nlptoolkit-classification 1.0.7 → 1.0.9

package/dist/Model/Ensemble/RandomForestModel.js

@@ -0,0 +1,34 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.RandomForestModel = void 0;
+const TreeEnsembleModel_1 = require("./TreeEnsembleModel");
+const InstanceList_1 = require("../../InstanceList/InstanceList");
+const DecisionTree_1 = require("../DecisionTree/DecisionTree");
+const DecisionNode_1 = require("../DecisionTree/DecisionNode");
+class RandomForestModel extends TreeEnsembleModel_1.TreeEnsembleModel {
+    /**
+     * Training algorithm for random forest classifier. Basically the algorithm creates K distinct decision trees from
+     * K bootstrap samples of the original training set.
+     *
+     * @param trainSet   Training data given to the algorithm
+     * @param parameters Parameters of the bagging trees algorithm. ensembleSize returns the number of trees in the random forest.
+     */
+    train(trainSet, parameters) {
+        let forestSize = parameters.getEnsembleSize();
+        this.forest = new Array();
+        for (let i = 0; i < forestSize; i++) {
+            let bootstrap = trainSet.bootstrap(i);
+            let tree = new DecisionTree_1.DecisionTree(new DecisionNode_1.DecisionNode(new InstanceList_1.InstanceList(bootstrap.getSample()), undefined, parameters, false));
+            this.forest.push(tree);
+        }
+    }
+    /**
+     * Loads the random forest model from an input file.
+     * @param fileName File name of the random forest model.
+     */
+    loadModel(fileName) {
+        this.constructor2(fileName);
+    }
+}
+exports.RandomForestModel = RandomForestModel;
+//# sourceMappingURL=RandomForestModel.js.map

package/dist/Model/Ensemble/RandomForestModel.js.map

@@ -0,0 +1 @@
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package/dist/Model/Ensemble/TreeEnsembleModel.d.ts

@@ -0,0 +1,32 @@
+import { Model } from "../Model";
+import { Instance } from "../../Instance/Instance";
+import { DecisionTree } from "../DecisionTree/DecisionTree";
+export declare abstract class TreeEnsembleModel extends Model {
+    protected forest: Array<DecisionTree>;
+    /**
+     * A constructor which sets the {@link Array} of {@link DecisionTree} with given input.
+     *
+     * @param forest An {@link Array} of {@link DecisionTree}.
+     */
+    constructor1(forest: Array<DecisionTree>): void;
+    /**
+     * Loads a tree ensemble model such as Random Forest model or Bagging model from an input model file.
+     * @param fileName Model file name.
+     */
+    constructor2(fileName: string): void;
+    /**
+     * The predict method takes an {@link Instance} as an input and loops through the {@link ArrayList} of {@link DecisionTree}s.
+     * Makes prediction for the items of that ArrayList and returns the maximum item of that ArrayList.
+     *
+     * @param instance Instance to make prediction.
+     * @return The maximum prediction of a given Instance.
+     */
+    predict(instance: Instance): string;
+    /**
+     * Calculates the posterior probability distribution for the given instance according to ensemble tree model.
+     * @param instance Instance for which posterior probability distribution is calculated.
+     * @return Posterior probability distribution for the given instance.
+     */
+    predictProbability(instance: Instance): Map<string, number>;
+    saveTxt(fileName: string): void;
+}

