arXiv subjects

Paul Taylor

Publications and source records attributed to Paul Taylor.

15 recordsLinked to original sources

arXiv2026

Seeking Necessary and Sufficient Information from Multimodal Medical Data

Learning multimodal representations from medical images and other data sources can provide richer information for decision-making. While various multimodal models have been developed for this, they overlook learning features that are both necessary (must be present for the outcome to occur) and sufficient (enough to determine the outcome). We argue learning such features is crucial as they can improve model performance by capturing essential predictive information, and enhance model robustness to missing modalities as each modality can provide adequate predictive signals. Such features can be learned by leveraging the Probability of Necessity and Sufficiency (PNS) as a learning objective, an approach that has proven effective in unimodal settings. However, extending PNS to multimodal scenarios remains underexplored and is non-trivial as key conditions of PNS estimation are violated. We address this by decomposing multimodal representations into modality-invariant and modality-specific components, then deriving tractable PNS objectives for each. Experiments on synthetic and real-world medical datasets demonstrate our method's effectiveness. Code will be available on GitHub.

cs.CV↗

arXiv2025

A computationally frugal open-source foundation model for thoracic disease detection in lung cancer screening programs

Low-dose computed tomography (LDCT) imaging employed in lung cancer screening (LCS) programs is increasing in uptake worldwide. LCS programs herald a generational opportunity to simultaneously detect cancer and non-cancer-related early-stage lung disease. Yet these efforts are hampered by a shortage of radiologists to interpret scans at scale. Here, we present TANGERINE, a computationally frugal, open-source vision foundation model for volumetric LDCT analysis. Designed for broad accessibility and rapid adaptation, TANGERINE can be fine-tuned off the shelf for a wide range of disease-specific tasks with limited computational resources and training data. Relative to models trained from scratch, TANGERINE demonstrates fast convergence during fine-tuning, thereby requiring significantly fewer GPU hours, and displays strong label efficiency, achieving comparable or superior performance with a fraction of fine-tuning data. Pretrained using self-supervised learning on over 98,000 thoracic LDCTs, including the UK's largest LCS initiative to date and 27 public datasets, TANGERINE achieves state-of-the-art performance across 14 disease classification tasks, including lung cancer and multiple respiratory diseases, while generalising robustly across diverse clinical centres. By extending a masked autoencoder framework to 3D imaging, TANGERINE offers a scalable solution for LDCT analysis, departing from recent closed, resource-intensive models by combining architectural simplicity, public availability, and modest computational requirements. Its accessible, open-source lightweight design lays the foundation for rapid integration into next-generation medical imaging tools that could transform LCS initiatives, allowing them to pivot from a singular focus on lung cancer detection to comprehensive respiratory disease management in high-risk populations.

eess.IV↗

arXiv2025

Minuscule Cell Detection in AS-OCT Images with Progressive Field-of-View Focusing

Anterior Segment Optical Coherence Tomography (AS-OCT) is an emerging imaging technique with great potential for diagnosing anterior uveitis, a vision-threatening ocular inflammatory condition. A hallmark of this condition is the presence of inflammatory cells in the eye's anterior chamber, and detecting these cells using AS-OCT images has attracted research interest. While recent efforts aim to replace manual cell detection with automated computer vision approaches, detecting extremely small (minuscule) objects in high-resolution images, such as AS-OCT, poses substantial challenges: (1) each cell appears as a minuscule particle, representing less than 0.005\% of the image, making the detection difficult, and (2) OCT imaging introduces pixel-level noise that can be mistaken for cells, leading to false positive detections. To overcome these challenges, we propose a minuscule cell detection framework through a progressive field-of-view focusing strategy. This strategy systematically refines the detection scope from the whole image to a target region where cells are likely to be present, and further to minuscule regions potentially containing individual cells. Our framework consists of two modules. First, a Field-of-Focus module uses a vision foundation model to segment the target region. Subsequently, a Fine-grained Object Detection module introduces a specialized Minuscule Region Proposal followed by a Spatial Attention Network to distinguish individual cells from noise within the segmented region. Experimental results demonstrate that our framework outperforms state-of-the-art methods for cell detection, providing enhanced efficacy for clinical applications. Our code is publicly available at: https://github.com/joeybyc/MCD.

cs.CV↗

arXiv2024

Medical Image Quality Assessment based on Probability of Necessity and Sufficiency

