Strava – Tour de Richmond Park Clockwise

Screenshot 2019-05-22 at 15.24.51

Following my recent update on the Tour de Richmond Park leaderboard, a friend asked about the ideal weather conditions for a reverse lap, clockwise around the park. This is a less popular direction, because it involves turning right at each mini-roundabout, including Cancellara corner, where the great Swiss rouleur crashed in the 2012 London Olympics, costing him a chance of a medal.

An earlier analysis suggested that apart from choosing a warm day and avoiding traffic, the optimal wind direction for a conventional anticlockwise lap was a moderate easterly, offering a tailwind up Sawyers Hill. It does not immediately follow that a westerly wind would be best for a clockwise lap, because trees, buildings and the profile of the course affect the extent to which the wind helps or hinders a rider.

Currently there are over 280,000 clockwise laps recorded by nearly 35,000 riders, compared with more than a million anticlockwise laps by almost 55,000 riders. As before, I downloaded the top 1,000 entries from the leaderboard and then looked up the wind conditions when each time was set on a clockwise lap.

In the previous analysis, I took account of the prevailing wind direction in London. If wind had no impact, we would expect the distribution of wind directions for leaderboard entries to match the average distribution of winds over the year. I defined the wind direction advantage to be the difference between these two distributions and checked if it was statistically significant. These are the results for the clockwise lap.

RoseSegmentBarSegmentclockwise

The wind direction advantage was significant (at p=1.3%). Two directions stand out. A westerly provides a tailwind on the more exposed section of the park between Richmond Gate and Roehampton, which seems to be a help, even though it is largely downhill. A wind blowing from the NNW would be beneficial between Roehampton and Robin Hood Gate, but apparently does not provide much hindrance on the drag from Kingston Gate up to Richmond, perhaps because this section of the park is more sheltered. The prevailing southwesterly wind was generally unfavourable to riders setting PBs on a clockwise lap.

The excellent mywindsock web site provides very good analysis for avid wind dopers. This confirms that the wind was blowing predominantly from the west for the top ten riders on the leaderboard, including the KOM, though the wind strength was generally light.

The interesting thing about this exercise is that it demonstrates a convergence between our online and our offline lives, as increasing volumes of data are uploaded from mobile sensors. A detailed analysis of each section of the million laps riders have recorded for Richmond Park could reveal many subtleties about how the wind flows across the terrain, depending on strength and direction. This could be extended across the country or globally, potentially identifying local areas where funnelling effects might make a wind turbine economically viable.

References

Jupyter notebook for calculations

Can self-driving cars detect cyclists?

Screenshot 2019-05-10 at 14.05.59

Self-driving cars employ sophisticated software to interpret the world around them. How do these systems work? And how good are they at detecting cyclists? Can cyclists feel safe sharing roads with an increasing number of vehicles that make use of these systems?

How hard is it to spot a cyclist?

Vehicles can use a range of detection systems, including cameras, radar and lidar.  Deep learning techniques have become very good at identifying objects in photographic images. So one important question is how hard is it to spot a cyclist in a photo taken from a moving vehicle?

Researchers at Tsinghua University, working in collaboration with Daimler, created a publicly available collection of dashboard camera photos, where humans have painstakingly drawn boxes around other road users. The data set is used by academics to benchmark the performance of their image recognition algorithms. The images are rather grey and murky, reflecting the cloudy and polluted atmosphere of the Chinese city location. It is striking that, in the majority of cases, the cyclists are very small, representing around 900 pixels out of the 2048 x 1024 images, i.e. less than 0.05% of the total area. For example, the cyclist in the middle of the image above is pretty hard to make out, even for a human.

Object-detecting neural networks are typically trained to identify the subject of a photo, which normally takes up are significant portion of the image. Finding a tall, thin segment containing a cyclist is significantly more difficult.

If you think about it, the cyclist taking up the largest percentage of a dash cam image will be riding across the direction of travel, directly in front of the vehicle, at which point it may be too late to take action. So a crucial aspect of any successful algorithm is to find more distant cyclists, before they are too close.

Setting up the problem

Taking advantage of skills acquired on the fast.ai course on deep learning, I decided to have a go at training a neural network to detect cyclists. Many of the images in the Tsinghua Daimler data set include multiple cyclists. In order to make the problem more manageable, I set out to find the single largest cyclist in each image.

