Publication Research

While gradually building up a strong tradition in publishing, our research teams have developed an internal publication strategy where they work either individually or collaboratively on publications linked to their current projects.

To assist with their research they have established strong links with local universities, including Glasgow, Edinburgh, Heriot Watt, Aberdeen and St Andrews, and work with both clinical and academic collaborators to maintain a long term strategy to deliver new and exciting projects. To further support their research our scientists have opportunities to attend international conferences focused on medical imaging, deep learning and artificial intelligence.

2023

Liu, X., Thermos, S., Sanchez, P., O’Neil, A.Q. and Tsaftaris, S.A. (2023). HSIC-InfoGAN: Learning Unsupervised Disentangled Representations by Maximising Approximated Mutual Information. In Medical Applications with Disentanglements: First MICCAI Workshop (MAD) (pp. 15-21). Springer, Cham.

2022

Dalla Serra, F., Clackett, W., MacKinnon, H., Wang, C., Deligianni, F., Dalton, J. and O’Neil, A.Q.. Multimodal Generation of Radiology Reports using Knowledge-Grounded Extraction of Entities and Relations. ACL-IJCNLP 2022.

Dalla Serra, F., Jacenków, G., Deligianni, F., Dalton, J. and O’Neil, A.Q. (2022). Improving Image Representations via MoCo Pre-training for Multimodal CXR Classification. In Annual Conference on Medical Image Understanding and Analysis (MIUA) pp. 623-635. Springer, Cham.

Fisher S, Hung R, Andersen D et al. Investigating the transcriptome of adenomatous colorectal polyps in the context of metachronous recurrence [version 1; not peer reviewed]. F1000Research 2022, 11:1325 (poster) F1000research.1119211.1 (poster)

Hung R, Fisher S, Andersen D, Lynch G, Maka N, Hay J, Jawny J, Sloan W, McSorley S, Edwards J, and Poole I. Machine learning identifies weak prognostic signal in colorectal polyp’s transcriptome [version 1; not peer reviewed].  F1000Research 2022, 11:1324 (poster)

Jacenków, G., O’Neil, A.Q. and Tsaftaris, S.A. (2022). Indication as Prior Knowledge for Multimodal Disease Classification in Chest Radiographs with Transformers. In 2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI) (pp. 1-5). IEEE.

Kascenas, A., Pugeault, N. and O'Neil, A.Q. (2022). Denoising Autoencoders for Unsupervised Anomaly Detection in Brain MRI. In Medical Imaging with Deep Learning (MIDL).

Kascenas, A., Young, R., Jensen, B.S., Pugeault, N. and O’Neil, A.Q. (2022). Anomaly Detection via Context and Local Feature Matching. In 2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI) (pp. 1-5). IEEE.

Liu, X., Thermos, S., Sanchez, P., O’Neil, A.Q. and Tsaftaris, S.A. (2022). vMFNet: Compositionality Meets Domain-Generalised Segmentation. In International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) pp. 704-714.

Liu, X., Sanchez, P., Thermos, S., O’Neil, A.Q. and Tsaftaris, S.A. (2022). Learning disentangled representations in the imaging domain. Medical Image Analysis (MedIA), p.102516.

Park EH, Watson HI, Mehendale FV, O'Neil AQ. Evaluating the Impact on Clinical Task Efficiency of a Natural Language Processing Algorithm for Searching Medical Documents: Prospective Crossover Study. JMIR Med Inform 2022;10(10):e39616

Sanchez, P., Kascenas, A., Liu, X., O’Neil, A.Q. and Tsaftaris, S.A. (2022). What is Healthy? Generative Counterfactual Diffusion for Lesion Localization. In MICCAI Workshop on Deep Generative Models (pp. 34-44). Springer, Cham.

Sanchez, P., Voisey, J.P., Xia, T., Watson, H.I., O’Neil, A.Q. and Tsaftaris, S.A. (2022). Causal machine learning for healthcare and precision medicine. Royal Society Open Science, 9(8), p.220638.

