Automated neuroradiological support systems for multiple cerebrovascular disease markers -- A systematic review and meta-analysis

Cerebrovascular diseases (CVD) can lead to stroke and dementia. Stroke is the second leading cause of death world wide and dementia incidence is increasing by the year. There are several markers of CVD that are visible on brain imaging, including: white matter hyperintensities (WMH), acute and chronic ischaemic stroke lesions (ISL), lacunes, enlarged perivascular spaces (PVS), acute and chronic haemorrhagic lesions, and cerebral microbleeds (CMB). Brain atrophy also occurs in CVD. These markers are important for patient management and intervention, since they indicate elevated risk of future stroke and dementia. We systematically reviewed automated systems designed to support radiologists reporting on these CVD imaging findings. We considered commercially available software and research publications which identify at least two CVD markers. In total, we included 29 commercial products and 13 research publications. Two distinct types of commercial support system were available: those which identify acute stroke lesions (haemorrhagic and ischaemic) from computed tomography (CT) scans, mainly for the purpose of patient triage; and those which measure WMH and atrophy regionally and longitudinally. In research, WMH and ISL were the markers most frequently analysed together, from magnetic resonance imaging (MRI) scans; lacunes and PVS were each targeted only twice and CMB only once. For stroke, commercially available systems largely support the emergency setting, whilst research systems consider also follow-up and routine scans. The systems to quantify WMH and atrophy are focused on neurodegenerative disease support, where these CVD markers are also of significance. There are currently no openly validated systems, commercially, or in research, performing a comprehensive joint analysis of all CVD markers (WMH, ISL, lacunes, PVS, haemorrhagic lesions, CMB, and atrophy).

Zero-Shot Medical Phrase Grounding with Off-the-shelf Diffusion Models

Localizing the exact pathological regions in a given medical scan is an important imaging problem that requires a large amount of bounding box ground truth annotations to be accurately solved. However, there exist alternative, potentially weaker, forms of supervision, such as accompanying free-text reports, which are readily available. The task of performing localization with textual guidance is commonly referred to as phrase grounding. In this work, we use a publicly available Foundation Model, namely the Latent Diffusion Model, to solve this challenging task. This choice is supported by the fact that the Latent Diffusion Model, despite being generative in nature, contains mechanisms (cross-attention) that implicitly align visual and textual features, thus leading to intermediate representations that are suitable for the task at hand. In addition, we aim to perform this task in a zero-shot manner, i.e., without any further training on target data, meaning that the model's weights remain frozen. To this end, we devise strategies to select features and also refine them via post-processing without extra learnable parameters. We compare our proposed method with state-of-the-art approaches which explicitly enforce image-text alignment in a joint embedding space via contrastive learning. Results on a popular chest X-ray benchmark indicate that our method is competitive wih SOTA on different types of pathology, and even outperforms them on average in terms of two metrics (mean IoU and AUC-ROC). Source code will be released upon acceptance.

Group Distributionally Robust Knowledge Distillation

Knowledge distillation enables fast and effective transfer of features learned from a bigger model to a smaller one. However, distillation objectives are susceptible to sub-population shifts, a common scenario in medical imaging analysis which refers to groups/domains of data that are underrepresented in the training set. For instance, training models on health data acquired from multiple scanners or hospitals can yield subpar performance for minority groups. In this paper, inspired by distributionally robust optimization (DRO) techniques, we address this shortcoming by proposing a group-aware distillation loss. During optimization, a set of weights is updated based on the per-group losses at a given iteration. This way, our method can dynamically focus on groups that have low performance during training. We empirically validate our method, GroupDistil on two benchmark datasets (natural images and cardiac MRIs) and show consistent improvement in terms of worst-group accuracy.

Compositional Representation Learning for Brain Tumour Segmentation

For brain tumour segmentation, deep learning models can achieve human expert-level performance given a large amount of data and pixel-level annotations. However, the expensive exercise of obtaining pixel-level annotations for large amounts of data is not always feasible, and performance is often heavily reduced in a low-annotated data regime. To tackle this challenge, we adapt a mixed supervision framework, vMFNet, to learn robust compositional representations using unsupervised learning and weak supervision alongside non-exhaustive pixel-level pathology labels. In particular, we use the BraTS dataset to simulate a collection of 2-point expert pathology annotations indicating the top and bottom slice of the tumour (or tumour sub-regions: peritumoural edema, GD-enhancing tumour, and the necrotic / non-enhancing tumour) in each MRI volume, from which weak image-level labels that indicate the presence or absence of the tumour (or the tumour sub-regions) in the image are constructed. Then, vMFNet models the encoded image features with von-Mises-Fisher (vMF) distributions, via learnable and compositional vMF kernels which capture information about structures in the images. We show that good tumour segmentation performance can be achieved with a large amount of weakly labelled data but only a small amount of fully-annotated data. Interestingly, emergent learning of anatomical structures occurs in the compositional representation even given only supervision relating to pathology (tumour).