If you are not interested in the technical bit, just scroll down to the results.

The technical bit

In order to save space on my drive, I downloaded about a third of the training set. The 3209 images were split 80:20 to create a training and validation sets. I also downloaded 641 unseen images that were excluded from training and used only for testing the final model.

I used transfer learning to fine-tune a neural network using a pre-trained ResNet34 backbone, with a customised head designed to generate four numbers representing the coordinates of a bounding box around the largest object in each image. All images were scaled down to 224 pixel squares, without cropping. Data augmentation added variation to the training images, including small rotations, horizontal flips and adjustments to lighting.

It took a couple of hours to train the network on my MacBook Pro, without needing to resort to a cloud-based GPU, to produce bounding boxes with an average error of just 12 pixels on each coordinate. The network had learned to do a pretty good job at detecting cyclists in the training set.

Results

The key step was to test my neural network on the set of 641 unseen images. The results were impressive: the average error on the bounding box coordinates was just 14 pixels. The network was surprisingly good at detecting cyclists.

oosImages

The 16 photos above were taken at random from the test set. The cyan box shows the predicted position of the largest cyclist in the image, while the white box shows the human annotation. There is a high degree of overlap for eleven cyclists 2, 3, 4, 5, 6, 8, 11, 12, 14, 15 and 16. Box 9 was close, falling between two similar sized riders, but 7 was a miss. The algorithm failed on the very distant cyclists in 1, 10 and 13. If you rank the photos, based on the size of the cyclist, we can see that the network had a high success rate for all but the smallest of cyclists.

In conclusion, as long as the cyclists were not too far away, it was surprisingly easy to detect riders pretty reliably, using a neural network trained over an afternoon.  With all the resources available to Google, Uber and the big car manufacturers, we can be sure that much more sophisticated systems have been developed. I did not consider, for example, using a sequence of images to detect motion or combining them with data about the motion of the camera vehicle. Nor did I attempt to distinguish cyclists from other road users, such as pedestrians or motorbikes.

After completing this project, I feel reassured that cyclists of the future will be spotted by self-driving cars. The riders in the data set generally did not wear reflective clothing and did not have rear lights. These basic safety measures make cyclists, particularly commuters, more obvious to all road users, whether human or AI.

Car manufacturers could potentially develop significant goodwill and credibility in their commitment to road safety by offering cyclists lightweight and efficient beacons that would make them more obvious to automated driving systems.

References

“A new benchmark for vision-based cyclist detection”, X. Li, F. Flohr, Y. Yang, H. Xiong, M. Braun, S. Pan, K. Li and D. M. Gavrila, in proceedings of IEEE Intelligent Vehicles Symposium (IV), pages 1028-1033, June 2016

Link to Jupyter notebook

Don’t ride your bike like an astronaut

Screenshot 2019-04-05 at 17.13.59

Astronauts return from the International Space Station with weak bones, due to the lack of gravitational forces. It is surprising to learn that competitive cyclists can experience similar losses in bone density over the period of a race season.

The problem is called Relative Energy Deficiency is Sport (RED-S). This occurs when lean athletes reach a tipping point where the benefits of losing weight become overwhelmed by negative impacts on health. When deprived of sufficient energy intake to match training load, certain metabolic systems become impaired or shut down.

Colleagues from Durham University and I recently published a study investigating what cyclists at risk of RED-S can do to improve their health and performance. It is freely available and written in an accessible way, without the requirement for specialist expertise.

Race performance

Race performance was measured by the number of British Cycling points accumulated over the season. This was correlated with power (FTP and FTP/kg) and training load. However, changes in energy availability proved to be an important factor. After adjusting for FTP, cyclists who improved their fuelling (green triangles) gained, on average, 95 points more than those who made no change. In contrast, those who restricted their nutrition (red crosses) accumulated 95 fewer points and reported fatigue, illness and injury.

Figure2 600
Race Performance versus FTP and changes in Energy Availability (EA)

The nutritional advice included recommendations on adequate fuelling before, during and after rides. Also see my previous article on fuelling for the work required.

Bone health

Competitive road cyclists can fall into an energy deficit due to the long hours of training they complete. Although an initial loss of excess body weight can lead to performance improvements, athletes need to maintain a healthy body mass. The lumbar spine is particularly sensitive to deficiencies of energy availability.