Thompson, B.H., Di Caterina, G. and Voisey, J.P. (2022). Pseudo-label refinement using superpixels for semi-supervised brain tumour segmentation. In 2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI) (pp. 1-5). IEEE.

Zimmerer, D., Full, P.M., Isensee, F., Jäger, P., Adler, T., Petersen, J., Köhler, G., Ross, T., Reinke, A., Kascenas, A., Jensen, B.S., O’Neil, A.Q., Tan, J., Hou, B., Batten, J., Qiu, H., Kainz, B., Shvetsova, N., Fedulova, I., Dylov, D.V., Yu, B., Zhai, J., Hu, J., Si, R., Zhou, S., Wang, S., Li, X., Chen, X., Zhao, Y., Naval Marimont, S., Tarroni, G., Saase, V., Maier-Hein, L. & Maier-Hein, K. (2022). MOOD 2020: A public Benchmark for Out-of-Distribution Detection and Localization on medical Images. IEEE Transactions on Medical Imaging.

2021

Anderson, O., Kidd, A.C., Goatman, K.A., Weir, A.J., Voisey, J.P., Dilys, V., Siebert, J.P., and Blyth, K.G (2021). Estimating the False Positive Prediction Rate in Automated Volumetric Measurements of Malignant Pleural Mesothelioma. Biomedical Engineering Systems and Technologies.

Juanco Müller, Á.V., Mota, J.F.C., and Hoogendoorn, C. (2021). Segmentation of Skin Lesions by Superpixel Classification with Graph-Context CNN. In 25th UK Conference on Medical Image Understanding and Analysis.

Juanco-Müller, Á.V., Mota, J.F., Goatman, K. and Hoogendoorn, C. (2021). Deep supervoxel segmentation for survival analysis in head and neck cancer patients. In 3D Head and Neck Tumor Segmentation in PET/CT (HEKTOR) Challenge (pp. 257-265), MICCAI. Springer, Cham.

Liu, X., Thermos, S., Chartsias, A., O'Neil, A. and Tsaftaris, S.A. (2021). Disentangled Representations for Domain-Generalized Cardiac Segmentation. In MICCAI workshop on “Statistical Atlases and Computational Models of the Heart” (STACOM), submission to the Multi-Centre, Multi-Vendor & Multi-Disease Cardiac Image Segmentation (M&Ms) Challenge.

Liu, X., Thermos, S., O’Neil, A. and Tsaftaris, S.A. (2021). Semi-supervised Meta-learning with Disentanglement for Domain-generalised Medical Image Segmentation. In International Conference on Medical Image Computing and Computer-Assisted Intervention (pp. 307-317). Springer, Cham.

Schrempf, P., Watson, H., Park, E., Pajak, M., MacKinnon, H., Muir, K.W., Harris-Birtill, D. and O’Neil, A.Q. (2021). Templated text synthesis for expert-guided multi-label extraction from radiology reports. Machine Learning and Knowledge Extraction, 3(2), pp.299-317.

Thermos, S., Liu, X., O’Neil, A. and Tsaftaris, S.A. (2021). Controllable cardiac synthesis via disentangled anatomy arithmetic. In International Conference on Medical Image Computing and Computer-Assisted Intervention (pp. 160-170). Springer, Cham.

2020

Anderson, O., Kidd, A.C., Goatman, K.A., Weir, A.J., Voisey, J., Dilys, V., Siebert, J.P., and Blyth, K.G. (2020). Fully automated volumetric measurement of malignant pleural mesothelioma from computed tomography images by deep learning: Preliminary results of an internal validation. In Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020) - Volume 2: BIOIMAGING, pp. 64–73, SCITEPRESS.

Elskhawy, A., Lisowska, A., Keicher, M., Henry, J., Thomson, P. and Navab, N. (2020). Continual Class Incremental Learning for CT Thoracic Segmentation. In MICCAI workshop on  “Domain Adaptation and Representation Transfer” (DART).

Jacenków, G., O’Neil, A.Q., Mohr, B. and Tsaftaris, S.A. (2020). INSIDE: Steering Spatial Attention with Non-imaging Information in CNNs. In International Conference on Medical Image Computing and Computer-Assisted Intervention (pp. 385-395). Springer, Cham.

