arXiv subjects

Sotirios A. Tsaftaris

Publications and source records attributed to Sotirios A. Tsaftaris.

At least 73 records · Page 4Linked to original sources

arXiv2022

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.

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arXiv2022

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.

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arXiv2022

Re-using Adversarial Mask Discriminators for Test-time Training under Distribution Shifts

Thanks to their ability to learn flexible data-driven losses, Generative Adversarial Networks (GANs) are an integral part of many semi- and weakly-supervised methods for medical image segmentation. GANs jointly optimise a generator and an adversarial discriminator on a set of training data. After training is complete, the discriminator is usually discarded, and only the generator is used for inference. But should we discard discriminators? In this work, we argue that training stable discriminators produces expressive loss functions that we can re-use at inference to detect and \textit{correct} segmentation mistakes. First, we identify key challenges and suggest possible solutions to make discriminators re-usable at inference. Then, we show that we can combine discriminators with image reconstruction costs (via decoders) to endow a causal perspective to test-time training and further improve the model. Our method is simple and improves the test-time performance of pre-trained GANs. Moreover, we show that it is compatible with standard post-processing techniques and it has the potential to be used for Online Continual Learning. With our work, we open new research avenues for re-using adversarial discriminators at inference. Our code is available at https://vios-s.github.io/adversarial-test-time-training.

cs.CV↗

arXiv2022

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.

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arXiv2022

Diffusion Causal Models for Counterfactual Estimation

We consider the task of counterfactual estimation from observational imaging data given a known causal structure. In particular, quantifying the causal effect of interventions for high-dimensional data with neural networks remains an open challenge. Herein we propose Diff-SCM, a deep structural causal model that builds on recent advances of generative energy-based models. In our setting, inference is performed by iteratively sampling gradients of the marginal and conditional distributions entailed by the causal model. Counterfactual estimation is achieved by firstly inferring latent variables with deterministic forward diffusion, then intervening on a reverse diffusion process using the gradients of an anti-causal predictor w.r.t the input. Furthermore, we propose a metric for evaluating the generated counterfactuals. We find that Diff-SCM produces more realistic and minimal counterfactuals than baselines on MNIST data and can also be applied to ImageNet data. Code is available https://github.com/vios-s/Diff-SCM.

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arXiv2022

Measuring Unintended Memorisation of Unique Private Features in Neural Networks

Neural networks pose a privacy risk to training data due to their propensity to memorise and leak information. Focusing on image classification, we show that neural networks also unintentionally memorise unique features even when they occur only once in training data. An example of a unique feature is a person's name that is accidentally present on a training image. Assuming access to the inputs and outputs of a trained model, the domain of the training data, and knowledge of unique features, we develop a score estimating the model's sensitivity to a unique feature by comparing the KL divergences of the model's output distributions given modified out-of-distribution images. Our results suggest that unique features are memorised by multi-layer perceptrons and convolutional neural networks trained on benchmark datasets, such as MNIST, Fashion-MNIST and CIFAR-10. We find that strategies to prevent overfitting (e.g.\ early stopping, regularisation, batch normalisation) do not prevent memorisation of unique features. These results imply that neural networks pose a privacy risk to rarely occurring private information. These risks can be more pronounced in healthcare applications if patient information is present in the training data.

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arXiv2022

Indication as Prior Knowledge for Multimodal Disease Classification in Chest Radiographs with Transformers

When a clinician refers a patient for an imaging exam, they include the reason (e.g. relevant patient history, suspected disease) in the scan request; this appears as the indication field in the radiology report. The interpretation and reporting of the image are substantially influenced by this request text, steering the radiologist to focus on particular aspects of the image. We use the indication field to drive better image classification, by taking a transformer network which is unimodally pre-trained on text (BERT) and fine-tuning it for multimodal classification of a dual image-text input. We evaluate the method on the MIMIC-CXR dataset, and present ablation studies to investigate the effect of the indication field on the classification performance. The experimental results show our approach achieves 87.8 average micro AUROC, outperforming the state-of-the-art methods for unimodal (84.4) and multimodal (86.0) classification. Our code is available at https://github.com/jacenkow/mmbt.

