Stephen Bonner

ORCID: 0000-0001-6008-358X
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About
Contact & Profiles
Research Areas
  • Advanced Graph Neural Networks
  • SARS-CoV-2 and COVID-19 Research
  • COVID-19 Clinical Research Studies
  • Complex Network Analysis Techniques
  • Bioinformatics and Genomic Networks
  • Sepsis Diagnosis and Treatment
  • Intensive Care Unit Cognitive Disorders
  • Computational Drug Discovery Methods
  • Recommender Systems and Techniques
  • Airway Management and Intubation Techniques
  • Neural dynamics and brain function
  • Advanced Bandit Algorithms Research
  • Cloud Computing and Resource Management
  • Topic Modeling
  • Organ Donation and Transplantation
  • Machine Learning in Materials Science
  • SARS-CoV-2 detection and testing
  • Intracranial Aneurysms: Treatment and Complications
  • Respiratory Support and Mechanisms
  • Frailty in Older Adults
  • EEG and Brain-Computer Interfaces
  • Traumatic Brain Injury and Neurovascular Disturbances
  • Advanced Malware Detection Techniques
  • Animal Virus Infections Studies
  • Nosocomial Infections in ICU

James Cook University Hospital
2013-2023

South Tees Hospitals NHS Foundation Trust
2015-2022

Imperial College London
2022

Quadram Institute
2022

AstraZeneca (United Kingdom)
2022

AstraZeneca (Australia)
2022

Durham University
2013-2021

Weatherford College
2021

Flint Institute Of Arts
2021

Newcastle University
2019-2021

Many current applications use recommendations in order to modify the natural user behavior, such as increase number of sales or time spent on a website. This results gap between final recommendation objective and classical setup where candidates are evaluated by their coherence with past predicting either missing entries user-item matrix, most likely next event. To bridge this gap, we optimize policy for task increasing desired outcome versus organic behavior. We show is equivalent learning...

10.1145/3240323.3240360 preprint EN 2018-09-27

Deep learning is rapidly becoming a go-to tool for many artificial intelligence problems due to its ability outperform other approaches and even humans at problems. Despite popularity we are still unable accurately predict the time it will take train deep network solve given problem. This training can be seen as product of per epoch number epochs which need performed reach desired level accuracy. Some work has been carried out an - most have based around assumption that linearly related...

10.1109/bigdata.2018.8622396 article EN 2021 IEEE International Conference on Big Data (Big Data) 2018-12-01

Background Early physical rehabilitation in the intensive care unit (ICU) has been shown to improve short-term clinical outcomes but long-term benefit not proven and optimum intensity of is known. Methods We conducted a randomised, parallel-group, allocation-concealed, assessor-blinded, controlled trial patients who had received at least 48 hours invasive or non-invasive ventilation. Participants were randomised 1:1 ratio, stratified by admitting ICU, admission type level independence. The...

10.1136/thoraxjnl-2016-209858 article EN cc-by Thorax 2017-08-05

Abstract Background The nature of multiple organ dysfunction syndrome (MODS) after traumatic injury is evolving as resuscitation practices advance and more patients survive their injuries to reach critical care. aim this study was characterize contemporary MODS subtypes in trauma care at a population level. Methods Adult admitted major centre units were enrolled 4-week point-prevalence study. defined by daily total Sequential Organ Failure Assessment (SOFA) score than 5. Hierarchical...

10.1002/bjs.11361 article EN cc-by British journal of surgery 2019-11-06

BackgroundVentilator-associated pneumonia is the most common intensive care unit (ICU)-acquired infection, yet accurate diagnosis remains difficult, leading to overuse of antibiotics. Low concentrations IL-1β and IL-8 in bronchoalveolar lavage fluid have been validated as effective markers for exclusion ventilator-associated pneumonia. The VAPrapid2 trial aimed determine whether measurement could effectively safely improve antibiotic stewardship patients with clinically suspected...

10.1016/s2213-2600(19)30367-4 article EN cc-by The Lancet Respiratory Medicine 2019-12-04
Thushan I. de Silva Guihai Liu Benjamin B. Lindsey Danning Dong Shona C. Moore and 95 more Sharon Hsu Dhruv R. Shah Dannielle Wellington Alexander J. Mentzer Adrienn Angyal Rebecca Brown Matthew Parker Zixi Ying Xuan Yao Lance Turtle Susanna Dunachie Mala K. Maini Graham S. Ogg Julian C. Knight Yanchun Peng Sarah L. Rowland-Jones Tao Dong David M. Aanensen Khalil Abudahab Helen Adams Alexander Adams Safiah Afifi Dinesh Aggarwal Shazaad S.Y. Ahmad Louise Aigrain Adela Alcolea-Medina Nabil-Fareed Alikhan Elias Allara Roberto Amato Tara Annett Stephen Aplin Cristina V. Ariani Hibo Asad Amy Ash Paula Ashfield Fiona Ashford Laura Atkinson Stephen W. Attwood Cressida Auckland Alp Aydin David Baker Paul Baker Carlos E. Balcazar Jonathan Ball Jeffrey C. Barrett Magdalena Barrow Edward Barton Matthew Bashton Andrew R. Bassett Rahul Batra Chris Baxter Nadua Bayzid Charlotte Beaver Angela H. Beckett Shaun M. Beckwith Luke Bedford Robert Beer Andrew D. Beggs Katherine L. Bellis Louise Berry Beatrice Bertolusso Angus Best Emma Betteridge David C. Bibby Kelly Bicknell Debbie Binns Alec Birchley Paul Bird Chloe Bishop Rachel Blacow Victoria Blakey Beth Blane Frances Bolt James Bonfield Stephen Bonner David Bonsall Tim Boswell Andrew Bosworth Yann Bourgeois Olivia Boyd Declan T. Bradley Cassie Breen Catherine Bresner Judith Breuer Stephen Bridgett Iraad F. Bronner Ellena Brooks Alice Broos Julianne R. Brown Giselda Bucca Sarah L. Buchan David Buck Matthew Bull Phillipa Burns Shirelle Burton-Fanning

