Raphael Sonabend

RPTU - Rheinland-Pfälzische Technische Universität Kaiserslautern Landau | TUK

As the SARS-CoV-2 pandemic progressed, distinct variants emerged and dominated in England. These variants, Wildtype, Alpha, Delta, and Omicron were characterized by variations in transmissibility and severity. We used a robust mathematical model and Bayesian inference framework to analyse epidemiological surveillance data from England. We quantifie...

The influx of deep learning (DL) techniques into the field of survival analysis in recent years, coupled with the increasing availability of high-dimensional omics data and unstructured data like images or text, has led to substantial methodological progress; for instance, learning from such high-dimensional or unstructured data. Numerous modern DL...

As the SARS-CoV-2 pandemic progressed, distinct variants emerged and dominated in England. These variants, Wildtype, Alpha, Delta, and Omicron were characterized by variations in transmissibility and severity. We used a robust mathematical model and Bayesian inference framework to analyse epidemiological surveillance data from England. We quantifie...

Background: The UK was the first country to start national COVID-19 vaccination programmes, initially administering doses 3 weeks apart. However, early evidence of high vaccine effectiveness after the first dose and the emergence of the SARS-CoV-2 alpha variant prompted the UK to extend the interval between doses to 12 weeks. In this study, we aim...

Scoring rules promote rational and good decision making and predictions by models, this is increasingly important for automated procedures of `auto-ML'. The Brier score and Log loss are well-established scoring rules for classification and regression and possess the `strict properness' property that encourages optimal predictions. In this paper we...

Purpose: Algorithmic fairness is an increasingly important field concerned with detecting and mitigating biases in machine learning models. There has been a wealth of literature for algorithmic fairness in regression and classification however there has been little exploration of the field for survival analysis. Survival analysis is the prediction...

Background The UK was the first country to start national COVID-19 vaccination programmes, initially administering doses 3-weeks apart. However, early evidence of high vaccine effectiveness after the first dose and the emergence of the Alpha variant prompted the UK to extend the interval between doses to 12-weeks. In this study, we quantify the imp...

Motivation In this paper we consider how to evaluate survival distribution predictions with measures of discrimination. This is non-trivial as discrimination measures are the most commonly used in survival analysis and yet there is no clear method to derive a risk prediction from a distribution prediction. We survey methods proposed in literature a...

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Gamma variant of concern has spread rapidly across Brazil since late 2020, causing substantial infection and death waves. Here we used individual-level patient records after hospitalization with suspected or confirmed coronavirus disease 2019 (COVID-19) between 20 January 2020 and 26...

Algorithmic fairness is an increasingly important field concerned with detecting and mitigating biases in machine learning models. There has been a wealth of literature for algorithmic fairness in regression and classification however there has been little exploration of the field for survival analysis. Survival analysis is the prediction task in w...

In this paper we consider how to evaluate survival distribution predictions with measures of discrimination. This is a non-trivial problem as discrimination measures are the most commonly used in survival analysis and yet there is no clear method to derive a risk prediction from a distribution prediction. We survey methods proposed in literature an...

One sentence summary COVID-19 in-hospital fatality rates fluctuate dramatically in Brazil, and these fluctuations are primarily associated with geographic inequities and shortages in healthcare capacity. Abstract The SARS-CoV-2 Gamma variant spread rapidly across Brazil, causing substantial infection and death waves. We use individual-level patient...

The SARS-CoV-2 Gamma variant spread rapidly across Brazil, causing substantial infection and death waves. We use individual-level patient records following hospitalisation with suspected or confirmed COVID-19 to document the extensive shocks in hospital fatality rates that followed Gamma’s spread across 14 state capitals, and in which more than hal...

Background: Specialized Rehabilitation Services (SRSs) are designed to offer intensive multidisciplinary rehabilitation to patients with complex needs, who are expected to make significant functional gains in their ADLs over a relatively limited period of time. Although national guidelines offer a guidance on how to band patients by complexity, th...

Background England's COVID-19 roadmap out of lockdown policy set out the timeline and conditions for the stepwise lifting of non-pharmaceutical interventions (NPIs) as vaccination roll-out continued, with step one starting on March 8, 2021. In this study, we assess the roadmap, the impact of the delta (B.1.617.2) variant of SARS-CoV-2, and potentia...

While craft apprenticeship can be understood as socially mediated individual learning, the ensuing prediction of individual and cultural object traits within craft communities has not been investigated. Here we provide an assessment of vessel shape variations occurring through cultural transmission and their visual perception by the craftsmen. To t...

