David Wood

David A. Wood, Jeremy Lynch, Sina Kafiabadi et al.

Labelling large datasets for training high-capacity neural networks is a major obstacle to the development of deep learning-based medical imaging applications. Here we present a transformer-based network for magnetic resonance imaging (MRI) radiology report classification which automates this task by assigning image labels on the basis of free-text expert radiology reports. Our model's performance is comparable to that of an expert radiologist, and better than that of an expert physician, demonstrating the feasibility of this approach. We make code available online for researchers to label their own MRI datasets for medical imaging applications.

Karan Daga, Siddharth Agarwal, Zaeem Moti et al.

Purpose: Subarachnoid haemorrhage is a potentially fatal consequence of intracranial aneurysm rupture, however, it is difficult to predict if aneurysms will rupture. Prophylactic treatment of an intracranial aneurysm also involves risk, hence identifying rupture-prone aneurysms is of substantial clinical importance. This systematic review aims to evaluate the performance of machine learning algorithms for predicting intracranial aneurysm rupture risk. Methods: MEDLINE, Embase, Cochrane Library and Web of Science were searched until December 2023. Studies incorporating any machine learning algorithm to predict the risk of rupture of an intracranial aneurysm were included. Risk of bias was assessed using the Prediction Model Risk of Bias Assessment Tool (PROBAST). PROSPERO registration: CRD42023452509. Results: Out of 10,307 records screened, 20 studies met the eligibility criteria for this review incorporating a total of 20,286 aneurysm cases. The machine learning models gave a 0.66-0.90 range for performance accuracy. The models were compared to current clinical standards in six studies and gave mixed results. Most studies posed high or unclear risks of bias and concerns for applicability, limiting the inferences that can be drawn from them. There was insufficient homogenous data for a meta-analysis. Conclusions: Machine learning can be applied to predict the risk of rupture for intracranial aneurysms. However, the evidence does not comprehensively demonstrate superiority to existing practice, limiting its role as a clinical adjunct. Further prospective multicentre studies of recent machine learning tools are needed to prove clinical validation before they are implemented in the clinic.

David A. Wood, Emily Guilhem, Sina Kafiabadi et al.

Artificial neural networks trained on large, expert-labelled datasets are considered state-of-the-art for a range of medical image recognition tasks. However, categorically labelled datasets are time-consuming to generate and constrain classification to a pre-defined, fixed set of classes. For neuroradiological applications in particular, this represents a barrier to clinical adoption. To address these challenges, we present a self-supervised text-vision framework that learns to detect clinically relevant abnormalities in brain MRI scans by directly leveraging the rich information contained in accompanying free-text neuroradiology reports. Our training approach consisted of two-steps. First, a dedicated neuroradiological language model - NeuroBERT - was trained to generate fixed-dimensional vector representations of neuroradiology reports (N = 50,523) via domain-specific self-supervised learning tasks. Next, convolutional neural networks (one per MRI sequence) learnt to map individual brain scans to their corresponding text vector representations by optimising a mean square error loss. Once trained, our text-vision framework can be used to detect abnormalities in unreported brain MRI examinations by scoring scans against suitable query sentences (e.g., 'there is an acute stroke', 'there is hydrocephalus' etc.), enabling a range of classification-based applications including automated triage. Potentially, our framework could also serve as a clinical decision support tool, not only by suggesting findings to radiologists and detecting errors in provisional reports, but also by retrieving and displaying examples of pathologies from historical examinations that could be relevant to the current case based on textual descriptors.

Siddharth Agarwal, David A. Wood, Mariusz Grzeda et al.

Purpose: Most studies evaluating artificial intelligence (AI) models that detect abnormalities in neuroimaging are either tested on unrepresentative patient cohorts or are insufficiently well-validated, leading to poor generalisability to real-world tasks. The aim was to determine the diagnostic test accuracy and summarise the evidence supporting the use of AI models performing first-line, high-volume neuroimaging tasks. Methods: Medline, Embase, Cochrane library and Web of Science were searched until September 2021 for studies that temporally or externally validated AI capable of detecting abnormalities in first-line CT or MR neuroimaging. A bivariate random-effects model was used for meta-analysis where appropriate. PROSPERO: CRD42021269563. Results: Only 16 studies were eligible for inclusion. Included studies were not compromised by unrepresentative datasets or inadequate validation methodology. Direct comparison with radiologists was available in 4/16 studies. 15/16 had a high risk of bias. Meta-analysis was only suitable for intracranial haemorrhage detection in CT imaging (10/16 studies), where AI systems had a pooled sensitivity and specificity 0.90 (95% CI 0.85 - 0.94) and 0.90 (95% CI 0.83 - 0.95) respectively. Other AI studies using CT and MRI detected target conditions other than haemorrhage (2/16), or multiple target conditions (4/16). Only 3/16 studies implemented AI in clinical pathways, either for pre-read triage or as post-read discrepancy identifiers. Conclusion: The paucity of eligible studies reflects that most abnormality detection AI studies were not adequately validated in representative clinical cohorts. The few studies describing how abnormality detection AI could impact patients and clinicians did not explore the full ramifications of clinical implementation.

