@datagrok-libraries/utils 0.0.3 → 0.0.7
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/package.json +8 -4
- package/src/bit-array.js +666 -0
- package/src/bit-array.ts +767 -0
- package/src/operations.js +144 -0
- package/src/operations.ts +160 -0
- package/src/reduce-dimensionality.js +233 -0
- package/src/reduce-dimensionality.ts +278 -0
- package/src/sequence-encoder.js +117 -0
- package/src/sequence-encoder.ts +132 -0
- package/src/spe.js +151 -0
- package/src/spe.ts +172 -0
- package/src/string-measure.js +46 -0
- package/src/string-measure.ts +54 -0
- package/src/string-utils.js +9 -0
- package/src/string-utils.ts +8 -0
- package/src/table-validation.js +47 -0
- package/src/table-validation.ts +67 -0
- package/src/test-utils.js +81 -0
- package/src/test-utils.ts +97 -0
- package/src/type_declarations.js +37 -0
- package/src/type_declarations.ts +54 -0
|
@@ -0,0 +1,144 @@
|
|
|
1
|
+
import { Vector } from './type_declarations';
|
|
2
|
+
/**
|
|
3
|
+
* Asserts a condition by throwing an Error.
|
|
4
|
+
*
|
|
5
|
+
* @export
|
|
6
|
+
* @param {boolean} [condition=false] Condition to assert.
|
|
7
|
+
* @param {string} [message='Assertion error.'] Message to output.
|
|
8
|
+
* @throws {Error}
|
|
9
|
+
*/
|
|
10
|
+
export function assert(condition = false, message = 'Assertion error.') {
|
|
11
|
+
if (!condition) {
|
|
12
|
+
throw new Error(message);
|
|
13
|
+
}
|
|
14
|
+
}
|
|
15
|
+
/**
|
|
16
|
+
* Generates single random integer from 0 to range.
|
|
17
|
+
*
|
|
18
|
+
* @export
|
|
19
|
+
* @param {number} range Max generating value.
|
|
20
|
+
* @return {number} A random integer generated.
|
|
21
|
+
*/
|
|
22
|
+
export function randomInt(range) {
|
|
23
|
+
return Math.floor(Math.random() * range);
|
|
24
|
+
}
|
|
25
|
+
/**
|
|
26
|
+
* Creates new two-dimensional array and fills it with the value given.
|
|
27
|
+
*
|
|
28
|
+
* @param {number} dimension1 The first dimension of the coordinates (number of rows).
|
|
29
|
+
* @param {number} dimension2 The second dimension of the coordinates (number of columns).
|
|
30
|
+
* @param {number} [fill=0] A value to fill the coordinates with.
|
|
31
|
+
* @return {Coordinates} A two-dimensional filled with the value given.
|
|
32
|
+
* @todo Might be slow since used Array.map. Probably needs performance revision.
|
|
33
|
+
*/
|
|
34
|
+
function initCoordinates(dimension1, dimension2, fill = 0) {
|
|
35
|
+
return new Array(dimension1).fill(fill).map(() => (new Vector(dimension2).fill(fill)));
|
|
36
|
+
}
|
|
37
|
+
/**
|
|
38
|
+
* Transpose matrix.
|
|
39
|
+
*
|
|
40
|
+
* @export
|
|
41
|
+
* @param {Matrix} matrix The matrix to be transposed.
|
|
42
|
+
* @return {Matrix} Transposed matrix.
|
|
43
|
+
* @todo Might be slow since used Array.map. Probably needs performance revision.
|
|
44
|
+
*/
|
|
45
|
+
export function transposeMatrix(matrix) {
|
|
46
|
+
return new Array(matrix[0].length).fill(0).map((_, i) => (new Vector(matrix.length).fill(0).map((_, j) => (matrix[j][i]))));
|
|
47
|
+
}
|
|
48
|
+
/**
|
|
49
|
+
* Adds two vectors with the second one to be multiplied by the given ratio.
|
|
50
|
+
*
|
|
51
|
+
* @export
|
|
52
|
+
* @param {Vector} p The first vector to add.
|
|
53
|
+
* @param {Vector} q The second vector to add.
|
|
54
|
+
* @param {number} [multiplier=1] A multiplier to be used before the second vector is added.
