feat(lib): Allow per-column standardisation (#202)

BREAKING CHANGE: standardise does not allow boolean values anymore,
meand and variance are no longer returned

README.md

@@ -53,33 +53,23 @@ Advanced usage:
 ```js
 import loadCsv from 'tensorflow-load-csv';
 
-const {
-  features,
-  labels,
-  testFeatures,
-  testLabels,
-  mean, // tensor holding mean of features, ignores testFeatures
-  variance, // tensor holding variance of features, ignores testFeatures
-} = loadCsv('./data.csv', {
+const { features, labels, testFeatures, testLabels } = loadCsv('./data.csv', {
   featureColumns: ['lat', 'lng', 'height'],
   labelColumns: ['temperature'],
   mappings: {
     height: (ft) => ft * 0.3048, // feet to meters
     temperature: (f) => (f < 50 ? [1, 0] : [0, 1]), // cold or hot classification
   }, // Map values based on which column they are in before they are loaded into tensors.
   flatten: ['temperature'], // Flattens the array result of a mapping so that each member is a new column.
-  shuffle: true, // Pass true to shuffle with a fixed seed, or a string to use it as a seed for the shuffling.
-  splitTest: true, // Splits your data in half. You can also provide a certain row count for the test data, or a percentage string (e.g. 10%).
-  prependOnes: true, // Prepends a column of 1s to your features and testFeatures tensors, useful for linear regression.
-  standardise: true, // Calculates mean and variance for each feature column using data only in features, then standardises the values in features and testFeatures. Does not touch labels.
+  shuffle: true, // Pass true to shuffle with a fixed seed, or a string to use as a seed for the shuffling.
+  splitTest: true, // Splits your data in half. You can also provide a certain row count for the test data, or a percentage string (e.g. '10%').
+  standardise: ['height'], // Calculates mean and variance for each feature column using data only in features, then standardises the values in features and testFeatures. Does not touch labels.
+  prependOnes: true, // Prepends a column of 1s to your features and testFeatures tensors, useful for regression problems.
 });
 
 features.print();
 labels.print();
 
 testFeatures.print();
 testLabels.print();
-
-mean.print();
-variance.print();
 ```

jest.config.js

@@ -12,10 +12,10 @@ module.exports = {
   coveragePathIgnorePatterns: ['/node_modules/', '/tests/'],
   coverageThreshold: {
     global: {
-      branches: 90,
-      functions: 95,
-      lines: 95,
-      statements: 95,
+      branches: 100,
+      functions: 100,
+      lines: 100,
+      statements: 100,
     },
   },
   collectCoverageFrom: ['src/*.{js,ts}'],

src/loadCsv.models.ts

@@ -35,9 +35,9 @@ export interface CsvReadOptions {
    */
   prependOnes?: boolean;
   /**
-   * If true, calculates mean and variance for each feature column using data only in features, then standardises the values in features and testFeatures. Does not touch labels.
+   * Calculates mean and variance for given columns using data only in features, then standardises the values in features and testFeatures. Does not touch labels.
    */
-  standardise?: boolean | string[];
+  standardise?: string[];
   /**
    * Useful for classification problems, if you have mapped a column's values to an array using `mappings`, you can choose to flatten it here so that each element becomes a new column.
    *

src/loadCsv.ts

@@ -7,6 +7,7 @@ import filterColumns from './filterColumns';
 import splitTestData from './splitTestData';
 import applyMappings from './applyMappings';
 import shuffle from './shuffle';
+import standardise from './standardise';
 
 const defaultShuffleSeed = 'mncv9340ur';
 
@@ -31,10 +32,10 @@ const loadCsv = (
     featureColumns,
     labelColumns,
     mappings = {},
-    shuffle: shouldShuffle = false,
+    shuffle: shouldShuffleOrSeed = false,
     splitTest,
     prependOnes = false,
-    standardise = false,
+    standardise: columnsToStandardise = [],
     flatten = [],
   }: CsvReadOptions
 ) => {
@@ -54,11 +55,13 @@ const loadCsv = (
   };
 
   tables.labels.shift();
-  tables.features.shift();
+  const featureColumnNames = tables.features.shift() as string[];
 