package/dist/Model/Ensemble/TreeEnsembleModel.js

@@ -0,0 +1,61 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.TreeEnsembleModel = void 0;
+const Model_1 = require("../Model");
+const DecisionTree_1 = require("../DecisionTree/DecisionTree");
+const DiscreteDistribution_1 = require("nlptoolkit-math/dist/DiscreteDistribution");
+const FileContents_1 = require("nlptoolkit-util/dist/FileContents");
+const DecisionNode_1 = require("../DecisionTree/DecisionNode");
+class TreeEnsembleModel extends Model_1.Model {
+    forest;
+    /**
+     * A constructor which sets the {@link Array} of {@link DecisionTree} with given input.
+     *
+     * @param forest An {@link Array} of {@link DecisionTree}.
+     */
+    constructor1(forest) {
+        this.forest = forest;
+    }
+    /**
+     * Loads a tree ensemble model such as Random Forest model or Bagging model from an input model file.
+     * @param fileName Model file name.
+     */
+    constructor2(fileName) {
+        let input = new FileContents_1.FileContents(fileName);
+        let numberOfTrees = parseInt(input.readLine());
+        this.forest = new Array();
+        for (let i = 0; i < numberOfTrees; i++) {
+            this.forest.push(new DecisionTree_1.DecisionTree(new DecisionNode_1.DecisionNode(input)));
+        }
+    }
+    /**
+     * The predict method takes an {@link Instance} as an input and loops through the {@link ArrayList} of {@link DecisionTree}s.
+     * Makes prediction for the items of that ArrayList and returns the maximum item of that ArrayList.
+     *
+     * @param instance Instance to make prediction.
+     * @return The maximum prediction of a given Instance.
+     */
+    predict(instance) {
+        let distribution = new DiscreteDistribution_1.DiscreteDistribution();
+        for (let tree of this.forest) {
+            distribution.addItem(tree.predict(instance));
+        }
+        return distribution.getMaxItem();
+    }
+    /**
+     * Calculates the posterior probability distribution for the given instance according to ensemble tree model.
+     * @param instance Instance for which posterior probability distribution is calculated.
+     * @return Posterior probability distribution for the given instance.
+     */
+    predictProbability(instance) {
+        let distribution = new DiscreteDistribution_1.DiscreteDistribution();
+        for (let tree of this.forest) {
+            distribution.addItem(tree.predict(instance));
+        }
+        return distribution.getProbabilityDistribution();
+    }
+    saveTxt(fileName) {
+    }
+}
+exports.TreeEnsembleModel = TreeEnsembleModel;
+//# sourceMappingURL=TreeEnsembleModel.js.map

package/dist/Model/Ensemble/TreeEnsembleModel.js.map

@@ -0,0 +1 @@
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package/dist/Model/Model.d.ts

@@ -3,10 +3,14 @@ import { FileContents } from "nlptoolkit-util/dist/FileContents";
 import { InstanceList } from "../InstanceList/InstanceList";
 import { Matrix } from "nlptoolkit-math/dist/Matrix";
 import { DiscreteDistribution } from "nlptoolkit-math/dist/DiscreteDistribution";
+import { Parameter } from "../Parameter/Parameter";
+import { Performance } from "../Performance/Performance";
 export declare abstract class Model {
     abstract predict(instance: Instance): string;
     abstract predictProbability(instance: Instance): Map<string, number>;
     abstract saveTxt(fileName: String): void;
+    abstract train(trainSet: InstanceList, parameters: Parameter): void;
+    abstract loadModel(fileName: string): void;
     /**
      * Given an array of class labels, returns the maximum occurred one.
      *
@@ -14,8 +18,54 @@ export declare abstract class Model {
      * @return The class label that occurs most in the array of class labels (mod of class label list).
      */
     static getMaximum(classLabels: Array<string>): string;
+    /**
+     * Loads a single instance from a single line.
+     * @param line Line containing the instance.
+     * @param attributeTypes Type of the attributes of the instance. If th attribute is discrete, it is "DISCRETE",
+     *                       otherwise it is "CONTINUOUS".
+     * @return Instance read from the line.
+     */
     loadInstance(line: string, attributeTypes: string[]): Instance;
+    /**
+     * Loads a discrete distribution from an input model file
+     * @param input Input model file.
+     * @return Discrete distribution read from an input model file.
+     */
     static loadDiscreteDistribution(input: FileContents): DiscreteDistribution;
+    /**
+     * Loads an instance list from an input model file.
+     * @param input Input model file.
+     * @return Instance list read from an input model file.
+     */
     loadInstanceList(input: FileContents): InstanceList;
+    /**
+     * Loads a matrix from an input model file.
+     * @param input Input model file.
+     * @return Matrix read from the input model file.
+     */
     loadMatrix(input: FileContents): Matrix;
+    /**
+     * Checks given instance's attribute and returns true if it is a discrete indexed attribute, false otherwise.
+     *
+     * @param instance Instance to check.
+     * @return True if instance is a discrete indexed attribute, false otherwise.
+     */
+    discreteCheck(instance: Instance): boolean;
+    /**
+     * TestClassification an instance list with the current model.
+     *
+     * @param testSet Test data (list of instances) to be tested.
+     * @return The accuracy (and error) of the model as an instance of Performance class.
+     */
+    test(testSet: InstanceList): Performance;
+    /**
+     * Runs current classifier with the given train and test data.
+     *
+     * @param parameter Parameter of the classifier to be trained.
+     * @param trainSet  Training data to be used in training the classifier.
+     * @param testSet   Test data to be tested after training the model.
+     * @return The accuracy (and error) of the trained model as an instance of Performance class.
+     * @throws DiscreteFeaturesNotAllowed Exception for discrete features.
+     */
+    singleRun(parameter: Parameter, trainSet: InstanceList, testSet: InstanceList): Performance;
 }

