arXiv subjects

Kathleen M. Curran

Publications and source records attributed to Kathleen M. Curran.

34 records · Page 2Linked to original sources

arXiv2024

Lightweight Framework for Automated Kidney Stone Detection using coronal CT images

Kidney stone disease results in millions of annual visits to emergency departments in the United States. Computed tomography (CT) scans serve as the standard imaging modality for efficient detection of kidney stones. Various approaches utilizing convolutional neural networks (CNNs) have been proposed to implement automatic diagnosis of kidney stones. However, there is a growing interest in employing fast and efficient CNNs on edge devices in clinical practice. In this paper, we propose a lightweight fusion framework for kidney detection and kidney stone diagnosis on coronal CT images. In our design, we aim to minimize the computational costs of training and inference while implementing an automated approach. The experimental results indicate that our framework can achieve competitive outcomes using only 8\% of the original training data. These results include an F1 score of 96\% and a False Negative (FN) error rate of 4\%. Additionally, the average detection time per CT image on a CPU is 0.62 seconds. Reproducibility: Framework implementation and models available on GitHub.

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arXiv2024

Evaluate Fine-tuning Strategies for Fetal Head Ultrasound Image Segmentation with U-Net

Fetal head segmentation is a crucial step in measuring the fetal head circumference (HC) during gestation, an important biometric in obstetrics for monitoring fetal growth. However, manual biometry generation is time-consuming and results in inconsistent accuracy. To address this issue, convolutional neural network (CNN) models have been utilized to improve the efficiency of medical biometry. But training a CNN network from scratch is a challenging task, we proposed a Transfer Learning (TL) method. Our approach involves fine-tuning (FT) a U-Net network with a lightweight MobileNet as the encoder to perform segmentation on a set of fetal head ultrasound (US) images with limited effort. This method addresses the challenges associated with training a CNN network from scratch. It suggests that our proposed FT strategy yields segmentation performance that is comparable when trained with a reduced number of parameters by 85.8%. And our proposed FT strategy outperforms other strategies with smaller trainable parameter sizes below 4.4 million. Thus, we contend that it can serve as a dependable FT approach for reducing the size of models in medical image analysis. Our key findings highlight the importance of the balance between model performance and size in developing Artificial Intelligence (AI) applications by TL methods. Code is available at https://github.com/13204942/FT_Methods_for_Fetal_Head_Segmentation.

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arXiv2024

Generative Diffusion Model Bootstraps Zero-shot Classification of Fetal Ultrasound Images In Underrepresented African Populations

Developing robust deep learning models for fetal ultrasound image analysis requires comprehensive, high-quality datasets to effectively learn informative data representations within the domain. However, the scarcity of labelled ultrasound images poses substantial challenges, especially in low-resource settings. To tackle this challenge, we leverage synthetic data to enhance the generalizability of deep learning models. This study proposes a diffusion-based method, Fetal Ultrasound LoRA (FU-LoRA), which involves fine-tuning latent diffusion models using the LoRA technique to generate synthetic fetal ultrasound images. These synthetic images are integrated into a hybrid dataset that combines real-world and synthetic images to improve the performance of zero-shot classifiers in low-resource settings. Our experimental results on fetal ultrasound images from African cohorts demonstrate that FU-LoRA outperforms the baseline method by a 13.73% increase in zero-shot classification accuracy. Furthermore, FU-LoRA achieves the highest accuracy of 82.40%, the highest F-score of 86.54%, and the highest AUC of 89.78%. It demonstrates that the FU-LoRA method is effective in the zero-shot classification of fetal ultrasound images in low-resource settings. Our code and data are publicly accessible on https://github.com/13204942/FU-LoRA.

