Outputs

Publications, talks, public engagement activities and other outputs generated by the CDT students.

Publications

2021

Angeletos Chrysaitis Nikitas, Jardri R, Denève S, Seriès P (2021) No increased circular inference in adults with high levels of autistic traits or autism. PLOS Computational Biology 17(9): e1009006. https://doi.org/10.1371/journal.pcbi.1009006

Corponi, Filippo, Zorkina, Y., Stahl, D., Murru, A., Vieta, E., Serretti, A., Morozova, А., Reznik, A., Kostyuk, G. and Chekhonin, V.P. (2021). Frontal lobes dysfunction across clinical clusters of acute schizophrenia. Revista de Psiquiatría y Salud Mental. https://doi.org/10.1016/j.rpsm.2021.12.002

Falis, Matúš, Dong, H., Birch, A., & Alex, B. (Accepted/In press). CoPHE: A Count-Preserving Hierarchical Evaluation Metric in Large-Scale Multi-Label Text Classification. In Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing (EMNLP 2021)

Stam Michael, Wood C W, DE-STRESS: a user-friendly web application for the evaluation of protein designs, Protein Engineering, Design and Selection, Volume 34, 2021, gzab029, https://doi.org/10.1093/protein/gzab029

Beltramo, G., Skraba, P., Andreeva, Rayna, Sarkar, R., Giarratano, Y. and Bernabeu, M., (2021). Euler characteristic surfaces. Foundations of Data Sciences http://dx.doi.org/10.3934/fods.2021027

Saadat-Yazdi A., Andreeva Rayna, Sarkar R. (2021) Topological Detection of Alzheimer’s Disease Using Betti Curves. In: Reyes M. et al. (eds) Interpretability of Machine Intelligence in Medical Image Computing, and Topological Data Analysis and Its Applications for Medical Data. IMIMIC 2021, TDA4MedicalData 2021. Lecture Notes in Computer Science, vol 12929. Springer, Cham. https://doi.org/10.1007/978-3-030-87444-5_12

(Preprint) PDBench: Evaluating Computational Methods for Protein Sequence Design. Leonardo Castorina, R Petrenas, K Subr, CW Wood

(Preprint) Super-Resolution of Magnetic Resonance Images Acquired Under Clinical Protocols using Deep Attention-based Method. Bryan Li, Leonardo Castorina, Maria del C. Valdés-Hernández, Una Clancy, Stewart J. Wiseman, Eleni Sakka, Amos J. Storkey, Daniela Jaime Garcia, Yajun Cheng, Fergus Doubal, Michael T. Thrippleton, Michael Stringer, Joanna M. Wardlaw medRxiv 2022.01.24.22269144; doi: https://doi.org/10.1101/2022.01.24.22269144

(Preprint) Challenges of building medical image datasets for development of deep learning software in stroke. Wenwen Li, Grant Mair, Alessandro Fontanella, Antreas Antoniou, Eleanor Platt , Chloe Martin, Paul Armitage , Emanuele Trucco, Amos Storkey, Joanna Wardlaw

(Preprint) Designing human Sphingosine-1-phosphate lyases using a temporal Dirichlet variational autoencoder. Evgenii Lobzaev, Michael A. Herrera, Dominic J. Campopiano, Giovanni Stracquadanio bioRxiv 2022.02.14.480330; doi: https://doi.org/10.1101/2022.02.14.480330

(Preprint) DNA Methylation scores augment 10-year risk prediction of diabetes. Yipeng Cheng, Danni A Gadd, Christian Gieger, Karla Monterrubio-Gómez, Yufei Zhang, Imrich Berta, Michael Stam, Natalia Szlachetka, Evgenii Lobzaev, Archie Campbell, Cliff Nangle, Rosie M Walker, Chloe Fawns-Ritchie, Annette Peters, Wolfgang Rathmann, David J Porteous, Kathryn L Evans, Andrew M McIntosh, Timothy I Cannings, Melanie Waldenberger, Andrea Ganna, Daniel L McCartney, Catalina A Vallejos, Riccardo E Marioni

medRxiv 2021.11.19.21266469; doi: https://doi.org/10.1101/2021.11.19.21266469

2020

Andreeva, Rayna, Fontanella, Alessandro, Giarratano Y., Bernabeu M.O. (2020) DR Detection Using Optical Coherence Tomography Angiography (OCTA): A Transfer Learning Approach with Robustness Analysis. In: Fu H., Garvin M.K., MacGillivray T., Xu Y., Zheng Y. (eds) Ophthalmic Medical Image Analysis. OMIA 2020. Lecture Notes in Computer Science, vol 12069. Springer, Cham. https://doi.org/10.1007/978-3-030-63419-3_2