package/dist/Model/Model.js

@@ -1,84 +1,143 @@
-(function (factory) {
-    if (typeof module === "object" && typeof module.exports === "object") {
-        var v = factory(require, exports);
-        if (v !== undefined) module.exports = v;
-    }
-    else if (typeof define === "function" && define.amd) {
-        define(["require", "exports", "../Instance/Instance", "nlptoolkit-datastructure/dist/CounterHashMap", "../InstanceList/InstanceList", "nlptoolkit-math/dist/Matrix", "nlptoolkit-math/dist/DiscreteDistribution"], factory);
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.Model = void 0;
+const Instance_1 = require("../Instance/Instance");
+const CounterHashMap_1 = require("nlptoolkit-datastructure/dist/CounterHashMap");
+const InstanceList_1 = require("../InstanceList/InstanceList");
+const Matrix_1 = require("nlptoolkit-math/dist/Matrix");
+const DiscreteDistribution_1 = require("nlptoolkit-math/dist/DiscreteDistribution");
+const DiscreteAttribute_1 = require("../Attribute/DiscreteAttribute");
+const DiscreteIndexedAttribute_1 = require("../Attribute/DiscreteIndexedAttribute");
+const ConfusionMatrix_1 = require("../Performance/ConfusionMatrix");
+const DetailedClassificationPerformance_1 = require("../Performance/DetailedClassificationPerformance");
+class Model {
+    /**
+     * Given an array of class labels, returns the maximum occurred one.
+     *
+     * @param classLabels An array of class labels.
+     * @return The class label that occurs most in the array of class labels (mod of class label list).
+     */
+    static getMaximum(classLabels) {
+        let frequencies = new CounterHashMap_1.CounterHashMap();
+        for (let label of classLabels) {
+            frequencies.put(label);
+        }
+        return frequencies.max();
     }
-})(function (require, exports) {
-    "use strict";
-    Object.defineProperty(exports, "__esModule", { value: true });
-    exports.Model = void 0;
-    const Instance_1 = require("../Instance/Instance");
-    const CounterHashMap_1 = require("nlptoolkit-datastructure/dist/CounterHashMap");
-    const InstanceList_1 = require("../InstanceList/InstanceList");
-    const Matrix_1 = require("nlptoolkit-math/dist/Matrix");
-    const DiscreteDistribution_1 = require("nlptoolkit-math/dist/DiscreteDistribution");
-    class Model {
-        /**
-         * Given an array of class labels, returns the maximum occurred one.
-         *
-         * @param classLabels An array of class labels.
-         * @return The class label that occurs most in the array of class labels (mod of class label list).
-         */
-        static getMaximum(classLabels) {
-            let frequencies = new CounterHashMap_1.CounterHashMap();
-            for (let label of classLabels) {
-                frequencies.put(label);
+    /**
+     * Loads a single instance from a single line.
+     * @param line Line containing the instance.
+     * @param attributeTypes Type of the attributes of the instance. If th attribute is discrete, it is "DISCRETE",
+     *                       otherwise it is "CONTINUOUS".
+     * @return Instance read from the line.
+     */
+    loadInstance(line, attributeTypes) {
+        let items = line.split(",");
+        let instance = new Instance_1.Instance(items[items.length - 1]);
+        for (let i = 0; i < items.length - 1; i++) {
+            switch (attributeTypes[i]) {
+                case "DISCRETE":
+                    instance.addAttribute(items[i]);
+                    break;
+                case "CONTINUOUS":
+                    instance.addAttribute(parseFloat(items[i]));
+                    break;
             }
-            return frequencies.max();
         }
-        loadInstance(line, attributeTypes) {
-            let items = line.split(",");
-            let instance = new Instance_1.Instance(items[items.length - 1]);
-            for (let i = 0; i < items.length - 1; i++) {
-                switch (attributeTypes[i]) {
-                    case "DISCRETE":
-                        instance.addAttribute(items[i]);
-                        break;
-                    case "CONTINUOUS":
-                        instance.addAttribute(parseFloat(items[i]));
-                        break;
-                }
+        return instance;
+    }
+    /**
+     * Loads a discrete distribution from an input model file
+     * @param input Input model file.
+     * @return Discrete distribution read from an input model file.
+     */
+    static loadDiscreteDistribution(input) {
+        let distribution = new DiscreteDistribution_1.DiscreteDistribution();
+        let size = parseInt(input.readLine());
+        for (let i = 0; i < size; i++) {
+            let line = input.readLine();
+            let items = line.split(" ");
+            let count = parseInt(items[1]);
