Benchmarking Counterfactual Image Generation

Counterfactual image generation is pivotal for understanding the causal relations of variables, with applications in interpretability and generation of unbiased synthetic data. However, evaluating image generation is a long-standing challenge in itself. The need to evaluate counterfactual generation compounds on this challenge, precisely because counterfactuals, by definition, are hypothetical scenarios without observable ground truths. In this paper, we present a novel comprehensive framework aimed at benchmarking counterfactual image generation methods. We incorporate metrics that focus on evaluating diverse aspects of counterfactuals, such as composition, effectiveness, minimality of interventions, and image realism. We assess the performance of three distinct conditional image generation model types, based on the Structural Causal Model paradigm. Our work is accompanied by a user-friendly Python package which allows to further evaluate and benchmark existing and future counterfactual image generation methods. Our framework is extendable to additional SCM and other causal methods, generative models, and datasets.

Non-parametric identifiability and sensitivity analysis of synthetic control models

Quantifying cause and effect relationships is an important problem in many domains. The gold standard solution is to conduct a randomised controlled trial. However, in many situations such trials cannot be performed. In the absence of such trials, many methods have been devised to quantify the causal impact of an intervention from observational data given certain assumptions. One widely used method are synthetic control models. While identifiability of the causal estimand in such models has been obtained from a range of assumptions, it is widely and implicitly assumed that the underlying assumptions are satisfied for all time periods both pre- and post-intervention. This is a strong assumption, as synthetic control models can only be learned in pre-intervention period. In this paper we address this challenge, and prove identifiability can be obtained without the need for this assumption, by showing it follows from the principle of invariant causal mechanisms. Moreover, for the first time, we formulate and study synthetic control models in Pearl's structural causal model framework. Importantly, we provide a general framework for sensitivity analysis of synthetic control causal inference to violations of the assumptions underlying non-parametric identifiability. We end by providing an empirical demonstration of our sensitivity analysis framework on simulated and real data in the widely-used linear synthetic control framework.

Self-Supervised 3D Human Pose Estimation in Static Video Via Neural Rendering

Inferring 3D human pose from 2D images is a challenging and long-standing problem in the field of computer vision with many applications including motion capture, virtual reality, surveillance or gait analysis for sports and medicine. We present preliminary results for a method to estimate 3D pose from 2D video containing a single person and a static background without the need for any manual landmark annotations. We achieve this by formulating a simple yet effective self-supervision task: our model is required to reconstruct a random frame of a video given a frame from another timepoint and a rendered image of a transformed human shape template. Crucially for optimisation, our ray casting based rendering pipeline is fully differentiable, enabling end to end training solely based on the reconstruction task.

Adnexal Mass Segmentation with Ultrasound Data Synthesis

Ovarian cancer is the most lethal gynaecological malignancy. The disease is most commonly asymptomatic at its early stages and its diagnosis relies on expert evaluation of transvaginal ultrasound images. Ultrasound is the first-line imaging modality for characterising adnexal masses, it requires significant expertise and its analysis is subjective and labour-intensive, therefore open to error. Hence, automating processes to facilitate and standardise the evaluation of scans is desired in clinical practice. Using supervised learning, we have demonstrated that segmentation of adnexal masses is possible, however, prevalence and label imbalance restricts the performance on under-represented classes. To mitigate this we apply a novel pathology-specific data synthesiser. We create synthetic medical images with their corresponding ground truth segmentations by using Poisson image editing to integrate less common masses into other samples. Our approach achieves the best performance across all classes, including an improvement of up to 8% when compared with nnU-Net baseline approaches.

nnOOD: A Framework for Benchmarking Self-supervised Anomaly Localisation Methods

The wide variety of in-distribution and out-of-distribution data in medical imaging makes universal anomaly detection a challenging task. Recently a number of self-supervised methods have been developed that train end-to-end models on healthy data augmented with synthetic anomalies. However, it is difficult to compare these methods as it is not clear whether gains in performance are from the task itself or the training pipeline around it. It is also difficult to assess whether a task generalises well for universal anomaly detection, as they are often only tested on a limited range of anomalies. To assist with this we have developed nnOOD, a framework that adapts nnU-Net to allow for comparison of self-supervised anomaly localisation methods. By isolating the synthetic, self-supervised task from the rest of the training process we perform a more faithful comparison of the tasks, whilst also making the workflow for evaluating over a given dataset quick and easy. Using this we have implemented the current state-of-the-art tasks and evaluated them on a challenging X-ray dataset.