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arXiv2024

Segmenting Fetal Head with Efficient Fine-tuning Strategies in Low-resource Settings: an empirical study with U-Net

Accurate measurement of fetal head circumference is crucial for estimating fetal growth during routine prenatal screening. Prior to measurement, it is necessary to accurately identify and segment the region of interest, specifically the fetal head, in ultrasound images. Recent advancements in deep learning techniques have shown significant progress in segmenting the fetal head using encoder-decoder models. Among these models, U-Net has become a standard approach for accurate segmentation. However, training an encoder-decoder model can be a time-consuming process that demands substantial computational resources. Moreover, fine-tuning these models is particularly challenging when there is a limited amount of data available. There are still no "best-practice" guidelines for optimal fine-tuning of U-net for fetal ultrasound image segmentation. This work summarizes existing fine-tuning strategies with various backbone architectures, model components, and fine-tuning strategies across ultrasound data from Netherlands, Spain, Malawi, Egypt and Algeria. Our study shows that (1) fine-tuning U-Net leads to better performance than training from scratch, (2) fine-tuning strategies in decoder are superior to other strategies, (3) network architecture with less number of parameters can achieve similar or better performance. We also demonstrate the effectiveness of fine-tuning strategies in low-resource settings and further expand our experiments into few-shot learning. Lastly, we publicly released our code and specific fine-tuned weights.

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arXiv2024

Rethinking Knee Osteoarthritis Severity Grading: A Few Shot Self-Supervised Contrastive Learning Approach

Knee Osteoarthritis (OA) is a debilitating disease affecting over 250 million people worldwide. Currently, radiologists grade the severity of OA on an ordinal scale from zero to four using the Kellgren-Lawrence (KL) system. Recent studies have raised concern in relation to the subjectivity of the KL grading system, highlighting the requirement for an automated system, while also indicating that five ordinal classes may not be the most appropriate approach for assessing OA severity. This work presents preliminary results of an automated system with a continuous grading scale. This system, namely SS-FewSOME, uses self-supervised pre-training to learn robust representations of the features of healthy knee X-rays. It then assesses the OA severity by the X-rays' distance to the normal representation space. SS-FewSOME initially trains on only 'few' examples of healthy knee X-rays, thus reducing the barriers to clinical implementation by eliminating the need for large training sets and costly expert annotations that existing automated systems require. The work reports promising initial results, obtaining a positive Spearman Rank Correlation Coefficient of 0.43, having had access to only 30 ground truth labels at training time.

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arXiv2024

Accelerating Cardiac MRI Reconstruction with CMRatt: An Attention-Driven Approach

Cine cardiac magnetic resonance (CMR) imaging is recognised as the benchmark modality for the comprehensive assessment of cardiac function. Nevertheless, the acquisition process of cine CMR is considered as an impediment due to its prolonged scanning time. One commonly used strategy to expedite the acquisition process is through k-space undersampling, though it comes with a drawback of introducing aliasing effects in the reconstructed image. Lately, deep learning-based methods have shown remarkable results over traditional approaches in rapidly achieving precise CMR reconstructed images. This study aims to explore the untapped potential of attention mechanisms incorporated with a deep learning model within the context of the CMR reconstruction problem. We are motivated by the fact that attention has proven beneficial in downstream tasks such as image classification and segmentation, but has not been systematically analysed in the context of CMR reconstruction. Our primary goal is to identify the strengths and potential limitations of attention algorithms when integrated with a convolutional backbone model such as a U-Net. To achieve this, we benchmark different state-of-the-art spatial and channel attention mechanisms on the CMRxRecon dataset and quantitatively evaluate the quality of reconstruction using objective metrics. Furthermore, inspired by the best performing attention mechanism, we propose a new, simple yet effective, attention pipeline specifically optimised for the task of cardiac image reconstruction that outperforms other state-of-the-art attention methods. The layer and model code will be made publicly available.

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arXiv2023

Interpretable Weighted Siamese Network to Predict the Time to Onset of Alzheimer's Disease from MRI Images

Alzheimer's Disease (AD) is a progressive disease preceded by Mild Cognitive Impairment (MCI). Early detection of AD is crucial for making treatment decisions. However, most of the literature on computer-assisted detection of AD focuses on classifying brain images into one of three major categories: healthy, MCI, and AD; or categorizing MCI patients into (1) progressive: those who progress from MCI to AD at a future examination time, and (2) stable: those who stay as MCI and never progress to AD. This misses the opportunity to accurately identify the trajectory of progressive MCI patients. In this paper, we revisit the brain image classification task for AD identification and re-frame it as an ordinal classification task to predict how close a patient is to the severe AD stage. To this end, we select progressive MCI patients from the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset and construct an ordinal dataset with a prediction target that indicates the time to progression to AD. We train a Siamese network model to predict the time to onset of AD based on MRI brain images. We also propose a Weighted variety of Siamese network and compare its performance to a baseline model. Our evaluations show that incorporating a weighting factor to Siamese networks brings considerable performance gain at predicting how close input brain MRI images are to progressing to AD. Moreover, we complement our results with an interpretation of the learned embedding space of the Siamese networks using a model explainability technique.