Schrempf, P., Watson, H., Mikhael, S., Pajak, M., Falis, M., Lisowska, A., Muir, K.W., Harris-Birtill, D. and O’Neil, A.Q. (2020). Paying Per-Label Attention for Multi-label Extraction from Radiology Reports. In MICCAI workshop on “Large-scale Annotation of Biomedical Data and Expert Label Synthesis” (LABELS).

Shaw, S., Pajak, M., Lisowska, A., Tsaftaris, S.A., O’Neil, A.Q., (2020). Teacher-Student chain for efficient semi-supervised histology image classification. In ICLR workshop on “AI for Affordable Healthcare” (AI4AH).

2019

Appelgren, M., Schrempf, P., Falis, M., Ikeda, S. and O'Neil, A.Q., (2019). Language Transfer for Early Warning of Epidemics from Social Media. In NeurIPS workshop on “Artificial Intelligence for Humanitarian Assistance and Disaster Response” (AI+HADR).

Falis, M., Pajak, M., Lisowska, A., Schrempf, P., Deckers, L., Mikhael, S., Tsaftaris, S. and O’Neil, A. Q., (2019). Ontological attention ensembles for capturing semantic concepts in ICD code prediction from clinical text. In EM NLP Workshop “Tenth International Workshop on Health Text Mining and Information Analysis” (LOUHI), p. 168-177.

Grob, D., Oostveen, L., Rühaak, J., Heldmann, S., Mohr, B., Michielsen, K., Dorn, S., Prokop, M., Kachelrieβ, M., Brink, M. and Sechopoulos, I. (2019). Accuracy of registration algorithms in subtraction CT of the lungs: A digital phantom study. Medical physics, 46(5), pp.2264-2274.

Jacenków, G., Chartsias, A., Mohr, B. and Tsaftaris, S.A. (2019). Conditioning Convolutional Segmentation Architectures with Non-Imaging Data. Medical Imaging with Deep Learning (Extended Abstract Track).

Mikhael, S.S., Mair, G., Valdes-Hernandez, M., Hoogendoorn, C., Wardlaw, J.M., Bastin, M.E. and Pernet, C., 2019. Manually-parcellated gyral data accounting for all known anatomical variability. Scientific data, 6, p.190001

Mikhael, S.S. and Pernet, C. (2019). A controlled comparison of thickness, volume and surface areas from multiple cortical parcellation packages. BMC bioinformatics, 20(1), p.55.

Zotova, D., Lisowska, A., Anderson, O., Dilys, V. and O’Neil, A. Q., (2019). Comparison of active learning strategies applied to lung nodule segmentation in CT scans. In MICCAI workshop on “Large-scale Annotation of Biomedical Data and Expert Label Synthesis” (LABELS).

2018

Daykin, M., Sellathurai, M. and Poole, I., 2018, July. A Comparison of Unsupervised Abnormality Detection Methods for Interstitial Lung Disease . In Annual Conference on Medical Image Understanding and Analysis (pp. 287-298). Springer, Cham.

Lisowska, A., O'Neil, A. and Poole, I. (2018) Cross-cohort Evaluation of Machine Learning Approaches to Fall Detection from Accelerometer Data . In Proceedings of the 11th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 5: HEALTHINF, January 2018, ISBN 978-989-758-281-3, pages 77-82.

Mikhael, S. and Gray, C. (2018) Masks2Metrics (M2M): A Matlab Toolbox for Gold Standard Morphometrics . Journal of Open Source Software, 3(22), 436.

O'Neil, A.Q., Kascenas, A., Henry, J., Wyeth, D., Shepherd, M., Beveridge, E., Clunie, L., Sansom, C., Šeduikytė, E., Muir, K. and Poole, I., (2018). Attaining human-level performance with atlas location autocontext for anatomical landmark detection in 3D CT data . ECCV 2018 Workshop "Geometry Meets Deep Learning".

