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Book ; Online: Scoring rules in survival analysis

Sonabend, Raphael

2022

Abstract: 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 ...

Abstract	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 survey proposed scoring rules for survival analysis, establish the first clear definition of `(strict) properness' for survival scoring rules, and determine which losses are proper and improper. We prove that commonly utilised scoring rules that are claimed to be proper are in fact improper. We further prove that under a strict set of assumptions a class of scoring rules is strictly proper for, what we term, `approximate' survival losses. We hope these findings encourage further research into robust validation of survival models and promote honest evaluation.
Keywords	Mathematics - Statistics Theory ; Computer Science - Machine Learning ; Statistics - Applications
Subject code	006
Publishing date	2022-12-10
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: FAIR-USE4OS: Guidelines for creating impactful open-source software.

Sonabend, Raphael / Gruson, Hugo / Wolansky, Leo / Kiragga, Agnes / Katz, Daniel S

PLoS computational biology

2024 Volume 20, Issue 5, Page(s) e1012045

Abstract: This paper extends the FAIR (Findable, Accessible, Interoperable, Reusable) guidelines to provide criteria for assessing if software conforms to best practices in open source. By adding "USE" (User-Centered, Sustainable, Equitable), software development ... ...

Abstract	This paper extends the FAIR (Findable, Accessible, Interoperable, Reusable) guidelines to provide criteria for assessing if software conforms to best practices in open source. By adding "USE" (User-Centered, Sustainable, Equitable), software development can adhere to open source best practice by incorporating user-input early on, ensuring front-end designs are accessible to all possible stakeholders, and planning long-term sustainability alongside software design. The FAIR-USE4OS guidelines will allow funders and researchers to more effectively evaluate and plan open-source software projects. There is good evidence of funders increasingly mandating that all funded research software is open source; however, even under the FAIR guidelines, this could simply mean software released on public repositories with a Zenodo DOI. By creating FAIR-USE software, best practice can be demonstrated from the very beginning of the design process and the software has the greatest chance of success by being impactful.
MeSH term(s)	Software ; Guidelines as Topic ; Computational Biology/methods ; Software Design ; Humans
Language	English
Publishing date	2024-05-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1012045
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Avoiding C-hacking when evaluating survival distribution predictions with discrimination measures.

Sonabend, Raphael / Bender, Andreas / Vollmer, Sebastian

Bioinformatics (Oxford, England)

2022 Volume 38, Issue 17, Page(s) 4178–4184

Abstract: Motivation: In this article, 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 ... ...

Abstract	Motivation: In this article, 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 and software and consider their respective advantages and disadvantages. Results: Whilst distributions are frequently evaluated by discrimination measures, we find that the method for doing so is rarely described in the literature and often leads to unfair comparisons or 'C-hacking'. We demonstrate by example how simple it can be to manipulate results and use this to argue for better reporting guidelines and transparency in the literature. We recommend that machine learning survival analysis software implements clear transformations between distribution and risk predictions in order to allow more transparent and accessible model evaluation. Availability and implementation: The code used in the final experiment is available at https://github.com/RaphaelS1/distribution_discrimination.
MeSH term(s)	Software ; Machine Learning ; Publications
Language	English
Publishing date	2022-07-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btac451
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Article ; Online: The Wolfson Assessment Matrix: a potential tool to support clinicians in establishing access to specialized neuro rehabilitation by capturing important prognostic factors. Sharing more equitable and transparent criteria.

Saverino, Alessia / Sonabend, Raphael / Wong, Sancho / Symeon, Christopher

European journal of physical and rehabilitation medicine

2021 Volume 58, Issue 2, Page(s) 161–170

Abstract: 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 ... ...