Giarratano, Y., Pavel, A., Lian, J., Andreeva, Rayna, Fontanella, Alessandro, Sarkar, R., Reid, L., Forbes, S., Pugh, D., Farrah, T., Dhaun, N., Dhillon, B., MacGillivray, T. and Bernabeu, M., 2020. A Framework for the Discovery of Retinal Biomarkers in Optical Coherence Tomography Angiography (OCTA). Ophthalmic Medical Image Analysis, pp.155-164.OMIA 2020. Lecture Notes in Computer Science, vol 12069. Springer, Cham. https://doi.org/10.1007/978-3-030-63419-3_16

Fontanella, Alessandro, Pead, E.,Macgillivray, T., Bernabeu, M., & Storkey, A. (2020). Classification with a domain shift in medical imaging. Med-NeurIPS 2020: Medical Imaging meets NeurIPS Workshop http://www.cse.cuhk.edu.hk/~qdou/public/medneurips2020/43_Classification_with_a_domain_shift_in_medical_imaging.pdf

Talks

2022

Alessandro Fontanella: 'The Challenges and Applications of Deep Learning Methods on Medical Imaging for Acute Ischemic Stroke', HDR UK - Applied Analytics seminar

2021

Rayna Andreeva: 'Automatic papillae identification using discrete curvature analysis', Food Oral Processing 2021, Early Career Researcher session

Rayna Andreeva: A Geometric Approach to Papillae Identification in 3D Meshes, Young Researchers Forum, 37th Symposium on Computational Geometry 2021

https://cse.buffalo.edu/socg21/program.html

Matúš Falis: 'Towards Better Use of Ontological Structure in the Evaluation of Automated ICD Coding', HealTAC Healthcare Text Analytics Conference 2021

Alessandro Fontanella: 'Deep learning methods to identify ischemic stroke lesions from CT scans of the brain', SICSA Conference 2021

Evgenii Lobzaev: 'Primer on Variational Inference and its application to Deep Learning', 6th Winter School on Data Analytics (DA 2021)

Evgenii Lobzaev: 'AI-driven design of enzyme replacement therapies', SICSA Conference 2021

2020

Rayna Andreeva: 'DR Detection Using Optical Coherence Tomography Angiography (OCTA): A Transfer Learning Approach with Robustness Analysis', 7th MICCAI Workshop on Ophthalmic Medical Image Analysis (OMIA7)

Rayna Andreeva, Alessandro Fontanella: 'Identifying patient status using optical coherence tomography angiography (OCTA): A transfer learning approach', 12th SINAPSE Annual Scientific Meeting

Alessandro Fontanella: 'Classification with a domain shift in medical imaging', NEURIPS- Medical imaging meets NEURIPS workshop

Posters

2022

Evgenii Lobzaev: 'Designing Human Sphingosine-1-phosphate Lyases Using Generative Deep Learning', Glycolipid and Sphingolipid Biology GRC

Leonardo Castorina: 'Machine Learning for Protein Design', APFED22

Matúš Falis: 'Horses to Zebras: Ontology-Guided Data Augmentation and Synthesis for ICD-9 Coding', ACL 2022

Michael Stam: 'Data-driven prediction of antibody expression', APFED22

Rayna Andreeva: 'Topological data analysis for papillae classification', SINAPSE Annual Scientific Meeting

2021

Rayna Andreeva: 'Automatic papillae identification using discrete curvature analysis', Food Oral Processing 2021, Early Career Researcher session

Domas Linkevicius: 'Modeling the dynamics of partially known systems via the integration of a system of ordinary differential equations into a recurrent neural network', CNS*2021

Domas Linkevicius: 'Combining neural ODEs and incomplete ODE systems to model complex, under-parameterised synaptic biochemical networks', Neuroscience 2021

Filippo Corponi: 'Definition of early age at onset in bipolar disorder according to distinctive neurodevelopmental pathways: insights from the FACE-BD study', French Congress of Psychiatry

Li W, Fontanella Alessandro, Antoniou A, Platt E., Martin C., Mair G., Trucco E., Storkey A., Wardlaw J.: 'Acute ischaemic stroke (AIS) lesion detection with a convolutional deep learning model', 7th European Stroke Organisation Conference ESOC 2021

Mair G., Li W., Martin C., Fontanella, Alessandro, Trucco E., Storkey A., Wardlaw J.: 'Challenges of delivering medical image sets for development of deep learning software in stroke', Artificial intelligence in practice 2021

Public Engagement and EDI initiatives

Katarzyna Szymaniak: Co-Creation Workshop with IntellSensing Lab at Newcastle University (2021)

Rayna Andreeva, Natalia Szlachetka, Katarzyna Szymaniak:  Panel participation: Women in AI event hosted by UCL (2020)

Rayna Andreeva: EDI in STEM: Race and Disability Workshop. Participation in an EDI workshop as part of the Women in STEM and CompSoc's equality, diversity, and inclusion (EDI) series with Dr Frantzana (2020)