nlptoolkit-classification 1.0.0

package/dist/InstanceList/InstanceList.js

@@ -0,0 +1,517 @@
+(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", "../DataSet/DataDefinition", "fs", "../Attribute/BinaryAttribute", "../Attribute/DiscreteAttribute", "../Attribute/ContinuousAttribute", "../Attribute/AttributeType", "nlptoolkit-sampling/dist/Bootstrap", "../Instance/CompositeInstance", "../Model/Model", "../Attribute/DiscreteIndexedAttribute", "nlptoolkit-math/dist/DiscreteDistribution", "nlptoolkit-math/dist/Matrix"], factory);
+    }
+})(function (require, exports) {
+    "use strict";
+    Object.defineProperty(exports, "__esModule", { value: true });
+    exports.InstanceList = void 0;
+    const Instance_1 = require("../Instance/Instance");
+    const DataDefinition_1 = require("../DataSet/DataDefinition");
+    const fs = require("fs");
+    const BinaryAttribute_1 = require("../Attribute/BinaryAttribute");
+    const DiscreteAttribute_1 = require("../Attribute/DiscreteAttribute");
+    const ContinuousAttribute_1 = require("../Attribute/ContinuousAttribute");
+    const AttributeType_1 = require("../Attribute/AttributeType");
+    const Bootstrap_1 = require("nlptoolkit-sampling/dist/Bootstrap");
+    const CompositeInstance_1 = require("../Instance/CompositeInstance");
+    const Model_1 = require("../Model/Model");
+    const DiscreteIndexedAttribute_1 = require("../Attribute/DiscreteIndexedAttribute");
+    const DiscreteDistribution_1 = require("nlptoolkit-math/dist/DiscreteDistribution");
+    const Matrix_1 = require("nlptoolkit-math/dist/Matrix");
+    class InstanceList {
+        /**
+         * Constructor for an instance list with a given data definition, data file and a separator character. Each instance
+         * must be stored in a separate line separated with the character separator. The last item must be the class label.
+         * The function reads the file line by line and for each line; depending on the data definition, that is, type of
+         * the attributes, adds discrete and continuous attributes to a new instance. For example, given the data set file
+         * <p>
+         * red;1;0.4;true
+         * green;-1;0.8;true
+         * blue;3;1.3;false
+         * <p>
+         * where the first attribute is a discrete attribute, second and third attributes are continuous attributes, the
+         * fourth item is the class label.
+         *
+         * @param definition Data definition of the data set.
+         * @param separator  Separator character which separates the attribute values in the data file.
+         * @param fileName   Name of the data set file.
+         */
+        constructor(definition, separator, fileName) {
+            this.list = new Array();
+            if (definition != undefined) {
+                if (definition instanceof DataDefinition_1.DataDefinition) {
+                    let data = fs.readFileSync(fileName, 'utf8');
+                    let lines = data.split("\n");
+                    for (let line of lines) {
+                        let attributeList = line.split(separator);
+                        if (attributeList.length == definition.attributeCount() + 1) {
+                            let current = new Instance_1.Instance(attributeList[attributeList.length - 1]);
+                            for (let i = 0; i < attributeList.length - 1; i++) {
+                                switch (definition.getAttributeType(i)) {
+                                    case AttributeType_1.AttributeType.DISCRETE:
+                                        current.addAttribute(new DiscreteAttribute_1.DiscreteAttribute(attributeList[i]));
+                                        break;
+                                    case AttributeType_1.AttributeType.BINARY:
+                                        if (attributeList[i].toLowerCase() == "yes" || attributeList[i] == "1") {
+                                            current.addAttribute(new BinaryAttribute_1.BinaryAttribute(true));
+                                        }
+                                        else {
+                                            current.addAttribute(new BinaryAttribute_1.BinaryAttribute(false));
+                                        }
+                                        break;
+                                    case AttributeType_1.AttributeType.CONTINUOUS:
+                                        current.addAttribute(new ContinuousAttribute_1.ContinuousAttribute(Number.parseFloat(attributeList[i])));
+                                        break;
+                                }
+                            }
+                            this.list.push(current);
+                        }
+                    }
+                }
+                else {
+                    this.list = definition;
+                }
+            }
+        }
+        /**
+         * Adds instance to the instance list.
