XGBoost Metrics & Early Stopping
Recently we upgraded access to the xgboost machine learning system to include metrics and early stopping. This document will be a quick walkthough using the Ames housing prices dataset to show how to use both systems.
Dataset Processing
Our goal is to end up with float64 columns with no missing values. This is a fast rough pass and isn’t anywhere near ideal. For instance many of the string columns should be encoded to preserve semantic order. Regardless this will show some minimal processing and the general pathway in order to do simple machine learning.
user> (require '[tech.v3.dataset :as ds])
nil
user> (def ames (ds/->dataset "https://github.com/techascent/tech.ml/raw/master/test/data/train.csv.gz"
{:file-type :csv :gzipped? true}))
#'user/ames
user> (ds/columns-with-missing-seq ames)
({:column-name "LotFrontage", :missing-count 259}
{:column-name "Alley", :missing-count 1369}
{:column-name "MasVnrType", :missing-count 8}
{:column-name "MasVnrArea", :missing-count 8}
{:column-name "BsmtQual", :missing-count 37}
{:column-name "BsmtCond", :missing-count 37}
{:column-name "BsmtExposure", :missing-count 38}
{:column-name "BsmtFinType1", :missing-count 37}
{:column-name "BsmtFinType2", :missing-count 38}
{:column-name "Electrical", :missing-count 1}
{:column-name "FireplaceQu", :missing-count 690}
{:column-name "GarageType", :missing-count 81}
{:column-name "GarageYrBlt", :missing-count 81}
{:column-name "GarageFinish", :missing-count 81}
{:column-name "GarageQual", :missing-count 81}
{:column-name "GarageCond", :missing-count 81}
{:column-name "PoolQC", :missing-count 1453}
{:column-name "Fence", :missing-count 1179}
{:column-name "MiscFeature", :missing-count 1406})
user> (->> (map (comp :datatype meta) (vals ames))
(frequencies))
{:int16 36, :string 42, :int32 2, :boolean 1}
user> (require '[tech.v3.dataset.column-filters :as cf])
nil
user> (def ames-missing-1 (ds/replace-missing-value ames cf/string "NA"))
#'user/ames-missing-1
user> (ds/columns-with-missing-seq ames-missing-1)
({:column-name "LotFrontage", :missing-count 259}
{:column-name "MasVnrArea", :missing-count 8}
{:column-name "GarageYrBlt", :missing-count 81})
user> (def ames-missing-2 (ds/replace-missing-value ames-missing-1 :all 0))
#'user/ames-missing-2
user> (ds/columns-with-missing-seq ames-missing-2)
nil
user> (def all-numeric (ds/categorical->number ames-missing-2 cf/string))
#'user/all-numeric
user> (->> (map (comp :datatype meta) (vals all-numeric))
(frequencies))
{:int16 36, :float64 42, :int32 2, :boolean 1}
Training with XGBoost
Since we set the inference target on the dataset, we can quickly train a model.
user> (require '[tech.v3.ml :as ml])
nil
user> (require '[tech.v3.libs.xgboost])
nil
user> (require '[tech.v3.dataset.modelling :as ds-mod])
nil
user> (def ames-processed (ds-mod/set-inference-target all-numeric "SalePrice"))
#'user/ames-processed
We split the dataset up into train/test datasets where we can train on one dataset and test on another.
user> (def train-test-split (ds-mod/train-test-split ames-processed))
#'user/train-test-split
user> (def model (ml/train {:model-type :xgboost/regression}
(:train-ds train-test-split)))
#'user/model
user> (def prediction (ml/predict (:test-ds train-test-split) model))
#'user/prediction
user> prediction
:_unnamed [438 1]:
| SalePrice |
|-----------|
| 1.904E+05 |
| 2.000E+05 |
| 1.944E+05 |
| 2.392E+05 |
| 1.766E+05 |
...
user> (meta prediction)
{:name :_unnamed, :model-type :regression}
Now we can say something about how good the model is. Let’s analyze this with mean average error:
user> (require '[tech.v3.ml.loss :as loss])
nil
user> (loss/mae (prediction "SalePrice")
((:test-ds train-test-split) "SalePrice"))
18439.617499643264
What is going on? Well, one question we want to to ask is what variables is xgboost using to decide how to predict SalePrice.