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arXiv2023

Distance-Aware eXplanation Based Learning

eXplanation Based Learning (XBL) is an interactive learning approach that provides a transparent method of training deep learning models by interacting with their explanations. XBL augments loss functions to penalize a model based on deviation of its explanations from user annotation of image features. The literature on XBL mostly depends on the intersection of visual model explanations and image feature annotations. We present a method to add a distance-aware explanation loss to categorical losses that trains a learner to focus on important regions of a training dataset. Distance is an appropriate approach for calculating explanation loss since visual model explanations such as Gradient-weighted Class Activation Mapping (Grad-CAMs) are not strictly bounded as annotations and their intersections may not provide complete information on the deviation of a model's focus from relevant image regions. In addition to assessing our model using existing metrics, we propose an interpretability metric for evaluating visual feature-attribution based model explanations that is more informative of the model's performance than existing metrics. We demonstrate performance of our proposed method on three image classification tasks.

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arXiv2023

Unlearning Spurious Correlations in Chest X-ray Classification

Medical image classification models are frequently trained using training datasets derived from multiple data sources. While leveraging multiple data sources is crucial for achieving model generalization, it is important to acknowledge that the diverse nature of these sources inherently introduces unintended confounders and other challenges that can impact both model accuracy and transparency. A notable confounding factor in medical image classification, particularly in musculoskeletal image classification, is skeletal maturation-induced bone growth observed during adolescence. We train a deep learning model using a Covid-19 chest X-ray dataset and we showcase how this dataset can lead to spurious correlations due to unintended confounding regions. eXplanation Based Learning (XBL) is a deep learning approach that goes beyond interpretability by utilizing model explanations to interactively unlearn spurious correlations. This is achieved by integrating interactive user feedback, specifically feature annotations. In our study, we employed two non-demanding manual feedback mechanisms to implement an XBL-based approach for effectively eliminating these spurious correlations. Our results underscore the promising potential of XBL in constructing robust models even in the presence of confounding factors.

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arXiv2023

Learning from Exemplary Explanations

eXplanation Based Learning (XBL) is a form of Interactive Machine Learning (IML) that provides a model refining approach via user feedback collected on model explanations. Although the interactivity of XBL promotes model transparency, XBL requires a huge amount of user interaction and can become expensive as feedback is in the form of detailed annotation rather than simple category labelling which is more common in IML. This expense is exacerbated in high stakes domains such as medical image classification. To reduce the effort and expense of XBL we introduce a new approach that uses two input instances and their corresponding Gradient Weighted Class Activation Mapping (GradCAM) model explanations as exemplary explanations to implement XBL. Using a medical image classification task, we demonstrate that, using minimal human input, our approach produces improved explanations (+0.02, +3%) and achieves reduced classification performance (-0.04, -4%) when compared against a model trained without interactions.

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arXiv2023

FewSOME: One-Class Few Shot Anomaly Detection with Siamese Networks

Recent Anomaly Detection techniques have progressed the field considerably but at the cost of increasingly complex training pipelines. Such techniques require large amounts of training data, resulting in computationally expensive algorithms that are unsuitable for settings where only a small amount of normal samples are available for training. We propose 'Few Shot anOMaly detection' (FewSOME), a deep One-Class Anomaly Detection algorithm with the ability to accurately detect anomalies having trained on 'few' examples of the normal class and no examples of the anomalous class. We describe FewSOME to be of low complexity given its low data requirement and short training time. FewSOME is aided by pretrained weights with an architecture based on Siamese Networks. By means of an ablation study, we demonstrate how our proposed loss, 'Stop Loss', improves the robustness of FewSOME. Our experiments demonstrate that FewSOME performs at state-of-the-art level on benchmark datasets MNIST, CIFAR-10, F-MNIST and MVTec AD while training on only 30 normal samples, a minute fraction of the data that existing methods are trained on. Moreover, our experiments show FewSOME to be robust to contaminated datasets. We also report F1 score and balanced accuracy in addition to AUC as a benchmark for future techniques to be compared against. Code available; https://github.com/niamhbelton/FewSOME.

