Causal Machine Learning for Healthcare and Precision Medicine

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.

Adversarial Counterfactual Augmentation: Application in Alzheimer's Disease Classification

Data augmentation has been widely used in deep learning to reduce over-fitting and improve the robustness of models. However, traditional data augmentation techniques, e.g., rotation, cropping, flipping, etc., do not consider \textit{semantic} transformations, e.g., changing the age of a brain image. Previous works tried to achieve semantic augmentation by generating \textit{counterfactuals}, but they focused on how to train deep generative models and randomly created counterfactuals with the generative models without considering which counterfactuals are most \textit{effective} for improving downstream training. Different from these approaches, in this work, we propose a novel adversarial counterfactual augmentation scheme that aims to find the most \textit{effective} counterfactuals to improve downstream tasks with 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. The key idea is to find conditional factors that can result in \textit{hard} counterfactuals for the classifier. 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 the downstream task based on a pre-trained brain ageing synthesis model. We show the proposed approach improves test accuracy and can alleviate spurious correlations. Code will be released upon acceptance.

Augmented Reality and Robotics: A Survey and Taxonomy for AR-enhanced Human-Robot Interaction and Robotic Interfaces

This paper contributes to a taxonomy of augmented reality and robotics based on a survey of 460 research papers. Augmented and mixed reality (AR/MR) have emerged as a new way to enhance human-robot interaction (HRI) and robotic interfaces (e.g., actuated and shape-changing interfaces). Recently, an increasing number of studies in HCI, HRI, and robotics have demonstrated how AR enables better interactions between people and robots. However, often research remains focused on individual explorations and key design strategies, and research questions are rarely analyzed systematically. In this paper, we synthesize and categorize this research field in the following dimensions: 1) approaches to augmenting reality; 2) characteristics of robots; 3) purposes and benefits; 4) classification of presented information; 5) design components and strategies for visual augmentation; 6) interaction techniques and modalities; 7) application domains; and 8) evaluation strategies. We formulate key challenges and opportunities to guide and inform future research in AR and robotics.

Advancing COVID-19 Diagnosis with Privacy-Preserving Collaboration in Artificial Intelligence

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.

Deep Multi-attribute Graph Representation Learning on Protein Structures

Graphs as a type of data structure have recently attracted significant attention. Representation learning of geometric graphs has achieved great success in many fields including molecular, social, and financial networks. It is natural to present proteins as graphs in which nodes represent the residues and edges represent the pairwise interactions between residues. However, 3D protein structures have rarely been studied as graphs directly. The challenges include: 1) Proteins are complex macromolecules composed of thousands of atoms making them much harder to model than micro-molecules. 2) Capturing the long-range pairwise relations for protein structure modeling remains under-explored. 3) Few studies have focused on learning the different attributes of proteins together. To address the above challenges, we propose a new graph neural network architecture to represent the proteins as 3D graphs and predict both distance geometric graph representation and dihedral geometric graph representation together. This gives a significant advantage because this network opens a new path from the sequence to structure. We conducted extensive experiments on four different datasets and demonstrated the effectiveness of the proposed method.

Pseudo-healthy synthesis with pathology disentanglement and adversarial learning

Pseudo-healthy synthesis is the task of creating a subject-specific `healthy' image from a pathological one. Such images can be helpful in tasks such as anomaly detection and understanding changes induced by pathology and disease. In this paper, we present a model that is encouraged to disentangle the information of pathology from what seems to be healthy. We disentangle what appears to be healthy and where disease is as a segmentation map, which are then recombined by a network to reconstruct the input disease image. We train our models adversarially using either paired or unpaired settings, where we pair disease images and maps when available. We quantitatively and subjectively, with a human study, evaluate the quality of pseudo-healthy images using several criteria. We show in a series of experiments, performed on ISLES, BraTS and Cam-CAN datasets, that our method is better than several baselines and methods from the literature. We also show that due to better training processes we could recover deformations, on surrounding tissue, caused by disease. Our implementation is publicly available at \url{https://tobeprovided.upon.acceptance}

AlignTTS: Efficient Feed-Forward Text-to-Speech System without Explicit Alignment

Targeting at both high efficiency and performance, we propose AlignTTS to predict the mel-spectrum in parallel. AlignTTS is based on a Feed-Forward Transformer which generates mel-spectrum from a sequence of characters, and the duration of each character is determined by a duration predictor.Instead of adopting the attention mechanism in Transformer TTS to align text to mel-spectrum, the alignment loss is presented to consider all possible alignments in training by use of dynamic programming. Experiments on the LJSpeech dataset show that our model achieves not only state-of-the-art performance which outperforms Transformer TTS by 0.03 in mean option score (MOS), but also a high efficiency which is more than 50 times faster than real-time.

Learning to synthesise the ageing brain without longitudinal data

Brain ageing is a continuous process that is affected by many factors including neurodegenerative diseases. Understanding this process is of great value for both neuroscience research and clinical applications. However, revealing underlying mechanisms is challenging due to the lack of longitudinal data. In this paper, we propose a deep learning-based method that learns to simulate subject-specific brain ageing trajectories without relying on longitudinal data. Our method synthesises aged images using a network conditioned on two clinical variables: age as a continuous variable, and health state, i.e. status of Alzheimer's Disease (AD) for this work, as an ordinal variable. We adopt an adversarial loss to learn the joint distribution of brain appearance and clinical variables and define reconstruction losses that help preserve subject identity. To demonstrate our model, we compare with several approaches using two widely used datasets: Cam-CAN and ADNI. We use ground-truth longitudinal data from ADNI to evaluate the quality of synthesised images. A pre-trained age predictor, which estimates the apparent age of a brain image, is used to assess age accuracy. In addition, we show that we can train the model on Cam-CAN data and evaluate on the longitudinal data from ADNI, indicating the generalisation power of our approach. Both qualitative and quantitative results show that our method can progressively simulate the ageing process by synthesising realistic brain images. The code will be made publicly available at: https://github.com/xiat0616/BrainAgeing.