user> (ml/explain model)
_unnamed [70 3]:
| :importance-type | :colname | :gain |
|------------------|--------------|----------------|
| gain | OverallQual | 2.63303470E+11 |
| gain | KitchenQual | 5.15596265E+10 |
| gain | TotRmsAbvGrd | 4.91487037E+10 |
| gain | GrLivArea | 3.93336045E+10 |
| gain | GarageCars | 3.66395853E+10 |
| gain | BsmtFinSF1 | 1.28130489E+10 |
| gain | TotalBsmtSF | 1.04417586E+10 |
| gain | BsmtQual | 8.16779754E+09 |
| gain | MSZoning | 7.97729807E+09 |
| gain | 1stFlrSF | 6.55107315E+09 |
| gain | BsmtExposure | 6.07410704E+09 |
| gain | 2ndFlrSF | 5.68743133E+09 |
| gain | Alley | 5.56387533E+09 |
| gain | Fireplaces | 4.28944688E+09 |
| gain | YearBuilt | 3.90289328E+09 |
| gain | LotFrontage | 3.21221797E+09 |
| gain | GarageFinish | 3.10737368E+09 |
| gain | YearRemodAdd | 3.08412712E+09 |
| gain | GarageYrBlt | 3.01600398E+09 |
| gain | SaleType | 2.76226739E+09 |
| gain | LandSlope | 2.70233190E+09 |
| gain | LotArea | 2.42620203E+09 |
| gain | BsmtFinType2 | 2.29969101E+09 |
| gain | Foundation | 2.27973530E+09 |
| gain | BsmtFullBath | 2.17456462E+09 |
These seem logical. In fact, it would appear that these columns are in this case somewhat correlated with the pearson correlation table for sale price:
user> (require '[tech.v3.dataset.math :as ds-math])
nil
user> (ds-math/correlation-table all-numeric :colname-seq ["SalePrice"])
WARNING - excluding non-numeric columns:
[CentralAir]
{"SalePrice"
(["SalePrice" 1.0]
["OverallQual" 0.7909816005838052]
["GrLivArea" 0.7086244776126517]
["ExterQual" 0.6501302285588267]
["GarageCars" 0.6404091972583521]
["GarageArea" 0.6234314389183621]
["KitchenQual" 0.6192349321077227]
...)}
Gridsearching
We can gridsearch through the xgboost options in order to find the ‘best’ options for a dataset.
We first build out an option map where some of the keys map to gridsearch commands. The xgboost model can fill out gridsearch options:
user> (ml/hyperparameters :xgboost/regression)
{:subsample
{:tech.v3.ml.gridsearch/type :linear,
:start 0.7,
:end 1.0,
:n-steps 3,
:result-space :float64},
:scale-pos-weight
{:tech.v3.ml.gridsearch/type :linear,
:start 0.7,
:end 1.31,
:n-steps 6,
:result-space :float64},
:max-depth
{:tech.v3.ml.gridsearch/type :linear,
:start 1.0,
:end 10.0,
:n-steps 10,
:result-space :int64},
Once we have a map where some of the keys map to gridsearch entries, we can use the automatic gridsearch facility in tech.ml to search over the space:
user> (require '[tech.v3.ml.gridsearch :as gs])
nil
user> (def gridsearchable-options (merge {:model-type :xgboost/regression} (ml/hyperparameters :xgboost/regression)))
#'user/gridsearchable-options
user> (def option-seq (take 100 (gs/sobol-gridsearch gridsearchable-options)))
#'user/option-seq
user> (take 5 option-seq)
({:subsample 0.85,
:scale-pos-weight 1.066,
:lambda 0.16517241379310346,
:round 25,
:model-type :xgboost/regression,
:gamma 0.556,
:alpha 0.16517241379310346,
:max-depth 6,
:eta 0.5555555555555556}
{:subsample 1.0,
:scale-pos-weight 0.822,
:lambda 0.08241379310344828,
:round 15,
:model-type :xgboost/regression,
:gamma 0.778,
:alpha 0.23758620689655172,
:max-depth 3,
:eta 0.7777777777777778}
...