|
|
55
|
+
* @return {Vector} New vector contained the result of operation p+multiplier*q.
|
|
56
|
+
*/
|
|
57
|
+
export function vectorAdd(p, q, multiplier = 1) {
|
|
58
|
+
const nItems = p.length;
|
|
59
|
+
assert(nItems == q.length, 'Vector lengths do not match.');
|
|
60
|
+
let total = new Vector(nItems);
|
|
61
|
+
for (let i = 0; i < p.length; ++i) {
|
|
62
|
+
total[i] = p[i] + multiplier * q[i];
|
|
63
|
+
}
|
|
64
|
+
return total;
|
|
65
|
+
}
|
|
66
|
+
/**
|
|
67
|
+
* Sums the vector's items.
|
|
68
|
+
*
|
|
69
|
+
* @param {Vector} v The vector to be summed.
|
|
70
|
+
* @return {number} The vector's items sum.
|
|
71
|
+
*/
|
|
72
|
+
function itemsSum(v) {
|
|
73
|
+
let total = 0;
|
|
74
|
+
for (let i = 0; i < v.length; ++i) {
|
|
75
|
+
total += v[i];
|
|
76
|
+
}
|
|
77
|
+
return total;
|
|
78
|
+
}
|
|
79
|
+
/**
|
|
80
|
+
* Suqares the vector's items.
|
|
81
|
+
*
|
|
82
|
+
* @param {Vector} v The vector to square.
|
|
83
|
+
* @return {Vector} A new vector containing the original's items squared.
|
|
84
|
+
*/
|
|
85
|
+
function vectorSquare(v) {
|
|
86
|
+
const nItems = v.length;
|
|
87
|
+
let total = new Vector(nItems);
|
|
88
|
+
for (let i = 0; i < v.length; ++i) {
|
|
89
|
+
total[i] = v[i] * v[i];
|
|
90
|
+
}
|
|
91
|
+
return total;
|
|
92
|
+
}
|
|
93
|
+
/**
|
|
94
|
+
* Creates a matrix filled with random floating point values.
|
|
95
|
+
*
|
|
96
|
+
* @export
|
|
97
|
+
* @param {number} dimension1 The first dimension of the matrix.
|
|
98
|
+
* @param {number} dimension2 The second dimension of the matrix.
|
|
99
|
+
* @param {number} [scale=1.] Max value given by random generator.
|
|
100
|
+
* @return {Matrix} A new matrix filled with random floating point values.
|
|
101
|
+
*/
|
|
102
|
+
export function fillRandomMatrix(dimension1, dimension2, scale = 1.) {
|
|
103
|
+
let matrix = initCoordinates(dimension1, dimension2);
|
|
104
|
+
for (let i = 0; i < dimension1; ++i) {
|
|
105
|
+
for (let j = 0; j < dimension2; ++j) {
|
|
106
|
+
matrix[i][j] = Math.random() * scale;
|
|
107
|
+
}
|
|
108
|
+
}
|
|
109
|
+
return matrix;
|
|
110
|
+
}
|
|
111
|
+
/**
|
|
112
|
+
* Calculates Euclidean distance between two vectors.
|
|
113
|
+
*
|
|
114
|
+
* @export
|
|
115
|
+
* @param {Vector} p The first vector.
|
|
116
|
+
* @param {Vector} q The second vector.
|
|
117
|
+
* @return {number} Euclidean distance between the given vectors.
|
|
118
|
+
*/
|
|
119
|
+
export function calculateEuclideanDistance(p, q) {
|
|
120
|
+
const diff = vectorAdd(p, q, -1);
|
|
121
|
+
const sqdiff = vectorSquare(diff);
|
|
122
|
+
const sqdiffSumm = itemsSum(sqdiff);
|
|
123
|
+
return Math.sqrt(sqdiffSumm);
|
|
124
|
+
}
|
|
125
|
+
/**
|
|
126
|
+
* Creates a distance matrix using a custom distance function.
|
|
127
|
+
*
|
|
128
|
+
* @export
|
|
129
|
+
* @param {Vectors} data Input vectors to calculate distances.
|
|
130
|
+
* @param {DistanceMetric} distance Custom distance function.
|
|
131
|
+
* @return {Matrix} Calculated custom distance matrix.