Medical image quality assessment (MIQA) is essential for reliable medical image analysis. While deep learning has shown promise in this field, current models could be misled by spurious correlations learned from data and struggle with out-of-distribution (OOD) scenarios. To that end, we propose an MIQA framework based on a concept from causal inference: Probability of Necessity and Sufficiency (PNS). PNS measures how likely a set of features is to be both necessary (always present for an outcome) and sufficient (capable of guaranteeing an outcome) for a particular result. Our approach leverages this concept by learning hidden features from medical images with high PNS values for quality prediction. This encourages models to capture more essential predictive information, enhancing their robustness to OOD scenarios. We evaluate our framework on an Anterior Segment Optical Coherence Tomography (AS-OCT) dataset for the MIQA task and experimental results demonstrate the effectiveness of our framework.

cs.CV↗

arXiv2024

Advancing Cell Detection in Anterior Segment Optical Coherence Tomography Images

Anterior uveitis, a common form of eye inflammation, can lead to permanent vision loss if not promptly diagnosed. Monitoring this condition involves quantifying inflammatory cells in the anterior chamber (AC) of the eye, which can be captured using Anterior Segment Optical Coherence Tomography (AS-OCT). However, manually identifying cells in AS-OCT images is time-consuming and subjective. Moreover, existing automated approaches may have limitations in both the effectiveness of detecting cells and the reliability of their detection results. To address these challenges, we propose an automated framework to detect cells in the AS-OCT images. This framework consists of a zero-shot chamber segmentation module and a cell detection module. The first module segments the AC area in the image without requiring human-annotated training data. Subsequently, the second module identifies individual cells within the segmented AC region. Through experiments, our framework demonstrates superior performance compared to current state-of-the-art methods for both AC segmentation and cell detection tasks. Notably, we find that previous cell detection approaches could suffer from low recall, potentially overlooking a significant number of cells. In contrast, our framework offers an improved solution, which could benefit the diagnosis and study of anterior uveitis. Our code for cell detection is publicly available at: https://github.com/joeybyc/cell_detection.

eess.IV↗

arXiv2024

Privacy Preserved Blood Glucose Level Cross-Prediction: An Asynchronous Decentralized Federated Learning Approach

Newly diagnosed Type 1 Diabetes (T1D) patients often struggle to obtain effective Blood Glucose (BG) prediction models due to the lack of sufficient BG data from Continuous Glucose Monitoring (CGM), presenting a significant "cold start" problem in patient care. Utilizing population models to address this challenge is a potential solution, but collecting patient data for training population models in a privacy-conscious manner is challenging, especially given that such data is often stored on personal devices. Considering the privacy protection and addressing the "cold start" problem in diabetes care, we propose "GluADFL", blood Glucose prediction by Asynchronous Decentralized Federated Learning. We compared GluADFL with eight baseline methods using four distinct T1D datasets, comprising 298 participants, which demonstrated its superior performance in accurately predicting BG levels for cross-patient analysis. Furthermore, patients' data might be stored and shared across various communication networks in GluADFL, ranging from highly interconnected (e.g., random, performs the best among others) to more structured topologies (e.g., cluster and ring), suitable for various social networks. The asynchronous training framework supports flexible participation. By adjusting the ratios of inactive participants, we found it remains stable if less than 70% are inactive. Our results confirm that GluADFL offers a practical, privacy-preserving solution for BG prediction in T1D, significantly enhancing the quality of diabetes management.

cs.LG↗

arXiv2024

A Data-driven Approach for Rapid Detection of Aeroelastic Modes from Flutter Flight Test Based on Limited Sensor Measurements

Flutter flight test involves the evaluation of the airframes aeroelastic stability by applying artificial excitation on the aircraft lifting surfaces. The subsequent responses are captured and analyzed to extract the frequencies and damping characteristics of the system. However, noise contamination, turbulence, non-optimal excitation of modes, and sensor malfunction in one or more sensors make it time-consuming and corrupt the extraction process. In order to expedite the process of identifying and analyzing aeroelastic modes, this study implements a time-delay embedded Dynamic Mode Decomposition technique. This approach is complemented by Robust Principal Component Analysis methodology, and a sparsity promoting criterion which enables the automatic and optimal selection of sparse modes. The anonymized flutter flight test data, provided by the fifth author of this research paper, is utilized in this implementation. The methodology assumes no knowledge of the input excitation, only deals with the responses captured by accelerometer channels, and rapidly identifies the aeroelastic modes. By incorporating a compressed sensing algorithm, the methodology gains the ability to identify aeroelastic modes, even when the number of available sensors is limited. This augmentation greatly enhances the methodology's robustness and effectiveness, making it an excellent choice for real-time implementation during flutter test campaigns.

eess.SP↗

arXiv2024

GARNN: An Interpretable Graph Attentive Recurrent Neural Network for Predicting Blood Glucose Levels via Multivariate Time Series

