, structure-specific variables while producing locally coherent and effective counterfactuals. We demonstrate the capability of generating realistic chest radiographs, and we show promising results for modeling coronary artery disease. Code: https://github.com/biomedia-mira/seg-cft.

Melanie Roschewitz, Fabio De Sousa Ribeiro, Tian Xia et al.

Contrastive pretraining is well-known to improve downstream task performance and model generalisation, especially in limited label settings. However, it is sensitive to the choice of augmentation pipeline. Positive pairs should preserve semantic information while destroying domain-specific information. Standard augmentation pipelines emulate domain-specific changes with pre-defined photometric transformations, but what if we could simulate realistic domain changes instead? In this work, we show how to utilise recent progress in counterfactual image generation to this effect. We propose CF-SimCLR, a counterfactual contrastive learning approach which leverages approximate counterfactual inference for positive pair creation. Comprehensive evaluation across five datasets, on chest radiography and mammography, demonstrates that CF-SimCLR substantially improves robustness to acquisition shift with higher downstream performance on both in- and out-of-distribution data, particularly for domains which are under-represented during training.

Xiang Bai, Hanchen Wang, Liya Ma et al.

Artificial intelligence (AI) provides a promising substitution for streamlining COVID-19 diagnoses. However, concerns surrounding security and trustworthiness impede the collection of large-scale representative medical data, posing a considerable challenge for training a well-generalised model in clinical practices. To address this, we launch the Unified CT-COVID AI Diagnostic Initiative (UCADI), where the AI model can be distributedly trained and independently executed at each host institution under a federated learning framework (FL) without data sharing. Here we show that our FL model outperformed all the local models by a large yield (test sensitivity /specificity in China: 0.973/0.951, in the UK: 0.730/0.942), achieving comparable performance with a panel of professional radiologists. We further evaluated the model on the hold-out (collected from another two hospitals leaving out the FL) and heterogeneous (acquired with contrast materials) data, provided visual explanations for decisions made by the model, and analysed the trade-offs between the model performance and the communication costs in the federated training process. Our study is based on 9,573 chest computed tomography scans (CTs) from 3,336 patients collected from 23 hospitals located in China and the UK. Collectively, our work advanced the prospects of utilising federated learning for privacy-preserving AI in digital health.