David A. Wood

Clinical neuroimaging data is naturally hierarchical. Different magnetic resonance imaging (MRI) sequences within a series, different slices covering the head, and different regions within each slice all confer different information. In this work we present a hierarchical attention network for abnormality detection using MRI scans obtained in a clinical hospital setting. The proposed network is suitable for non-volumetric data (i.e. stacks of high-resolution MRI slices), and can be trained from binary examination-level labels. We show that this hierarchical approach leads to improved classification, while providing interpretability through either coarse inter- and intra-slice abnormality localisation, or giving importance scores for different slices and sequences, making our model suitable for use as an automated triaging system in radiology departments.

David A. Wood, Sina Kafiabadi, Ayisha Al Busaidi et al.

The growing demand for head magnetic resonance imaging (MRI) examinations, along with a global shortage of radiologists, has led to an increase in the time taken to report head MRI scans around the world. For many neurological conditions, this delay can result in increased morbidity and mortality. An automated triaging tool could reduce reporting times for abnormal examinations by identifying abnormalities at the time of imaging and prioritizing the reporting of these scans. In this work, we present a convolutional neural network for detecting clinically-relevant abnormalities in $\text{T}_2$-weighted head MRI scans. Using a validated neuroradiology report classifier, we generated a labelled dataset of 43,754 scans from two large UK hospitals for model training, and demonstrate accurate classification (area under the receiver operating curve (AUC) = 0.943) on a test set of 800 scans labelled by a team of neuroradiologists. Importantly, when trained on scans from only a single hospital the model generalized to scans from the other hospital ($Δ$AUC $\leq$ 0.02). A simulation study demonstrated that our model would reduce the mean reporting time for abnormal examinations from 28 days to 14 days and from 9 days to 5 days at the two hospitals, demonstrating feasibility for use in a clinical triage environment.

Syed Yousaf Shah, Dhaval Patel, Long Vu et al.

A large number of time series forecasting models including traditional statistical models, machine learning models and more recently deep learning have been proposed in the literature. However, choosing the right model along with good parameter values that performs well on a given data is still challenging. Automatically providing a good set of models to users for a given dataset saves both time and effort from using trial-and-error approaches with a wide variety of available models along with parameter optimization. We present AutoAI for Time Series Forecasting (AutoAI-TS) that provides users with a zero configuration (zero-conf ) system to efficiently train, optimize and choose best forecasting model among various classes of models for the given dataset. With its flexible zero-conf design, AutoAI-TS automatically performs all the data preparation, model creation, parameter optimization, training and model selection for users and provides a trained model that is ready to use. For given data, AutoAI-TS utilizes a wide variety of models including classical statistical models, Machine Learning (ML) models, statistical-ML hybrid models and deep learning models along with various transformations to create forecasting pipelines. It then evaluates and ranks pipelines using the proposed T-Daub mechanism to choose the best pipeline. The paper describe in detail all the technical aspects of AutoAI-TS along with extensive benchmarking on a variety of real world data sets for various use-cases. Benchmark results show that AutoAI-TS, with no manual configuration from the user, automatically trains and selects pipelines that on average outperform existing state-of-the-art time series forecasting toolkits.

David A. Wood, Sina Kafiabadi, Aisha Al Busaidi et al.

Natural language processing (NLP) shows promise as a means to automate the labelling of hospital-scale neuroradiology magnetic resonance imaging (MRI) datasets for computer vision applications. To date, however, there has been no thorough investigation into the validity of this approach, including determining the accuracy of report labels compared to image labels as well as examining the performance of non-specialist labellers. In this work, we draw on the experience of a team of neuroradiologists who labelled over 5000 MRI neuroradiology reports as part of a project to build a dedicated deep learning-based neuroradiology report classifier. We show that, in our experience, assigning binary labels (i.e. normal vs abnormal) to images from reports alone is highly accurate. In contrast to the binary labels, however, the accuracy of more granular labelling is dependent on the category, and we highlight reasons for this discrepancy. We also show that downstream model performance is reduced when labelling of training reports is performed by a non-specialist. To allow other researchers to accelerate their research, we make our refined abnormality definitions and labelling rules available, as well as our easy-to-use radiology report labelling app which helps streamline this process.

David Wood, James Cole, Thomas Booth

Deep learning is attracting significant interest in the neuroimaging community as a means to diagnose psychiatric and neurological disorders from structural magnetic resonance images. However, there is a tendency amongst researchers to adopt architectures optimized for traditional computer vision tasks, rather than design networks customized for neuroimaging data. We address this by introducing NEURO-DRAM, a 3D recurrent visual attention model tailored for neuroimaging classification. The model comprises an agent which, trained by reinforcement learning, learns to navigate through volumetric images, selectively attending to the most informative regions for a given task. When applied to Alzheimer's disease prediction, NEURODRAM achieves state-of-the-art classification accuracy on an out-of-sample dataset, significantly outperforming a baseline convolutional neural network. When further applied to the task of predicting which patients with mild cognitive impairment will be diagnosed with Alzheimer's disease within two years, the model achieves state-of-the-art accuracy with no additional training. Encouragingly, the agent learns, without explicit instruction, a search policy in agreement with standardized radiological hallmarks of Alzheimer's disease, suggesting a route to automated biomarker discovery for more poorly understood disorders.