Aonghus Lawlor

Niamh Belton, Misgina Tsighe Hagos, Aonghus Lawlor et al.

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.

Niamh Belton, Aonghus Lawlor, Kathleen M. Curran

The diagnostic accuracy and subjectivity of existing Knee Osteoarthritis (OA) ordinal grading systems has been a subject of on-going debate and concern. Existing automated solutions are trained to emulate these imperfect systems, whilst also being reliant on large annotated databases for fully-supervised training. This work proposes a three stage approach for automated continuous grading of knee OA that is built upon the principles of Anomaly Detection (AD); learning a robust representation of healthy knee X-rays and grading disease severity based on its distance to the centre of normality. In the first stage, SS-FewSOME is proposed, a self-supervised AD technique that learns the 'normal' representation, requiring only examples of healthy subjects and <3% of the labels that existing methods require. In the second stage, this model is used to pseudo label a subset of unlabelled data as 'normal' or 'anomalous', followed by denoising of pseudo labels with CLIP. The final stage involves retraining on labelled and pseudo labelled data using the proposed Dual Centre Representation Learning (DCRL) which learns the centres of two representation spaces; normal and anomalous. Disease severity is then graded based on the distance to the learned centres. The proposed methodology outperforms existing techniques by margins of up to 24% in terms of OA detection and the disease severity scores correlate with the Kellgren-Lawrence grading system at the same level as human expert performance. Code available at https://github.com/niamhbelton/SS-FewSOME_Disease_Severity_Knee_Osteoarthritis.

Edoardo D'Amico, Khalil Muhammad, Elias Tragos et al.

Graph Convolutional Networks (GCN) have been recently employed as core component in the construction of recommender system algorithms, interpreting user-item interactions as the edges of a bipartite graph. However, in the absence of side information, the majority of existing models adopt an approach of randomly initialising the user embeddings and optimising them throughout the training process. This strategy makes these algorithms inherently transductive, curtailing their ability to generate predictions for users that were unseen at training time. To address this issue, we propose a convolution-based algorithm, which is inductive from the user perspective, while at the same time, depending only on implicit user-item interaction data. We propose the construction of an item-item graph through a weighted projection of the bipartite interaction network and to employ convolution to inject higher order associations into item embeddings, while constructing user representations as weighted sums of the items with which they have interacted. Despite not training individual embeddings for each user our approach achieves state of-the-art recommendation performance with respect to transductive baselines on four real-world datasets, showing at the same time robust inductive performance.

Haiwen Du, Zheng Ju, Yu An et al.

Spectrum analysis systems in online water quality testing are designed to detect types and concentrations of pollutants and enable regulatory agencies to respond promptly to pollution incidents. However, spectral data-based testing devices suffer from complex noise patterns when deployed in non-laboratory environments. To make the analysis model applicable to more environments, we propose a noise patterns transferring model, which takes the spectrum of standard water samples in different environments as cases and learns the differences in their noise patterns, thus enabling noise patterns to transfer to unknown samples. Unfortunately, the inevitable sample-level baseline noise makes the model unable to obtain the paired data that only differ in dataset-level environmental noise. To address the problem, we generate a sample-to-sample case-base to exclude the interference of sample-level noise on dataset-level noise learning, enhancing the system's learning performance. Experiments on spectral data with different background noises demonstrate the good noise-transferring ability of the proposed method against baseline systems ranging from wavelet denoising, deep neural networks, and generative models. From this research, we posit that our method can enhance the performance of DL models by generating high-quality cases. The source code is made publicly available online at https://github.com/Magnomic/CNST.

Niamh Belton, Victoria Joppin, Aonghus Lawlor et al.