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arXiv2022

OMASGAN: Out-of-Distribution Minimum Anomaly Score GAN for Sample Generation on the Boundary

Generative models trained in an unsupervised manner may set high likelihood and low reconstruction loss to Out-of-Distribution (OoD) samples. This increases Type II errors and leads to missed anomalies, overall decreasing Anomaly Detection (AD) performance. In addition, AD models underperform due to the rarity of anomalies. To address these limitations, we propose the OoD Minimum Anomaly Score GAN (OMASGAN). OMASGAN generates, in a negative data augmentation manner, anomalous samples on the estimated distribution boundary. These samples are then used to refine an AD model, leading to more accurate estimation of the underlying data distribution including multimodal supports with disconnected modes. OMASGAN performs retraining by including the abnormal minimum-anomaly-score OoD samples generated on the distribution boundary in a self-supervised learning manner. For inference, for AD, we devise a discriminator which is trained with negative and positive samples either generated (negative or positive) or real (only positive). OMASGAN addresses the rarity of anomalies by generating strong and adversarial OoD samples on the distribution boundary using only normal class data, effectively addressing mode collapse. A key characteristic of our model is that it uses any f-divergence distribution metric in its variational representation, not requiring invertibility. OMASGAN does not use feature engineering and makes no assumptions about the data distribution. The evaluation of OMASGAN on image data using the leave-one-out methodology shows that it achieves an improvement of at least 0.24 and 0.07 points in AUROC on average on the MNIST and CIFAR-10 datasets, respectively, over other benchmark and state-of-the-art models for AD.

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arXiv2022

FROB: Few-shot ROBust Model for Classification and Out-of-Distribution Detection

Nowadays, classification and Out-of-Distribution (OoD) detection in the few-shot setting remain challenging aims due to rarity and the limited samples in the few-shot setting, and because of adversarial attacks. Accomplishing these aims is important for critical systems in safety, security, and defence. In parallel, OoD detection is challenging since deep neural network classifiers set high confidence to OoD samples away from the training data. To address such limitations, we propose the Few-shot ROBust (FROB) model for classification and few-shot OoD detection. We devise FROB for improved robustness and reliable confidence prediction for few-shot OoD detection. We generate the support boundary of the normal class distribution and combine it with few-shot Outlier Exposure (OE). We propose a self-supervised learning few-shot confidence boundary methodology based on generative and discriminative models. The contribution of FROB is the combination of the generated boundary in a self-supervised learning manner and the imposition of low confidence at this learned boundary. FROB implicitly generates strong adversarial samples on the boundary and forces samples from OoD, including our boundary, to be less confident by the classifier. FROB achieves generalization to unseen OoD with applicability to unknown, in the wild, test sets that do not correlate to the training datasets. To improve robustness, FROB redesigns OE to work even for zero-shots. By including our boundary, FROB reduces the threshold linked to the model's few-shot robustness; it maintains the OoD performance approximately independent of the number of few-shots. The few-shot robustness analysis evaluation of FROB on different sets and on One-Class Classification (OCC) data shows that FROB achieves competitive performance and outperforms benchmarks in terms of robustness to the outlier few-shot sample population and variability.

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arXiv2022

Boundary of Distribution Support Generator (BDSG): Sample Generation on the Boundary

Generative models, such as Generative Adversarial Networks (GANs), have been used for unsupervised anomaly detection. While performance keeps improving, several limitations exist particularly attributed to difficulties at capturing multimodal supports and to the ability to approximate the underlying distribution closer to the tails, i.e. the boundary of the distribution's support. This paper proposes an approach that attempts to alleviate such shortcomings. We propose an invertible-residual-network-based model, the Boundary of Distribution Support Generator (BDSG). GANs generally do not guarantee the existence of a probability distribution and here, we use the recently developed Invertible Residual Network (IResNet) and Residual Flow (ResFlow), for density estimation. These models have not yet been used for anomaly detection. We leverage IResNet and ResFlow for Out-of-Distribution (OoD) sample detection and for sample generation on the boundary using a compound loss function that forces the samples to lie on the boundary. The BDSG addresses non-convex support, disjoint components, and multimodal distributions. Results on synthetic data and data from multimodal distributions, such as MNIST and CIFAR-10, demonstrate competitive performance compared to methods from the literature.