|
|
132
|
+
*/
|
|
133
|
+
export function calcDistanceMatrix(data, distance) {
|
|
134
|
+
const nItems = data.length;
|
|
135
|
+
let matrix = initCoordinates(nItems, nItems, 0);
|
|
136
|
+
for (let i = 0; i < nItems; ++i) {
|
|
137
|
+
for (let j = i + 1; j < nItems; ++j) {
|
|
138
|
+
const d = (data[i] == null) || (data[j] == null) ? 0 : distance(data[i], data[j]);
|
|
139
|
+
matrix[i][j] = matrix[j][i] = d;
|
|
140
|
+
}
|
|
141
|
+
}
|
|
142
|
+
return matrix;
|
|
143
|
+
}
|
|
144
|
+
//# sourceMappingURL=data:application/json;base64,{"version":3,"file":"operations.js","sourceRoot":"","sources":["operations.ts"],"names":[],"mappings":"AAAA,OAAO,EAAS,MAAM,EAAuC,MAAM,qBAAqB,CAAC;AAEzF;;;;;;;GAOG;AACH,MAAM,UAAU,MAAM,CAAC,YAAqB,KAAK,EAAE,UAAkB,kBAAkB;IACrF,IAAI,CAAC,SAAS,EAAE;QACd,MAAM,IAAI,KAAK,CAAC,OAAO,CAAC,CAAC;KAC1B;AACH,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,SAAS,CAAC,KAAa;IACrC,OAAO,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,GAAG,KAAK,CAAC,CAAC;AAC3C,CAAC;AAED;;;;;;;;GAQG;AACH,SAAS,eAAe,CAAC,UAAkB,EAAE,UAAkB,EAAE,OAAe,CAAC;IAC/E,OAAO,IAAI,KAAK,CAAC,UAAU,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,CAAC,IAAI,MAAM,CAAC,UAAU,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;AACzF,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,eAAe,CAAC,MAAc;IAC5C,OAAO,IAAI,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,IAAI,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;AAC9H,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,SAAS,CAAC,CAAS,EAAE,CAAS,EAAE,aAAqB,CAAC;IACpE,MAAM,MAAM,GAAG,CAAC,CAAC,MAAM,CAAC;IAExB,MAAM,CAAC,MAAM,IAAI,CAAC,CAAC,MAAM,EAAE,8BAA8B,CAAC,CAAA;IAE1D,IAAI,KAAK,GAAG,IAAI,MAAM,CAAC,MAAM,CAAC,CAAC;IAE/B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;QACjC,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAC,UAAU,GAAC,CAAC,CAAC,CAAC,CAAC,CAAC;KACjC;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED;;;;;GAKG;AACH,SAAS,QAAQ,CAAC,CAAS;IACzB,IAAI,KAAK,GAAG,CAAC,CAAC;IAEd,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;QACjC,KAAK,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;KACf;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED;;;;;GAKG;AACH,SAAS,YAAY,CAAC,CAAS;IAC7B,MAAM,MAAM,GAAG,CAAC,CAAC,MAAM,CAAC;IACxB,IAAI,KAAK,GAAG,IAAI,MAAM,CAAC,MAAM,CAAC,CAAC;IAE/B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;QACjC,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAC,CAAC,CAAC,CAAC,CAAC,CAAC;KACtB;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,gBAAgB,CAAC,UAAkB,EAAE,UAAkB,EAAE,QAAgB,EAAE;IACzF,IAAI,MAAM,GAAG,eAAe,CAAC,UAAU,EAAE,UAAU,CAAC,CAAC;IAErD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,EAAE,CAAC,EAAE;QACnC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,EAAE,CAAC,EAAE;YACnC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,GAAG,KAAK,CAAC;SACtC;KACF;IACD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,0BAA0B,CAAC,CAAS,EAAE,CAAS;IAC7D,MAAM,IAAI,GAAG,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;IACjC,MAAM,MAAM,GAAG,YAAY,CAAC,IAAI,CAAC,CAAC;IAClC,MAAM,UAAU,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC;IACpC,OAAO,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;AAC/B,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,kBAAkB,CAAC,IAAa,EAAE,QAAwB;IACxE,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC;IAC3B,IAAI,MAAM,GAAG,eAAe,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC,CAAC,CAAC;IAEhD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,EAAE,CAAC,EAAE;QAC/B,KAAK,IAAI,CAAC,GAAG,CAAC,GAAC,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,EAAE,CAAC,EAAE;YACjC,MAAM,CAAC,GAAW,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;YAC1F,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;SACjC;KACF;IACD,OAAO,MAAM,CAAC;AAChB,CAAC","sourcesContent":["import {Matrix, Vector, Coordinates, Vectors, DistanceMetric} from './type_declarations';\r\n\r\n/**\r\n * Asserts a condition by throwing an Error.