This work introduces DyABD, a novel and complex benchmark dataset of dynamic abdominal MRIs from patients with abdominal hernias and associated high quality abdominal muscle annotations. DyABD is the first-of-its-kind in four key ways; (1) it proposes the first abdominal muscle segmentation task, (2) the dynamic MRIs are acquired whilst the patients perform various exercises, introducing extreme anatomical variability, making it one of the most challenging segmentation datasets to date, (3) it includes both pre and post corrective MRIs and (4) DyABD promotes clinical research into the high recurrence rates of abdominal hernias. Beyond dataset introduction, this work provides a comprehensive evaluation of the generalisation capabilities of existing segmentation models across Supervised, Few Shot and Zero Shot paradigms on the unseen DyABD dataset. This work reveals that there is still room for substantial improvement in the field of medical image segmentation, with the majority of techniques achieving a Dice Coefficient of 0.82. This work therefore sheds light on the true progress of the field and redefines the benchmark for progress in medical image segmentation.

Siteng Ma, Haochang Wu, Aonghus Lawlor et al.

Active learning (AL) has found wide applications in medical image segmentation, aiming to alleviate the annotation workload and enhance performance. Conventional uncertainty-based AL methods, such as entropy and Bayesian, often rely on an aggregate of all pixel-level metrics. However, in imbalanced settings, these methods tend to neglect the significance of target regions, eg., lesions, and tumors. Moreover, uncertainty-based selection introduces redundancy. These factors lead to unsatisfactory performance, and in many cases, even underperform random sampling. To solve this problem, we introduce a novel approach called the Selective Uncertainty-based AL, avoiding the conventional practice of summing up the metrics of all pixels. Through a filtering process, our strategy prioritizes pixels within target areas and those near decision boundaries. This resolves the aforementioned disregard for target areas and redundancy. Our method showed substantial improvements across five different uncertainty-based methods and two distinct datasets, utilizing fewer labeled data to reach the supervised baseline and consistently achieving the highest overall performance. Our code is available at https://github.com/HelenMa9998/Selective\_Uncertainty\_AL.

Siteng Ma, Honghui Du, Prateek Mathur et al.

Detecting changes in longitudinal medical imaging using deep learning requires a substantial amount of accurately labeled data. However, labeling these images is notably more costly and time-consuming than labeling other image types, as it requires labeling across various time points, where new lesions can be minor, and subtle changes are easily missed. Deep Active Learning (DAL) has shown promise in minimizing labeling costs by selectively querying the most informative samples, but existing studies have primarily focused on static tasks like classification and segmentation. Consequently, the conventional DAL approach cannot be directly applied to change detection tasks, which involve identifying subtle differences across multiple images. In this study, we propose a novel DAL framework, named Longitudinal Medical Imaging Active Learning (LMI-AL), tailored specifically for longitudinal medical imaging. By pairing and differencing all 2D slices from baseline and follow-up 3D images, LMI-AL iteratively selects the most informative pairs for labeling using DAL, training a deep learning model with minimal manual annotation. Experimental results demonstrate that, with less than 8% of the data labeled, LMI-AL can achieve performance comparable to models trained on fully labeled datasets. We also provide a detailed analysis of the method's performance, as guidance for future research. The code is publicly available at https://github.com/HelenMa9998/Longitudinal_AL.

Niamh Belton, Ivan Welaratne, Adil Dahlan et al.

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.

Honghui Du, Leandro Minku, Aonghus Lawlor et al.

Label concepts in multi-label data streams often experience drift in non-stationary environments, either independently or in relation to other labels. Transferring knowledge between related labels can accelerate adaptation, yet research on multi-label transfer learning for data streams remains limited. To address this, we propose two novel transfer learning methods: BR-MARLENE leverages knowledge from different labels in both source and target streams for multi-label classification; BRPW-MARLENE builds on this by explicitly modelling and transferring pairwise label dependencies to enhance learning performance. Comprehensive experiments show that both methods outperform state-of-the-art multi-label stream approaches in non-stationary environments, demonstrating the effectiveness of inter-label knowledge transfer for improved predictive performance.

Siteng Ma, Honghui Du, Yu An et al.

