Athanasios Vlontzos

Hadrien Reynaud, Athanasios Vlontzos, Mischa Dombrowski et al.

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 to answer 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, while modifying 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.

Athanasios Vlontzos, Daniel Rueckert, Bernhard Kainz

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.

Matthew Baugh, Jeremy Tan, Athanasios Vlontzos et al.

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.

Clara Lebbos, Jen Barcroft, Jeremy Tan et al.

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.

Luca Schmidtke, Benjamin Hou, Athanasios Vlontzos et al.

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.

Jakob Zeitler, Athanasios Vlontzos, Ciaran M. Gilligan-Lee

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.

Thomas Melistas, Nikos Spyrou, Nefeli Gkouti et al.

Generative AI has revolutionised visual content editing, empowering users to effortlessly modify images and videos. However, not all edits are equal. To perform realistic edits in domains such as natural image or medical imaging, modifications must respect causal relationships inherent to the data generation process. Such image editing falls into the counterfactual image generation regime. Evaluating counterfactual image generation is substantially complex: not only it lacks observable ground truths, but also requires adherence to causal constraints. Although several counterfactual image generation methods and evaluation metrics exist, a comprehensive comparison within a unified setting is lacking. We present a comparison framework to thoroughly benchmark counterfactual image generation methods. We integrate all models that have been used for the task at hand and expand them to novel datasets and causal graphs, demonstrating the superiority of Hierarchical VAEs across most datasets and metrics. Our framework is implemented in a user-friendly Python package that can be extended to incorporate additional SCMs, causal methods, generative models, and datasets for the community to build on. Code: https://github.com/gulnazaki/counterfactual-benchmark.

Athanasios Vlontzos, Hadrien Reynaud, Bernhard Kainz

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.

Jake Fawkes, Michael O'Riordan, Athanasios Vlontzos et al.

Observational data is often readily available in large quantities, but can lead to biased causal effect estimates due to the presence of unobserved confounding. Recent works attempt to remove this bias by supplementing observational data with experimental data, which, when available, is typically on a smaller scale due to the time and cost involved in running a randomised controlled trial. In this work, we prove a theorem that places fundamental limits on this ``best of both worlds'' approach. Using the framework of impossible inference, we show that although it is possible to use experimental data to \emph{falsify} causal effect estimates from observational data, in general it is not possible to \emph{validate} such estimates. Our theorem proves that while experimental data can be used to detect bias in observational studies, without additional assumptions on the smoothness of the correction function, it can not be used to remove it. We provide a practical example of such an assumption, developing a novel Gaussian Process based approach to construct intervals which contain the true treatment effect with high probability, both inside and outside of the support of the experimental data. We demonstrate our methodology on both simulated and semi-synthetic datasets and make the \href{https://github.com/Jakefawkes/Obs_and_exp_data}{code available}.

Hadrien Reynaud, Athanasios Vlontzos, Benjamin Hou et al.

Cardiac ultrasound imaging is used to diagnose various heart diseases. Common analysis pipelines involve manual processing of the video frames by expert clinicians. This suffers from intra- and inter-observer variability. We propose a novel approach to ultrasound video analysis using a transformer architecture based on a Residual Auto-Encoder Network and a BERT model adapted for token classification. This enables videos of any length to be processed. We apply our model to the task of End-Systolic (ES) and End-Diastolic (ED) frame detection and the automated computation of the left ventricular ejection fraction. We achieve an average frame distance of 3.36 frames for the ES and 7.17 frames for the ED on videos of arbitrary length. Our end-to-end learnable approach can estimate the ejection fraction with a MAE of 5.95 and $R^2$ of 0.52 in 0.15s per video, showing that segmentation is not the only way to predict ejection fraction. Code and models are available at https://github.com/HReynaud/UVT.

Oriol Corcoll Andreu, Athanasios Vlontzos, Michael O'Riordan et al.

Estimating causal effects is vital for decision making. In standard causal effect estimation, treatments are usually binary- or continuous-valued. However, in many important real-world settings, treatments can be structured, high-dimensional objects, such as text, video, or audio. This provides a challenge to traditional causal effect estimation. While leveraging the shared structure across different treatments can help generalize to unseen treatments at test time, we show in this paper that using such structure blindly can lead to biased causal effect estimation. We address this challenge by devising a novel contrastive approach to learn a representation of the high-dimensional treatments, and prove that it identifies underlying causal factors and discards non-causally relevant factors. We prove that this treatment representation leads to unbiased estimates of the causal effect, and empirically validate and benchmark our results on synthetic and real-world datasets.

