Counterfactual contrastive learning: robust representations via causal image synthesis

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.

Mitigating attribute amplification in counterfactual image generation

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.

Average Calibration Error: A Differentiable Loss for Improved Reliability in Image Segmentation

Deep neural networks for medical image segmentation often produce overconfident results misaligned with empirical observations. Such miscalibration, challenges their clinical translation. We propose to use marginal L1 average calibration error (mL1-ACE) as a novel auxiliary loss function to improve pixel-wise calibration without compromising segmentation quality. We show that this loss, despite using hard binning, is directly differentiable, bypassing the need for approximate but differentiable surrogate or soft binning approaches. Our work also introduces the concept of dataset reliability histograms which generalises standard reliability diagrams for refined visual assessment of calibration in semantic segmentation aggregated at the dataset level. Using mL1-ACE, we reduce average and maximum calibration error by 45% and 55% respectively, maintaining a Dice score of 87% on the BraTS 2021 dataset. We share our code here: https://github.com/cai4cai/ACE-DLIRIS

Demystifying Variational Diffusion Models

Despite the growing popularity of diffusion models, gaining a deep understanding of the model class remains somewhat elusive for the uninitiated in non-equilibrium statistical physics. With that in mind, we present what we believe is a more straightforward introduction to diffusion models using directed graphical modelling and variational Bayesian principles, which imposes relatively fewer prerequisites on the average reader. Our exposition constitutes a comprehensive technical review spanning from foundational concepts like deep latent variable models to recent advances in continuous-time diffusion-based modelling, highlighting theoretical connections between model classes along the way. We provide additional mathematical insights that were omitted in the seminal works whenever possible to aid in understanding, while avoiding the introduction of new notation. We envision this article serving as a useful educational supplement for both researchers and practitioners in the area, and we welcome feedback and contributions from the community at https://github.com/biomedia-mira/demystifying-diffusion.

Robust semi-supervised segmentation with timestep ensembling diffusion models

Medical image segmentation is a challenging task, made more difficult by many datasets' limited size and annotations. Denoising diffusion probabilistic models (DDPM) have recently shown promise in modelling the distribution of natural images and were successfully applied to various medical imaging tasks. This work focuses on semi-supervised image segmentation using diffusion models, particularly addressing domain generalisation. Firstly, we demonstrate that smaller diffusion steps generate latent representations that are more robust for downstream tasks than larger steps. Secondly, we use this insight to propose an improved esembling scheme that leverages information-dense small steps and the regularising effect of larger steps to generate predictions. Our model shows significantly better performance in domain-shifted settings while retaining competitive performance in-domain. Overall, this work highlights the potential of DDPMs for semi-supervised medical image segmentation and provides insights into optimising their performance under domain shift.

Analysing race and sex bias in brain age prediction

Brain age prediction from MRI has become a popular imaging biomarker associated with a wide range of neuropathologies. The datasets used for training, however, are often skewed and imbalanced regarding demographics, potentially making brain age prediction models susceptible to bias. We analyse the commonly used ResNet-34 model by conducting a comprehensive subgroup performance analysis and feature inspection. The model is trained on 1,215 T1-weighted MRI scans from Cam-CAN and IXI, and tested on UK Biobank (n=42,786), split into six racial and biological sex subgroups. With the objective of comparing the performance between subgroups, measured by the absolute prediction error, we use a Kruskal-Wallis test followed by two post-hoc Conover-Iman tests to inspect bias across race and biological sex. To examine biases in the generated features, we use PCA for dimensionality reduction and employ two-sample Kolmogorov-Smirnov tests to identify distribution shifts among subgroups. Our results reveal statistically significant differences in predictive performance between Black and White, Black and Asian, and male and female subjects. Seven out of twelve pairwise comparisons show statistically significant differences in the feature distributions. Our findings call for further analysis of brain age prediction models.

Distance Matters For Improving Performance Estimation Under Covariate Shift

Performance estimation under covariate shift is a crucial component of safe AI model deployment, especially for sensitive use-cases. Recently, several solutions were proposed to tackle this problem, most leveraging model predictions or softmax confidence to derive accuracy estimates. However, under dataset shifts, confidence scores may become ill-calibrated if samples are too far from the training distribution. In this work, we show that taking into account distances of test samples to their expected training distribution can significantly improve performance estimation under covariate shift. Precisely, we introduce a "distance-check" to flag samples that lie too far from the expected distribution, to avoid relying on their untrustworthy model outputs in the accuracy estimation step. We demonstrate the effectiveness of this method on 13 image classification tasks, across a wide-range of natural and synthetic distribution shifts and hundreds of models, with a median relative MAE improvement of 27% over the best baseline across all tasks, and SOTA performance on 10 out of 13 tasks. Our code is publicly available at https://github.com/melanibe/distance_matters_performance_estimation.

Robustness Stress Testing in Medical Image Classification

Deep neural networks have shown impressive performance for image-based disease detection. Performance is commonly evaluated through clinical validation on independent test sets to demonstrate clinically acceptable accuracy. Reporting good performance metrics on test sets, however, is not always a sufficient indication of the generalizability and robustness of an algorithm. In particular, when the test data is drawn from the same distribution as the training data, the iid test set performance can be an unreliable estimate of the accuracy on new data. In this paper, we employ stress testing to assess model robustness and subgroup performance disparities in disease detection models. We design progressive stress testing using five different bidirectional and unidirectional image perturbations with six different severity levels. As a use case, we apply stress tests to measure the robustness of disease detection models for chest X-ray and skin lesion images, and demonstrate the importance of studying class and domain-specific model behaviour. Our experiments indicate that some models may yield more robust and equitable performance than others. We also find that pretraining characteristics play an important role in downstream robustness. We conclude that progressive stress testing is a viable and important tool and should become standard practice in the clinical validation of image-based disease detection models.

No Fair Lunch: A Causal Perspective on Dataset Bias in Machine Learning for Medical Imaging

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.

Unsupervised Conditional Slot Attention for Object Centric Learning

Extracting object-level representations for downstream reasoning tasks is an emerging area in AI. Learning object-centric representations in an unsupervised setting presents multiple challenges, a key one being binding an arbitrary number of object instances to a specialized object slot. Recent object-centric representation methods like Slot Attention utilize iterative attention to learn composable representations with dynamic inference level binding but fail to achieve specialized slot level binding. To address this, in this paper we propose Unsupervised Conditional Slot Attention using a novel Probabilistic Slot Dictionary (PSD). We define PSD with (i) abstract object-level property vectors as key and (ii) parametric Gaussian distribution as its corresponding value. We demonstrate the benefits of the learnt specific object-level conditioning distributions in multiple downstream tasks, namely object discovery, compositional scene generation, and compositional visual reasoning. We show that our method provides scene composition capabilities and a significant boost in a few shot adaptability tasks of compositional visual reasoning, while performing similarly or better than slot attention in object discovery tasks