Automated clinical coding using off-the-shelf large language models

The task of assigning diagnostic ICD codes to patient hospital admissions is typically performed by expert human coders. Efforts towards automated ICD coding are dominated by supervised deep learning models. However, difficulties in learning to predict the large number of rare codes remain a barrier to adoption in clinical practice. In this work, we leverage off-the-shelf pre-trained generative large language models (LLMs) to develop a practical solution that is suitable for zero-shot and few-shot code assignment. Unsupervised pre-training alone does not guarantee precise knowledge of the ICD ontology and specialist clinical coding task, therefore we frame the task as information extraction, providing a description of each coded concept and asking the model to retrieve related mentions. For efficiency, rather than iterating over all codes, we leverage the hierarchical nature of the ICD ontology to sparsely search for relevant codes. Then, in a second stage, which we term 'meta-refinement', we utilise GPT-4 to select a subset of the relevant labels as predictions. We validate our method using Llama-2, GPT-3.5 and GPT-4 on the CodiEsp dataset of ICD-coded clinical case documents. Our tree-search method achieves state-of-the-art performance on rarer classes, achieving the best macro-F1 of 0.225, whilst achieving slightly lower micro-F1 of 0.157, compared to 0.216 and 0.219 respectively from PLM-ICD. To the best of our knowledge, this is the first method for automated ICD coding requiring no task-specific learning.

Finding-Aware Anatomical Tokens for Chest X-Ray Automated Reporting

The task of radiology reporting comprises describing and interpreting the medical findings in radiographic images, including description of their location and appearance. Automated approaches to radiology reporting require the image to be encoded into a suitable token representation for input to the language model. Previous methods commonly use convolutional neural networks to encode an image into a series of image-level feature map representations. However, the generated reports often exhibit realistic style but imperfect accuracy. Inspired by recent works for image captioning in the general domain in which each visual token corresponds to an object detected in an image, we investigate whether using local tokens corresponding to anatomical structures can improve the quality of the generated reports. We introduce a novel adaptation of Faster R-CNN in which finding detection is performed for the candidate bounding boxes extracted during anatomical structure localisation. We use the resulting bounding box feature representations as our set of finding-aware anatomical tokens. This encourages the extracted anatomical tokens to be informative about the findings they contain (required for the final task of radiology reporting). Evaluating on the MIMIC-CXR dataset of chest X-Ray images, we show that task-aware anatomical tokens give state-of-the-art performance when integrated into an automated reporting pipeline, yielding generated reports with improved clinical accuracy.

Compositionally Equivariant Representation Learning

Deep learning models often need sufficient supervision (i.e. labelled data) in order to be trained effectively. By contrast, humans can swiftly learn to identify important anatomy in medical images like MRI and CT scans, with minimal guidance. This recognition capability easily generalises to new images from different medical facilities and to new tasks in different settings. This rapid and generalisable learning ability is largely due to the compositional structure of image patterns in the human brain, which are not well represented in current medical models. In this paper, we study the utilisation of compositionality in learning more interpretable and generalisable representations for medical image segmentation. Overall, we propose that the underlying generative factors that are used to generate the medical images satisfy compositional equivariance property, where each factor is compositional (e.g. corresponds to the structures in human anatomy) and also equivariant to the task. Hence, a good representation that approximates well the ground truth factor has to be compositionally equivariant. By modelling the compositional representations with learnable von-Mises-Fisher (vMF) kernels, we explore how different design and learning biases can be used to enforce the representations to be more compositionally equivariant under un-, weakly-, and semi-supervised settings. Extensive results show that our methods achieve the best performance over several strong baselines on the task of semi-supervised domain-generalised medical image segmentation. Code will be made publicly available upon acceptance at https://github.com/vios-s.

The role of noise in denoising models for anomaly detection in medical images

Pathological brain lesions exhibit diverse appearance in brain images, in terms of intensity, texture, shape, size, and location. Comprehensive sets of data and annotations are difficult to acquire. Therefore, unsupervised anomaly detection approaches have been proposed using only normal data for training, with the aim of detecting outlier anomalous voxels at test time. Denoising methods, for instance classical denoising autoencoders (DAEs) and more recently emerging diffusion models, are a promising approach, however naive application of pixelwise noise leads to poor anomaly detection performance. We show that optimization of the spatial resolution and magnitude of the noise improves the performance of different model training regimes, with similar noise parameter adjustments giving good performance for both DAEs and diffusion models. Visual inspection of the reconstructions suggests that the training noise influences the trade-off between the extent of the detail that is reconstructed and the extent of erasure of anomalies, both of which contribute to better anomaly detection performance. We validate our findings on two real-world datasets (tumor detection in brain MRI and hemorrhage/ischemia/tumor detection in brain CT), showing good detection on diverse anomaly appearances. Overall, we find that a DAE trained with coarse noise is a fast and simple method that gives state-of-the-art accuracy. Diffusion models applied to anomaly detection are as yet in their infancy and provide a promising avenue for further research.

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.