-
Notifications
You must be signed in to change notification settings - Fork 10
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #31 from behrica/addModelIntegrationTest
Add model integration test
- Loading branch information
Showing
10 changed files
with
273 additions
and
234 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -39,3 +39,4 @@ book | |
| test/noj_book/ | ||
|
|
||
| .venv/ | ||
| docs/ | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,169 @@ | ||
| (ns model-integration-test | ||
| (:require [scicloj.metamorph.core :as mm] | ||
| [scicloj.metamorph.ml :as ml] | ||
| [scicloj.metamorph.ml.loss :as loss] | ||
| [scicloj.metamorph.ml.toydata :as data] | ||
| [tech.v3.dataset.categorical :as ds-cat] | ||
| [tablecloth.api :as tc] | ||
| [clojure.string :as str] | ||
| [clojure.set :as set] | ||
| [clojure.test :refer [is deftest]] | ||
| [tech.v3.dataset :as ds]) | ||
| (:import | ||
| (smile.base.mlp ActivationFunction Cost HiddenLayerBuilder LayerBuilder OutputFunction OutputLayerBuilder)) | ||
| ) | ||
|
|
||
| (def mlp-hidden-layer-builder | ||
| (HiddenLayerBuilder. 1 (ActivationFunction/linear))) | ||
|
|
||
| (def mlp-output-layer-builder | ||
| (OutputLayerBuilder. 3 OutputFunction/LINEAR Cost/MEAN_SQUARED_ERROR)) | ||
|
|
||
|
|
||
| (require '[scicloj.metamorph.ml.classification] | ||
| '[scicloj.ml.smile.classification] | ||
| '[scicloj.ml.tribuo] | ||
| '[scicloj.sklearn-clj.ml] | ||
| '[scicloj.ml.xgboost] | ||
| ) | ||
|
|
||
| (def min-accuracies | ||
| {:smile.classification/linear-discriminant-analysis 0.85}) | ||
|
|
||
| (def smile-model-specs | ||
| (map | ||
| #(vector (get min-accuracies % 0.95) | ||
| {:model-type %}) | ||
| (->> (ml/model-definition-names) | ||
| (filter #(str/starts-with? (namespace %) "smile.classification")) | ||
| set | ||
| ((fn [x] (set/difference | ||
| x | ||
| #{:smile.classification/sparse-svm | ||
| :smile.classification/maxent-binomial | ||
| :smile.classification/maxent-multinomial | ||
| :smile.classification/mlp | ||
| :smile.classification/svm | ||
| :smile.classification/sparse-logistic-regression | ||
| :smile.classification/discrete-naive-bayes})))))) | ||
|
|
||
|
|
||
|
|
||
| (def sklearn-model-specs | ||
| (map | ||
| #(vector 0.90 | ||
| {:model-type %}) | ||
| (->> (ml/model-definition-names) | ||
| (filter #(str/starts-with? (namespace %) "sklearn.classification" )) | ||
| set | ||
| ((fn [x] (set/difference | ||
| x | ||
| #{:sklearn.classification/perceptron | ||
| :sklearn.classification/sgd-classifier | ||
| :sklearn.classification/svc | ||
|
|
||
| }))) | ||
| ))) | ||
|
|
||
|
|
||
| (def model-specs | ||
| (concat | ||
| [ | ||
| [0.98 { | ||
| ;; :validate-parameters 1 | ||
| ;; :round 10 | ||
| ;; :silent 0 | ||
| ;; :verbosity 3 | ||
| :model-type :xgboost/classification}] | ||
| [0.30 {:model-type :smile.classification/mlp | ||
| :layer-builders [mlp-hidden-layer-builder mlp-output-layer-builder]}] | ||
| [0.95 {:model-type :sklearn.classification/decision-tree-classifier}] | ||
| [0.95 {:model-type :sklearn.classification/random-forest-classifier}] | ||
| [0.95 {:model-type :sklearn.classification/logistic-regression}] | ||
| [0.93 {:model-type :scicloj.ml.tribuo/classification | ||
| :tribuo-components [{:name "logistic" | ||
| :type "org.tribuo.classification.sgd.linear.LinearSGDTrainer" | ||
| :properties {:seed "1234" | ||
| :shuffle "false" | ||
| :epochs "10"}}] | ||
| :tribuo-trainer-name "logistic"}] | ||
| [0.94 {:model-type :scicloj.ml.tribuo/classification | ||
| :tribuo-components [{:name "random-forest" | ||
| :type "org.tribuo.classification.dtree.CARTClassificationTrainer" | ||
| :properties {:maxDepth "8" | ||
| :useRandomSplitPoints "false" | ||
| :fractionFeaturesInSplit "0.5"}}] | ||
| :tribuo-trainer-name "random-forest"}] | ||
| [0.30 {:model-type :metamorph.ml/dummy-classifier}] | ||
| ] | ||
| smile-model-specs | ||
| ;sklearn-model-specs | ||
| )) | ||
|
|
||
|
|
||
|
|
||
|
|
||
|
|
||
| (defn my-classification-accuracy [lhs rhs] | ||
| ;(println :lhs (meta lhs)) | ||
| ;(println :rhs (meta rhs)) | ||
|
|
||
| (loss/classification-accuracy lhs rhs) | ||
| ) | ||
|
|
||
| (defn verify-classification [model-spec expected-accuracy ds] | ||
| (println :verify (:model-type model-spec)) | ||
| (let [ | ||
| train-test-split | ||
| (tc/split->seq ds :kfold {:seed 1234 :k 10}) | ||
|
|
||
| pipe | ||
| (mm/pipeline | ||
| {:metamorph/id :model} | ||
| (ml/model model-spec)) | ||
|
|
||
| result | ||
| (ml/evaluate-pipelines | ||
| [pipe] | ||
| train-test-split | ||
| my-classification-accuracy | ||
| :accuracy) | ||
| accuracy (-> result first first :train-transform :mean) | ||
| ] | ||
|
|
||
| (is (>= accuracy expected-accuracy) | ||
| (format "%s: expect at least: %s, found : %s" | ||
| (:model-type model-spec) | ||
| expected-accuracy accuracy)))) | ||
|
|
||
|
|
||
| (deftest verify-classifictions-iris | ||
| (run! | ||
| (fn [[acc spec]] (verify-classification spec acc (data/iris-ds))) | ||
| model-specs)) | ||
|
|
||
|
|
||
| (def iris-2 | ||
| (-> | ||
| (data/iris-ds) | ||
| ds-cat/reverse-map-categorical-xforms | ||
| )) | ||
|
|
||
| ;; (deftest verify-classification-iris-2 | ||
| ;; (run! | ||
| ;; (fn [[acc spec]] (verify-classification spec acc iris-2)) | ||
| ;; smile-model-specs)) | ||
|
|
||
|
|
||
| (def iris-3 | ||
| (-> | ||
| (data/iris-ds) | ||
| (ds/assoc-metadata [:species] :categorical-map nil) | ||
| )) | ||
|
|
||
|
|
||
| (deftest verify-classification-iris-3 | ||
| (run! | ||
| (fn [[acc spec]] (verify-classification spec acc iris-3)) | ||
| smile-model-specs)) | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.