Accurate prediction of future blood glucose (BG) levels can effectively improve BG management for people living with diabetes, thereby reducing complications and improving quality of life. The state of the art of BG prediction has been achieved by leveraging advanced deep learning methods to model multi-modal data, i.e., sensor data and self-reported event data, organised as multi-variate time series (MTS). However, these methods are mostly regarded as ``black boxes'' and not entirely trusted by clinicians and patients. In this paper, we propose interpretable graph attentive recurrent neural networks (GARNNs) to model MTS, explaining variable contributions via summarizing variable importance and generating feature maps by graph attention mechanisms instead of post-hoc analysis. We evaluate GARNNs on four datasets, representing diverse clinical scenarios. Upon comparison with twelve well-established baseline methods, GARNNs not only achieve the best prediction accuracy but also provide high-quality temporal interpretability, in particular for postprandial glucose levels as a result of corresponding meal intake and insulin injection. These findings underline the potential of GARNN as a robust tool for improving diabetes care, bridging the gap between deep learning technology and real-world healthcare solutions.

cs.LG↗

arXiv2023

Exploring Multimodal Large Language Models for Radiology Report Error-checking

This paper proposes one of the first clinical applications of multimodal large language models (LLMs) as an assistant for radiologists to check errors in their reports. We created an evaluation dataset from real-world radiology datasets (including X-rays and CT scans). A subset of original reports was modified to contain synthetic errors by introducing three types of mistakes: "insert", "remove", and "substitute". The evaluation contained two difficulty levels: SIMPLE for binary error-checking and COMPLEX for identifying error types. At the SIMPLE level, our fine-tuned model significantly enhanced performance by 47.4% and 25.4% on MIMIC-CXR and IU X-ray data, respectively. This performance boost is also observed in unseen modality, CT scans, as the model performed 19.46% better than the baseline model. The model also surpassed the domain expert's accuracy in the MIMIC-CXR dataset by 1.67%. Notably, among the subsets (N=21) of the test set where a clinician did not achieve the correct conclusion, the LLaVA ensemble mode correctly identified 71.4% of these cases. However, all models performed poorly in identifying mistake types, underscoring the difficulty of the COMPLEX level. This study marks a promising step toward utilizing multimodal LLMs to enhance diagnostic accuracy in radiology. The ensemble model demonstrated comparable performance to clinicians, even capturing errors overlooked by humans.

cs.CL↗

arXiv2022

Optimising Chest X-Rays for Image Analysis by Identifying and Removing Confounding Factors

During the COVID-19 pandemic, the sheer volume of imaging performed in an emergency setting for COVID-19 diagnosis has resulted in a wide variability of clinical CXR acquisitions. This variation is seen in the CXR projections used, image annotations added and in the inspiratory effort and degree of rotation of clinical images. The image analysis community has attempted to ease the burden on overstretched radiology departments during the pandemic by developing automated COVID-19 diagnostic algorithms, the input for which has been CXR imaging. Large publicly available CXR datasets have been leveraged to improve deep learning algorithms for COVID-19 diagnosis. Yet the variable quality of clinically-acquired CXRs within publicly available datasets could have a profound effect on algorithm performance. COVID-19 diagnosis may be inferred by an algorithm from non-anatomical features on an image such as image labels. These imaging shortcuts may be dataset-specific and limit the generalisability of AI systems. Understanding and correcting key potential biases in CXR images is therefore an essential first step prior to CXR image analysis. In this study, we propose a simple and effective step-wise approach to pre-processing a COVID-19 chest X-ray dataset to remove undesired biases. We perform ablation studies to show the impact of each individual step. The results suggest that using our proposed pipeline could increase accuracy of the baseline COVID-19 detection algorithm by up to 13%.

eess.IV↗

arXiv2020

Dual Encoder Fusion U-Net (DEFU-Net) for Cross-manufacturer Chest X-ray Segmentation