-  if (shouldShuffle) {
+  if (shouldShuffleOrSeed) {
     const seed =
-      typeof shouldShuffle === 'string' ? shouldShuffle : defaultShuffleSeed;
+      typeof shouldShuffleOrSeed === 'string'
+        ? shouldShuffleOrSeed
+        : defaultShuffleSeed;
     tables.features = shuffle(tables.features, seed);
     tables.labels = shuffle(tables.labels, seed);
   }
@@ -76,11 +79,14 @@ const loadCsv = (
   const labels = tf.tensor(tables.labels);
   const testLabels = tf.tensor(tables.testLabels);
 
-  const { mean, variance } = tf.moments(features, 0);
-
-  if (standardise) {
-    features = features.sub(mean).div(variance.pow(0.5));
-    testFeatures = testFeatures.sub(mean).div(variance.pow(0.5));
+  if (columnsToStandardise.length > 0) {
+    const result = standardise(
+      features,
+      testFeatures,
+      featureColumnNames.map((c) => columnsToStandardise.includes(c))
+    );
+    features = result.features;
+    testFeatures = result.testFeatures;
   }
 
   if (prependOnes) {
@@ -93,8 +99,6 @@ const loadCsv = (
     labels,
     testFeatures,
     testLabels,
-    mean,
-    variance,
   };
 };
 

src/standardise.ts

@@ -0,0 +1,68 @@
+import * as tf from '@tensorflow/tfjs';
+
+const standardise = (
+  features: tf.Tensor<tf.Rank>,
+  testFeatures: tf.Tensor<tf.Rank>,
+  indicesToStandardise: boolean[]
+): {
+  features: tf.Tensor<tf.Rank>;
+  testFeatures: tf.Tensor<tf.Rank>;
+} => {
+  let newFeatures, newTestFeatures;
+
+  if (features.shape.length < 2 || testFeatures.shape.length < 2) {
+    throw new Error(
+      'features and testFeatures must have at least two dimensions'
+    );
+  }
+
+  if (features.shape[1] !== testFeatures.shape[1]) {
+    throw new Error(
+      'Length of the second dimension of features and testFeatures must be the same'
+    );
+  }
+
+  if (features.shape[1] !== indicesToStandardise.length) {
+    throw new Error(
+      'Length of indicesToStandardise must match the length of the second dimension of features'
+    );
+  }
+
+  if (features.shape[1] === 0) {
+    return { features, testFeatures };
+  }
+
+  for (let i = 0; i < features.shape[1]; i++) {
+    let featureSlice = features.slice([0, i], [features.shape[0], 1]);
+    let testFeatureSlice = testFeatures.slice(
+      [0, i],
+      [testFeatures.shape[0], 1]
+    );
+    if (indicesToStandardise[i]) {
+      const sliceMoments = tf.moments(featureSlice);
+      featureSlice = featureSlice
+        .sub(sliceMoments.mean)
+        .div(sliceMoments.variance.pow(0.5));
+      testFeatureSlice = testFeatureSlice
+        .sub(sliceMoments.mean)
+        .div(sliceMoments.variance.pow(0.5));
+    }
+    if (!newFeatures) {
+      newFeatures = featureSlice;
+    } else {
+      newFeatures = newFeatures.concat(featureSlice, 1);
+    }
+    if (!newTestFeatures) {
+      newTestFeatures = testFeatureSlice;
+    } else {
+      newTestFeatures = newTestFeatures.concat(testFeatureSlice, 1);
+    }
+  }
+
+  return {
+    features: newFeatures as tf.Tensor<tf.Rank>,
+    testFeatures: newTestFeatures as tf.Tensor<tf.Rank>,
+  };
+};
+
+export default standardise;

tests/loadCsv.test.ts

@@ -46,95 +46,54 @@ test('Loading with only the required options should work', () => {
   ]);
 });
 
