Machine learning for a medical study of cyclists

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This blog provides a technical explanation of the analysis underlying the medical paper about male cyclists described previously. Part of the skill of a data scientist is to choose from the arsenal of machine learning techniques the tools that are appropriate for the problem at hand. In the study of male cyclists, I was asked to identify significant features of a medical data set. This article describes how the problem was tackled.

Data

Fifty road racing cyclists, riding at the equivalent of British Cycling 2nd category or above, were asked to complete a questionnaire, provide a blood sample and undergo a DXA scan – a low intensity X-ray used to measure bone density and body composition. I used Python to load and clean up the data, so that all the information could be represented in Pandas DataFrames. As expected this time-consuming, but essential step required careful attention and cross-checking, combined with the perseverance that is always necessary to be sure of working with a clean data set.

The questionnaire included numerical data and text relating to cycling performance, training, nutrition and medical history. As a result of interviewing each cyclist, a specialist sports endocrinologist identified a number of individuals who were at risk of low energy availability (EA), due to a mismatch between nutrition and training load.

Bone density was measured throughout the body, but the key site of interest was the lumbar spine (L1-L4). Since bone density varies with age and between males and females, it was logical to use the male, age-adjusted Z-score, expressing values in standard deviations above or below the comparable population mean.

The measured blood markers were provided in the relevant units, alongside the normal range. Since the normal range is defined to cover 95% of the population, I assumed that the population could be modelled by a gaussian distribution in order to convert each blood result into a Z-score. This aligned the scale of the blood results with the bone density measures.

Analysis

I decided to use the Orange machine learning and data visualisation toolkit for this project. It was straightforward to load the data set of 46 features for each of the 50 cyclists. The two target variables were lumbar spine Z-score (bone health) and 60 minute FTP watts per kilo (performance). The statistics confirmed the researchers’ suspicion that the lumbar spine bone density of the cyclists would be below average, partly due to the non-weight-bearing nature of the sport. Some of the readings were extremely low (verging on osteoporosis) and the question was why.

Given the relatively small size of the data set (a sample of 50), the most straightforward approach for identifying the key explanatory variables was to search for an optimal Decision Tree. Interestingly, low EA turned out to be the most important variable in explaining lumbar spine bone density, followed by prior participation in a weight-bearing sport and levels of vitamin D (which was, in most cases, below the ideal level of athletes). Since I had used all the data to generate the tree, I made use of Orange’s data sampler to confirm that these results were highly robust. This had some similarities with the Random Forest approach. Although Orange produces some simple graphical tools like the following, I use Python to generate my own versions for the final publication.

Decision Tree from Orange

Published Decision Tree

Finding a robust decision tree is one thing, but it was essential to verify whether the decision variables were statistically significant. For this, Orange provides box plots for discrete variables. For my own peace of mind, I recalculated all of the Student’s T-statistics to confirm that they were correct and significant. The charts below show an example of an Orange box plot and the final graphic used in the publication.

Orange Box Plot

Final Box Plots

The Orange toolkit includes other nice data visualisation tools. I particularly liked the flexibility available to make scatter plots. This inspired the third figure in the publication, which showed the most important variable explaining performance. This chart highlights a cluster of three cyclists with low EA, whose FTP watts/kg were lower than expected, based on their high training load. I independently checked the T-statistics of the regression coefficients to identify relationships that were significant, like training load, or insignificant, like percentage body fat.

Orange Scatter Plot

Published Scatter Plot

Conclusions

The Orange toolkit turned out to be extremely helpful in identifying relationships that fed directly into the conclusions of an important medical paper highlighting potential health risks and performance drivers for high level cyclists. Restricting nutrition through diet or fasted rides can lead to low energy availability, that can cause endocrine responses in the body that reduce lumbar spine bone density, resulting in vulnerability to fracture and slow recovery. This is know as Relative Energy Deficiency in Sport (RED-S). Despite the obsession of many cyclists to reduce body fat, the key variable explaining functional threshold power watts/kg was weekly training load.