+            for (let j = 0; j < count; j++) {
+                distribution.addItem(items[0]);
             }
-            return instance;
         }
-        static loadDiscreteDistribution(input) {
-            let distribution = new DiscreteDistribution_1.DiscreteDistribution();
-            let size = parseInt(input.readLine());
-            for (let i = 0; i < size; i++) {
-                let line = input.readLine();
-                let items = line.split(" ");
-                let count = parseInt(items[1]);
-                for (let j = 0; j < count; j++) {
-                    distribution.addItem(items[0]);
-                }
-            }
-            return distribution;
+        return distribution;
+    }
+    /**
+     * Loads an instance list from an input model file.
+     * @param input Input model file.
+     * @return Instance list read from an input model file.
+     */
+    loadInstanceList(input) {
+        let types = input.readLine().split(" ");
+        let instanceCount = parseInt(input.readLine());
+        let instanceList = new InstanceList_1.InstanceList();
+        for (let i = 0; i < instanceCount; i++) {
+            instanceList.add(this.loadInstance(input.readLine(), types));
         }
-        loadInstanceList(input) {
-            let types = input.readLine().split(" ");
-            let instanceCount = parseInt(input.readLine());
-            let instanceList = new InstanceList_1.InstanceList();
-            for (let i = 0; i < instanceCount; i++) {
-                instanceList.add(this.loadInstance(input.readLine(), types));
+        return instanceList;
+    }
+    /**
+     * Loads a matrix from an input model file.
+     * @param input Input model file.
+     * @return Matrix read from the input model file.
+     */
+    loadMatrix(input) {
+        let items = input.readLine().split(" ");
+        let matrix = new Matrix_1.Matrix(parseInt(items[0]), parseInt(items[1]));
+        for (let j = 0; j < matrix.getRow(); j++) {
+            let line = input.readLine();
+            items = line.split(" ");
+            for (let k = 0; k < matrix.getColumn(); k++) {
+                matrix.setValue(j, k, parseFloat(items[k]));
             }
-            return instanceList;
         }
-        loadMatrix(input) {
-            let items = input.readLine().split(" ");
-            let matrix = new Matrix_1.Matrix(parseInt(items[0]), parseInt(items[1]));
-            for (let j = 0; j < matrix.getRow(); j++) {
-                let line = input.readLine();
-                items = line.split(" ");
-                for (let k = 0; k < matrix.getColumn(); k++) {
-                    matrix.setValue(j, k, parseFloat(items[k]));
-                }
+        return matrix;
+    }
+    /**
+     * Checks given instance's attribute and returns true if it is a discrete indexed attribute, false otherwise.
+     *
+     * @param instance Instance to check.
+     * @return True if instance is a discrete indexed attribute, false otherwise.
+     */
+    discreteCheck(instance) {
+        for (let i = 0; i < instance.attributeSize(); i++) {
+            if (instance.getAttribute(i) instanceof DiscreteAttribute_1.DiscreteAttribute &&
+                !(instance.getAttribute(i) instanceof DiscreteIndexedAttribute_1.DiscreteIndexedAttribute)) {
+                return false;
             }
-            return matrix;
         }
+        return true;
+    }
+    /**
+     * TestClassification an instance list with the current model.
+     *
+     * @param testSet Test data (list of instances) to be tested.
+     * @return The accuracy (and error) of the model as an instance of Performance class.
+     */
+    test(testSet) {
+        let classLabels = testSet.getUnionOfPossibleClassLabels();
+        let confusion = new ConfusionMatrix_1.ConfusionMatrix(classLabels);
+        for (let i = 0; i < testSet.size(); i++) {
+            let instance = testSet.get(i);
+            confusion.classify(instance.getClassLabel(), this.predict(instance));
+        }
+        return new DetailedClassificationPerformance_1.DetailedClassificationPerformance(confusion);
+    }
+    /**
+     * Runs current classifier with the given train and test data.
+     *
+     * @param parameter Parameter of the classifier to be trained.
+     * @param trainSet  Training data to be used in training the classifier.
+     * @param testSet   Test data to be tested after training the model.
+     * @return The accuracy (and error) of the trained model as an instance of Performance class.
+     * @throws DiscreteFeaturesNotAllowed Exception for discrete features.
+     */
+    singleRun(parameter, trainSet, testSet) {
+        this.train(trainSet, parameter);
+        return this.test(testSet);
     }
-    exports.Model = Model;
-});
+}
+exports.Model = Model;
 //# sourceMappingURL=Model.js.map

