Rethinking Generalization: The Impact of Annotation Style on Medical Image Segmentation

Generalization is an important attribute of machine learning models, particularly for those that are to be deployed in a medical context, where unreliable predictions can have real world consequences. While the failure of models to generalize across datasets is typically attributed to a mismatch in the data distributions, performance gaps are often a consequence of biases in the ``ground-truth" label annotations. This is particularly important in the context of medical image segmentation of pathological structures (e.g. lesions), where the annotation process is much more subjective, and affected by a number underlying factors, including the annotation protocol, rater education/experience, and clinical aims, among others. In this paper, we show that modeling annotation biases, rather than ignoring them, poses a promising way of accounting for differences in annotation style across datasets. To this end, we propose a generalized conditioning framework to (1) learn and account for different annotation styles across multiple datasets using a single model, (2) identify similar annotation styles across different datasets in order to permit their effective aggregation, and (3) fine-tune a fully trained model to a new annotation style with just a few samples. Next, we present an image-conditioning approach to model annotation styles that correlate with specific image features, potentially enabling detection biases to be more easily identified.

Diffusion Models for Causal Discovery via Topological Ordering

Discovering causal relations from observational data becomes possible with additional assumptions such as considering the functional relations to be constrained as nonlinear with additive noise. In this case, the Hessian of the data log-likelihood can be used for finding leaf nodes in a causal graph. Topological ordering approaches for causal discovery exploit this by performing graph discovery in two steps, first sequentially identifying nodes in reverse order of depth (topological ordering), and secondly pruning the potential relations. This is more efficient since the search is performed over a permutation rather than a graph space. However, existing computational methods for obtaining the Hessian still do not scale as the number of variables and the number of samples are increased. Therefore, inspired by recent innovations in diffusion probabilistic models (DPMs), we propose DiffAN, a topological ordering algorithm that leverages DPMs. Further, we introduce theory for updating the learned Hessian without re-training the neural network, and we show that computing with a subset of samples gives an accurate approximation of the ordering, which allows scaling to datasets with more samples and variables. We show empirically that our method scales exceptionally well to datasets with up to $500$ nodes and up to $10^5$ samples while still performing on par over small datasets with state-of-the-art causal discovery methods. Implementation is available at https://github.com/vios-s/DiffAN .

HSIC-InfoGAN: Learning Unsupervised Disentangled Representations by Maximising Approximated Mutual Information

Learning disentangled representations requires either supervision or the introduction of specific model designs and learning constraints as biases. InfoGAN is a popular disentanglement framework that learns unsupervised disentangled representations by maximising the mutual information between latent representations and their corresponding generated images. Maximisation of mutual information is achieved by introducing an auxiliary network and training with a latent regression loss. In this short exploratory paper, we study the use of the Hilbert-Schmidt Independence Criterion (HSIC) to approximate mutual information between latent representation and image, termed HSIC-InfoGAN. Directly optimising the HSIC loss avoids the need for an additional auxiliary network. We qualitatively compare the level of disentanglement in each model, suggest a strategy to tune the hyperparameters of HSIC-InfoGAN, and discuss the potential of HSIC-InfoGAN for medical applications.

What is Healthy? Generative Counterfactual Diffusion for Lesion Localization

Reducing the requirement for densely annotated masks in medical image segmentation is important due to cost constraints. In this paper, we consider the problem of inferring pixel-level predictions of brain lesions by only using image-level labels for training. By leveraging recent advances in generative diffusion probabilistic models (DPM), we synthesize counterfactuals of "How would a patient appear if X pathology was not present?". The difference image between the observed patient state and the healthy counterfactual can be used for inferring the location of pathology. We generate counterfactuals that correspond to the minimal change of the input such that it is transformed to healthy domain. This requires training with healthy and unhealthy data in DPMs. We improve on previous counterfactual DPMs by manipulating the generation process with implicit guidance along with attention conditioning instead of using classifiers. Code is available at https://github.com/vios-s/Diff-SCM.

Why patient data cannot be easily forgotten?