Deep learning has achieved significant breakthroughs in medical imaging, but these advancements are often dependent on large, well-annotated datasets. However, obtaining such datasets poses a significant challenge, as it requires time-consuming and labor-intensive annotations from medical experts. Consequently, there is growing interest in learning paradigms such as incomplete, inexact, and absent supervision, which are designed to operate under limited, inexact, or missing labels. This survey categorizes and reviews the evolving research in these areas, analyzing around 600 notable contributions since 2018. It covers tasks such as image classification, segmentation, and detection across various medical application areas, including but not limited to brain, chest, and cardiac imaging. We attempt to establish the relationships among existing research studies in related areas. We provide formal definitions of different learning paradigms and offer a comprehensive summary and interpretation of various learning mechanisms and strategies, aiding readers in better understanding the current research landscape and ideas. We also discuss potential future research challenges.

Niamh Belton, Misgina Tsighe Hagos, Aonghus Lawlor et al.

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.

Edoardo D'Amico, Aonghus Lawlor, Neil Hurley

The use of graph convolution in the development of recommender system algorithms has recently achieved state-of-the-art results in the collaborative filtering task (CF). While it has been demonstrated that the graph convolution operation is connected to a filtering operation on the graph spectral domain, the theoretical rationale for why this leads to higher performance on the collaborative filtering problem remains unknown. The presented work makes two contributions. First, we investigate the effect of using graph convolution throughout the user and item representation learning processes, demonstrating how the latent features learned are pushed from the filtering operation into the subspace spanned by the eigenvectors associated with the highest eigenvalues of the normalised adjacency matrix, and how vectors lying on this subspace are the optimal solutions for an objective function related to the sum of the prediction function over the training data. Then, we present an approach that directly leverages the eigenvectors to emulate the solution obtained through graph convolution, eliminating the requirement for a time-consuming gradient descent training procedure while also delivering higher performance on three real-world datasets.

Niamh Belton, Aonghus Lawlor, Kathleen M. Curran

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.

Sixun Ouyang, Aonghus Lawlor, Felipe Costa et al.

An important task for a recommender system to provide interpretable explanations for the user. This is important for the credibility of the system. Current interpretable recommender systems tend to focus on certain features known to be important to the user and offer their explanations in a structured form. It is well known that user generated reviews and feedback from reviewers have strong leverage over the users' decisions. On the other hand, recent text generation works have been shown to generate text of similar quality to human written text, and we aim to show that generated text can be successfully used to explain recommendations. In this paper, we propose a framework consisting of popular review-oriented generation models aiming to create personalised explanations for recommendations. The interpretations are generated at both character and word levels. We build a dataset containing reviewers' feedback from the Amazon books review dataset. Our cross-domain experiments are designed to bridge from natural language processing to the recommender system domain. Besides language model evaluation methods, we employ DeepCoNN, a novel review-oriented recommender system using a deep neural network, to evaluate the recommendation performance of generated reviews by root mean square error (RMSE). We demonstrate that the synthetic personalised reviews have better recommendation performance than human written reviews. To our knowledge, this presents the first machine-generated natural language explanations for rating prediction.

Felipe Costa, Sixun Ouyang, Peter Dolog et al.

An important task for recommender system is to generate explanations according to a user's preferences. Most of the current methods for explainable recommendations use structured sentences to provide descriptions along with the recommendations they produce. However, those methods have neglected the review-oriented way of writing a text, even though it is known that these reviews have a strong influence over user's decision. In this paper, we propose a method for the automatic generation of natural language explanations, for predicting how a user would write about an item, based on user ratings from different items' features. We design a character-level recurrent neural network (RNN) model, which generates an item's review explanations using long-short term memories (LSTM). The model generates text reviews given a combination of the review and ratings score that express opinions about different factors or aspects of an item. Our network is trained on a sub-sample from the large real-world dataset BeerAdvocate. Our empirical evaluation using natural language processing metrics shows the generated text's quality is close to a real user written review, identifying negation, misspellings, and domain specific vocabulary.