In cyclists, the lower back also fails to benefit from the gravitational stresses of weight-bearing sports. This is why, in addition to nutritional advice, study participants were recommended some basic skeletal loading exercises (yes, that is me in the pictures).

The cyclists fell into three general groups: those who made positive changes to nutrition and skeletal loading, those who made negative changes and the remainder. The resulting changes in bone mineral density over a six month period were striking, with highly statistically significant differences observed between the groups.

Those making positive changes (green triangles) saw significant gains in bone mineral density, while those making negative changes (red crosses) saw equally significant negative losses in bone density. Any individual observation outside the band of the least significant change (LSC) is indicative of a material change in bone health.

Figure1 600
Changes in Lumbar Bone Mineral Density versus Behaviour Changes

Conclusions

The study provided strong evidence of the benefits of positive changes and the costs of negative changes in nutrition and skeletal loading exercises. It was noted that certain cyclists found it hard to overcome psychological barriers preventing them from deviating from their current routines. It is hoped that such strong statistical results will help these vulnerable athletes make beneficial behavioural changes

References

Clinical evaluation of education relating to nutrition and skeletal loading in competitive male road cyclists at risk of relative energy deficiency in sports (RED-S): 6-month randomised controlled trial, Nicola Keay, Gavin Francis, Ian Entwistle, Karen Hind. BMJ Open Sport and Exercise Medicine Journal, Volume 5, Issue 1. http://dx.doi.org/10.1136/bmjsem-2019-000523

 

 

Learning the language of the Giro

Fausto_Coppi

Computers are becoming ever better at natural language processing (NLP). I set up a neural network as a language model and loaded a set of pre-trained weights on my MacBook Pro, to see what it could do. After priming it with some text about the Giro d’Italia, this is what the model produced as a continuation.

Priming text: The Giro d’ Italia (Italian pronunciation: [ˈdʒiːro diˈtaːlja]; English: Tour of Italy; also known as the Giro) is an annual multiple-stage bicycle race primarily held in Italy, while also occasionally passing through nearby countries. The first race was organized in 1909 to increase sales of the newspaper La Gazzetta dello Sport; however it is currently run by RCS Sport. The race has been held annually since its first edition in 1909, except when it was stopped for the two world wars. As the Giro gained prominence and popularity the race was lengthened, and the peloton expanded from primarily Italian participation to riders from all over the world.

Computer generated continuation:  the race was won by the italian rider , giovanni di u_n , who won the race in the first leg of the race . the race was won by italian rider giovanni u_n , who won the race by a margin of two lengths .
= = = world tour = = =
the tour de france was the first of the tour de france . the tour de france was won by the reigning world champion , the reigning world champion , who had won the tour de france in the previous year ‘s race …

The output may not make a lot of sense, but the point is that it looks like English (in lower case). The grammar is reasonable, with commas, fullstops and a header inserted in  a logical way. Furthermore, the model has demonstrated some understanding of the context by suggesting that the Giro could be won by an Italian ride called Giovanni. The word “u_n” stands for unknown, which is consistent with the idea that an Italian surname may not be a familiar English word. It turns out that a certain Giovanni Di Santi raced against Fausto Coppi (pictured above) in the 1940 Giro, though he did not win the first stage. In addition to this, the model somehow knew that the Giro, in common with the Tour the France, is a World Tour event that could be won by the reigning world champion.

I found this totally amazing. And it was not a one off: further examples on random topics are included below. This neural network is just an architecture, defining a collection of matrix multiplications and transformations, along with a set of connection weights. Admittedly there are a lot of connection weights: 115.6 million of them, but they are just numbers. It was not explicitly provided with any rules about English grammar or any domain knowledge.

How could this possibly work?

In machine learning, language models are assessed on a simple metric: accuracy in predicting the next word of a sentence. The neural network approach has proved to be remarkably successful. Given enough data and a suitable architecture, deep learning now far outstrips traditional methods that relied on linguistic expertise to parse sentences and apply grammatical rules that differ across languages.

I was experimenting with an AWD-LSTM model originally created by Stephen Merity. This is a recurrent neural network (RNN) with three LSTM layers that include dropout. The pre-trained weights for the wt103 model were generated by Jeremy Howard of fast.ai, using a large corpus of text from Wikipedia.