-test('Shuffling should work and preserve feature - label pairs', () => {
-  const { features, labels } = loadCsv(filePath, {
+test('Loading with all extra options should work', () => {
+  const { features, labels, testFeatures, testLabels } = loadCsv(filePath, {
     featureColumns: ['lat', 'lng'],
     labelColumns: ['country'],
+    mappings: {
+      country: (name) => (name as string).toUpperCase(),
+      lat: (lat) => ((lat as number) > 0 ? [0, 1] : [1, 0]), // South or North classification
+    },
+    flatten: ['lat'],
     shuffle: true,
+    splitTest: true,
+    prependOnes: true,
+    standardise: ['lng'],
   });
   // @ts-ignore
   expect(features.arraySync()).toBeDeepCloseTo(
     [
-      [5, 40.34],
-      [0.234, 1.47],
-      [-93.2, 103.34],
-      [102, -164],
+      [1, 0, 1, 1],
+      [1, 0, 1, -1],
     ],
     3
   );
-  expect(labels.arraySync()).toMatchObject([
-    ['Landistan'],
-    ['SomeCountria'],
-    ['SomeOtherCountria'],
-    ['Landotzka'],
-  ]);
-});
-
-test('Shuffling with a custom seed should work', () => {
-  const { features, labels } = loadCsv(filePath, {
-    featureColumns: ['lat', 'lng'],
-    labelColumns: ['country'],
-    shuffle: 'hello-is-it-me-you-are-looking-for',
-  });
+  expect(labels.arraySync()).toMatchObject([['LANDISTAN'], ['SOMECOUNTRIA']]);
   // @ts-ignore
-  expect(features.arraySync()).toBeDeepCloseTo(
+  expect(testFeatures.arraySync()).toBeDeepCloseTo(
     [
-      [-93.2, 103.34],
-      [102, -164],
-      [5, 40.34],
-      [0.234, 1.47],
+      [1, 1, 0, 4.241],
+      [1, 0, 1, -9.514],
     ],
     3
   );
-  expect(labels.arraySync()).toMatchObject([
-    ['SomeOtherCountria'],
-    ['Landotzka'],
-    ['Landistan'],
-    ['SomeCountria'],
+  expect(testLabels.arraySync()).toMatchObject([
+    ['SOMEOTHERCOUNTRIA'],
+    ['LANDOTZKA'],
   ]);
 });
 
-test('Loading with all extra options other than shuffle as true should work', () => {
-  const {
-    features,
-    labels,
-    testFeatures,
-    testLabels,
-    mean,
-    variance,
-  } = loadCsv(filePath, {
+test('Loading with custom seed should use the custom seed', () => {
+  const { features } = loadCsv(filePath, {
     featureColumns: ['lat', 'lng'],
     labelColumns: ['country'],
-    mappings: {
-      country: (name) => (name as string).toUpperCase(),
-    },
-    splitTest: true,
-    prependOnes: true,
-    standardise: true,
+    shuffle: true,
+  });
+  const { features: featuresCustom } = loadCsv(filePath, {
+    featureColumns: ['lat', 'lng'],
+    labelColumns: ['country'],
+    shuffle: 'sdhjhdf',
   });
   // @ts-ignore
-  expect(features.arraySync()).toBeDeepCloseTo(
-    [
-      [1, 1, -1],
-      [1, -1, 1],
-    ],
-    3
-  );
-  expect(labels.arraySync()).toMatchObject([
-    ['SOMECOUNTRIA'],
-    ['SOMEOTHERCOUNTRIA'],
-  ]);
-  // @ts-ignore
-  expect(testFeatures.arraySync()).toBeDeepCloseTo(
-    [
-      [1, 1.102, -0.236],
-      [1, 3.178, -4.248],
-    ],
-    3
-  );
-  expect(testLabels.arraySync()).toMatchObject([['LANDISTAN'], ['LANDOTZKA']]);
-  // @ts-ignore
-  expect(mean.arraySync()).toBeDeepCloseTo([-46.482, 52.404], 3);
-  // @ts-ignore
-  expect(variance.arraySync()).toBeDeepCloseTo([2182.478, 2594.374], 3);
+  expect(features).not.toBeDeepCloseTo(featuresCustom, 1);
 });