Abstract	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, there is no consensus on how to screen patients with regard to rehabilitation prognosis. Aim: The aim of this study was to improve the selection of patients admitted to an SRS, defining transparent and equitable prognostic criteria to guide clinicians' decision making. Design: This is a retrospective observational study SETTING: an SRS in the UK. Population: We included 121 patients affected by a neurological condition consecutively admitted for multidisciplinary rehabilitation. Methods: Rehabilitation Complexity Scale Extended is used to describe rehabilitation complexity. A short list of potential barriers to rehabilitation was analysed to predict the functional outcome measured by the Functional Independent Measure and the Barthel Index. Results: Older age, a heavier burden of co-morbidities, pre-morbid cognitive difficulties or dementia and a lower function level at admission were the most important variables to predict a lower functional gain. Conclusions: We have used this list of barriers to create the Wolfson Assessment Matrix as a potential support tool to guide clinicians navigating through the different rehabilitation service options when assessing complex patients for eligibility to an SRS. Clinical rehabilitation impact: SRSs are highly expensive services representing a possible step along the rehabilitation pathway for patients with complex needs. A tool such as the Wolfson Assessment Matrix would represent a step forward to help consistency in decision making regarding appropriateness for SRSs. It would also help to set realistic long-term goals with patients and families and support Health Services in the further development of alternative rehabilitation settings.
MeSH term(s)	Activities of Daily Living ; Comorbidity ; Consensus ; Hospitalization ; Humans ; Prognosis
Language	English
Publishing date	2021-11-26
Publishing country	Italy
Document type	Journal Article ; Observational Study
ZDB-ID	2426908-6
ISSN	1973-9095 ; 1973-9087
ISSN (online)	1973-9095
ISSN	1973-9087
DOI	10.23736/S1973-9087.21.07022-2
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Article ; Online: The impact of health inequity on regional variation of COVID-19 transmission in England

Rawson, Thomas / Hinsley, Wes / Sonabend, Raphael / Semenova, Elizaveta / Cori, Anne / Ferguson, Neil M

medRxiv

Abstract: Considerable spatial heterogeneity has been observed in COVID-19 transmission across administrative regions of England throughout the pandemic. This study investigates what drives these differences. We constructed a probabilistic case count model for 306 ...

Abstract	Considerable spatial heterogeneity has been observed in COVID-19 transmission across administrative regions of England throughout the pandemic. This study investigates what drives these differences. We constructed a probabilistic case count model for 306 administrative regions of England across 95 weeks, fit using a Bayesian evidence synthesis framework. We include the mechanistic impact of acquired immunity, of spatial exportation of cases, and 16 spatially-varying socio-economic, socio-demographic, health, and mobility variables. Model comparison assesses the relative contributions of these respective mechanisms. We find that regionally-varying and time-varying differences in week-to-week transmission were definitively associated with differences in: time spent at home, variant-of-concern proportion, and adult social care funding. However, model comparison demonstrates that the mechanistic impact of these terms was of negligible impact compared to the role of spatial exportation between regions. While these results confirm the impact of some, but not all, measures of regional inequity in England, our work corroborates the finding that observed differences in regional disease transmission during the pandemic were predominantly driven by underlying epidemiological factors rather than the demography and health inequity between regions.
Keywords	covid19
Language	English
Publishing date	2024-04-22
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2024.04.20.24306121
Database	COVID19

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Book ; Online: Deep Learning for Survival Analysis

Wiegrebe, Simon / Kopper, Philipp / Sonabend, Raphael / Bischl, Bernd / Bender, Andreas

A Review

2023

Abstract: The influx of deep learning (DL) techniques into the field of survival analysis in recent years has led to substantial methodological progress; for instance, learning from unstructured or high-dimensional data such as images, text or omics data. In this ... ...

Abstract	The influx of deep learning (DL) techniques into the field of survival analysis in recent years has led to substantial methodological progress; for instance, learning from unstructured or high-dimensional data such as images, text or omics data. In this work, we conduct a comprehensive systematic review of DL-based methods for time-to-event analysis, characterizing them according to both survival- and DL-related attributes. In summary, the reviewed methods often address only a small subset of tasks relevant to time-to-event data - e.g., single-risk right-censored data - and neglect to incorporate more complex settings. Our findings are summarized in an editable, open-source, interactive table: https://survival-org.github.io/DL4Survival. As this research area is advancing rapidly, we encourage community contribution in order to keep this database up to date. Comment: 29 pages, 7 figures, 2 tables, 1 interactive table
Keywords	Statistics - Machine Learning ; Computer Science - Machine Learning
Subject code	004
Publishing date	2023-05-24
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: distr6

Sonabend, Raphael / Kiraly, Franz

R6 Object-Oriented Probability Distributions Interface in R

2020

Abstract: 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 ...

