Fabio De Sousa Ribeiro

Miguel Monteiro, Fabio De Sousa Ribeiro, Nick Pawlowski et al. · microsoft-research

We present a general framework for evaluating image counterfactuals. The power and flexibility of deep generative models make them valuable tools for learning mechanisms in structural causal models. However, their flexibility makes counterfactual identifiability impossible in the general case. Motivated by these issues, we revisit Pearl's axiomatic definition of counterfactuals to determine the necessary constraints of any counterfactual inference model: composition, reversibility, and effectiveness. We frame counterfactuals as functions of an input variable, its parents, and counterfactual parents and use the axiomatic constraints to restrict the set of functions that could represent the counterfactual, thus deriving distance metrics between the approximate and ideal functions. We demonstrate how these metrics can be used to compare and choose between different approximate counterfactual inference models and to provide insight into a model's shortcomings and trade-offs.

Charles Jones, Daniel C. Castro, Fabio De Sousa Ribeiro et al. · microsoft-research

As machine learning methods gain prominence within clinical decision-making, addressing fairness concerns becomes increasingly urgent. Despite considerable work dedicated to detecting and ameliorating algorithmic bias, today's methods are deficient with potentially harmful consequences. Our causal perspective sheds new light on algorithmic bias, highlighting how different sources of dataset bias may appear indistinguishable yet require substantially different mitigation strategies. We introduce three families of causal bias mechanisms stemming from disparities in prevalence, presentation, and annotation. Our causal analysis underscores how current mitigation methods tackle only a narrow and often unrealistic subset of scenarios. We provide a practical three-step framework for reasoning about fairness in medical imaging, supporting the development of safe and equitable AI prediction models.

Margherita Rosnati, Fabio De Sousa Ribeiro, Miguel Monteiro et al. · microsoft-research

Image segmentation is important in medical imaging, providing valuable, quantitative information for clinical decision-making in diagnosis, therapy, and intervention. The state-of-the-art in automated segmentation remains supervised learning, employing discriminative models such as U-Net. However, training these models requires access to large amounts of manually labelled data which is often difficult to obtain in real medical applications. In such settings, semi-supervised learning (SSL) attempts to leverage the abundance of unlabelled data to obtain more robust and reliable models. Recently, generative models have been proposed for semantic segmentation, as they make an attractive choice for SSL. Their ability to capture the joint distribution over input images and output label maps provides a natural way to incorporate information from unlabelled images. This paper analyses whether deep generative models such as the SemanticGAN are truly viable alternatives to tackle challenging medical image segmentation problems. To that end, we thoroughly evaluate the segmentation performance, robustness, and potential subgroup disparities of discriminative and generative segmentation methods when applied to large-scale, publicly available chest X-ray datasets.

Fabio De Sousa Ribeiro, Tian Xia, Miguel Monteiro et al.

We present a general causal generative modelling framework for accurate estimation of high fidelity image counterfactuals with deep structural causal models. Estimation of interventional and counterfactual queries for high-dimensional structured variables, such as images, remains a challenging task. We leverage ideas from causal mediation analysis and advances in generative modelling to design new deep causal mechanisms for structured variables in causal models. Our experiments demonstrate that our proposed mechanisms are capable of accurate abduction and estimation of direct, indirect and total effects as measured by axiomatic soundness of counterfactuals.

Melanie Bernhardt, Fabio De Sousa Ribeiro, Ben Glocker

Failure detection in automated image classification is a critical safeguard for clinical deployment. Detected failure cases can be referred to human assessment, ensuring patient safety in computer-aided clinical decision making. Despite its paramount importance, there is insufficient evidence about the ability of state-of-the-art confidence scoring methods to detect test-time failures of classification models in the context of medical imaging. This paper provides a reality check, establishing the performance of in-domain misclassification detection methods, benchmarking 9 widely used confidence scores on 6 medical imaging datasets with different imaging modalities, in multiclass and binary classification settings. Our experiments show that the problem of failure detection is far from being solved. We found that none of the benchmarked advanced methods proposed in the computer vision and machine learning literature can consistently outperform a simple softmax baseline, demonstrating that improved out-of-distribution detection or model calibration do not necessarily translate to improved in-domain misclassification detection. Our developed testbed facilitates future work in this important area

Fabio De Sousa Ribeiro, Kevin Duarte, Miles Everett et al.

Capsule networks were proposed as an alternative approach to Convolutional Neural Networks (CNNs) for learning object-centric representations, which can be leveraged for improved generalization and sample complexity. Unlike CNNs, capsule networks are designed to explicitly model part-whole hierarchical relationships by using groups of neurons to encode visual entities, and learn the relationships between those entities. Promising early results achieved by capsule networks have motivated the deep learning community to continue trying to improve their performance and scalability across several application areas. However, a major hurdle for capsule network research has been the lack of a reliable point of reference for understanding their foundational ideas and motivations. The aim of this survey is to provide a comprehensive overview of the capsule network research landscape, which will serve as a valuable resource for the community going forward. To that end, we start with an introduction to the fundamental concepts and motivations behind capsule networks, such as equivariant inference in computer vision. We then cover the technical advances in the capsule routing mechanisms and the various formulations of capsule networks, e.g. generative and geometric. Additionally, we provide a detailed explanation of how capsule networks relate to the popular attention mechanism in Transformers, and highlight non-trivial conceptual similarities between them in the context of representation learning. Afterwards, we explore the extensive applications of capsule networks in computer vision, video and motion, graph representation learning, natural language processing, medical imaging and many others. To conclude, we provide an in-depth discussion regarding the main hurdles in capsule network research, and highlight promising research directions for future work.