A Review of Causality for Learning Algorithms in Medical Image Analysis

Medical image analysis is a vibrant research area that offers doctors and medical practitioners invaluable insight and the ability to accurately diagnose and monitor disease. Machine learning provides an additional boost for this area. However, machine learning for medical image analysis is particularly vulnerable to natural biases like domain shifts that affect algorithmic performance and robustness. In this paper we analyze machine learning for medical image analysis within the framework of Technology Readiness Levels and review how causal analysis methods can fill a gap when creating robust and adaptable medical image analysis algorithms. We review methods using causality in medical imaging AI/ML and find that causal analysis has the potential to mitigate critical problems for clinical translation but that uptake and clinical downstream research has been limited so far.

Is More Data All You Need? A Causal Exploration

Curating a large scale medical imaging dataset for machine learning applications is both time consuming and expensive. Balancing the workload between model development, data collection and annotations is difficult for machine learning practitioners, especially under time constraints. Causal analysis is often used in medicine and economics to gain insights about the effects of actions and policies. In this paper we explore the effect of dataset interventions on the output of image classification models. Through a causal approach we investigate the effects of the quantity and type of data we need to incorporate in a dataset to achieve better performance for specific subtasks. The main goal of this paper is to highlight the potential of causal analysis as a tool for resource optimization for developing medical imaging ML applications. We explore this concept with a synthetic dataset and an exemplary use-case for Diabetic Retinopathy image analysis.

D'ARTAGNAN: Counterfactual Video Generation

Causally-enabled machine learning frameworks could help clinicians to identify the best course of treatments by answering counterfactual questions. We explore this path for the case of echocardiograms by looking into the variation of the Left Ventricle Ejection Fraction, the most essential clinical metric gained from these examinations. We combine deep neural networks, twin causal networks and generative adversarial methods for the first time to build D'ARTAGNAN (Deep ARtificial Twin-Architecture GeNerAtive Networks), a novel causal generative model. We demonstrate the soundness of our approach on a synthetic dataset before applying it to cardiac ultrasound videos by answering the question: "What would this echocardiogram look like if the patient had a different ejection fraction?". To do so, we generate new ultrasound videos, retaining the video style and anatomy of the original patient, with variations of the Ejection Fraction conditioned on a given input. We achieve an SSIM score of 0.79 and an R2 score of 0.51 on the counterfactual videos. Code and models are available at https://github.com/HReynaud/dartagnan.

Estimating the probabilities of causation via deep monotonic twin networks

There has been much recent work using machine learning to answer causal queries. Most focus on interventional queries, such as the conditional average treatment effect. However, as noted by Pearl, interventional queries only form part of a larger hierarchy of causal queries, with counterfactuals sitting at the top. Despite this, our community has not fully succeeded in adapting machine learning tools to answer counterfactual queries. This work addresses this challenge by showing how to implement twin network counterfactual inference -- an alternative to abduction, action, & prediction counterfactual inference -- with deep learning to estimate counterfactual queries. We show how the graphical nature of twin networks makes them particularly amenable to deep learning, yielding simple neural network architectures that, when trained, are capable of counterfactual inference. Importantly, we show how to enforce known identifiability constraints during training, ensuring the answer to each counterfactual query is uniquely determined. We demonstrate our approach by using it to accurately estimate the probabilities of causation -- important counterfactual queries that quantify the degree to which one event was a necessary or sufficient cause of another -- on both synthetic and real data.

Detecting Hypo-plastic Left Heart Syndrome in Fetal Ultrasound via Disease-specific Atlas Maps

Fetal ultrasound screening during pregnancy plays a vital role in the early detection of fetal malformations which have potential long-term health impacts. The level of skill required to diagnose such malformations from live ultrasound during examination is high and resources for screening are often limited. We present an interpretable, atlas-learning segmentation method for automatic diagnosis of Hypo-plastic Left Heart Syndrome (HLHS) from a single `4 Chamber Heart' view image. We propose to extend the recently introduced Image-and-Spatial Transformer Networks (Atlas-ISTN) into a framework that enables sensitising atlas generation to disease. In this framework we can jointly learn image segmentation, registration, atlas construction and disease prediction while providing a maximum level of clinical interpretability compared to direct image classification methods. As a result our segmentation allows diagnoses competitive with expert-derived manual diagnosis and yields an AUC-ROC of 0.978 (1043 cases for training, 260 for validation and 325 for testing).