A number of methods based on deep learning have been applied to medical image segmentation and have achieved state-of-the-art performance. Due to the importance of chest x-ray data in studying COVID-19, there is a demand for state-of-the-art models capable of precisely segmenting soft tissue on the chest x-rays. The dataset for exploring best segmentation model is from Montgomery and Shenzhen hospital which had opened in 2014. The most famous technique is U-Net which has been used to many medical datasets including the Chest X-rays. However, most variant U-Nets mainly focus on extraction of contextual information and skip connections. There is still a large space for improving extraction of spatial features. In this paper, we propose a dual encoder fusion U-Net framework for Chest X-rays based on Inception Convolutional Neural Network with dilation, Densely Connected Recurrent Convolutional Neural Network, which is named DEFU-Net. The densely connected recurrent path extends the network deeper for facilitating contextual feature extraction. In order to increase the width of network and enrich representation of features, the inception blocks with dilation are adopted. The inception blocks can capture globally and locally spatial information from various receptive fields. At the same time, the two paths are fused by summing features, thus preserving the contextual and spatial information for decoding part. This multi-learning-scale model is benefiting in Chest X-ray dataset from two different manufacturers (Montgomery and Shenzhen hospital). The DEFU-Net achieves the better performance than basic U-Net, residual U-Net, BCDU-Net, R2U-Net and attention R2U-Net. This model has proved the feasibility for mixed dataset and approaches state-of-the-art. The source code for this proposed framework is public https://github.com/uceclz0/DEFU-Net.

eess.IV↗

arXiv2010

An extensible web interface for databases and its application to storing biochemical data

This paper presents a generic web-based database interface implemented in Prolog. We discuss the advantages of the implementation platform and demonstrate the system's applicability in providing access to integrated biochemical data. Our system exploits two libraries of SWI-Prolog to create a schema-transparent interface within a relational setting. As is expected in declarative programming, the interface was written with minimal programming effort due to the high level of the language and its suitability to the task. We highlight two of Prolog's features that are well suited to the task at hand: term representation of structured documents and relational nature of Prolog which facilitates transparent integration of relational databases. Although we developed the system for accessing in-house biochemical and genomic data the interface is generic and provides a number of extensible features. We describe some of these features with references to our research databases. Finally we outline an in-house library that facilitates interaction between Prolog and the R statistical package. We describe how it has been employed in the present context to store output from statistical analysis on to the database.

cs.PL↗

arXiv2006

Computably Based Locally Compact Spaces

ASD (Abstract Stone Duality) is a re-axiomatisation of general topology in which the topology on a space is treated, not as an infinitary lattice, but as an exponential object of the same category as the original space, with an associated lambda-calculus. In this paper, this is shown to be equivalent to a notion of computable basis for locally compact sober spaces or locales, involving a family of open subspaces and accompanying family of compact ones. This generalises Smyth's effectively given domains and Jung's strong proximity lattices. Part of the data for a basis is the inclusion relation of compact subspaces within open ones, which is formulated in locale theory as the way-below relation on a continuous lattice. The finitary properties of this relation are characterised here, including the Wilker condition for the cover of a compact space by two open ones. The real line is used as a running example, being closely related to Scott's domain of intervals. ASD does not use the category of sets, but the full subcategory of overt discrete objects plays this role; it is an arithmetic universe (pretopos with lists). In particular, we use this subcategory to translate computable bases for classical spaces into objects in the ASD calculus.

math.GN↗

arXiv2003

Relational Grid Monitoring Architecture (R-GMA)

We describe R-GMA (Relational Grid Monitoring Architecture) which has been developed within the European DataGrid Project as a Grid Information and Monitoring System. Is is based on the GMA from GGF, which is a simple Consumer-Producer model. The special strength of this implementation comes from the power of the relational model. We offer a global view of the information as if each Virtual Organisation had one large relational database. We provide a number of different Producer types with different characteristics; for example some support streaming of information. We also provide combined Consumer/Producers, which are able to combine information and republish it. At the heart of the system is the mediator, which for any query is able to find and connect to the best Producers for the job. We have developed components to allow a measure of inter-working between MDS and R-GMA. We have used it both for information about the grid (primarily to find out about what services are available at any one time) and for application monitoring. R-GMA has been deployed in various testbeds; we describe some preliminary results and experiences of this deployment.

cs.DC↗

arXiv2003

R-GMA: First results after deployment

We describe R-GMA (Relational Grid Monitoring Architecture) which is being developed within the European DataGrid Project as an Grid Information and Monitoring System. Is is based on the GMA from GGF, which is a simple Consumer-Producer model. The special strength of this implementation comes from the power of the relational model. We offer a global view of the information as if each VO had one large relational database. We provide a number of different Producer types with different characteristics; for example some support streaming of information. We also provide combined Consumer/Producers, which are able to combine information and republish it. At the heart of the system is the mediator, which for any query is able to find and connect to the best Producers to do the job. We are able to invoke MDS info-provider scripts and publish the resulting information via R-GMA in addition to having some of our own sensors. APIs are available which allow the user to deploy monitoring and information services for any application that may be needed in the future. We have used it both for information about the grid (primarily to find what services are available at any one time) and for application monitoring. R-GMA has been deployed in Grid testbeds, we describe the results and experiences of this deployment.

cs.DC↗