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arXiv2022

Tail of Distribution GAN (TailGAN): Generative-Adversarial-Network-Based Boundary Formation

Generative Adversarial Networks (GAN) are a powerful methodology and can be used for unsupervised anomaly detection, where current techniques have limitations such as the accurate detection of anomalies near the tail of a distribution. GANs generally do not guarantee the existence of a probability density and are susceptible to mode collapse, while few GANs use likelihood to reduce mode collapse. In this paper, we create a GAN-based tail formation model for anomaly detection, the Tail of distribution GAN (TailGAN), to generate samples on the tail of the data distribution and detect anomalies near the support boundary. Using TailGAN, we leverage GANs for anomaly detection and use maximum entropy regularization. Using GANs that learn the probability of the underlying distribution has advantages in improving the anomaly detection methodology by allowing us to devise a generator for boundary samples, and use this model to characterize anomalies. TailGAN addresses supports with disjoint components and achieves competitive performance on images. We evaluate TailGAN for identifying Out-of-Distribution (OoD) data and its performance evaluated on MNIST, CIFAR-10, Baggage X-Ray, and OoD data shows competitiveness compared to methods from the literature.

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arXiv2022

MyoPS: A Benchmark of Myocardial Pathology Segmentation Combining Three-Sequence Cardiac Magnetic Resonance Images

Assessment of myocardial viability is essential in diagnosis and treatment management of patients suffering from myocardial infarction, and classification of pathology on myocardium is the key to this assessment. This work defines a new task of medical image analysis, i.e., to perform myocardial pathology segmentation (MyoPS) combining three-sequence cardiac magnetic resonance (CMR) images, which was first proposed in the MyoPS challenge, in conjunction with MICCAI 2020. The challenge provided 45 paired and pre-aligned CMR images, allowing algorithms to combine the complementary information from the three CMR sequences for pathology segmentation. In this article, we provide details of the challenge, survey the works from fifteen participants and interpret their methods according to five aspects, i.e., preprocessing, data augmentation, learning strategy, model architecture and post-processing. In addition, we analyze the results with respect to different factors, in order to examine the key obstacles and explore potential of solutions, as well as to provide a benchmark for future research. We conclude that while promising results have been reported, the research is still in the early stage, and more in-depth exploration is needed before a successful application to the clinics. Note that MyoPS data and evaluation tool continue to be publicly available upon registration via its homepage (www.sdspeople.fudan.edu.cn/zhuangxiahai/0/myops20/).

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arXiv2021

Semi-supervised Meta-learning with Disentanglement for Domain-generalised Medical Image Segmentation

Generalising deep models to new data from new centres (termed here domains) remains a challenge. This is largely attributed to shifts in data statistics (domain shifts) between source and unseen domains. Recently, gradient-based meta-learning approaches where the training data are split into meta-train and meta-test sets to simulate and handle the domain shifts during training have shown improved generalisation performance. However, the current fully supervised meta-learning approaches are not scalable for medical image segmentation, where large effort is required to create pixel-wise annotations. Meanwhile, in a low data regime, the simulated domain shifts may not approximate the true domain shifts well across source and unseen domains. To address this problem, we propose a novel semi-supervised meta-learning framework with disentanglement. We explicitly model the representations related to domain shifts. Disentangling the representations and combining them to reconstruct the input image allows unlabeled data to be used to better approximate the true domain shifts for meta-learning. Hence, the model can achieve better generalisation performance, especially when there is a limited amount of labeled data. Experiments show that the proposed method is robust on different segmentation tasks and achieves state-of-the-art generalisation performance on two public benchmarks.

cs.CV↗

arXiv2021

Learning to synthesise the ageing brain without longitudinal data

How will my face look when I get older? Or, for a more challenging question: How will my brain look when I get older? To answer this question one must devise (and learn from data) a multivariate auto-regressive function which given an image and a desired target age generates an output image. While collecting data for faces may be easier, collecting longitudinal brain data is not trivial. We propose a deep learning-based method that learns to simulate subject-specific brain ageing trajectories without relying on longitudinal data. Our method synthesises images conditioned on two factors: age (a continuous variable), and status of Alzheimer's Disease (AD, an ordinal variable). With an adversarial formulation we learn the joint distribution of brain appearance, age and AD status, and define reconstruction losses to address the challenging problem of preserving subject identity. We compare with several benchmarks using two widely used datasets. We evaluate the quality and realism of synthesised images using ground-truth longitudinal data and a pre-trained age predictor. We show that, despite the use of cross-sectional data, our model learns patterns of gray matter atrophy in the middle temporal gyrus in patients with AD. To demonstrate generalisation ability, we train on one dataset and evaluate predictions on the other. In conclusion, our model shows an ability to separate age, disease influence and anatomy using only 2D cross-sectional data that should be useful in large studies into neurodegenerative disease, that aim to combine several data sources. To facilitate such future studies by the community at large our code is made available at https://github.com/xiat0616/BrainAgeing.

