diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 0aafe8c..140244a 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -28,5 +28,7 @@ }, "remoteUser": "vscode", - "postStartCommand": "poetry install --sync" + "postStartCommand": {"install python packages": "poetry install --sync" , + "add link to python executable": "sudo ln -s /usr/bin/python3 /usr/local/bin/python" + } } diff --git a/.gitignore b/.gitignore index 129ba5c..9784716 100644 --- a/.gitignore +++ b/.gitignore @@ -39,3 +39,4 @@ book test/noj_book/ .venv/ +docs/ \ No newline at end of file diff --git a/build.clj b/build.clj index 104dd5f..d6184d8 100644 --- a/build.clj +++ b/build.clj @@ -52,8 +52,8 @@ :src-dirs ["src"] :pom-data (pom-template version)))) -(defn generate-tests [opts] - (let [basis (b/create-basis {:aliases [:dev]}) +(defn generate-tests [_] + (let [basis (b/create-basis {:aliases [:gen-tests :model-integration-tests :test]}) cmds (b/java-command {:basis basis @@ -63,7 +63,7 @@ (when-not (zero? exit) (throw (ex-info "Tests generation failed" {}))))) (def opts {}) (defn ci "Run the CI pipeline of tests (and build the JAR)." [opts] - (generate-tests (assoc opts :aliases [:dev])) + (generate-tests nil) (test (assoc opts :aliases [:dev :test])) (b/delete {:path "target"}) (let [opts (jar-opts opts)] @@ -80,3 +80,16 @@ (dd/deploy {:installer :remote :artifact (b/resolve-path jar-file) :pom-file (b/pom-path (select-keys opts [:lib :class-dir]))})) opts) + + +(defn models-integration-tests "Run integration tests." [opts] + (let [basis (b/create-basis { :aliases [:model-integration-tests ]}) + cmds (b/java-command + {:basis basis + :main 'clojure.main + :main-args ["-m" "cognitect.test-runner" "-d" "model-integration-tests"]})] + (b/process cmds) + )opts) + + + diff --git a/deps.edn b/deps.edn index 68d220f..9710598 100644 --- a/deps.edn +++ b/deps.edn @@ -5,35 +5,44 @@ org.scicloj/kindly {:mvn/version "4-beta12"} generateme/fastmath {:mvn/version "3.0.0-alpha1"} aerial.hanami/aerial.hanami {:mvn/version "0.20.0"} - org.scicloj/hanamicloth {:mvn/version "1-alpha8" - :exclusions [scicloj/metamorph.ml]} - scicloj/metamorph.ml {:git/url "https://github.com/scicloj/metamorph.ml.git" - :git/sha "50f47dad934a2786b3cf025bef509f1f3d1a7e1d" - :exclusions [generateme/fastmath]} - org.scicloj/scicloj.ml.tribuo {:mvn/version "0.1.1-branch-noj-2-alpha4-SNAPSHOT" - :exclusions [scicloj/metamorph.ml]} - org.tribuo/tribuo-regression-sgd {:mvn/version "4.3.1"} - org.tribuo/tribuo-regression-tree {:mvn/version "4.3.1"} - org.tribuo/tribuo-regression-xgboost {:mvn/version "4.3.1"} - org.tribuo/tribuo-classification-sgd {:mvn/version "4.3.1"} - org.tribuo/tribuo-classification-tree {:mvn/version "4.3.1"} - org.tribuo/tribuo-classification-xgboost {:mvn/version "4.3.1"} + org.scicloj/hanamicloth {:mvn/version "1-alpha8"} + org.scicloj/metamorph.ml {:mvn/version "0.9.0"} + org.scicloj/scicloj.ml.tribuo {:mvn/version "0.1.2"} + org.tribuo/tribuo-regression-sgd {:mvn/version "4.2.0"} + org.tribuo/tribuo-regression-tree {:mvn/version "4.2.0"} + org.tribuo/tribuo-classification-sgd {:mvn/version "4.2.0"} + org.tribuo/tribuo-classification-tree {:mvn/version "4.2.0"} clj-python/libpython-clj {:mvn/version "2.025"} org.scicloj/kind-pyplot {:mvn/version "1-beta1"} scicloj/clojisr {:mvn/version "1.0.0"}} :aliases - {:build {:deps {io.github.clojure/tools.build {:mvn/version "0.9.6"} + {:gen-tests {:extra-paths ["build"]} + + :build {:deps {io.github.clojure/tools.build {:mvn/version "0.9.6"} slipset/deps-deploy {:mvn/version "0.2.1"}} :ns-default build} :test {:extra-paths ["test" "notebooks"] :extra-deps {org.clojure/test.check {:mvn/version "1.1.1"} - io.github.cognitect-labs/test-runner - {:git/tag "v0.5.1" :git/sha "dfb30dd"} + io.github.cognitect-labs/test-runner {:git/tag "v0.5.1" :git/sha "dfb30dd"} + same/ish {:mvn/version "0.1.6"} org.scicloj/clay {:mvn/version "2-beta16"}}} - :dev {:extra-paths ["notebooks" "build"] - :extra-deps {org.scicloj/clay {:mvn/version "2-beta16"} - scicloj/scicloj.ml.smile {:mvn/version "7.4.1"} - org.scicloj/sklearn-clj {:mvn/version "0.4.1"} - }}}} + + :model-integration-tests + {:extra-paths ["model-integration-tests"] + :extra-deps {org.scicloj/scicloj.ml.smile {:mvn/version "7.4.2"} + org.scicloj/sklearn-clj {:mvn/version "0.4.1"} + scicloj/scicloj.ml.xgboost {:mvn/version "6.0.0"} + + org.bytedeco/arpack-ng {:mvn/version "3.7.0-1.5.4"} + org.bytedeco/openblas-platform {:mvn/version "0.3.10-1.5.4"} + org.bytedeco/arpack-ng-platform {:mvn/version "3.7.0-1.5.4"} + org.bytedeco/openblas {:mvn/version "0.3.10-1.5.4"} + org.bytedeco/javacpp {:mvn/version "1.5.4"} + org.scicloj/metamorph.ml {:mvn/version "0.9.0"} + io.github.cognitect-labs/test-runner {:git/tag "v0.5.1" :git/sha "dfb30dd"} + }} + + :dev {:extra-paths ["notebooks"] + :extra-deps {org.scicloj/clay {:mvn/version "2-beta16"}}}}} diff --git a/model-integration-tests/model_integration_test.clj b/model-integration-tests/model_integration_test.clj new file mode 100644 index 0000000..006bf39 --- /dev/null +++ b/model-integration-tests/model_integration_test.clj @@ -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)) + diff --git a/notebooks/noj_book/automl.clj b/notebooks/noj_book/automl.clj index 6600cd4..dcca883 100644 --- a/notebooks/noj_book/automl.clj +++ b/notebooks/noj_book/automl.clj @@ -277,11 +277,9 @@ ctx-after-train (require '[scicloj.metamorph.ml :as ml] '[scicloj.metamorph.ml.loss :as loss] '[scicloj.metamorph.core :as mm] - '[scicloj.ml.tribuo] ;; register the tribuo models - '[scicloj.ml.smile.classification] ;; register the smile classification models - '[scicloj.metamorph.ml.classification] ;; register dummy classifier - '[scicloj.sklearn-clj.ml] ;; register all sklern models classifier - ) + '[scicloj.ml.tribuo] + '[scicloj.ml.xgboost] + '[scicloj.sklearn-clj.ml]) ;; ## Finding the best model automatically @@ -312,26 +310,23 @@ ctx-after-train (-> titanic-k-fold count) ;; The list of the model types we want to try: -(def models [{:model-type :metamorph.ml/dummy-classifier} - +(def models [{ :model-type :xgboost/classification + :round 10} + {:model-type :sklearn.classification/decision-tree-classifier} {:model-type :sklearn.classification/logistic-regression} - - {:model-type :smile.classification/random-forest} - - {:model-type :scicloj.ml.tribuo/classification - :tribuo-components [{:name "logistic" - :type "org.tribuo.classification.sgd.linear.LinearSGDTrainer"}] - :tribuo-trainer-name "logistic"} - {: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"} - - - ]) + {:model-type :sklearn.classification/random-forest-classifier} + {:model-type :metamorph.ml/dummy-classifier} + {:model-type :scicloj.ml.tribuo/classification + :tribuo-components [{:name "logistic" + :type "org.tribuo.classification.sgd.linear.LinearSGDTrainer"}] + :tribuo-trainer-name "logistic"} + {: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"}]) ;; This uses models from Smile and Tribuo, but could be any @@ -383,7 +378,8 @@ ctx-after-train titanic-k-fold loss/classification-accuracy :accuracy - {:return-best-crossvalidation-only false + {:map-fn :map + :return-best-crossvalidation-only false :return-best-pipeline-only false})) diff --git a/notebooks/noj_book/ml_basic.clj b/notebooks/noj_book/ml_basic.clj index f76c953..ff3fd06 100644 --- a/notebooks/noj_book/ml_basic.clj +++ b/notebooks/noj_book/ml_basic.clj @@ -11,12 +11,29 @@ (:require [tablecloth.api :as tc] [scicloj.metamorph.ml.toydata :as data] [tech.v3.dataset :as ds] + [same.core :as same] + [same.compare :as compare] [camel-snake-kebab.core :as csk] [scicloj.kindly.v4.kind :as kind] [scicloj.kindly.v4.api :as kindly])) +(defn round + [n scale rm] + (.setScale ^java.math.BigDecimal (bigdec n) + (int scale) + ^RoundingMode (if (instance? java.math.RoundingMode rm) + rm + (java.math.RoundingMode/valueOf + (str (if (ident? rm) (symbol rm) rm)))))) +(defn set-sameish-comparator! [scale] + (same/set-comparator! (fn [a b] + (let [a-rounded (round a scale :HALF_UP) + b-rounded (round b scale :HALF_UP)] + (= a-rounded + b-rounded))))) + ;; ## Inspect data ;; @@ -191,7 +208,7 @@ split (loss/classification-accuracy (:survived (ds-cat/reverse-map-categorical-xforms (:test split))) - (:survived (ds-cat/reverse-map-categorical-xforms lreg-prediction))) + (:survived lreg-prediction)) (kindly/check = 0.7373737373737373) ;; Its performance is better, 73 % @@ -208,19 +225,21 @@ split (def rf-prediction (ml/predict (:test split) rf-model)) +(set-sameish-comparator! 1) ;; First five prediction including the probability distributions ;; are (-> rf-prediction (tc/head) (tc/rows)) -(kindly/check = - [["no" 0.6470588235294118 0.35294117647058826] - ["no" 0.5714285714285714 0.42857142857142855] - ["no" 0.8529411764705882 0.14705882352941177] - ["no" 0.8879310344827587 0.11206896551724138] - ["no" 0.8879310344827587 0.11206896551724138]]) +(kindly/check same/ish? + [["no" 0.64 0.35] + ["no" 0.57 0.42] + ["no" 0.85 0.14] + ["no" 0.88 0.11] + ["no" 0.88 0.11]]) + (loss/classification-accuracy (:survived (ds-cat/reverse-map-categorical-xforms (:test split))) diff --git a/poetry.lock b/poetry.lock index 4cdffbd..38f0047 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,99 +1,5 @@ # This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. -[[package]] -name = "attrs" -version = "24.2.0" -description = "Classes Without Boilerplate" -optional = false -python-versions = ">=3.7" -files = [ - 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