We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several nucleocapsid and ORF3a have arisen independently in multiple lineages result loss of recognition epitope-specific cells assessed IFN-γ cytotoxic killing assays. Complete responsiveness was seen due to Q213K the A∗01:01-restricted CD8+ epitope FTSDYYQLY207-215; P13L, P13S, P13T B∗27:05-restricted QRNAPRITF9-17; T362I P365S A∗03:01/A∗11:01-restricted KTFPPTEPK361-369. lines...

10.1016/j.isci.2021.103353 article EN cc-by iScience 2021-10-28
Kerstin Kläser Erika Molteni Mark S. Graham Liane S. Canas Marc F. Österdahl and 95 more Michela Antonelli Liyuan Chen Jie Deng Benjamin Murray Eric Kerfoot Jonathan Wolf Anna May Ben Fox Joan Capdevila Pujol David M. Aanensen Khalil Abudahab Helen Adams Alexander Adams Safiah Afifi Dinesh Aggarwal Shazaad S. Y. Ahmad Louise Aigrain Adela Alcolea-Medina Nabil-Fareed Alikhan Elias Allara Roberto Amato Adrienn Angyal Tara Annett Stephen Aplin Cristina V. Ariani Hibo Asad Amy Ash Paula Ashfield Fiona Ashford Laura Atkinson Stephen W. Attwood Cressida Auckland Alp Aydin David Baker Paul Baker Carlos E. Balcazar Jonathan K. Ball Jeffrey C. Barrett Magdalena Barrow Edward Barton Matthew Bashton Andrew R. Bassett Rahul Batra Chris Baxter Nadua Bayzid Charlotte Beaver Angela H. Beckett Shaun M. Beckwith Luke Bedford Robert Beer Andrew D. Beggs Katherine L. Bellis Louise Berry Beatrice Bertolusso Angus Best Emma Betteridge David Bibby Kelly Bicknell Debbie Binns Alec Birchley Paul Bird Chloe Bishop Rachel Blacow Victoria Blakey Beth Blane Frances Bolt James Bonfield Stephen Bonner David Bonsall Tim Boswell Andrew Bosworth Yann Bourgeois Olivia Boyd Declan Bradley Cassie Breen Catherine Bresner Judith Breuer Stephen Bridgett Iraad F. Bronner Ellena Brooks Alice Broos Julianne R. Brown Giselda Bucca Sarah L. Buchan David Buck Matthew Bull Phillipa Burns Shirelle Burton-Fanning Timothy Byaruhanga Matthew Byott Sharon L. Campbell Alessandro M. Carabelli James S. Cargill Matthew Carlile Silvia Carvalho

The Delta (B.1.617.2) variant was the predominant UK circulating SARS-CoV-2 strain between May and December 2021. How infection compares with previous variants is unknown. This prospective observational cohort study assessed symptomatic adults participating in app-based COVID Symptom Study who tested positive for from 26 to July 1, 2021 (Delta overwhelmingly variant), compared (1:1, age- sex-matched) individuals presenting 28, 2020 6, (Alpha (B.1.1.7) variant). We illness (symptoms,...

10.1038/s41598-022-14016-0 article EN cc-by Scientific Reports 2022-06-28

Knowledge Graphs (KG) and associated Graph Embedding (KGE) models have recently begun to be explored in the context of drug discovery potential assist key challenges such as target identification. In domain, KGs can employed part a process which result lab-based experiments being performed, or impact on other decisions, incurring significant time financial costs most importantly, ultimately influencing patient healthcare. For KGE this better understanding not only performance, but also...

10.1016/j.ailsci.2022.100036 article EN cc-by-nc-nd Artificial Intelligence in the Life Sciences 2022-05-26

Evidence is limited for the effectiveness of interventions survivors critical illness after hospital discharge. We explored effect an 8-week hospital-based exercise-training programme on physical fitness and quality-of-life.In a parallel-group minimized controlled trial, patients were recruited before discharge or in intensive care follow-up clinic enrolled 8-16 weeks Each week, intervention comprised two sessions physiotherapist-led cycle ergometer exercise (30 min, moderate intensity) plus...

