Risk prediction models need thorough validation to assess their performance. Validation of models for survival outcomes poses challenges due to the censoring of observations and the varying time... Show moreRisk prediction models need thorough validation to assess their performance. Validation of models for survival outcomes poses challenges due to the censoring of observations and the varying time horizon at which predictions can be made. This article describes measures to evaluate predictions and the potential improvement in decision making from survival models based on Cox proportional hazards regression.As a motivating case study, the authors consider the prediction of the composite outcome of recurrence or death (the "event ") in patients with breast cancer after surgery. They developed a simple Cox regression model with 3 predictors, as in the Nottingham Prognostic Index, in 2982 women (1275 events over 5 years of follow-up) and externally validated this model in 686 women (285 events over 5 years). Improvement in performance was assessed after the addition of progesterone receptor as a prognostic biomarker.The model predictions can be evaluated across the full range of observed follow-up times or for the event occurring by the end of a fixed time horizon of interest. The authors first discuss recommended statistical measures that evaluate model performance in terms of discrimination, calibration, or overall performance. Further, they evaluate the potential clinical utility of the model to support clinical decision making according to a net benefit measure. They provide SAS and R code to illustrate internal and external validation.The authors recommend the proposed set of performance measures for transparent reporting of the validity of predictions from survival models. Show less
Ratna, M.B.; Bhattacharya, S.; Geloven, N. van; McLernon, D.J. 2022
STUDY QUESTION Can we develop an IVF prediction model to estimate individualized chances of a live birth over multiple complete cycles of IVF in couples embarking on their second complete cycle of... Show moreSTUDY QUESTION Can we develop an IVF prediction model to estimate individualized chances of a live birth over multiple complete cycles of IVF in couples embarking on their second complete cycle of treatment? SUMMARY ANSWER Yes, our prediction model can estimate individualized chances of cumulative live birth over three additional complete cycles of IVF. WHAT IS KNOWN ALREADY After the completion of a first complete cycle of IVF, couples who are unsuccessful may choose to undergo further treatment to have their first child, while those who have had a live birth may decide to have more children. Existing prediction models can estimate the overall chances of success in couples before commencing IVF but are unable to revise these chances on the basis of the couple's response to a first treatment cycle in terms of the number of eggs retrieved and pregnancy outcome. This makes it difficult for couples to plan and prepare emotionally and financially for the next step in their treatment. STUDY DESIGN, SIZE, DURATION For model development, a population-based cohort was used of 49 314 women who started their second cycle of IVF including ICSI in the UK from 1999 to 2008 using their own oocytes and their partners' sperm. External validation was performed on data from 39 442 women who underwent their second cycle from 2010 to 2016. PARTICIPANTS/MATERIALS, SETTING, METHODS Data about all UK IVF treatments were obtained from the Human Fertilisation and Embryology Authority (HFEA) database. Using a discrete time logistic regression model, we predicted the cumulative probability of live birth from the second up to and including the fourth complete cycles of IVF. Inverse probability weighting was used to account for treatment discontinuation. Discrimination was assessed using c-statistic and calibration was assessed using calibration-in-the-large and calibration slope. MAIN RESULTS AND THE ROLE OF CHANCE Following exclusions, 49 314 women with 73 053 complete cycles were included. 12 408 (25.2%) had a live birth resulting from their second complete cycle. Cumulatively, 17 394 (35.3%) had a live birth over complete cycles two to four. The model showed moderate discriminative ability (c-statistic: 0.65, 95% CI: 0.64 to 0.65) and evidence of overprediction (calibration-in-the-large = -0.08) and overfitting (calibration slope 0.85, 95% CI: 0.81 to 0.88) in the validation cohort. However, after recalibration the fit was much improved. The recalibrated model identified the following key predictors of live birth: female age (38 versus 32 years-adjusted odds ratio: 0.59, 95% CI: 0.57 to 0.62), number of eggs retrieved in the first complete cycle (12 versus 4 eggs; 1.34, 1.30 to 1.37) and outcome of the first complete cycle (live birth versus no pregnancy; 1.78, 1.66 to 1.91; live birth versus pregnancy loss; 1.29, 1.23 to 1.36). As an example, a 32-year-old with 2 years of non-tubal infertility who had 12 eggs retrieved from her first stimulation and had a live birth during her first complete cycle has a 46% chance of having a further live birth from the second complete cycle of IVF and an 81% chance over a further three cycles. LIMITATIONS, REASONS FOR CAUTION The developed model was updated using validation data that was 6 to 12 years old. IVF practice continues to evolve over time, which may affect the accuracy of predictions from the model. We were unable to adjust for some potentially important predictors, e.g. BMI, smoking and alcohol intake in women, as well as measures of ovarian reserve such as antral follicle count.These were not available in the linked HFEA dataset. WIDER IMPLICATIONS OF THE FINDINGS By appropriately adjusting for couples who discontinue treatment, our novel prediction model will provide more realistic chances of live birth in couples starting a second complete cycle of IVF. Clinicians can use these predictions to inform discussion with couples who wish to plan ahead. This prediction tool will enable couples to prepare emotionally, financially and logistically for IVF treatment. STUDY FUNDING/COMPETING INTEREST(S) This study was supported by an Elphinstone scholarship scheme at the University of Aberdeen and Aberdeen Fertility Centre, University of Aberdeen. The authors have no conflict of interest. Show less
Calster, B. van; McLernon, D.J.; Smeden, M. van; Wynants, L.; Steyerberg, E.W.; STRATOS Initiative 2019
Background: The assessment of calibration performance of risk prediction models based on regression or more flexible machine learning algorithms receives little attention.Main text: Herein, we... Show moreBackground: The assessment of calibration performance of risk prediction models based on regression or more flexible machine learning algorithms receives little attention.Main text: Herein, we argue that this needs to change immediately because poorly calibrated algorithms can be misleading and potentially harmful for clinical decision-making. We summarize how to avoid poor calibration at algorithm development and how to assess calibration at algorithm validation, emphasizing balance between model complexity and the available sample size. At external validation, calibration curves require sufficiently large samples. Algorithm updating should be considered for appropriate support of clinical practice.Conclusion: Efforts are required to avoid poor calibration when developing prediction models, to evaluate calibration when validating models, and to update models when indicated. The ultimate aim is to optimize the utility of predictive analytics for shared decision-making and patient counseling. Show less
Eekelen, R. van; Putter, H.; McLernon, D.J.; Eijkemans, M.J.; Geloven, N. van 2019