\r\n *\r\n * @export\r\n * @param {boolean} [condition=false] Condition to assert.\r\n * @param {string} [message='Assertion error.'] Message to output.\r\n * @throws {Error}\r\n */\r\nexport function assert(condition: boolean = false, message: string = 'Assertion error.') {\r\n  if (!condition) {\r\n    throw new Error(message);\r\n  }\r\n}\r\n\r\n/**\r\n * Generates single random integer from 0 to range.\r\n *\r\n * @export\r\n * @param {number} range Max generating value.\r\n * @return {number} A random integer generated.\r\n */\r\nexport function randomInt(range: number): number {\r\n  return Math.floor(Math.random() * range);\r\n}\r\n\r\n/**\r\n * Creates new two-dimensional array and fills it with the value given.\r\n *\r\n * @param {number} dimension1 The first dimension of the coordinates (number of rows).\r\n * @param {number} dimension2 The second dimension of the coordinates (number of columns).\r\n * @param {number} [fill=0] A value to fill the coordinates with.\r\n * @return {Coordinates} A two-dimensional filled with the value given.\r\n * @todo Might be slow since used Array.map. Probably needs performance revision.\r\n */\r\nfunction initCoordinates(dimension1: number, dimension2: number, fill: number = 0): Coordinates {\r\n  return new Array(dimension1).fill(fill).map(() => (new Vector(dimension2).fill(fill)));\r\n}\r\n\r\n/**\r\n * Transpose matrix.\r\n *\r\n * @export\r\n * @param {Matrix} matrix The matrix to be transposed.\r\n * @return {Matrix} Transposed matrix.\r\n * @todo Might be slow since used Array.map. Probably needs performance revision.\r\n */\r\nexport function transposeMatrix(matrix: Matrix): Matrix {\r\n  return new Array(matrix[0].length).fill(0).map((_, i) => (new Vector(matrix.length).fill(0).map((_, j) => (matrix[j][i]))));\r\n}\r\n\r\n/**\r\n * Adds two vectors with the second one to be multiplied by the given ratio.\r\n *\r\n * @export\r\n * @param {Vector} p The first vector to add.\r\n * @param {Vector} q The second vector to add.\r\n * @param {number} [multiplier=1] A multiplier to be used before the second vector is added.\r\n * @return {Vector} New vector contained the result of operation p+multiplier*q.\r\n */\r\nexport function vectorAdd(p: Vector, q: Vector, multiplier: number = 1): Vector {\r\n  const nItems = p.length;\r\n\r\n  assert(nItems == q.length, 'Vector lengths do not match.')\r\n\r\n  let total = new Vector(nItems);\r\n\r\n  for (let i = 0; i < p.length; ++i) {\r\n    total[i] = p[i]+multiplier*q[i];\r\n  }\r\n  return total;\r\n}\r\n\r\n/**\r\n * Sums the vector's items.\r\n *\r\n * @param {Vector} v The vector to be summed.\r\n * @return {number} The vector's items sum.\r\n */\r\nfunction itemsSum(v: Vector): number {\r\n  let total = 0;\r\n\r\n  for (let i = 0; i < v.length; ++i) {\r\n    total += v[i];\r\n  }\r\n  return total;\r\n}\r\n\r\n/**\r\n * Suqares the vector's items.\r\n *\r\n * @param {Vector} v The vector to square.\r\n * @return {Vector} A new vector containing the original's items squared.