Deep Structural Causal Models for Tractable Counterfactual Inference

We formulate a general framework for building structural causal models (SCMs) with deep learning components. The proposed approach employs normalising flows and variational inference to enable tractable inference of exogenous noise variables - a crucial step for counterfactual inference that is missing from existing deep causal learning methods. Our framework is validated on a synthetic dataset built on MNIST as well as on a real-world medical dataset of brain MRI scans. Our experimental results indicate that we can successfully train deep SCMs that are capable of all three levels of Pearl's ladder of causation: association, intervention, and counterfactuals, giving rise to a powerful new approach for answering causal questions in imaging applications and beyond. The code for all our experiments is available at https://github.com/biomedia-mira/deepscm.

Stochastic Segmentation Networks: Modelling Spatially Correlated Aleatoric Uncertainty

In image segmentation, there is often more than one plausible solution for a given input. In medical imaging, for example, experts will often disagree about the exact location of object boundaries. Estimating this inherent uncertainty and predicting multiple plausible hypotheses is of great interest in many applications, yet this ability is lacking in most current deep learning methods. In this paper, we introduce stochastic segmentation networks (SSNs), an efficient probabilistic method for modelling aleatoric uncertainty with any image segmentation network architecture. In contrast to approaches that produce pixel-wise estimates, SSNs model joint distributions over entire label maps and thus can generate multiple spatially coherent hypotheses for a single image. By using a low-rank multivariate normal distribution over the logit space to model the probability of the label map given the image, we obtain a spatially consistent probability distribution that can be efficiently computed by a neural network without any changes to the underlying architecture. We tested our method on the segmentation of real-world medical data, including lung nodules in 2D CT and brain tumours in 3D multimodal MRI scans. SSNs outperform state-of-the-art for modelling correlated uncertainty in ambiguous images while being much simpler, more flexible, and more efficient.

Unpaired Multi-modal Segmentation via Knowledge Distillation

Multi-modal learning is typically performed with network architectures containing modality-specific layers and shared layers, utilizing co-registered images of different modalities. We propose a novel learning scheme for unpaired cross-modality image segmentation, with a highly compact architecture achieving superior segmentation accuracy. In our method, we heavily reuse network parameters, by sharing all convolutional kernels across CT and MRI, and only employ modality-specific internal normalization layers which compute respective statistics. To effectively train such a highly compact model, we introduce a novel loss term inspired by knowledge distillation, by explicitly constraining the KL-divergence of our derived prediction distributions between modalities. We have extensively validated our approach on two multi-class segmentation problems: i) cardiac structure segmentation, and ii) abdominal organ segmentation. Different network settings, i.e., 2D dilated network and 3D U-net, are utilized to investigate our method's general efficacy. Experimental results on both tasks demonstrate that our novel multi-modal learning scheme consistently outperforms single-modal training and previous multi-modal approaches.

Causality matters in medical imaging

This article discusses how the language of causality can shed new light on the major challenges in machine learning for medical imaging: 1) data scarcity, which is the limited availability of high-quality annotations, and 2) data mismatch, whereby a trained algorithm may fail to generalize in clinical practice. Looking at these challenges through the lens of causality allows decisions about data collection, annotation procedures, and learning strategies to be made (and scrutinized) more transparently. We discuss how causal relationships between images and annotations can not only have profound effects on the performance of predictive models, but may even dictate which learning strategies should be considered in the first place. For example, we conclude that semi-supervision may be unsuitable for image segmentation---one of the possibly surprising insights from our causal analysis, which is illustrated with representative real-world examples of computer-aided diagnosis (skin lesion classification in dermatology) and radiotherapy (automated contouring of tumours). We highlight that being aware of and accounting for the causal relationships in medical imaging data is important for the safe development of machine learning and essential for regulation and responsible reporting. To facilitate this we provide step-by-step recommendations for future studies.

Universal Adversarial Perturbations to Understand Robustness of Texture vs. Shape-biased Training

Convolutional Neural Networks (CNNs) used on image classification tasks such as ImageNet have been shown to be biased towards recognizing textures rather than shapes. Recent work has attempted to alleviate this by augmenting the training dataset with shape-based examples to create Stylized-ImageNet. However, in this paper we show that models trained on this dataset remain vulnerable to Universal Adversarial Perturbations (UAPs). We use UAPs to evaluate and compare the robustness of CNN models with varying degrees of shape-based training. We also find that a posteriori fine-tuning on ImageNet negates features learned from training on Stylized-ImageNet. This study reveals an important limitation and reiterates the need for further research into understanding the robustness of CNNs for visual recognition.