Rights provisioned within data protection regulations, permit patients to request that knowledge about their information be eliminated by data holders. With the advent of AI learned on data, one can imagine that such rights can extent to requests for forgetting knowledge of patient's data within AI models. However, forgetting patients' imaging data from AI models, is still an under-explored problem. In this paper, we study the influence of patient data on model performance and formulate two hypotheses for a patient's data: either they are common and similar to other patients or form edge cases, i.e. unique and rare cases. We show that it is not possible to easily forget patient data. We propose a targeted forgetting approach to perform patient-wise forgetting. Extensive experiments on the benchmark Automated Cardiac Diagnosis Challenge dataset showcase the improved performance of the proposed targeted forgetting approach as opposed to a state-of-the-art method.

vMFNet: Compositionality Meets Domain-generalised Segmentation

Training medical image segmentation models usually requires a large amount of labeled data. By contrast, humans can quickly learn to accurately recognise anatomy of interest from medical (e.g. MRI and CT) images with some limited guidance. Such recognition ability can easily generalise to new images from different clinical centres. This rapid and generalisable learning ability is mostly due to the compositional structure of image patterns in the human brain, which is less incorporated in medical image segmentation. In this paper, we model the compositional components (i.e. patterns) of human anatomy as learnable von-Mises-Fisher (vMF) kernels, which are robust to images collected from different domains (e.g. clinical centres). The image features can be decomposed to (or composed by) the components with the composing operations, i.e. the vMF likelihoods. The vMF likelihoods tell how likely each anatomical part is at each position of the image. Hence, the segmentation mask can be predicted based on the vMF likelihoods. Moreover, with a reconstruction module, unlabeled data can also be used to learn the vMF kernels and likelihoods by recombining them to reconstruct the input image. Extensive experiments show that the proposed vMFNet achieves improved generalisation performance on two benchmarks, especially when annotations are limited. Code is publicly available at: https://github.com/vios-s/vMFNet.

Metrics reloaded: Pitfalls and recommendations for image analysis validation

The field of automatic biomedical image analysis crucially depends on robust and meaningful performance metrics for algorithm validation. Current metric usage, however, is often ill-informed and does not reflect the underlying domain interest. Here, we present a comprehensive framework that guides researchers towards choosing performance metrics in a problem-aware manner. Specifically, we focus on biomedical image analysis problems that can be interpreted as a classification task at image, object or pixel level. The framework first compiles domain interest-, target structure-, data set- and algorithm output-related properties of a given problem into a problem fingerprint, while also mapping it to the appropriate problem category, namely image-level classification, semantic segmentation, instance segmentation, or object detection. It then guides users through the process of selecting and applying a set of appropriate validation metrics while making them aware of potential pitfalls related to individual choices. In this paper, we describe the current status of the Metrics Reloaded recommendation framework, with the goal of obtaining constructive feedback from the image analysis community. The current version has been developed within an international consortium of more than 60 image analysis experts and will be made openly available as a user-friendly toolkit after community-driven optimization.

Causal Machine Learning for Healthcare and Precision Medicine

Causal machine learning (CML) has experienced increasing popularity in healthcare. Beyond the inherent capabilities of adding domain knowledge into learning systems, CML provides a complete toolset for investigating how a system would react to an intervention (e.g.\ outcome given a treatment). Quantifying effects of interventions allows actionable decisions to be made whilst maintaining robustness in the presence of confounders. Here, we explore how causal inference can be incorporated into different aspects of clinical decision support (CDS) systems by using recent advances in machine learning. Throughout this paper, we use Alzheimer's disease (AD) to create examples for illustrating how CML can be advantageous in clinical scenarios. Furthermore, we discuss important challenges present in healthcare applications such as processing high-dimensional and unstructured data, generalisation to out-of-distribution samples, and temporal relationships, that despite the great effort from the research community remain to be solved. Finally, we review lines of research within causal representation learning, causal discovery and causal reasoning which offer the potential towards addressing the aforementioned challenges.

Unintended memorisation of unique features in neural networks

Neural networks pose a privacy risk due to their propensity to memorise and leak training data. We show that unique features occurring only once in training data are memorised by discriminative multi-layer perceptrons and convolutional neural networks trained on benchmark imaging datasets. We design our method for settings where sensitive training data is not available, for example medical imaging. Our setting knows the unique feature, but not the training data, model weights or the unique feature's label. We develop a score estimating a model's sensitivity to a unique feature by comparing the KL divergences of the model's output distributions given modified out-of-distribution images. We find that typical strategies to prevent overfitting do not prevent unique feature memorisation. And that images containing a unique feature are highly influential, regardless of the influence the images's other features. We also find a significant variation in memorisation with training seed. These results imply that neural networks pose a privacy risk to rarely occurring private information. This risk is more pronounced in healthcare applications since sensitive patient information can be memorised when it remains in training data due to an imperfect data sanitisation process.