Jeremy Howard converted the Wikipedia text into tokens. A tokeniser, such as spaCy,  breaks text into words and punctuation, resulting in a vocabulary of tokens that are indexed as integers. This allows blocks of text to be fed into the neural network as lists of numbers. The outputs are numbers that can be converted back into the predicted words.

The wt103 model includes a linear encoder that creates embeddings of word tokens. These are passed through three LSTM layers whose states are able to retain a memory of previous words or context. The result is passed through a decoder, employing the same weights as the encoder, to produce a softmax output that can be treated as a set of probabilities, across the vocabulary, to predict the next word token. Special forms of dropout were employed, as described in the paper, to limit overfitting and make the model more robust.

The network was trained by minimising cross-entropy loss using stochastic gradient descent. A technique called back propagation through time (BPTT) introduced some random variation into the length of the blocks of text employed in each training batch. The connection weights were iteratively improved towards optimal values.

OK, but so what?

Impressive as it may be for a neural network to spout highly plausible but nonsensical English, what possible use could this have? Well, suppose you want to automate the separation of texts into different categories, for example, distinguish different authors or determine the sentiment of tweets or predict the reaction of the stock market to news items or identify the sentiment of movie reviews. Fine-tuning a neural network that already has a good knowledge of English provides a huge advantage over starting from scratch. In lesson 10 of the fast.ai course, Jeremy Howard demonstrates how this approach can be used to achieve state of the art results on the widely used IMDB movie review data set.

Further examples

In the first example, the network finishes the sentence about a hurricane in perfect English.  Next, it comes up with the name of a critic (actually a rock music critic rather than a book reviewer, but heh!) and it makes use of its LSTM to open and close quotation marks. In the bean example, it amazingly starts describing flowers and correctly converts their dimensions from centimetres to inches!

My code can be found here.

Priming text: Hurricane Ivan was a large long Cape Verde hurricane that caused widespread damage in the Caribbean and United States The cyclone was

Computer generated continuation:  the first hurricane to strike the united states since hurricane katrina in 2005 .

Priming text: The book was widely acclaimed by the critics.

Computer generated continuation: the book was published in the united states by the american library association on june 1 , 2006 .

= = = critical response = = =

the book received mixed reviews from critics . the new york times reviewer robert christgau called it ” a great book ” and ” a great book ” . he praised the book ‘s ” strong , strong , and well – written ” prose , and the ” excellent ” prose .

Priming text: Most varieties of bean grow either as an erect bush or as a climbing plant, but a few important kinds are of intermediate form. Dwarf and semiclimbers are grown extensively. When the climbing type is grown for its immature pods, artificial supports are necessary to facilitate harvesting. Varieties differ greatly in size, shape, colour, and fibrousness or tenderness of the immature pods. In general, varieties grown for dry mature seeds produce pods that are too fibrous to be eaten at any state of development. Most edible-podded beans produce relatively low yields of mature seeds, or seeds that are of low eating quality. Seed colours range from white through green, yellow, tan, pink, red, brown, and purple to black in solid colours and countless contrasting patterns. Seed shapes range from nearly spherical to flattened, elongated, and kidney-shaped. Pods are of various shades of green, yellow, red, and purple and splashed with red or purple; pod shapes range from flat to round, smooth to irregular, and straight to sharply curved; length ranges from 75 to 200 millimetres (3 to 8 inches) or more.

Computer generated continuation:  the most common form of the flower is the flower spike , which is a characteristic of the flower spike . the flower is made up of a series of small , cylindrical , cylindrical , cylindrical , cylindrical stems that are up to 10 cm ( 3.9 in ) long and 2.5 cm ( 0.98 in ) wide . the flower spikes are arranged in a series of three or four pairs of flowers 

 

 

Creating artistic images from Strava rides

firstimage
Four laps of Richmond Park

When you upload a ride, Strava draws a map using the longitude and latitude coordinates recorded by your GPS device. This article explores ways in which these numbers, along with other metrics, can be used to create interesting images that might have some artistic merit.

The idea was motivated by the huge advances made in the field of Deep Learning, particularly applications for image recognition. However, since datasets come in all shapes and forms, researchers have explored ways of converting different types of data into images.  In a paper published in 2015, the authors achieved success in identifying standard time series by converting them into images.

GPS bike computers typically record snapshots of information every second. What kind of images could these time series generate? It turns out that there are several ways to convert a time series into an image.