+         *
+         * @param instance Instance to be added.
+         */
+        add(instance) {
+            this.list.push(instance);
+        }
+        /**
+         * Adds a list of instances to the current instance list.
+         *
+         * @param instanceList List of instances to be added.
+         */
+        addAll(instanceList) {
+            for (let instance of instanceList) {
+                this.list.push(instance);
+            }
+        }
+        /**
+         * Returns size of the instance list.
+         *
+         * @return Size of the instance list.
+         */
+        size() {
+            return this.list.length;
+        }
+        /**
+         * Accessor for a single instance with the given index.
+         *
+         * @param index Index of the instance.
+         * @return Instance with index 'index'.
+         */
+        get(index) {
+            return this.list[index];
+        }
+        /**
+         * Sorts instance list according to the attribute with index 'attributeIndex'.
+         *
+         * @param attributeIndex index of the attribute.
+         */
+        sort(attributeIndex) {
+            if (attributeIndex == undefined) {
+                this.list.sort((a, b) => (a.getClassLabel() < b.getClassLabel() ? -1 :
+                    a.getClassLabel() > b.getClassLabel() ? 1 : 0));
+            }
+            else {
+                this.list.sort((a, b) => a.getAttribute(attributeIndex).getValue() < b.getAttribute(attributeIndex).getValue() ? -1 :
+                    a.getAttribute(attributeIndex).getValue() > b.getAttribute(attributeIndex).getValue() ? 1 : 0);
+            }
+        }
+        /**
+         * Shuffles the instance list.
+         * @param seed Seed is used for random number generation.
+         */
+        shuffle(seed) {
+        }
+        /**
+         * Creates a bootstrap sample from the current instance list.
+         *
+         * @param seed To create a different bootstrap sample, we need a new seed for each sample.
+         * @return Bootstrap sample.
+         */
+        bootstrap(seed) {
+            return new Bootstrap_1.Bootstrap(this.list, seed);
+        }
+        /**
+         * Extracts the class labels of each instance in the instance list and returns them in an array of {@link String}.
+         *
+         * @return An array list of class labels.
+         */
+        getClassLabels() {
+            let classLabels = new Array();
+            for (let instance of this.list) {
+                classLabels.push(instance.getClassLabel());
+            }
+            return classLabels;
+        }
+        /**
+         * Extracts the class labels of each instance in the instance list and returns them as a set.
+         *
+         * @return An {@link Array} of distinct class labels.
+         */
+        getDistinctClassLabels() {
+            let classLabels = new Array();
+            for (let instance of this.list) {
+                if (!classLabels.includes(instance.getClassLabel())) {
+                    classLabels.push(instance.getClassLabel());
+                }
+            }
+            return classLabels;
+        }
+        /**
+         * Extracts the possible class labels of each instance in the instance list and returns them as a set.
+         *
+         * @return An {@link Array} of distinct class labels.
+         */
+        getUnionOfPossibleClassLabels() {
+            let possibleClassLabels = new Array();
+            for (let instance of this.list) {
+                if (instance instanceof CompositeInstance_1.CompositeInstance) {
+                    let compositeInstance = instance;
+                    for (let possibleClassLabel of compositeInstance.getPossibleClassLabels()) {
+                        if (!possibleClassLabels.includes(possibleClassLabel)) {
+                            possibleClassLabels.push(possibleClassLabel);
+                        }
+                    }
+                }
+                else {
+                    if (!possibleClassLabels.includes(instance.getClassLabel())) {
+                        possibleClassLabels.push(instance.getClassLabel());
+                    }
+                }
+            }
+            return possibleClassLabels;
+        }
+        /**
+         * Extracts distinct discrete values of a given attribute as an array of strings.