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.

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

Contrastive pretraining can substantially increase model generalisation and downstream performance. However, the quality of the learned representations is highly dependent on the data augmentation strategy applied to generate positive pairs. Positive contrastive pairs should preserve semantic meaning while discarding unwanted variations related to the data acquisition domain. Traditional contrastive pipelines attempt to simulate domain shifts through pre-defined generic image transformations. However, these do not always mimic realistic and relevant domain variations for medical imaging, such as scanner differences. To tackle this issue, we herein introduce counterfactual contrastive learning, a novel framework leveraging recent advances in causal image synthesis to create contrastive positive pairs that faithfully capture relevant domain variations. Our method, evaluated across five datasets encompassing both chest radiography and mammography data, for two established contrastive objectives (SimCLR and DINO-v2), outperforms standard contrastive learning in terms of robustness to acquisition shift. Notably, counterfactual contrastive learning achieves superior downstream performance on both in-distribution and external datasets, especially for images acquired with scanners under-represented in the training set. Further experiments show that the proposed framework extends beyond acquisition shifts, with models trained with counterfactual contrastive learning reducing subgroup disparities across biological sex.

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.

Fabio De Sousa Ribeiro, Omar Todd, Charles Jones et al.

We introduce the Flow Stochastic Segmentation Network (Flow-SSN), a generative segmentation model family featuring discrete-time autoregressive and modern continuous-time flow variants. We prove fundamental limitations of the low-rank parameterisation of previous methods and show that Flow-SSNs can estimate arbitrarily high-rank pixel-wise covariances without assuming the rank or storing the distributional parameters. Flow-SSNs are also more efficient to sample from than standard diffusion-based segmentation models, thanks to most of the model capacity being allocated to learning the base distribution of the flow, constituting an expressive prior. We apply Flow-SSNs to challenging medical imaging benchmarks and achieve state-of-the-art results. Code available: https://github.com/biomedia-mira/flow-ssn.

Rajat Rasal, Avinash Kori, Fabio De Sousa Ribeiro et al.

Counterfactual image generation presents significant challenges, including preserving identity, maintaining perceptual quality, and ensuring faithfulness to an underlying causal model. While existing auto-encoding frameworks admit semantic latent spaces which can be manipulated for causal control, they struggle with scalability and fidelity. Advancements in diffusion models present opportunities for improving counterfactual image editing, having demonstrated state-of-the-art visual quality, human-aligned perception and representation learning capabilities. Here, we present a suite of diffusion-based causal mechanisms, introducing the notions of spatial, semantic and dynamic abduction. We propose a general framework that integrates semantic representations into diffusion models through the lens of Pearlian causality to edit images via a counterfactual reasoning process. To our knowledge, this is the first work to consider high-level semantic identity preservation for diffusion counterfactuals and to demonstrate how semantic control enables principled trade-offs between faithful causal control and identity preservation.

Mélanie Roschewitz, Raghav Mehta, Fabio de Sousa Ribeiro et al.

We conduct an extensive study on the state of calibration under real-world dataset shift for image classification. Our work provides important insights on the choice of post-hoc and in-training calibration techniques, and yields practical guidelines for all practitioners interested in robust calibration under shift. We compare various post-hoc calibration methods, and their interactions with common in-training calibration strategies (e.g., label smoothing), across a wide range of natural shifts, on eight different classification tasks across several imaging domains. We find that: (i) simultaneously applying entropy regularisation and label smoothing yield the best calibrated raw probabilities under dataset shift, (ii) post-hoc calibrators exposed to a small amount of semantic out-of-distribution data (unrelated to the task) are most robust under shift, (iii) recent calibration methods specifically aimed at increasing calibration under shifts do not necessarily offer significant improvements over simpler post-hoc calibration methods, (iv) improving calibration under shifts often comes at the cost of worsening in-distribution calibration. Importantly, these findings hold for randomly initialised classifiers, as well as for those finetuned from foundation models, the latter being consistently better calibrated compared to models trained from scratch. Finally, we conduct an in-depth analysis of ensembling effects, finding that (i) applying calibration prior to ensembling (instead of after) is more effective for calibration under shifts, (ii) for ensembles, OOD exposure deteriorates the ID-shifted calibration trade-off, (iii) ensembling remains one of the most effective methods to improve calibration robustness and, combined with finetuning from foundation models, yields best calibration results overall.

Raghav Mehta, Fabio De Sousa Ribeiro, Tian Xia et al.