Sloan, J., Goatman, K. and Siebert, J. (2018). Learning Rigid Image Registration - Utilizing Convolutional Neural Networks for Medical Image Registration . In Proceedings of the 11th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 2: BIOIMAGING, ISBN 978-989-758-278-3, pages 89-99.

2017

Daykin, M., Beveridge, E., Dilys, V., Lisowska, A., Muir, K., Sellathurai, M. and Poole, I., (2017). Evaluation of an Automatic ASPECT Scoring System for Acute Stroke in Non-Contrast CT . In Annual Conference on Medical Image Understanding and Analysis (pp. 537-547). Springer, Cham.

Lisowska, A., O’Neil, A., Dilys, V., Beveridge, E., Muir, K., Poole, I. (2017). Dense vessel detection using an anatomically-aware CNN in non-contrast CT scans . ‘Medical Imaging meets NIPS’ satellite workshop at NIPS 2017.

Lisowska, A., Beveridge, E., O’Neil, A., Dilys, V., Muir, K. and Poole, I. (2017). Evaluation of Dense Vessel Detection in NCCT Scans . In International Joint Conference on Biomedical Engineering Systems and Technologies (pp. 134-145). Springer, Cham.

Lisowska, A., Beveridge, E., Muir, K., & Poole, I. (2017). Thrombus Detection in CT Brain Scans using a Convolutional Neural Network . Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies, 24–33.

Lisowska, A., O’Neil, A., Dilys, V., Daykin, M., Beveridge, E., Muir, K., McLaughlin, S., Poole, I. (2017). Context-aware convolutional neural networks for stroke sign detection in non-contrast CT scans . In Communications in Computer and Information Science, MIUA (Vol. 723, pp. 494–505).

McNeil, A., Degano, G., Poole, I., Houston, G., & Trucco, E. (2017). Comparison of automatic vessel segmentation techniques for whole body magnetic resonance angiography with limited ground truth data . In Communications in Computer and Information Science: MIUA (Vol. 723, pp. 144–155).

Mikhael, S., Hoogendoorn, C., Valdes-Hernandez, M., Pernet, C (2017). A Critical Analysis of Neuroanatomical Software Protocols Reveals Clinically Relevant Differences in Parcellation Schemes . NeuroImage, 170, 348-364.

O’Neil, A., Shepherd, M., Beveridge, E. and Goatman, K., (2017). A Comparison of Texture Features Versus Deep Learning for Image Classification in Interstitial Lung Disease . In Annual Conference on Medical Image Understanding and Analysis (pp. 743-753). Springer, Cham.

O’Neil, A. Q., Murchison, J. T., Van Beek, E. J. R., & Goatman, K. A. (2017). Crowdsourcing labels for pathological patterns in CT lung scans: Can non-experts contribute expert-quality ground truth? In: Large-Scale Annotation of Biomedical Data and Expert Label Synthesis (MICCAI). LNCS, vol. 10552, pp. 96-105). Springer, Cham.

Tobon-Gomez, C., Stroud, T., Cameron, J., Elcock, D., Murray, A., Wyeth, D., Conway, C., Reynolds, S., Teixeira, P.A.G., Blum, A. and Plakas, C. (2017). Unfolded Cylindrical Projection for Rib Fracture Diagnosis . In International Workshop and Challenge on Computational Methods and Clinical Applications in Musculoskeletal Imaging (pp. 36-47). Springer, Cham.

2016

Blobel, J., Mews, J., Goatman, K.A., Schuijf, J.D. and Overlaet, W. (2016). Calibration of coronary calcium scores determined using iterative image reconstruction (AIDR 3D) at 120, 100, and 80 kVp . Medical physics, 43(4), pp.1921-1932.

Jimenez-Del-Toro O, Muller H, Krenn M, Gruenberg K, Taha AA, Winterstein M, Eggel I, Foncubierta-Rodriguez A, Goksel O, Jakab A, Kontokotsios G, Langs G, Menze BH, Salas Fernandez T, Schaer R, Walleyo A, Weber MA, Dicente Cid Y, Gass T, Heinrich M, Jia F, Kahl F, Kechichian R, Mai D, Spanier AB, Vincent G, Wang C, Wyeth D, and Hanbury A. (2016). Cloud-based evaluation of anatomical structure segmentation and landmark detection algorithms: VISCERAL anatomy benchmarks . IEEE transactions on medical imaging, 35(11), pp.2459-2475.