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arXiv2021

Measuring the Biases and Effectiveness of Content-Style Disentanglement

A recent spate of state-of-the-art semi- and un-supervised solutions disentangle and encode image "content" into a spatial tensor and image appearance or "style" into a vector, to achieve good performance in spatially equivariant tasks (e.g. image-to-image translation). To achieve this, they employ different model design, learning objective, and data biases. While considerable effort has been made to measure disentanglement in vector representations, and assess its impact on task performance, such analysis for (spatial) content - style disentanglement is lacking. In this paper, we conduct an empirical study to investigate the role of different biases in content-style disentanglement settings and unveil the relationship between the degree of disentanglement and task performance. In particular, we consider the setting where we: (i) identify key design choices and learning constraints for three popular content-style disentanglement models; (ii) relax or remove such constraints in an ablation fashion; and (iii) use two metrics to measure the degree of disentanglement and assess its effect on each task performance. Our experiments reveal that there is a "sweet spot" between disentanglement, task performance and - surprisingly - content interpretability, suggesting that blindly forcing for higher disentanglement can hurt model performance and content factors semanticness. Our findings, as well as the used task-independent metrics, can be used to guide the design and selection of new models for tasks where content-style representations are useful.

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arXiv2021

Self-supervised Multi-scale Consistency for Weakly Supervised Segmentation Learning

Collecting large-scale medical datasets with fine-grained annotations is time-consuming and requires experts. For this reason, weakly supervised learning aims at optimising machine learning models using weaker forms of annotations, such as scribbles, which are easier and faster to collect. Unfortunately, training with weak labels is challenging and needs regularisation. Herein, we introduce a novel self-supervised multi-scale consistency loss, which, coupled with an attention mechanism, encourages the segmentor to learn multi-scale relationships between objects and improves performance. We show state-of-the-art performance on several medical and non-medical datasets. The code used for the experiments is available at https://vios-s.github.io/multiscale-pyag.

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arXiv2021

Stop Throwing Away Discriminators! Re-using Adversaries for Test-Time Training

Thanks to their ability to learn data distributions without requiring paired data, Generative Adversarial Networks (GANs) have become an integral part of many computer vision methods, including those developed for medical image segmentation. These methods jointly train a segmentor and an adversarial mask discriminator, which provides a data-driven shape prior. At inference, the discriminator is discarded, and only the segmentor is used to predict label maps on test images. But should we discard the discriminator? Here, we argue that the life cycle of adversarial discriminators should not end after training. On the contrary, training stable GANs produces powerful shape priors that we can use to correct segmentor mistakes at inference. To achieve this, we develop stable mask discriminators that do not overfit or catastrophically forget. At test time, we fine-tune the segmentor on each individual test instance until it satisfies the learned shape prior. Our method is simple to implement and increases model performance. Moreover, it opens new directions for re-using mask discriminators at inference. We release the code used for the experiments at https://vios-s.github.io/adversarial-test-time-training.

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arXiv2021

Controllable cardiac synthesis via disentangled anatomy arithmetic

Acquiring annotated data at scale with rare diseases or conditions remains a challenge. It would be extremely useful to have a method that controllably synthesizes images that can correct such underrepresentation. Assuming a proper latent representation, the idea of a "latent vector arithmetic" could offer the means of achieving such synthesis. A proper representation must encode the fidelity of the input data, preserve invariance and equivariance, and permit arithmetic operations. Motivated by the ability to disentangle images into spatial anatomy (tensor) factors and accompanying imaging (vector) representations, we propose a framework termed "disentangled anatomy arithmetic", in which a generative model learns to combine anatomical factors of different input images such that when they are re-entangled with the desired imaging modality (e.g. MRI), plausible new cardiac images are created with the target characteristics. To encourage a realistic combination of anatomy factors after the arithmetic step, we propose a localized noise injection network that precedes the generator. Our model is used to generate realistic images, pathology labels, and segmentation masks that are used to augment the existing datasets and subsequently improve post-hoc classification and segmentation tasks. Code is publicly available at https://github.com/vios-s/DAA-GAN.

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