+         *
+         * @param attributeIndex Index of the discrete attribute.
+         * @return An array of distinct values of a discrete attribute.
+         */
+        getAttributeValueList(attributeIndex) {
+            let valueList = new Array();
+            for (let instance of this.list) {
+                if (!valueList.includes(instance.getAttribute(attributeIndex).getValue())) {
+                    valueList.push(instance.getAttribute(attributeIndex).getValue());
+                }
+            }
+            return valueList;
+        }
+        /**
+         * Calculates the mean of a single attribute for this instance list (m_i). If the attribute is discrete, the maximum
+         * occurring value for that attribute is returned. If the attribute is continuous, the mean value of the values of
+         * all instances are returned.
+         *
+         * @param index Index of the attribute.
+         * @return The mean value of the instances as an attribute.
+         */
+        attributeAverage(index) {
+            if (this.list[0].getAttribute(index) instanceof DiscreteAttribute_1.DiscreteAttribute) {
+                let values = new Array();
+                for (let instance of this.list) {
+                    values.push(instance.getAttribute(index).getValue());
+                }
+                return new DiscreteAttribute_1.DiscreteAttribute(Model_1.Model.getMaximum(values));
+            }
+            else {
+                if (this.list[0].getAttribute(index) instanceof ContinuousAttribute_1.ContinuousAttribute) {
+                    let sum = 0.0;
+                    for (let instance of this.list) {
+                        sum += instance.getAttribute(index).getValue();
+                    }
+                    return new ContinuousAttribute_1.ContinuousAttribute(sum / this.list.length);
+                }
+                else {
+                    return undefined;
+                }
+            }
+        }
+        /**
+         * Calculates the mean of a single attribute for this instance list (m_i).
+         *
+         * @param index Index of the attribute.
+         * @return The mean value of the instances as an attribute.
+         */
+        continuousAttributeAverage(index) {
+            if (index == undefined) {
+                let result = new Array();
+                for (let i = 0; i < this.list[0].attributeSize(); i++) {
+                    for (let attribute of this.continuousAttributeAverage(i)) {
+                        result.push(attribute);
+                    }
+                }
+                return result;
+            }
+            else {
+                if (this.list[0].getAttribute(index) instanceof DiscreteIndexedAttribute_1.DiscreteIndexedAttribute) {
+                    let maxIndexSize = this.list[0].getAttribute(index).getMaxIndex();
+                    let values = new Array();
+                    for (let i = 0; i < maxIndexSize; i++) {
+                        values.push(0.0);
+                    }
+                    for (let instance of this.list) {
+                        let valueIndex = instance.getAttribute(index).getIndex();
+                        values[valueIndex]++;
+                    }
+                    for (let i = 0; i < values.length; i++) {
+                        values[i] /= this.list.length;
+                    }
+                    return values;
+                }
+                else {
+                    if (this.list[0].getAttribute(index) instanceof ContinuousAttribute_1.ContinuousAttribute) {
+                        let sum = 0.0;
+                        for (let instance of this.list) {
+                            sum += instance.getAttribute(index).getValue();
+                        }
+                        let values = new Array();
+                        values.push(sum / this.list.length);
+                        return values;
+                    }
+                    else {
+                        return undefined;
+                    }
+                }
+            }
+        }
+        /**
+         * Calculates the standard deviation of a single attribute for this instance list (m_i). If the attribute is discrete,
+         * null returned. If the attribute is continuous, the standard deviation  of the values all instances are returned.
+         *
+         * @param index Index of the attribute.
+         * @return The standard deviation of the instances as an attribute.