Mohr, B., Brink, M., Oostveen, L.J., Schuijf, J.D. and Prokop, M., 2016, March. Lung iodine mapping by subtraction with image registration allowing for tissue sliding . In Medical Imaging 2016: Image Processing (Vol. 9784, p. 978442). International Society for Optics and Photonics.

Nakatsugawa, M., Cheng, Z., Goatman, K.A., Lee, J., Robinson, A., Choflet, A., Sakaue, K., Sugiyama, S.,Kiess, A.P., Wong, J.W., McNutt, T.R., Quon, H. (2016) Radiomic Analysis of Salivary Glands and Its Role for Predicting Xerostomia in Irradiated Head and Neck Cancer Patients . International Journal of Radiation Oncology, vol. 96, no. 2, p. S217.

O’Neil, A., Dabbah, M. and Poole, I., 2016, October. Cross-Modality Anatomical Landmark Detection Using Histograms of Unsigned Gradient Orientations and Atlas Location Autocontext . In: International Workshop on Machine Learning in Medical Imaging (MICCAI). LNCS, vol. 6893, pp. 139-146. Springer, Cham.

Rosmini, S., Treibel, T.A., Bandula, S., Stroud, T., Fontana, M., Hawkins, P.N. and Moon, J.C. (2016). Cardiac computed tomography for the detection of cardiac amyloidosis . Journal of cardiovascular computed tomography, 11(2), pp.155-156.

Sloan, J.M., Goatman, K. and Siebert, P. (2016). FASTR: using local structure tensors as a similarity metric. Procedia Computer Science, 90, pp.194-199.

2015

Fuchs, A., Kühl, J.T., Chen, M.Y., Helqvist, S., Razeto, M., Arakita, K., Steveson, C., Arai, A.E. and Kofoed, K.F. (2015). Feasibility of coronary calcium and stent image subtraction using 320-detector row CT angiography . Journal of cardiovascular computed tomography, 9(5), pp.393-398.

Lisowska, A., Wheeler, G., Inza, V. C., & Poole, I. (2015). An Evaluation of Supervised, Novelty-Based and Hybrid Approaches to Fall Detection Using Silmee Accelerometer Data .Proceedings of the IEEE International Conference on Computer Vision , 2015–Dec, 402–408.

O'Neil, A., Murphy, S. and Poole, I. (2015). Anatomical Landmark Detection in CT Data by Learned Atlas Location Autocontext . In MIUA (pp. 189-194).

Tamerus, A., Washbrook, A. and Wyeth, D. (2015) Acceleration of ensemble machine learning methods using many-core devices . Journal of Physics: Conference Series, vol. 664, no. 9, pp. 092026.

Tang, Q., Matthews, J., Razeto, M., Linde, J.J. and Nakanishi, S. (2015). Motion estimation and compensation for coronary artery and myocardium in cardiac CT . In Medical Imaging 2015: Physics of Medical Imaging (Vol. 9412, p. 94120Q). International Society for Optics and Photonics.

Wang, C., Goatman, K.A., MacGillivray, T., Beveridge, E., Koutraki, Y., Boardman, J., Stirrat, C., Sparrow, S., Moore, E., Paraky, R. and Alam, S. (2015). Automatic multi-parametric MR registration method using mutual information based on adaptive asymmetric k-means binning . In 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI) (pp. 1089-1092).

2014

Dabbah, M.A., Murphy, S., Pello, H., Courbon, R., Beveridge, E., Wiseman, S., Wyeth, D. and Poole, I. (2014). Detection and location of 127 anatomical landmarks in diverse CT datasets . In Medical Imaging 2014: Image Processing (Vol. 9034, p. 903415). International Society for Optics and Photonics.

Goatman, K., Plakas, C., Schuijf, J., Beveridge, E. and Prokop, M. (2014). Computed tomography lung iodine contrast mapping by image registration and subtraction. In Medical Imaging 2014: Image Processing (Vol. 9034, p. 90343I). International Society for Optics and Photonics.