Nikos Spyrou, Athanasios Vlontzos, Paraskevas Pegios et al.

Adapting text-to-image (T2I) latent diffusion models (LDMs) to video editing has shown strong visual fidelity and controllability, but challenges remain in maintaining causal relationships inherent to the video data generating process. Edits affecting causally dependent attributes often generate unrealistic or misleading outcomes if these relationships are ignored. In this work, we introduce a causally faithful framework for counterfactual video generation, formulated as an Out-of-Distribution (OOD) prediction problem. We embed prior causal knowledge by encoding the relationships specified in a causal graph into text prompts and guide the generation process by optimizing these prompts using a vision-language model (VLM)-based textual loss. This loss encourages the latent space of the LDMs to capture OOD variations in the form of counterfactuals, effectively steering generation toward causally meaningful alternatives. The proposed framework, dubbed CSVC, is agnostic to the underlying video editing system and does not require access to its internal mechanisms or fine-tuning. We evaluate our approach using standard video quality metrics and counterfactual-specific criteria, such as causal effectiveness and minimality. Experimental results show that CSVC generates causally faithful video counterfactuals within the LDM distribution via prompt-based causal steering, achieving state-of-the-art causal effectiveness without compromising temporal consistency or visual quality on real-world facial videos. Due to its compatibility with any black-box video editing system, our framework has significant potential to generate realistic 'what if' hypothetical video scenarios in diverse areas such as digital media and healthcare.

Athanasios Vlontzos, Bernhard Kainz, Ciaran M. Gilligan-Lee

Counterfactual inference is a powerful tool, capable of solving challenging problems in high-profile sectors. To perform counterfactual inference, one requires knowledge of the underlying causal mechanisms. However, causal mechanisms cannot be uniquely determined from observations and interventions alone. This raises the question of how to choose the causal mechanisms so that resulting counterfactual inference is trustworthy in a given domain. This question has been addressed in causal models with binary variables, but the case of categorical variables remains unanswered. We address this challenge by introducing for causal models with categorical variables the notion of counterfactual ordering, a principle that posits desirable properties causal mechanisms should posses, and prove that it is equivalent to specific functional constraints on the causal mechanisms. To learn causal mechanisms satisfying these constraints, and perform counterfactual inference with them, we introduce deep twin networks. These are deep neural networks that, when trained, are capable of twin network counterfactual inference -- an alternative to the abduction, action, & prediction method. We empirically test our approach on diverse real-world and semi-synthetic data from medicine, epidemiology, and finance, reporting accurate estimation of counterfactual probabilities while demonstrating the issues that arise with counterfactual reasoning when counterfactual ordering is not enforced.

Samuel Budd, Matthew Sinclair, Thomas Day et al.

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).

Tianrui Liu, Qingjie Meng, Jun-Jie Huang et al.

Intelligent video summarization algorithms allow to quickly convey the most relevant information in videos through the identification of the most essential and explanatory content while removing redundant video frames. In this paper, we introduce the 3DST-UNet-RL framework for video summarization. A 3D spatio-temporal U-Net is used to efficiently encode spatio-temporal information of the input videos for downstream reinforcement learning (RL). An RL agent learns from spatio-temporal latent scores and predicts actions for keeping or rejecting a video frame in a video summary. We investigate if real/inflated 3D spatio-temporal CNN features are better suited to learn representations from videos than commonly used 2D image features. Our framework can operate in both, a fully unsupervised mode and a supervised training mode. We analyse the impact of prescribed summary lengths and show experimental evidence for the effectiveness of 3DST-UNet-RL on two commonly used general video summarization benchmarks. We also applied our method on a medical video summarization task. The proposed video summarization method has the potential to save storage costs of ultrasound screening videos as well as to increase efficiency when browsing patient video data during retrospective analysis or audit without loosing essential information

Athanasios Vlontzos, Gabriel Sutherland, Siddha Ganju et al.

Future short or long-term space missions require a new generation of monitoring and diagnostic systems due to communication impasses as well as limitations in specialized crew and equipment. Machine learning supported diagnostic systems present a viable solution for medical and technical applications. We discuss challenges and applicability of such systems in light of upcoming missions and outline an example use case for a next-generation medical diagnostic system for future space operations. Additionally, we present approach recommendations and constraints for the successful generation and use of machine learning models aboard a spacecraft.

Luca Schmidtke, Athanasios Vlontzos, Simon Ellershaw et al.