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arXiv2022

Identifying Spurious Correlations and Correcting them with an Explanation-based Learning

Identifying spurious correlations learned by a trained model is at the core of refining a trained model and building a trustworthy model. We present a simple method to identify spurious correlations that have been learned by a model trained for image classification problems. We apply image-level perturbations and monitor changes in certainties of predictions made using the trained model. We demonstrate this approach using an image classification dataset that contains images with synthetically generated spurious regions and show that the trained model was overdependent on spurious regions. Moreover, we remove the learned spurious correlations with an explanation based learning approach.

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arXiv2022

Impact of Feedback Type on Explanatory Interactive Learning

Explanatory Interactive Learning (XIL) collects user feedback on visual model explanations to implement a Human-in-the-Loop (HITL) based interactive learning scenario. Different user feedback types will have different impacts on user experience and the cost associated with collecting feedback since different feedback types involve different levels of image annotation. Although XIL has been used to improve classification performance in multiple domains, the impact of different user feedback types on model performance and explanation accuracy is not well studied. To guide future XIL work we compare the effectiveness of two different user feedback types in image classification tasks: (1) instructing an algorithm to ignore certain spurious image features, and (2) instructing an algorithm to focus on certain valid image features. We use explanations from a Gradient-weighted Class Activation Mapping (GradCAM) based XIL model to support both feedback types. We show that identifying and annotating spurious image features that a model finds salient results in superior classification and explanation accuracy than user feedback that tells a model to focus on valid image features.

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arXiv2022

Cardiac Segmentation using Transfer Learning under Respiratory Motion Artifacts

Methods that are resilient to artifacts in the cardiac magnetic resonance imaging (MRI) while performing ventricle segmentation, are crucial for ensuring quality in structural and functional analysis of those tissues. While there has been significant efforts on improving the quality of the algorithms, few works have tackled the harm that the artifacts generate in the predictions. In this work, we study fine tuning of pretrained networks to improve the resilience of previous methods to these artifacts. In our proposed method, we adopted the extensive usage of data augmentations that mimic those artifacts. The results significantly improved the baseline segmentations (up to 0.06 Dice score, and 4mm Hausdorff distance improvement).

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arXiv2021

Optimising Knee Injury Detection with Spatial Attention and Validating Localisation Ability

This work employs a pre-trained, multi-view Convolutional Neural Network (CNN) with a spatial attention block to optimise knee injury detection. An open-source Magnetic Resonance Imaging (MRI) data set with image-level labels was leveraged for this analysis. As MRI data is acquired from three planes, we compare our technique using data from a single-plane and multiple planes (multi-plane). For multi-plane, we investigate various methods of fusing the planes in the network. This analysis resulted in the novel 'MPFuseNet' network and state-of-the-art Area Under the Curve (AUC) scores for detecting Anterior Cruciate Ligament (ACL) tears and Abnormal MRIs, achieving AUC scores of 0.977 and 0.957 respectively. We then developed an objective metric, Penalised Localisation Accuracy (PLA), to validate the model's localisation ability. This metric compares binary masks generated from Grad-Cam output and the radiologist's annotations on a sample of MRIs. We also extracted explainability features in a model-agnostic approach that were then verified as clinically relevant by the radiologist.

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arXiv2021

Semi-Supervised Siamese Network for Identifying Bad Data in Medical Imaging Datasets

Noisy data present in medical imaging datasets can often aid the development of robust models that are equipped to handle real-world data. However, if the bad data contains insufficient anatomical information, it can have a severe negative effect on the model's performance. We propose a novel methodology using a semi-supervised Siamese network to identify bad data. This method requires only a small pool of 'reference' medical images to be reviewed by a non-expert human to ensure the major anatomical structures are present in the Field of View. The model trains on this reference set and identifies bad data by using the Siamese network to compute the distance between the reference set and all other medical images in the dataset. This methodology achieves an Area Under the Curve (AUC) of 0.989 for identifying bad data. Code will be available at https://git.io/JYFuV.

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