user> (defn test-options
[options]
(let [model (ml/train (:train-ds train-test-split) options)
prediction (ml/predict (:test-ds train-test-split) model)]
(assoc model :loss (loss/mae (prediction "SalePrice")
((:test-ds train-test-split) "SalePrice")))))
#'user/test-options
user> (def search-results
(->> option-seq
(map test-options)
(sort-by :loss)
(take 10)))
#'user/search-results
user> (map :loss search-results)
(17407.003585188355
17640.71050049943
17647.76534853025
17656.68644763128
17748.619631135844
17873.145191210046
17911.20817280251
18073.004726740866
18221.194652539954
18305.031258918378)
Note that gridsearching saves out the option map so we can see what produced the best options or perform a new sub-gridsearch given ranges built from the return value of the previous gridsearch.
user> (:options (first search-results))
{:subsample 0.690625,
:scale-pos-weight 1.346875,
:lambda 0.6940625,
:model-type :xgboost/regression,
:gamma 0.052329911468149484,
:alpha 0.11984165845261181,
:max-depth 17,
:eta 0.15625}
Doing this over the return value of gridsearch is instructive. You can see what the various options mean here. Regardless, we will just use the best options for now:
user> (def model-options (:options (first search-results)))
#'user/model-options
Metrics
Metrics will help us see if the model itself is overtraining. When you setup xgboost options with one or more watch datasets, it will dump out the metrics generated during training to a map of the same name under the [:model-data :metrics] path:
user> (def model (ml/train (:train-ds train-test-split)
(assoc model-options
:watches {:test-ds (:test-ds train-test-split)}
:eval-metric "mae")))
#'user/model
user> (get-in model [:model :metrics])
nil
user> (get-in model [:model-data :metrics])
:metrics [35 1]:
| :test-ds |
|-----------------|
| 164215.03125000 |
| 145998.57812500 |
| 129672.75000000 |
| 115247.78906250 |
| 102420.60156250 |
...
user> (ds/tail (get-in model [:model-data :metrics]))
:metrics [5 1]:
| :test-ds |
|----------------|
| 17594.75390625 |
| 17569.87109375 |
| 17500.19921875 |
| 17438.49609375 |
| 17407.00390625 |
user> (loss/mae ((ml/predict (:test-ds train-test-split) model) "SalePrice")
((:test-ds train-test-split) "SalePrice"))
17407.003585188355
Our loss lines up with our metrics. In this case it appears the default number of training rounds, 25, works pretty well. That is luck and dataset dependent. For instance, we could just as easily chosen to train more rounds:
user> (def model (ml/train (:train-ds train-test-split)
(assoc model-options
:watches {:test-ds (:test-ds train-test-split)}
:eval-metric "mae"
:round 100)))
user> (ds/tail (get-in model [:model-data :metrics]) 20)
:metrics [20 1]:
| :test-ds |
|----------------|
| 17170.25976563 |
| 17169.70117188 |
| 17169.28906250 |
| 17170.50585938 |
| 17170.07226563 |
| 17168.27929688 |
| 17168.89062500 |
| 17173.72851563 |
| 17179.31640625 |
| 17177.67773438 |
| 17175.00000000 |
| 17172.91406250 |
| 17170.39257813 |
| 17166.40039063 |
| 17166.11132813 |
| 17162.64648438 |
| 17161.11328125 |
| 17161.10351563 |
| 17157.91796875 |
| 17159.54492188 |
Now we see a very common case. XGBoost is overtraining; the error on the validation set not improving while the model continues to train further. We can make this clearer by adding in the training dataset to the watches map:
user> (def model (ml/train (:train-ds train-test-split)
(assoc model-options
:watches train-test-split
:eval-metric "mae"
:round 100)))
#'user/model
user> (ds/tail (get-in model [:model-data :metrics]) 20)
:metrics [20 2]:
| :train-ds | :test-ds |
|--------------|----------------|
| 833.36267090 | 17170.25781250 |
| 802.52020264 | 17169.70117188 |
| 777.55834961 | 17169.28906250 |
| 742.71563721 | 17170.50585938 |
| 712.96319580 | 17170.07226563 |
| 697.16204834 | 17168.27734375 |
| 668.31335449 | 17168.89062500 |
| 636.66845703 | 17173.72851563 |
| 606.96020508 | 17179.31640625 |
| 583.48291016 | 17177.67773438 |
| 564.89141846 | 17175.00000000 |
| 542.37860107 | 17172.91406250 |
| 529.37158203 | 17170.39257813 |
| 515.00244141 | 17166.40039063 |
| 494.43447876 | 17166.11132813 |
| 473.96432495 | 17162.64648438 |
| 456.32290649 | 17161.11328125 |
| 448.66156006 | 17161.10351563 |
| 439.60934448 | 17157.91796875 |
| 425.91204834 | 17159.54492188 |
...
