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Ciaran Bench

Ciaran Bench contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
eess.IVphysics.med-phMachine Learning

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Published work

3 published item(s)

preprint2026arXiv

Uncertainty Reliability Under Domain Shift: An Investigation for Data-Driven Blood Pressure Estimation in Photoplethysmography

Uncertainty quantification (UQ) is critical for safety-critical domains like healthcare, yet it is rarely evaluated under realistic out-of-distribution (OOD) conditions. Here, we assessed predictive performance and uncertainty reliability for deep learning-based blood pressure (BP) estimation from photoplethysmography (PPG) signals under both in-distribution (ID) and OOD settings. Using an XResNet1D-50 trained on PulseDB and tested on four external datasets, we compared deep ensembles (DE) and Monte Carlo dropout (MCD) with Gaussian negative log-likelihood (GNLL) and mean squared error (MSE) losses, optionally followed by post-hoc recalibration via conformal prediction (CP), temperature scaling (TS), and isotonic regression (IR). The key findings of our study are as follows: (1) DE provides stronger predictive robustness under domain shift than MCD, an advantage that becomes clear primarily under external shift. (2) Recalibrated GNLL-based methods yield the best uncertainty calibration (e.g., GNLL+DE+CP for systolic blood pressure (SBP), GNLL+DE+TS for diastolic blood pressure (DBP)), while MSE-based uncertainty requires recalibration to become practically useful. (3) Across settings, CP and TS offer the most consistent gains, with IR remaining competitive in several cases. Overall, our results identify DE-based methods as most robust for predictive performance under domain shift, GNLL as strongest for native UQ, and recalibration as essential for making MSE-based uncertainty practical. These findings highlight the need to jointly assess predictive accuracy and calibration on external data for trustworthy cuffless BP estimation

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preprint2022arXiv

Unsupervised segmentation of biomedical hyperspectral image data: tackling high dimensionality with convolutional autoencoders

Information about the structure and composition of biopsy specimens can assist in disease monitoring and diagnosis. In principle, this can be acquired from Raman and infrared (IR) hyperspectral images (HSIs) that encode information about how a sample's constituent molecules are arranged in space. Each tissue section/component is defined by a unique combination of spatial and spectral features, but given the high dimensionality of HSI datasets, extracting and utilising them to segment images is non-trivial. Here, we show how networks based on deep convolutional autoencoders (CAEs) can perform this task in an end-to-end fashion by first detecting and compressing relevant features from patches of the HSI into low-dimensional latent vectors, and then performing a clustering step that groups patches containing similar spatio-spectral features together. We showcase the advantages of using this end-to-end spatio-spectral segmentation approach compared to i) the same spatio-spectral technique not trained in an end-to-end manner, and ii) a method that only utilises spectral features (spectral k-means) using simulated HSIs of porcine tissue as test examples. Secondly, we describe the potential advantages/limitations of using three different CAE architectures: a generic 2D CAE, a generic 3D CAE, and a 2D CNN architecture inspired by the recently proposed UwU-net that is specialised for extracting features from HSI data. We assess their performance on IR HSIs of real colon samples. We find that all architectures are capable of producing segmentations that show good correspondence with HE stained adjacent tissue slices used as approximate ground truths, indicating the robustness of the CAE-driven approach for segmenting biomedical HSI data. Additionally, we stress the need for more accurate ground truth information to rigorously compare the advantages offered by each architecture.

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preprint2020arXiv

Towards accurate quantitative photoacoustic imaging: learning vascular blood oxygen saturation in 3D

Significance: 2D fully convolutional neural networks have been shown capable of producing maps of sO$_2$ from 2D simulated images of simple tissue models. However, their potential to produce accurate estimates in vivo is uncertain as they are limited by the 2D nature of the training data when the problem is inherently 3D, and they have not been tested with realistic images. Aim: To demonstrate the capability of deep neural networks to process whole 3D images and output 3D maps of vascular sO$_2$ from realistic tissue models/images. Approach: Two separate fully convolutional neural networks were trained to produce 3D maps of vascular blood oxygen saturation and vessel positions from multiwavelength simulated images of tissue models. Results: The mean of the absolute difference between the true mean vessel sO$_2$ and the network output for 40 examples was 4.4% and the standard deviation was 4.5%. Conclusions: 3D fully convolutional networks were shown capable of producing accurate sO$_2$ maps using the full extent of spatial information contained within 3D images generated under conditions mimicking real imaging scenarios. This work demonstrates that networks can cope with some of the confounding effects present in real images such as limited-view artefacts, and have the potential to produce accurate estimates in vivo.

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