Murphy, S., Mohr, B., Fushimi, Y., Yamagata, H. and Poole, I. (2014). Fast, simple, accurate multi-atlas segmentation of the brain . In International Workshop on Biomedical Image Registration (pp. 1-10). Springer, Cham.

O'Neil, A., Beveridge, E., Houston, G., McCormick, L. and Poole, I. (2014). Arterial tree tracking from anatomical landmarks in magnetic resonance angiography scans . In Medical Imaging 2014: Image Processing (Vol. 9034, p. 90342S). International Society for Optics and Photonics.

Razeto, M., Mohr, B., Arakita, K., Schuijf, J.D., Fuchs, A., Kühl, J.T., Chen, M.Y. and Kofoed, K.F. (2014). Accurate, fully-automated registration of coronary arteries for volumetric CT digital subtraction angiography. In Medical Imaging 2014: Image Processing (Vol. 9034, p. 90343F). International Society for Optics and Photonics.

Tang, Q., Chiang, B., Akinyemi, A., Zamyatin, A., Shi, B. and Nakanishi, S., 2014, March. A combined local and global motion estimation and compensation method for cardiac CT . In Medical Imaging 2014: Physics of Medical Imaging (Vol. 9033, p. 903304). International Society for Optics and Photonics.

Teixeira, P.A.G., Hossu, G., Lecocq, S., Razeto, M., Louis, M. and Blum, A. (2014) ‘ Bone Marrow Edema Pattern Identification in Patients With Lytic Bone Lesions Using Digital Subtraction Angiography-Like Bone Subtraction on Large-Area Detector Computed Tomography ’. Investigative Radiology, vol. 49, no. 3, pp. 156-164

2013

Kirişli, H.A., Schaap, M., Metz, C.T., Dharampal, A.S., Meijboom, W.B., Papadopoulou, S.L., Dedic, A., Nieman, K., De Graaf, M.A., Meijs, M.F.L. and Cramer, M.J. (2013). Standardized evaluation framework for evaluating coronary artery stenosis detection, stenosis quantification and lumen segmentation algorithms in computed tomography angiography . Medical image analysis, 17(8), pp.859-876.

2012

Akinyemi, A., Plakas, C., Piper, J., Roberts, C., & Poole, I. (2012). Optimal Atlas Selection Using Image Similarities in a Trained Regression Model to Predict Performance . 2012 9th IEEE International Symposium on Biomedical Imaging (Isbi) , 1264–1267.

Dickie, D.A., Job, D.E., Poole, I., Ahearn, T.S., Staff, R.T., Murray, A.D. and Wardlaw, J.M., 2012. Do brain image databanks support understanding of normal ageing brain structure? A systematic review . European radiology, 22(7), pp.1385-1394.

Mohr, B., Masood, S. and Plakas, C., 2012. Accurate lumen segmentation and stenosis detection and quantification in coronary CTA . In Proceedings of 3D Cardiovascular Imaging: a MICCAI segmentation challenge workshop .

Murphy, S., Akinyemi, A., Steel, J., Petillot, Y., & Poole, I. Multi-compartment heart segmentation in CT angiography using a spatially varying Gaussian classifier . International Journal of Computer Assisted Radiology and Surgery 829–836 (2012).

Piper, J., Ikeda, Y., Fujisawa, Y., Ohno, Y., Yoshikawa, T., O’Neil, A. and Poole, I., 2012. Objective evaluation of the correction by non-rigid registration of abdominal organ motion in low-dose 4D dynamic contrast-enhanced CT . Physics in Medicine & Biology, 57(6), p.1701.

2010

Hernandez, M., Murphy, S., & Wardlaw, J. (2010). A comparison of four unsupervised clustering algorithms for segmenting brain tissue in multi-spectral MR data . In BIOSTECH.

2009

Akinyemi, A., Murphy, S., Poole, I., & Roberts, C. (2009). Automatic labelling of coronary arteries . In European Signal Processing Conference.