package/dist/Model/Model.js.map

@@ -1 +1 @@
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package/dist/Model/NeuralNetwork/DeepNetworkModel.d.ts

@@ -0,0 +1,47 @@
+import { NeuralNetworkModel } from "./NeuralNetworkModel";
+import { InstanceList } from "../../InstanceList/InstanceList";
+import { Parameter } from "../../Parameter/Parameter";
+export declare class DeepNetworkModel extends NeuralNetworkModel {
+    private weights;
+    private hiddenLayerSize;
+    private activationFunction;
+    /**
+     * The allocateWeights method takes {@link DeepNetworkParameter}s as an input. First it adds random weights to the {@link Array}
+     * of {@link Matrix} weights' first layer. Then it loops through the layers and adds random weights till the last layer.
+     * At the end it adds random weights to the last layer and also sets the hiddenLayerSize value.
+     *
+     * @param parameters {@link DeepNetworkParameter} input.
+     */
+    private allocateWeights;
+    /**
+     * The setBestWeights method creates an {@link Array} of Matrix as bestWeights and clones the values of weights {@link Array}
+     * into this newly created {@link Array}.
+     *
+     * @return An {@link Array} clones from the weights ArrayList.
+     */
+    private setBestWeights;
+    /**
+     * Loads a deep network model from an input model file.
+     * @param fileName Model file name.
+     */
+    constructor2(fileName: string): void;
+    /**
+     * The calculateOutput method loops size of the weights times and calculate one hidden layer at a time and adds bias term.
+     * At the end it updates the output y value.
+     */
+    protected calculateOutput(): void;
+    saveTxt(fileName: string): void;
+    /**
+     * Training algorithm for deep network classifier.
+     *
+     * @param train  Training data given to the algorithm.
+     * @param params Parameters of the deep network algorithm. crossValidationRatio and seed are used as parameters.
+     * @throws DiscreteFeaturesNotAllowed Exception for discrete features.
+     */
+    train(train: InstanceList, params: Parameter): void;
+    /**
+     * Loads the deep network model from an input file.
+     * @param fileName File name of the deep network model.
+     */
+    loadModel(fileName: string): void;
+}