Abstract	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 hazards and distribution function anti-derivatives. In addition to simple distributions, distr6 supports compositions such as truncation, mixtures, and product distributions. This paper presents the core functionality of the package and demonstrates examples for key use-cases. In addition this paper provides a critical review of the object-oriented programming paradigms in R and describes some novel implementations for design patterns and core object-oriented features introduced by the package for supporting distr6 components. Comment: Accepted in The R Journal
Keywords	Computer Science - Software Engineering ; Computer Science - Mathematical Software ; Statistics - Applications ; Statistics - Computation
Subject code	519
Publishing date	2020-09-07
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Assessing the influence of culture on craft skills: A quantitative study with expert Nepalese potters.

Gandon, Enora / Nonaka, Tetsushi / Sonabend, Raphael / Endler, John

PloS one

2020 Volume 15, Issue 10, Page(s) e0239139

Abstract: 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 ... ...

Abstract	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 skills. Our goal was to quantify the influence of three kinds of constraints: the transcultural constraints of wheel-throwing, the cultural constraints induced via cultural transmission, and the potters' individual constraints. Five expert Nepalese potters were invited to produce three familiar pottery types, each in five specimens. A total of 31 different fashioning hand positions were identified. Most of them (14) were cross-cultural, ten positions were cultural, five positions were individual, and two positions were unique. Statistical tests indicated that the subset of positions used by the participants in this study were distinct from those of other cultural groups. Behaviours described in terms of fashioning duration, number of gestures, and hand position repertoires size highlighted both individual and cross-cultural traits. We also analysed the time series of the successive hand positions used throughout the fashioning of each vessel. Results showed, for each pottery type, strong reproducible sequences at the individual level and a clearly higher level of variability between potters. Overall, our findings confirm the existence of a cultural transmission in craft skills but also demonstrated that the skill is not fully determined by a cultural marking. We conclude that the influence of culture on craft skills should not be overstated, even if its role is significant given the fact that it reflects the socially transmitted part of the skill. Such research offers insights into archaeological problems in providing a representative view of how cultural constraints influence the motor skills implied in artefact manufacturing.
MeSH term(s)	Adult ; Art ; Cross-Cultural Comparison ; Cultural Characteristics ; Gestures ; Hand ; Hinduism ; Humans ; Male ; Middle Aged ; Motor Skills ; Nepal
Language	English
Publishing date	2020-10-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0239139
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Book ; Online: Avoiding C-hacking when evaluating survival distribution predictions with discrimination measures

Sonabend, Raphael / Bender, Andreas / Vollmer, Sebastian

2021

Abstract: 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 ... ...

Abstract	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 and software and consider their respective advantages and disadvantages. Whilst distributions are frequently evaluated by discrimination measures, we find that the method for doing so is rarely described in the literature and often leads to unfair comparisons. We find that the most robust method of reducing a distribution to a risk is to sum over the predicted cumulative hazard. We recommend that machine learning survival analysis software implements clear transformations between distribution and risk predictions in order to allow more transparent and accessible model evaluation. The code used in the final experiment is available at https://github.com/RaphaelS1/distribution_discrimination.
Keywords	Statistics - Machine Learning ; Computer Science - Machine Learning ; Mathematics - Statistics Theory ; Statistics - Methodology
Subject code	310
Publishing date	2021-12-09
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: mlr3proba: an R package for machine learning in survival analysis.

Sonabend, Raphael / Király, Franz J / Bender, Andreas / Bischl, Bernd / Lang, Michel

Bioinformatics (Oxford, England)

2021 Volume 37, Issue 17, Page(s) 2789–2791

Abstract: Summary: 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 ... ...

Abstract	Summary: 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, bioinformatics, economics, engineering and more. mlr3proba provides a comprehensive machine-learning interface for survival analysis and connects with mlr3's general model tuning and benchmarking facilities to provide a systematic infrastructure for survival modelling and evaluation. Availability and implementation: mlr3proba is available under an LGPL-3 licence on CRAN and at https://github.com/mlr-org/mlr3proba, with further documentation at https://mlr3book.mlr-org.com/survival.html.
Language	English
Publishing date	2021-01-08
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btab039
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