+         */
+        attributeStandardDeviation(index) {
+            if (this.list[0].getAttribute(index) instanceof ContinuousAttribute_1.ContinuousAttribute) {
+                let sum = 0.0;
+                for (let instance of this.list) {
+                    sum += instance.getAttribute(index).getValue();
+                }
+                let average = sum / this.list.length;
+                sum = 0.0;
+                for (let instance of this.list) {
+                    sum += Math.pow(instance.getAttribute(index).getValue() - average, 2);
+                }
+                return new ContinuousAttribute_1.ContinuousAttribute(Math.sqrt(sum / (this.list.length - 1)));
+            }
+            else {
+                return undefined;
+            }
+        }
+        /**
+         * Calculates the standard deviation of a single continuous attribute for this instance list (m_i).
+         *
+         * @param index Index of the attribute.
+         * @return The standard deviation of the instances as an attribute.
+         */
+        continuousAttributeStandardDeviation(index) {
+            if (index == undefined) {
+                let result = new Array();
+                for (let i = 0; i < this.list[0].attributeSize(); i++) {
+                    for (let attribute of this.continuousAttributeStandardDeviation(i)) {
+                        result.push(attribute);
+                    }
+                }
+                return result;
+            }
+            else {
+                if (this.list[0].getAttribute(index) instanceof DiscreteIndexedAttribute_1.DiscreteIndexedAttribute) {
+                    let maxIndexSize = this.list[0].getAttribute(index).getMaxIndex();
+                    let averages = new Array();
+                    for (let i = 0; i < maxIndexSize; i++) {
+                        averages.push(0.0);
+                    }
+                    for (let instance of this.list) {
+                        let valueIndex = instance.getAttribute(index).getIndex();
+                        averages[valueIndex]++;
+                    }
+                    for (let i = 0; i < averages.length; i++) {
+                        averages[i] /= this.list.length;
+                    }
+                    let values = new Array();
+                    for (let i = 0; i < maxIndexSize; i++) {
+                        values.push(0.0);
+                    }
+                    for (let instance of this.list) {
+                        let valueIndex = instance.getAttribute(index).getIndex();
+                        for (let i = 0; i < maxIndexSize; i++) {
+                            if (i == valueIndex) {
+                                values[i] += Math.pow(1 - averages[i], 2);
+                            }
+                            else {
+                                values[i] += Math.pow(averages[i], 2);
+                            }
+                        }
+                    }
+                    for (let i = 0; i < values.length; i++) {
+                        values[i] = Math.sqrt(values[i] / (this.list.length - 1));
+                    }
+                    return values;
+                }
+                else {
+                    if (this.list[0].getAttribute(index) instanceof ContinuousAttribute_1.ContinuousAttribute) {
+                        let sum = 0.0;
+                        for (let instance of this.list) {
+                            sum += instance.getAttribute(index).getValue();
+                        }
+                        let average = sum / this.list.length;
+                        sum = 0.0;
+                        for (let instance of this.list) {
+                            sum += Math.pow(instance.getAttribute(index).getValue() - average, 2);
+                        }
+                        let result = new Array();
+                        result.push(Math.sqrt(sum / (this.list.length - 1)));
+                        return result;
+                    }
+                    else {
+                        return undefined;
+                    }
+                }
+            }
+        }
+        /**
+         * The attributeDistribution method takes an index as an input and if the attribute of the instance at given index is
+         * discrete, it returns the distribution of the attributes of that instance.
+         *
+         * @param index Index of the attribute.
+         * @return Distribution of the attribute.
+         */
+        attributeDistribution(index) {
+            let distribution = new DiscreteDistribution_1.DiscreteDistribution();
+            if (this.list[0].getAttribute(index) instanceof DiscreteAttribute_1.DiscreteAttribute) {
+                for (let instance of this.list) {
+                    distribution.addItem(instance.getAttribute(index).getValue());
+                }
+            }
+            return distribution;
+        }
+        /**
+         * The attributeClassDistribution method takes an attribute index as an input. It loops through the instances, gets
+         * the corresponding value of given attribute index and adds the class label of that instance to the discrete distributions list.