Spectrogram

Creating a spectrogram is a standard approach from signal processing that is particularly useful for analysing acoustic files. The spectrogram is a heat map that shows how the underlying frequencies contributing to the signal change over time. Technically, it is derived by calculating the discrete Fourier transform of a window that slides across the time series. I applied this to my regular Saturday morning club ride of four laps around Richmond Park. The image changes a bit once the ride gets going after about 1200 seconds (20 minutes), but, frankly, the result was not particularly illuminating. There is no obvious reason to consider cycling power data as a superposition of frequencies.

spectrogram

Ah! Now we are getting somewhere

The authors of the referenced paper took a different approach to produce things called Gramian Angular Summation Field (GASF), Gramian Angular Difference Field (GADF), and Markov Transition Field (MTF). Read the paper if want to know the details. I created these and something call a Recurrence Plot. All of these methods generate a matrix, by combining every element in the time series with every other element. The underling observations occurring at times t_{1} and t_{2} determine the colour of the pixel at position (t_{1}, t_{2}). Images are symmetric along the lower-left to upper-right diagonal, apart from GADF, which is antisymmetric.

Let’s see how do they look for on four laps of Richmond Park. We have six time series, with corresponding sets of images below. The segmentation of the images is due to periodicity of the data. This is particularly clear in the geographic data (longitude, latitude and altitude). The higher intensity of the main part of the ride is most obvious in the heart rate data. The MTF plots are quite interesting. Scroll down through the images to the next section

data1
Raw time series of power, heart rate, cadence, longitude, latitude and altitude
gasf
Gramian Angular Sum Field
gadf
Gramian Angular Difference Field
mtf
Markov Transition Field
rp
Recurrence Plot

From cycle ride to art

It is one thing to create an image of each item, but how can we combine these to summarise a ride in a single image. I considered two methods of combining time series into a single image: a) create a new image where the vertical and horizontal axes represent different series and b) create a new image by simply adding the corresponding values from two underlying images.

One problem is that some cyclists don’t have gadgets like heart rate monitors and power meters, so I initially restricted myself to just the longitude, latitude and altitude data. Nevertheless, as noted in an earlier blog, it is possible to work out speed, because the time interval is one second between each reading. Furthermore, one can estimate power, from the speed and changes in elevation.

Another problem is that rides differ in length. For this I split the ride into, say, 128 intervals and took the last observation in each interval. So for a 3 hour ride, I’d be sampling about once every 84 seconds.

The chart at the top of this blog was created by first normalising each series to a standard range (-1, +1). Method a) was used to create two images: longitude was added to latitude and altitude was multiplied by speed. These were added using method b). Using these measures will produce pretty much the same chart each time the ride is done. In contrast, an image that is totally unique to the ride can be produced using data relating to the individual rider. The image below uses the same recipe to combine speed, heart rate, power and cadence. If this had been a particularly special ride, the image would be a nice personal memento.

lastimage
A different take on four laps of Richmond Park

For anyone interested in the underlying code, I have posted a Jupyter notebook here.

References

Encoding Time Series as Images for Visual Inspection and Classification Using Tiled Convolutional Neural Networks, Wang Z Oates T, https://www.aaai.org/ocs/index.php/WS/AAAIW15/paper/viewFile/10179/10251

 

Fuel for the work required: periodisation of carbohydrate intake

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Fuel for the work required, Impey et al, Sports Med (2018) 48:1031–1048

Last week I attended an event announcing the forthcoming launch of a new fitness app called Pillar. It offers combined training and nutrition advice to help athletes achieve their goals. Pillar is backed by a strong scientific team including Professor James Morton, Team Sky Head of Performance Nutrition, and Professor Graeme Close, England Rugby Head of Performance Nutrition.

James Morton gave a fascinating presentation about the periodisation of carbohydrate (CHO) fuelling, including a detailed description of the nutrition strategy he created to support Chris Froome’s famous 80km attack on stage 19 of the 2018 Giro d’Italia. His recent paper explains the underlying science. These are some of the key points.