10.1093/bja/aeu051 article EN cc-by-nc British Journal of Anaesthesia 2014-03-07

We introduce style augmentation, a new form of data augmentation based on random transfer, for improving the robustness convolutional neural networks (CNN) over both classification and regression tasks. During training, our randomizes texture, contrast color, while preserving shape semantic content. This is accomplished by adapting an arbitrary transfer network to perform randomization, sampling input embeddings from multivariate normal distribution instead inferring them image. In addition...

10.48550/arxiv.1809.05375 preprint EN other-oa arXiv (Cornell University) 2018-01-01

In this paper, we propose a novel Convolutional Neural Network (CNN) approach for the classification of raw dry-EEG signals without any data pre-processing. To illustrate effectiveness our approach, utilise Steady State Visual Evoked Potential (SSVEP) paradigm as use case. SSVEP can be utilised to allow people with severe physical disabilities such Complete Locked-In Syndrome or Amyotrophic Lateral Sclerosis aided via BCI applications, it requires only subject fixate upon sensory stimuli...

10.1109/smc.2018.00631 article EN 2022 IEEE International Conference on Systems, Man, and Cybernetics (SMC) 2018-10-01

Despite significant recent progress in the area of Brain-Computer Interface (BCI), there are numerous shortcomings associated with collecting Electroencephalography (EEG) signals real-world environments. These include, but not limited to, subject and session data variance, long arduous calibration processes predictive generalisation issues across different subjects or sessions. This implies that many downstream applications, including Steady State Visual Evoked Potential (SSVEP) based...

10.1109/ijcnn.2019.8852227 article EN 2022 International Joint Conference on Neural Networks (IJCNN) 2019-07-01

Only a minority of intracranial aneurysms rupture to cause subarachnoid hemorrhage.To test the hypothesis that unruptured have different characteristics and risk factor profiles compared ruptured aneurysms.We recruited patients with or aneurysmal hemorrhages at 22 UK hospitals between 2011 2014. Demographic, clinical, imaging data were collected using standardized case report forms. We factors multivariable logistic regression.A total 2334 (1729 hemorrhage, 605 aneurysms) included (mean age...

10.1093/neuros/nyx365 article EN Neurosurgery 2017-06-06

Graph embeddings have become a key and widely used technique within the field of graph mining, proving to be successful across broad range domains including social, citation, transportation biological. Unsupervised embedding techniques aim automatically create low-dimensional representation given graph, which captures structural elements in resulting space. However, date, there has been little work exploring exactly topological structures are being learned embeddings, could possible way...

10.1007/s41019-019-0097-5 article EN cc-by Data Science and Engineering 2019-06-29

10.1093/bja/aei235 article EN publisher-specific-oa British Journal of Anaesthesia 2005-09-24

Objective: To investigate if the incidence of disorders spermatogenesis and testicular tissue morphology have changed in middle aged Finnish men over 10 years.Design: Two necropsy series completed 1981 1991.

10.1136/bmj.314.7073.35 article EN BMJ 1997-01-04

Brain stem death may be a difficult concept for relatives to understand. Our ITU practice follows published recommendations that the use of explanatory leaflets showing CT scans and observing brain testing in some cases help understand has occurred. Using this strategy, we interviewed 27 12 months after bereavement following certification by testing, investigating their understanding death, subsequent attitudes organ donation, grief reactions those who had observed tests. Most understood...

10.1111/j.1365-2044.2005.04297.x article EN Anaesthesia 2005-08-19

10.1093/bjaceaccp/mkt021 article EN publisher-specific-oa Continuing Education in Anaesthesia Critical Care & Pain 2013-07-12

Patients who survive critical illness often report deterioration in health related quality of life. This has not been shown to improve following post-intensive care unit (ICU) self-directed exercise. The Post Intensive Care eXercise (PIX) study demonstrated improved objectively measured fitness a supervised exercise programme and also suggested beneficial effects on physical mental health. qualitative arm the PIX reported here utilised focus groups explore more detail recovery from illness,...

10.1177/1751143714554896 article EN Journal of the Intensive Care Society 2014-12-09

Recommender Systems are becoming ubiquitous in many settings and take forms, from product recommendation e-commerce stores, to query suggestions search engines, friend social networks. Current research directions which largely based upon supervised learning historical data appear be showing diminishing returns with a lot of practitioners report discrepancy between improvements offline metrics for the online performance newly proposed models. One possible reason is that we using wrong...

10.48550/arxiv.1808.00720 preprint EN other-oa arXiv (Cornell University) 2018-01-01

Graphs have become a crucial way to represent large, complex and often temporal datasets across wide range of scientific disciplines. However, when graphs are used as input machine learning models, this rich information is frequently disregarded during the process, resulting in suboptimal performance on certain inference tasks. To combat this, we introduce Temporal Neighbourhood Aggregation (TNA), novel vertex representation model architecture designed capture both topological directly...

10.1109/bigdata47090.2019.9005545 article EN 2021 IEEE International Conference on Big Data (Big Data) 2019-12-01
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