+         *
+         * @param attributeIndex Index of the attribute.
+         * @return Distribution of the class labels.
+         */
+        attributeClassDistribution(attributeIndex) {
+            let distributions = new Array();
+            let valueList = this.getAttributeValueList(attributeIndex);
+            for (let ignored of valueList) {
+                distributions.push(new DiscreteDistribution_1.DiscreteDistribution());
+            }
+            for (let instance of this.list) {
+                distributions[valueList.indexOf(instance.getAttribute(attributeIndex).getValue())].addItem(instance.getClassLabel());
+            }
+            return distributions;
+        }
+        /**
+         * The discreteIndexedAttributeClassDistribution method takes an attribute index and an attribute value as inputs.
+         * It loops through the instances, gets the corresponding value of given attribute index and given attribute value.
+         * Then, adds the class label of that instance to the discrete indexed distributions list.
+         *
+         * @param attributeIndex Index of the attribute.
+         * @param attributeValue Value of the attribute.
+         * @return Distribution of the class labels.
+         */
+        discreteIndexedAttributeClassDistribution(attributeIndex, attributeValue) {
+            let distribution = new DiscreteDistribution_1.DiscreteDistribution();
+            for (let instance of this.list) {
+                if (instance.getAttribute(attributeIndex).getIndex() == attributeValue) {
+                    distribution.addItem(instance.getClassLabel());
+                }
+            }
+            return distribution;
+        }
+        /**
+         * The classDistribution method returns the distribution of all the class labels of instances.
+         *
+         * @return Distribution of the class labels.
+         */
+        classDistribution() {
+            let distribution = new DiscreteDistribution_1.DiscreteDistribution();
+            for (let instance of this.list) {
+                distribution.addItem(instance.getClassLabel());
+            }
+            return distribution;
+        }
+        /**
+         * The allAttributesDistribution method returns the distributions of all the attributes of instances.
+         *
+         * @return Distributions of all the attributes of instances.
+         */
+        allAttributesDistribution() {
+            let distributions = new Array();
+            for (let i = 0; i < this.list[0].attributeSize(); i++) {
+                distributions.push(this.attributeDistribution(i));
+            }
+            return distributions;
+        }
+        /**
+         * Returns the mean of all the attributes for instances in the list.
+         *
+         * @return Mean of all the attributes for instances in the list.
+         */
+        average() {
+            let result = new Instance_1.Instance(this.list[0].getClassLabel());
+            for (let i = 0; i < this.list[0].attributeSize(); i++) {
+                result.addAttribute(this.attributeAverage(i));
+            }
+            return result;
+        }
+        /**
+         * Returns the standard deviation of attributes for instances.
+         *
+         * @return Standard deviation of attributes for instances.
+         */
+        standardDeviation() {
+            let result = new Instance_1.Instance(this.list[0].getClassLabel());
+            for (let i = 0; i < this.list[0].attributeSize(); i++) {
+                result.addAttribute(this.attributeStandardDeviation(i));
+            }
+            return result;
+        }
+        /**
+         * Calculates a covariance {@link Matrix} by using an average {@link Vector}.
+         *
+         * @param average Vector input.
+         * @return Covariance {@link Matrix}.
+         */
+        covariance(average) {
+            let result = new Matrix_1.Matrix(this.list[0].continuousAttributeSize(), this.list[0].continuousAttributeSize());
+            for (let instance of this.list) {
+                let continuousAttributes = instance.continuousAttributes();
+                for (let i = 0; i < instance.continuousAttributeSize(); i++) {
+                    let xi = continuousAttributes[i];
+                    let mi = average.getValue(i);
+                    for (let j = 0; j < instance.continuousAttributeSize(); j++) {
+                        let xj = continuousAttributes[j];
+                        let mj = average.getValue(j);
+                        result.addValue(i, j, (xi - mi) * (xj - mj));
+                    }
+                }
+            }
+            result.divideByConstant(this.list.length - 1);
+            return result;
+        }
+        /**
+         * Accessor for the instances.