  • Always go into competition fully fuelled with carbohydrate
    • Well-fuelled athletes perform for longer at higher intensities than those with depleted reserves
    • Basic biochemistry: fat burning is too slow and supplies of the phosphocreatine are too small to sustain intensities over 85% of VO2max
    • Theory is backed up by experiment
  • There are pros and cons to training with low levels of carbohydrate
    • Positive effects: Improved fat burning, changes in cell signalling, gene expression and enzyme/protein activity, potential to save precious glycogen stores for crucial attacks later in a race
    • Negative effects: Inconsistent evidence of improved performance, ability to complete training session may be compromised, reduced immunity, risks to bone health, loss of top end for those on high fat/low carb (ketogenic) diet
  • Different ways to train with low carbohydrate
    • doing two sessions in one day with minimal refuelling
    • low carb evening meal and breakfast: sleep low, train low the next morning
    • fasted rides
    • high fat/low carb diet

Is there a structured method of training that provides the benefits without the negatives?

  • The authors propose a glycogen threshold hypothesis
    • Positive effects seem to be dependent on commencing with muscle glycogen levels within a specific range
    • Levels have to be low enough to promote positive effects
    • But when too low, protein synthesis may be impaired and the ability to complete sessions is compromised
  • This leads to the idea of periodising carbohydrate consumption, meal by meal, around planned training sessions
  • “Fuelling for the work required”
    • low carbs before and during lighter training sessions
    • high carbs in preparation for and during rides with greater intensities
    • always refuel after training
  • The diagram above provides an example for an elite endurance cyclist
    • The red, amber, green colour coding indicates low, medium or high carbohydrate consumption
    • On day 1, the athlete aims to “train high” for a hard session
    • A lighter evening meal on day 1 prepares to “sleep low, train low” ahead of a lower intensity session on day 2
    • Carbohydrate intake rises after exercise on day 2 in anticipation of a high intensity session on day 3
    • Fuelling is moderated on the evening of day 3 as day 4 is assigned as a recovery day
    • Carbohydrate rises later on day 4 to prepare for the next block of training
  • The Pillar app aims to provide these leading edge scientific principles to amateur cyclists and other athletes

In order to put this into action, you need to know how much carbohydrate you are consuming. My assumption has been that my diet is reasonably healthy, but I have never actually measured it. So I have been experimenting with free app MyFitnessPal that can be downloaded onto your phone. This provides a simple and convenient way to track the nutritional composition of your diet, including a barcode scanner that recognises most foods. You can link it to other apps such as Training Peaks to take account of energy expended. However, neither of these tools plans nutrition ahead of training sessions. Pillar aims to fill this gap. It will be interesting to see whether this turns out to be successful.

References

Fuel for the Work Required: A Theoretical Framework for Carbohydrate Periodization and the Glycogen Threshold Hypothesis, SG Impey, MA Hearris, KM Hammond, JD Bartlett, J Louis, G Close, JP Morton, Sports Med (2018) 48:1031–1048, https://doi.org/10.1007/s40279-018-0867-7

Fuel for the work required: a practical approach to amalgamating train-low paradigms for endurance athletes, Impey SG, Hammond KM, Shepherd SO, Sharples AP, Stewart C, Limb M, Smith K, Philp A, Jeromson S, Hamilton DL, Close GL, Morton JP, Physiol Rep. 2016 May;4(10). pii: e12803. doi: 10.14814/phy2.12803

Low carbohydrate, high fat diet impairs exercise economy and negates the performance benefit from intensified training in elite race walkers, Burke LM, Ross ML, Garvican-Lewis LA, Welvaert M, Heikura IA, Forbes SG, Mirtschin JG, Cato LE, Strobel N, Sharma AP, Hawley JA.  J Physiol. 2017;595:2785–807

Low energy availability assessed by a sport-specific questionnaire and clinical interview indicative of bone health, endocrine profile and cycling performance in competitive male cyclists, BMJ Open Sport & Exercise Medicine,https://doi.org/10.1136/bmjsem-2018-000424

Machine learning for a medical study of cyclists

Screen Shot 2018-10-11 at 15.28.46

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.

 

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.

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.

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.

References

Low energy availability assessed by a sport-specific questionnaire and clinical interview indicative of bone health, endocrine profile and cycling performance in competitive male cyclists, BMJ Open Sport & Exercise Medicine, https://doi.org/10.1136/bmjsem-2018-000424

Relative Energy Deficiency in Sport, British Association of Sports and Exercise Medicine

Synergistic interactions of steroid hormones, British Journal of Sports Medicine

Cyclists: Make No Bones About It, British Journal of Sports Medicine

Male Cyclists: bones, body composition, nutrition, performance, British Journal of Sports Medicine