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Statistically solvingsneezessniffles odsc2016

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http://ianozsvald.com/2016/05/07/statistically-solving-sneezes-and-sniffles-a-work-in-progress-report-at-pydatalondon-2016/

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Statistically solvingsneezessniffles odsc2016

  1. 1. Statistically Solving Sneezes and Sniffles - A Work In Progress #ODSC 2016 License: CC By Attribution Ian Ozsvald @IanOzsvald ModelInsight.io Giles Weaver @GilesWeaver
  2. 2. Ian.Ozsvald@ModelInsight.io ODSC 2016 @IanOzsvald @gilesweaver Who Are We? ● Ian - “Industrial Data Scientist” for 15 yrs ● Giles - bioinformatician turned Data Sci.
  3. 3. Ian.Ozsvald@ModelInsight.io ODSC 2016 @IanOzsvald @gilesweaver Goal ● Help my wife have a less sneezy life - therefore try to understand “what drives a person's Rhinitis?” (i.e. sneezes) ● Can we help folk reduce symptoms by explaining the drivers of those symptoms? A step towards “personalised medicine”? ● Could we help people reduce their medication? ● 10–30% of Western population affected by Allergic Rhinitis (overall ≈1.4 billion people?) ● Some antihistamines (AH) have negative health associations - (e.g. anticholinergics [inc. U.S. Benadryl] linked to Alzheimers) ● UK folk don't tend to use these AHs but nobody knows the consequences of long-term usage
  4. 4. Ian.Ozsvald@ModelInsight.io ODSC 2016 @IanOzsvald @gilesweaver Counts of daily sneezes & AH Using Seaborn and Pandas DataFrames for countplots
  5. 5. Ian.Ozsvald@ModelInsight.io ODSC 2016 @IanOzsvald @gilesweaver Hypothesis ● “Ian's wife Emily suffers from non-allergic Rhinitis” (not allergic or infectious Rhinitis) ● “Possibly it is weather related” ● “Alcohol might make things worse” ● “Airborne pollution might be a factor” ● We need to gather data so we can answer these questions ● Note - sneeze & AH behaviour similar out of the country and when at home (I'm not the cause! Nor, probably, is our cat, nor the apartment)
  6. 6. Ian.Ozsvald@ModelInsight.io ODSC 2016 @IanOzsvald @gilesweaver Data Gathering Methodology ● iOS ● Event logs ● GPS trace ● Editable history ● Open Src ● >1yr old github.com/radicalrobot/allergy-tracker
  7. 7. Ian.Ozsvald@ModelInsight.io ODSC 2016 @IanOzsvald @gilesweaver Some data issues ● Apple's DateTime epoch is != the Unix DateTime epoch (use ISO 8601!) ● GPS on London Underground on iPhone 6 confidently reports location (0,0) # Nigeria?! ● Weak experimental design (in hindsight) - we're logging positive events - does “0 events” mean “nothing happened” or “we forgot to log stuff”? ● SQLite→DataFrame with Python for clean-up
  8. 8. Ian.Ozsvald@ModelInsight.io ODSC 2016 @IanOzsvald @gilesweaver Sneezes and AH over 1yr Self-logged data by Emily
  9. 9. Ian.Ozsvald@ModelInsight.io ODSC 2016 @IanOzsvald @gilesweaver Sneezing by hour & day of week
  10. 10. Ian.Ozsvald@ModelInsight.io ODSC 2016 @IanOzsvald @gilesweaver How long does an AH last for? Uses: Plan your day? Compare effectiveness of different treatments?
  11. 11. Ian.Ozsvald@ModelInsight.io ODSC 2016 @IanOzsvald @gilesweaver Learning Relationships ● Antihistamine usage is ≈50/50 use/no use per day - treat as binary classification problem (not timeseries) ● We want a robust, interpretable model ● Logistic Regression with randomly shuffled rows and cross validation ● Can we find any strong features?
  12. 12. Ian.Ozsvald@ModelInsight.io ODSC 2016 @IanOzsvald @gilesweaver Features - weather and pollution Annual NO2 pollution via LondonAir.org.ukweatherData R package for Wunderground London City Airport
  13. 13. Ian.Ozsvald@ModelInsight.io ODSC 2016 @IanOzsvald @gilesweaver 1 Year Model ● 84 features (raw & augmented), 330 rows of daily data (resampled from sub-second timestamped raw events) ● Add diet tracker, GPS locations, use of London Underground (Oyster) ● Take a complex model, strip it down, remove everything that doesn't feel right... ● Left with few consistently predictive features - Sneezes per day, Previous day's AH usage <sigh> ● Everything else is not very predictive ● What's wrong with 1 year of data? ● Are signals like external humidity and temperature etc useful as a predictor in e.g. mid-summer or winter?
  14. 14. Ian.Ozsvald@ModelInsight.io ODSC 2016 @IanOzsvald @gilesweaver April-Aug 2015 Model Days when Emily exposed to 'the weather', not in a climate controlled office - suddenly some features emerge These boxplots show LogReg. coefs. from 5000 models built on 80% randomly sampled training data and scores on 20% test data Do we trust this?
  15. 15. Ian.Ozsvald@ModelInsight.io ODSC 2016 @IanOzsvald @gilesweaver Introducing ‘Nasalcrom’ ● “Part Two” - new treatment ● Discussed at Kings College with Professor Clive Page and colleague Dr. Emlyn Page (my PyDataLondon co-chair) ● Ruled out allergic reaction (yay!) ● Suggestion was to try Nasalcrom – probably more benign that Loratidine ● New Hypothesis - “NasalCrom is similarly effective to Loratidine”
  16. 16. Ian.Ozsvald@ModelInsight.io ODSC 2016 @IanOzsvald @gilesweaver Introducing ‘Nasalcrom’
  17. 17. Ian.Ozsvald@ModelInsight.io ODSC 2016 @IanOzsvald @gilesweaver Improving the App’s UI ● We need to log ‘no events happened’ rather than ‘nothing got recorded’ (which might mean we forgot to log events) ● We need feedback in UI to show that medication is being taken consistently ● Some trend display in the App would probably be useful ● Record “Feeling coldy”
  18. 18. Ian.Ozsvald@ModelInsight.io ODSC 2016 @IanOzsvald @gilesweaver Thoughts to pass on ● Do you have all the data you need to answer your questions? ● Is the data quality high enough? ● Feel free to use our data logger (link earlier) – could you tackle a similar challenge? ● Doing this has opened new doors...
  19. 19. Ian.Ozsvald@ModelInsight.io ODSC 2016 @IanOzsvald @gilesweaver Conclusion ● Challenging problem - we have found 1 potentially predictive signal from scratch ● We can answer “how effective is an antihistamine” ● Nasalcrom and Loratidine seem equally effective ● Thanks to:
  20. 20. Ian.Ozsvald@ModelInsight.io ODSC 2016 @IanOzsvald @gilesweaver Does Alcohol Increase Sneezing? "Possibly" - we need cleaner data. Hat tip to Jon Sedar for PyMC3 model

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