Domain Generalization via Model-Agnostic Learning of Semantic Features

Generalization capability to unseen domains is crucial for machine learning models when deploying to real-world conditions. We investigate the challenging problem of domain generalization, i.e., training a model on multi-domain source data such that it can directly generalize to target domains with unknown statistics. We adopt a model-agnostic learning paradigm with gradient-based meta-train and meta-test procedures to expose the optimization to domain shift. Further, we introduce two complementary losses which explicitly regularize the semantic structure of the feature space. Globally, we align a derived soft confusion matrix to preserve general knowledge about inter-class relationships. Locally, we promote domain-independent class-specific cohesion and separation of sample features with a metric-learning component. The effectiveness of our method is demonstrated with new state-of-the-art results on two common object recognition benchmarks. Our method also shows consistent improvement on a medical image segmentation task.

Vertebrae Detection and Localization in CT with Two-Stage CNNs and Dense Annotations

We propose a new, two-stage approach to the vertebrae centroid detection and localization problem. The first stage detects where the vertebrae appear in the scan using 3D samples, the second identifies the specific vertebrae within that region-of-interest using 2D slices. Our solution utilizes new techniques to improve the accuracy of the algorithm such as a revised approach to dense labelling from sparse centroid annotations and usage of large anisotropic kernels in the base level of a U-net architecture to maximize the receptive field. Our method improves the state-of-the-art's mean localization accuracy by 0.87mm on a publicly available spine CT benchmark.

Machine Learning with Multi-Site Imaging Data: An Empirical Study on the Impact of Scanner Effects

This is an empirical study to investigate the impact of scanner effects when using machine learning on multi-site neuroimaging data. We utilize structural T1-weighted brain MRI obtained from two different studies, Cam-CAN and UK Biobank. For the purpose of our investigation, we construct a dataset consisting of brain scans from 592 age- and sex-matched individuals, 296 subjects from each original study. Our results demonstrate that even after careful pre-processing with state-of-the-art neuroimaging pipelines a classifier can easily distinguish between the origin of the data with very high accuracy. Our analysis on the example application of sex classification suggests that current approaches to harmonize data are unable to remove scanner-specific bias leading to overly optimistic performance estimates and poor generalization. We conclude that multi-site data harmonization remains an open challenge and particular care needs to be taken when using such data with advanced machine learning methods for predictive modelling.

Needles in Haystacks: On Classifying Tiny Objects in Large Images

In some computer vision domains, such as medical or hyperspectral imaging, we care about the classification of tiny objects in large images. However, most Convolutional Neural Networks (CNNs) for image classification were developed and analyzed using biased datasets that contain large objects, most often, in central image positions. To assess whether classical CNN architectures work well for tiny object classification we build a comprehensive testbed containing two datasets: one derived from MNIST digits and other from histopathology images. This testbed allows us to perform controlled experiments to stress-test CNN architectures using a broad spectrum of signal-to-noise ratios. Our observations suggest that: (1) There exists a limit to signal-to-noise below which CNNs fail to generalize and that this limit is affected by dataset size - more data leading to better performances; however, the amount of training data required for the model to generalize scales rapidly with the inverse of the object-to-image ratio (2) in general, higher capacity models exhibit better generalization; (3) when knowing the approximate object sizes, adapting receptive field is beneficial; and (4) for very small signal-to-noise ratio the choice of global pooling operation affects optimization, whereas for relatively large signal-to-noise values, all tested global pooling operations exhibit similar performance.

Overfitting of neural nets under class imbalance: Analysis and improvements for segmentation

Overfitting in deep learning has been the focus of a number of recent works, yet its exact impact on the behavior of neural networks is not well understood. This study analyzes overfitting by examining how the distribution of logits alters in relation to how much the model overfits. Specifically, we find that when training with few data samples, the distribution of logit activations when processing unseen test samples of an under-represented class tends to shift towards and even across the decision boundary, while the over-represented class seems unaffected. In image segmentation, foreground samples are often heavily under-represented. We observe that sensitivity of the model drops as a result of overfitting, while precision remains mostly stable. Based on our analysis, we derive asymmetric modifications of existing loss functions and regularizers including a large margin loss, focal loss, adversarial training and mixup, which specifically aim at reducing the shift observed when embedding unseen samples of the under-represented class. We study the case of binary segmentation of brain tumor core and show that our proposed simple modifications lead to significantly improved segmentation performance over the symmetric variants.