Human pose estimation is a major computer vision problem with applications ranging from augmented reality and video capture to surveillance and movement tracking. In the medical context, the latter may be an important biomarker for neurological impairments in infants. Whilst many methods exist, their application has been limited by the need for well annotated large datasets and the inability to generalize to humans of different shapes and body compositions, e.g. children and infants. In this paper we present a novel method for learning pose estimators for human adults and infants in an unsupervised fashion. We approach this as a learnable template matching problem facilitated by deep feature extractors. Human-interpretable landmarks are estimated by transforming a template consisting of predefined body parts that are characterized by 2D Gaussian distributions. Enforcing a connectivity prior guides our model to meaningful human shape representations. We demonstrate the effectiveness of our approach on two different datasets including adults and infants.

Yueqi Cao, Athanasios Vlontzos, Luca Schmidtke et al.

Appropriately representing elements in a database so that queries may be accurately matched is a central task in information retrieval; recently, this has been achieved by embedding the graphical structure of the database into a manifold in a hierarchy-preserving manner using a variety of metrics. Persistent homology is a tool commonly used in topological data analysis that is able to rigorously characterize a database in terms of both its hierarchy and connectivity structure. Computing persistent homology on a variety of embedded datasets reveals that some commonly used embeddings fail to preserve the connectivity. We show that those embeddings which successfully retain the database topology coincide in persistent homology by introducing two dilation-invariant comparative measures to capture this effect: in particular, they address the issue of metric distortion on manifolds. We provide an algorithm for their computation that exhibits greatly reduced time complexity over existing methods. We use these measures to perform the first instance of topology-based information retrieval and demonstrate its increased performance over the standard bottleneck distance for persistent homology. We showcase our approach on databases of different data varieties including text, videos, and medical images.

Athanasios Vlontzos, Henrique Bergallo Rocha, Daniel Rueckert et al.

Estimating future events is a difficult task. Unlike humans, machine learning approaches are not regularized by a natural understanding of physics. In the wild, a plausible succession of events is governed by the rules of causality, which cannot easily be derived from a finite training set. In this paper we propose a novel theoretical framework to perform causal future prediction by embedding spatiotemporal information on a Minkowski space-time. We utilize the concept of a light cone from special relativity to restrict and traverse the latent space of an arbitrary model. We demonstrate successful applications in causal image synthesis and future video frame prediction on a dataset of images. Our framework is architecture- and task-independent and comes with strong theoretical guarantees of causal capabilities.

Athanasios Vlontzos, Samuel Budd, Benjamin Hou et al.

X-Ray imaging is quick, cheap and useful for front-line care assessment and intra-operative real-time imaging (e.g., C-Arm Fluoroscopy). However, it suffers from projective information loss and lacks vital volumetric information on which many essential diagnostic biomarkers are based on. In this paper we explore probabilistic methods to reconstruct 3D volumetric images from 2D imaging modalities and measure the models' performance and confidence. We show our models' performance on large connected structures and we test for limitations regarding fine structures and image domain sensitivity. We utilize fast end-to-end training of a 2D-3D convolutional networks, evaluate our method on 117 CT scans segmenting 3D structures from digitally reconstructed radiographs (DRRs) with a Dice score of $0.91 \pm 0.0013$. Source code will be made available by the time of the conference.

Tianrui Liu, Qingjie Meng, Athanasios Vlontzos et al.

Video is an essential imaging modality for diagnostics, e.g. in ultrasound imaging, for endoscopy, or movement assessment. However, video hasn't received a lot of attention in the medical image analysis community. In the clinical practice, it is challenging to utilise raw diagnostic video data efficiently as video data takes a long time to process, annotate or audit. In this paper we introduce a novel, fully automatic video summarization method that is tailored to the needs of medical video data. Our approach is framed as reinforcement learning problem and produces agents focusing on the preservation of important diagnostic information. We evaluate our method on videos from fetal ultrasound screening, where commonly only a small amount of the recorded data is used diagnostically. We show that our method is superior to alternative video summarization methods and that it preserves essential information required by clinical diagnostic standards.

Kara Lamb, Garima Malhotra, Athanasios Vlontzos et al.