Background: England's COVID-19 'roadmap out of lockdown' set out the timeline and conditions for the stepwise lifting of non-pharmaceutical interventions (NPIs) as vaccination roll-out continued. Here we assess the roadmap, the impact of the Delta variant, and potential future epidemic trajectories. Methods: We extended a model of SARS-CoV-2 transm...

Background: The multiple efficacious vaccines authorised for emergency use worldwide represent the first preventative intervention against coronavirus disease 2019 (COVID-19) that does not rely on social distancing measures. The speed at which data are emerging and the heterogeneities in study design, target populations, and implementation make it...

Survival analysis is an important field of Statistics concerned with making time-to-event predictions with ‘censored’ data. Machine learning, specifically supervised learning, is the field of Statistics concerned with using state-of-the-art algorithms in order to make predictions on unseen data. This thesis looks at unifying these two fields as cur...

distr6 is an object-oriented (OO) probability distributions interface leveraging the extensibil ity and scalability of R6 and the speed and efficiency of Rcpp. Over 50 probability distributions are currently implemented in the package with ‘core’ methods, including density, distribution, and gener ating functions, and more ‘exotic’ ones, including...

Unmitigated spread in Brazil Despite an extensive network of primary care availability, Brazil has suffered profoundly during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Using daily data from state health offices, Castro et al. analyzed the pattern of spread of COVID-19 cases and deaths in the country from February to...

Background: Health-related quality of life (HRQL) is important for evaluating the impact of a disease in the longer term across the physical and psychological domains of human functioning. The aim of this study is to evaluate HRQL in COVID-19 survivors in Italy using the short form 36-items questionnaire (SF-36). Methods: This is an observational s...

Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite high levels of previous infection there. Through genome sequencing of viruses sampled in Manaus between November 2020 and January 2021, we identified the emergence and circulation of a novel SARS-CoV-2 variant of concern, lineage P.1, that acquired 17 mutations, includi...

Motivation As machine learning has become increasingly popular over the last few decades, so too has the number of machine learning interfaces for implementing these models. Whilst many R libraries exist for machine learning, very few offer extended support for survival analysis. This is problematic considering its importance in fields like medicin...

Machine learning (ML) and AI toolboxes such as scikit-learn or Weka are workhorses of contemporary data scientific practice -- their central role being enabled by usable yet powerful designs that allow to easily specify, train and validate complex modeling pipelines. However, despite their universal success, the key design principles in their const...

Background: Executive dysregulation and impulsivity can both predispose individuals to risk-prone actions. Although the risk of falls is well established in people with poor executive function, its association to impulsivity is less clear. Purpose: To describe and assess the prognostic capabilities of the relationship between impulsivity, execut...

Objective: To describe the relationship between type 2 diabetes and all-cause mortality among adults with coronavirus disease 2019 (COVID-19) in the critical care setting. Research design and methods: This was a nationwide retrospective cohort study in people admitted to hospital in England with COVID-19 requiring admission to a high dependency...

Studies have documented that traditional motor skills (i.e. motor habits) are part of the cultural way of life that characterises each society. Yet, it is still unclear to what extent motor skills are inherited through culture. Drawing on ethnology and motor behaviour, we addressed this issue through a detailed description of traditional pottery sk...

distr6 is an object-oriented (OO) probability distributions interface leveraging the extensibility and scalability of R6, and the speed and efficiency of Rcpp. Over 50 probability distributions are currently implemented in the package with `core' methods including density, distribution, and generating functions, and more `exotic' ones including haz...

As machine learning has become increasingly popular over the last few decades, so too has the number of machine learning interfaces for implementing these models. Whilst many R libraries exist for machine learning, very few offer extended support for survival analysis. This is problematic considering its importance in fields like medicine, bioinfor...

Bilal Mateen and Raphael Sonabend are searching for Santa Claus, armed only with a statistical model to predict ear size based on age. The plan sounds ridiculous, but there's a serious lesson here about the limits of predictive models Bilal Mateen and Raphael Sonabend are searching for Santa Claus, armed only with a statistical model to predict ear...

Objective: To determine the completeness of argumentative steps necessary to conclude effectiveness of an algorithm in a sample of current ML/AI supervised learning literature. Data Sources: Papers published in the Neural Information Processing Systems (NeurIPS, n\'ee NIPS) journal where the official record showed a 2017 year of publication. Eligib...

Objective: To determine the completeness of argumentative steps necessary to conclude effectiveness of an algorithm in a sample of current ML/AI supervised learning literature. Data Sources: Papers published in the Neural Information Processing Systems (NeurIPS, née NIPS) journal where the official record showed a 2017 year of publication. Eligibil...