Segmenting anatomical structures in medical images plays an important role in the quantitative assessment of various diseases. However, accurate segmentation becomes significantly more challenging in the presence of disease. Disease patterns can alter the appearance of surrounding healthy tissues, introduce ambiguous boundaries, or even obscure critical anatomical structures. As such, segmentation models trained on real-world datasets may struggle to provide good anatomical segmentation, leading to potential misdiagnosis. In this paper, we generate counterfactual (CF) images to simulate how the same anatomy would appear in the absence of disease without altering the underlying structure. We then use these CF images to segment structures of interest, without requiring any changes to the underlying segmentation model. Our experiments on two real-world clinical chest X-ray datasets show that the use of counterfactual images improves anatomical segmentation, thereby aiding downstream clinical decision-making.

Avinash Kori, Francesco Locatello, Ainkaran Santhirasekaram et al.

Learning modular object-centric representations is crucial for systematic generalization. Existing methods show promising object-binding capabilities empirically, but theoretical identifiability guarantees remain relatively underdeveloped. Understanding when object-centric representations can theoretically be identified is crucial for scaling slot-based methods to high-dimensional images with correctness guarantees. To that end, we propose a probabilistic slot-attention algorithm that imposes an aggregate mixture prior over object-centric slot representations, thereby providing slot identifiability guarantees without supervision, up to an equivalence relation. We provide empirical verification of our theoretical identifiability result using both simple 2-dimensional data and high-resolution imaging datasets.

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.

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

Causal generative modelling is gaining interest in medical imaging due to its ability to answer interventional and counterfactual queries. Most work focuses on generating counterfactual images that look plausible, using auxiliary classifiers to enforce effectiveness of simulated interventions. We investigate pitfalls in this approach, discovering the issue of attribute amplification, where unrelated attributes are spuriously affected during interventions, leading to biases across protected characteristics and disease status. We show that attribute amplification is caused by the use of hard labels in the counterfactual training process and propose soft counterfactual fine-tuning to mitigate this issue. Our method substantially reduces the amplification effect while maintaining effectiveness of generated images, demonstrated on a large chest X-ray dataset. Our work makes an important advancement towards more faithful and unbiased causal modelling in medical imaging.

Fabio De Sousa Ribeiro, Ben Glocker

Despite the growing interest in diffusion models, gaining a deep understanding of the model class remains an elusive endeavour, particularly for the uninitiated in non-equilibrium statistical physics. Thanks to the rapid rate of progress in the field, most existing work on diffusion models focuses on either applications or theoretical contributions. Unfortunately, the theoretical material is often inaccessible to practitioners and new researchers, leading to a risk of superficial understanding in ongoing research. Given that diffusion models are now an indispensable tool, a clear and consolidating perspective on the model class is needed to properly contextualize recent advances in generative modelling and lower the barrier to entry for new researchers. To that end, we revisit predecessors to diffusion models like hierarchical latent variable models and synthesize a holistic perspective using only directed graphical modelling and variational inference principles. The resulting narrative is easier to follow as it imposes fewer prerequisites on the average reader relative to the view from non-equilibrium thermodynamics or stochastic differential equations.

Fabio De Sousa Ribeiro, Georgios Leontidis, Stefanos Kollias

Capsule networks are a recently proposed type of neural network shown to outperform alternatives in challenging shape recognition tasks. In capsule networks, scalar neurons are replaced with capsule vectors or matrices, whose entries represent different properties of objects. The relationships between objects and their parts are learned via trainable viewpoint-invariant transformation matrices, and the presence of a given object is decided by the level of agreement among votes from its parts. This interaction occurs between capsule layers and is a process called routing-by-agreement. In this paper, we propose a new capsule routing algorithm derived from Variational Bayes for fitting a mixture of transforming gaussians, and show it is possible transform our capsule network into a Capsule-VAE. Our Bayesian approach addresses some of the inherent weaknesses of MLE based models such as the variance-collapse by modelling uncertainty over capsule pose parameters. We outperform the state-of-the-art on smallNORB using 50% fewer capsules than previously reported, achieve competitive performances on CIFAR-10, Fashion-MNIST, SVHN, and demonstrate significant improvement in MNIST to affNIST generalisation over previous works.

Fabio De Sousa Ribeiro, Francesco Caliva, Mark Swainson et al.

Supervised Deep Learning has been highly successful in recent years, achieving state-of-the-art results in most tasks. However, with the ongoing uptake of such methods in industrial applications, the requirement for large amounts of annotated data is often a challenge. In most real world problems, manual annotation is practically intractable due to time/labour constraints, thus the development of automated and adaptive data annotation systems is highly sought after. In this paper, we propose both a (i) Deep Bayesian Self-Training methodology for automatic data annotation, by leveraging predictive uncertainty estimates using variational inference and modern Neural Network architectures, as well as (ii) a practical adaptation procedure for handling high label variability between different dataset distributions through clustering of Neural Network latent variable representations. An experimental study on both public and private datasets is presented illustrating the superior performance of the proposed approach over standard Self-Training baselines, highlighting the importance of predictive uncertainty estimates in safety-critical domains.