High energy particles originating from solar activity travel along the the Earth's magnetic field and interact with the atmosphere around the higher latitudes. These interactions often manifest as aurora in the form of visible light in the Earth's ionosphere. These interactions also result in irregularities in the electron density, which cause disruptions in the amplitude and phase of the radio signals from the Global Navigation Satellite Systems (GNSS), known as 'scintillation'. In this paper we use a multi-scale residual autoencoder (Res-AE) to show the correlation between specific dynamic structures of the aurora and the magnitude of the GNSS phase scintillations ($σ_φ$). Auroral images are encoded in a lower dimensional feature space using the Res-AE, which in turn are clustered with t-SNE and UMAP. Both methods produce similar clusters, and specific clusters demonstrate greater correlations with observed phase scintillations. Our results suggest that specific dynamic structures of auroras are highly correlated with GNSS phase scintillations.

Kara Lamb, Garima Malhotra, Athanasios Vlontzos et al.

A Global Navigation Satellite System (GNSS) uses a constellation of satellites around the earth for accurate navigation, timing, and positioning. Natural phenomena like space weather introduce irregularities in the Earth's ionosphere, disrupting the propagation of the radio signals that GNSS relies upon. Such disruptions affect both the amplitude and the phase of the propagated waves. No physics-based model currently exists to predict the time and location of these disruptions with sufficient accuracy and at relevant scales. In this paper, we focus on predicting the phase fluctuations of GNSS radio waves, known as phase scintillations. We propose a novel architecture and loss function to predict 1 hour in advance the magnitude of phase scintillations within a time window of plus-minus 5 minutes with state-of-the-art performance.

Benjamin Hou, Athanasios Vlontzos, Amir Alansary et al.

Real-world settings often do not allow acquisition of high-resolution volumetric images for accurate morphological assessment and diagnostic. In clinical practice it is frequently common to acquire only sparse data (e.g. individual slices) for initial diagnostic decision making. Thereby, physicians rely on their prior knowledge (or mental maps) of the human anatomy to extrapolate the underlying 3D information. Accurate mental maps require years of anatomy training, which in the first instance relies on normative learning, i.e. excluding pathology. In this paper, we leverage Bayesian Deep Learning and environment mapping to generate full volumetric anatomy representations from none to a small, sparse set of slices. We evaluate proof of concept implementations based on Generative Query Networks (GQN) and Conditional BRUNO using abdominal CT and brain MRI as well as in a clinical application involving sparse, motion-corrupted MR acquisition for fetal imaging. Our approach allows to reconstruct 3D volumes from 1 to 4 tomographic slices, with a SSIM of 0.7+ and cross-correlation of 0.8+ compared to the 3D ground truth.

Athanasios Vlontzos, Amir Alansary, Konstantinos Kamnitsas et al.

The detection of anatomical landmarks is a vital step for medical image analysis and applications for diagnosis, interpretation and guidance. Manual annotation of landmarks is a tedious process that requires domain-specific expertise and introduces inter-observer variability. This paper proposes a new detection approach for multiple landmarks based on multi-agent reinforcement learning. Our hypothesis is that the position of all anatomical landmarks is interdependent and non-random within the human anatomy, thus finding one landmark can help to deduce the location of others. Using a Deep Q-Network (DQN) architecture we construct an environment and agent with implicit inter-communication such that we can accommodate K agents acting and learning simultaneously, while they attempt to detect K different landmarks. During training the agents collaborate by sharing their accumulated knowledge for a collective gain. We compare our approach with state-of-the-art architectures and achieve significantly better accuracy by reducing the detection error by 50%, while requiring fewer computational resources and time to train compared to the naive approach of training K agents separately.

Athanasios Vlontzos, Krystian Mikolajczyk

In interventional radiology, short video sequences of vein structure in motion are captured in order to help medical personnel identify vascular issues or plan intervention. Semantic segmentation can greatly improve the usefulness of these videos by indicating exact position of vessels and instruments, thus reducing the ambiguity. We propose a real-time segmentation method for these tasks, based on U-Net network trained in a Siamese architecture from automatically generated annotations. We make use of noisy low level binary segmentation and optical flow to generate multi class annotations that are successively improved in a multistage segmentation approach. We significantly improve the performance of a state of the art U-Net at the processing speeds of 90fps.

Athanasios Vlontzos

In this paper we examine learning methods combining the Random Neural Network, a biologically inspired neural network and the Extreme Learning Machine that achieve state of the art classification performance while requiring much shorter training time. The Random Neural Network is a integrate and fire computational model of a neural network whose mathematical structure permits the efficient analysis of large ensembles of neurons. An activation function is derived from the RNN and used in an Extreme Learning Machine. We compare the performance of this combination against the ELM with various activation functions, we reduce the input dimensionality via PCA and compare its performance vs. autoencoder based versions of the RNN-ELM.