We see the loss continue to decrease on the training set while the loss on the test set is staying fairly constant.
Early Stopping
Using the built-in XGBoost early stopping we can avoid overtraining:
user> (def model (ml/train (:train-ds train-test-split)
(assoc model-options
:watches train-test-split
:eval-metric "mae"
:round 100
:early-stopping-round 4)))
09:34:35.063 [nREPL-session-d7c6e5a6-cc96-42d5-8435-99f1f16b6d1f] WARN tech.v3.libs.xgboost - Early stopping indicated but watches has undefined iteration order.
Early stopping will always use the 'last' of the watches as defined by the iteration
order of the watches map. Consider using a java.util.LinkedHashMap for watches.
https://github.com/dmlc/xgboost/blob/master/jvm-packages/xgboost4j/src/main/java/ml/dml
c/xgboost4j/java/XGBoost.java#L208
#'user/model
Oops! This is a implementation detail of xgboost. We have to use a map that retains insertion order in order to do early stopping or we have to have only one watch. XGBoost will use the last entry in the watches map to perform it’s early stopping checks.
user> (import '[java.util LinkedHashMap])
java.util.LinkedHashMap
user> (def watches (doto (LinkedHashMap.)
(.put :train-ds (:train-ds train-test-split))
(.put :test-ds (:test-ds train-test-split))))
#'user/watches
user> (def model (ml/train (:train-ds train-test-split)
(assoc model-options
:watches watches
:eval-metric "mae"
:round 100
:early-stopping-round 4)))
#'user/model
user> (ds/tail (get-in model [:model-data :metrics]))
:metrics [5 2]:
| :train-ds | :test-ds |
|-----------|----------|
| 0.0 | 0.0 |
| 0.0 | 0.0 |
| 0.0 | 0.0 |
| 0.0 | 0.0 |
| 0.0 | 0.0 |
...
So here we asked XGBoost to stop if the error on the evaluation dataset (the ‘last’ dataset in the watches map) rises 4 rounds consecutively. As a result, we see that the end of the metrics dataset is all zeros. What round did we actually get to?
user> (def final-metrics (-> (get-in model [:model-data :metrics])
(assoc :round (range 100))
(ds/filter-column :test-ds #(not= 0.0 (double %)))))
#'user/final-metrics
user> (ds/tail final-metrics)
:metrics [5 3]:
| :train-ds | :test-ds | :round |
|---------------|----------------|--------|
| 1799.49560547 | 17184.22460938 | 50 |
| 1751.87585449 | 17190.24023438 | 51 |
| 1715.23388672 | 17189.55859375 | 52 |
| 1690.89416504 | 17189.88085938 | 53 |
| 1653.31481934 | 17184.24023438 | 54 |
Caveat - Cleaning the Options Map
The options used to train the model are stored verbatim in the model map. This means that if you use watches and then save the model you will probably more data in your nippy than you had planned on and it might just not work at all:
user> (require '[taoensso.nippy :as nippy])
nil
user> (count (nippy/freeze model))
Execution error (ExceptionInfo) at taoensso.nippy/throw-unfreezable (nippy.clj:982).
Unfreezable type: class java.util.LinkedHashMap
So we just clean up the options map (and the metrics) before saving:
user> (-> (update model :model-data dissoc :metrics)
(update :options dissoc :watches)
(nippy/freeze)
(count))
248398
Conclusion
We grabbed a dataset, made it trainable (no missing, no strings, everything is a numeric datatype). We then trained an initial model and checked out which columns XGBoost found useful. We furthermore built out metrics using xgboost’s watches feature and observed error rates as XGBoost continued to train. We then ask xgboost to stop training if the error on a validation dataset (the last of the watches map by iteration) increased 4 rounds consecutively.
For this dataset specifically there are quite a lot of dataset-specific operations you can do to improve the results. The examples above are intended to show the range of training options that XGBoost provides out of the box. We hope you enjoy using this excellent software library and that these relatively simple techniques can allow you to get to great results quickly.