+         *
+         * @return Instances.
+         */
+        getInstances() {
+            return this.list;
+        }
+    }
+    exports.InstanceList = InstanceList;
+});
+//# sourceMappingURL=InstanceList.js.map

package/dist/InstanceList/InstanceList.js.map

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package/dist/InstanceList/InstanceListOfSameClass.d.ts

@@ -0,0 +1,16 @@
+import { InstanceList } from "./InstanceList";
+export declare class InstanceListOfSameClass extends InstanceList {
+    private classLabel;
+    /**
+     * Constructor for creating a new instance list with the same class label.
+     *
+     * @param classLabel Class label of instance list.
+     */
+    constructor(classLabel: string);
+    /**
+     * Accessor for the class label.
+     *
+     * @return Class label.
+     */
+    getClassLabel(): string;
+}

package/dist/InstanceList/InstanceListOfSameClass.js

@@ -0,0 +1,35 @@
+(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", "./InstanceList"], factory);
+    }
+})(function (require, exports) {
+    "use strict";
+    Object.defineProperty(exports, "__esModule", { value: true });
+    exports.InstanceListOfSameClass = void 0;
+    const InstanceList_1 = require("./InstanceList");
+    class InstanceListOfSameClass extends InstanceList_1.InstanceList {
+        /**
+         * Constructor for creating a new instance list with the same class label.
+         *
+         * @param classLabel Class label of instance list.
+         */
+        constructor(classLabel) {
+            super();
+            this.classLabel = classLabel;
+        }
+        /**
+         * Accessor for the class label.
+         *
+         * @return Class label.
+         */
+        getClassLabel() {
+            return this.classLabel;
+        }
+    }
+    exports.InstanceListOfSameClass = InstanceListOfSameClass;
+});
+//# sourceMappingURL=InstanceListOfSameClass.js.map

package/dist/InstanceList/InstanceListOfSameClass.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"InstanceListOfSameClass.js","sourceRoot":"","sources":["../../source/InstanceList/InstanceListOfSameClass.ts"],"names":[],"mappings":";;;;;;;;;;;;IAAA,iDAA4C;IAE5C,MAAa,uBAAwB,SAAQ,2BAAY;QAIrD;;;;WAIG;QACH,YAAY,UAAkB;YAC1B,KAAK,EAAE,CAAC;YACR,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAChC,CAAC;QAED;;;;WAIG;QACH,aAAa;YACT,OAAO,IAAI,CAAC,UAAU,CAAA;QAC1B,CAAC;KACJ;IAtBD,0DAsBC"}

package/dist/InstanceList/Partition.d.ts

@@ -0,0 +1,31 @@
+import { InstanceList } from "./InstanceList";
+import { Instance } from "../Instance/Instance";
+export declare class Partition {
+    private multiList;
+    constructor(instanceList?: InstanceList, attributeIndex?: number, stratifiedOrValue?: any);
+    /**
+     * Adds given instance list to the list of instance lists.
+     *
+     * @param list Instance list to add.
+     */
+    add(list: InstanceList): void;
+    /**
+     * Returns the size of the list of instance lists.
+     *
+     * @return The size of the list of instance lists.
+     */
+    size(): number;
+    /**
+     * Returns the corresponding instance list at given index of list of instance lists.
+     *
+     * @param index Index of the instance list.
+     * @return Instance list at given index of list of instance lists.
+     */
+    get(index: number): InstanceList;
+    /**
+     * Returns the instances of the items at the list of instance lists.
+     *
+     * @return Instances of the items at the list of instance lists.
+     */
+    getLists(): Array<Array<Instance>>;
+}