First take on the Kaggle West Nile Virus Competition

Technology|Data Science|Machine Learning| May 11, 2015| HenriDw

I joined Dataiku this week as their first New York based hire. In order to get more familiar with Data Science Studio (DSS), I used it in a machine learning competition, which I've described for you in this blog post.

Kaggle recently launched the West Nile Virus Competition. All of my previous data science projects were done directly in R, python or Julia. With DSS, I was impressed by the fact that I didn’t lose flexibility and actually felt like I was working faster and increasingly able to focus on making the important decisions. In addition, I really liked having a visible and easily reproducible workflow.

Competition Overview

Chicago mosquitos sometimes have the West Nile virus. The goal here is to build a model to better predict when and where in Chicago captured mosquitos will have the west nile virus.

There are 3 different datasets:

-Mosquito trap data: location of traps, how many mosquitos on which date, and whether they have the west nile virus

-Weather data: 2 Chicago weather stations report with many indicators (temperature, dew point, sunset, …)

-Spray data: gis data for insecticide spraying by the city.

Import and Clean the Data

The datasets were compressed csv files which can be directly imported into the application.

First, I stacked the test and train in order to do the same transformations and feature engineering to both. Before training the model, I will split them back.

The test and train datasets only needed the date parsed (which DSS does easily). A quick look at the prediction column, using the analyze feature, showed that the classes were very imbalanced: 95% of the training set captures did not detect the virus.

The weather data was a bit more messy. There were missing values, and some columns were interpreted incorrectly (for example Depart had so many missing values, stored as ‘M’, that DSS thought it was a gender column).

Each date had 2 records, 1 for each station. Since this I was planing to join this dataset to the training data on the date, I merged the 2 station records together using a custom python processor. Then I noticed that most of the missing values were due to the fact that station 2 never reports certain values, so I deleted those columns.

Finally, the remaining missing values were fixed by copying the same value of the other station.

Joining Datasets

Now that the weather datasets and test and train datasets were cleaned, they could be joined using the DSS join action. Here is what the workflow looks like so far:

Here I could have done some additional processing and feature engineering before building a model. For this first take, I just removed some redundant or usuless columns (namely the address of the weather columns)

Building a model

I split the data back into train and test (based on whether the west nile virus column is present or not), and built a model using the analyze function. The default model choice selection optimized the AUC which is this competition’s metric. It was also possible to specify how to handle cross validation, how to do feature scaling, how to deal with the missing data, and which algorithms to use. In addition, Data Science Studio automatically took care of categorical features by creating indicator variables for each possible value.

The only thing I changed from the defaults was the CodeSum column, which was a space delimited list of weather codes (e.g. TS for thunderstorm, or RA BR for rain and mist). Rather than treating is as categorical, it made more sense to use counts vectorization (in this case the counts will be 0 or 1 for each code).

Once the model was trained, it was very straightforward to apply it to the test set, and export the predictions as a csv in order to submit to kaggle.

The final workflow looked like this:

Results

On May 8th, there were 411 teams in the leaderboard. This submission placed me 60th. Not so bad for a first try!

To rank higher, I could do more advanced feature engineering. For example, I could take into account the weather station locations compared to where the traps are, use the number of mosquitos captured, and incorporate the spray dataset.

If you want to work efficiently on a data science project, while focusing on the fun part - feature engineering and model optimization - download the community edition and try it out!

Feel free to contact me (henri.dwyer@dataiku.com) if you have questions or want to use this first take solution.

Good luck!

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