\r\n */\r\nfunction vectorSquare(v: Vector): Vector {\r\n  const nItems = v.length;\r\n  let total = new Vector(nItems);\r\n\r\n  for (let i = 0; i < v.length; ++i) {\r\n    total[i] = v[i]*v[i];\r\n  }\r\n  return total;\r\n}\r\n\r\n/**\r\n * Creates a matrix filled with random floating point values.\r\n *\r\n * @export\r\n * @param {number} dimension1 The first dimension of the matrix.\r\n * @param {number} dimension2 The second dimension of the matrix.\r\n * @param {number} [scale=1.] Max value given by random generator.\r\n * @return {Matrix} A new matrix filled with random floating point  values.\r\n */\r\nexport function fillRandomMatrix(dimension1: number, dimension2: number, scale: number = 1.): Matrix {\r\n  let matrix = initCoordinates(dimension1, dimension2);\r\n\r\n  for (let i = 0; i < dimension1; ++i) {\r\n    for (let j = 0; j < dimension2; ++j) {\r\n      matrix[i][j] = Math.random() * scale;\r\n    }\r\n  }\r\n  return matrix;\r\n}\r\n\r\n/**\r\n * Calculates Euclidean distance between two vectors.\r\n *\r\n * @export\r\n * @param {Vector} p The first vector.\r\n * @param {Vector} q The second vector.\r\n * @return {number} Euclidean distance between the given vectors.\r\n */\r\nexport function calculateEuclideanDistance(p: Vector, q: Vector): number {\r\n  const diff = vectorAdd(p, q, -1);\r\n  const sqdiff = vectorSquare(diff);\r\n  const sqdiffSumm = itemsSum(sqdiff);\r\n  return Math.sqrt(sqdiffSumm);\r\n}\r\n\r\n/**\r\n * Creates a distance matrix using a custom distance function.\r\n *\r\n * @export\r\n * @param {Vectors} data Input vectors to calculate distances.\r\n * @param {DistanceMetric} distance Custom distance function.\r\n * @return {Matrix} Calculated custom distance matrix.\r\n */\r\nexport function calcDistanceMatrix(data: Vectors, distance: DistanceMetric): Matrix {\r\n  const nItems = data.length;\r\n  let matrix = initCoordinates(nItems, nItems, 0);\r\n\r\n  for (let i = 0; i < nItems; ++i) {\r\n    for (let j = i+1; j < nItems; ++j) {\r\n      const d: number = (data[i] == null) || (data[j] == null) ? 0 : distance(data[i], data[j]);\r\n      matrix[i][j] = matrix[j][i] = d;\r\n    }\r\n  }\r\n  return matrix;\r\n}\r\n"]}
|
|
@@ -0,0 +1,160 @@
|
|
|
1
|
+
import {Matrix, Vector, Coordinates, Vectors, DistanceMetric} from './type_declarations';
|
|
2
|
+
|
|
3
|
+
/**
|
|
4
|
+
* Asserts a condition by throwing an Error.
|
|
5
|
+
*
|
|
6
|
+
* @export
|
|
7
|
+
* @param {boolean} [condition=false] Condition to assert.
|
|
8
|
+
* @param {string} [message='Assertion error.'] Message to output.
|
|
9
|
+
* @throws {Error}
|
|
10
|
+
*/
|
|
11
|
+
export function assert(condition: boolean = false, message: string = 'Assertion error.') {
|
|
12
|
+
if (!condition) {
|
|
13
|
+
throw new Error(message);
|
|
14
|
+
}
|
|
15
|
+
}
|
|
16
|
+
|
|
17
|
+
/**
|
|
18
|
+
* Generates single random integer from 0 to range.
|
|
19
|
+
*
|
|
20
|
+
* @export
|
|
21
|
+
* @param {number} range Max generating value.
|
|
22
|
+
* @return {number} A random integer generated.
|
|
23
|
+
*/
|
|
24
|
+
export function randomInt(range: number): number {
|
|
25
|
+
return Math.floor(Math.random() * range);
|
|
26
|
+
}
|
|
27
|
+
|
|
28
|
+
/**
|
|
29
|
+
* Creates new two-dimensional array and fills it with the value given.
|
|
30
|
+
*
|
|
31
|
+
* @param {number} dimension1 The first dimension of the coordinates (number of rows).
|
|
32
|
+
* @param {number} dimension2 The second dimension of the coordinates (number of columns).
|
|
33
|
+
* @param {number} [fill=0] A value to fill the coordinates with.
|
|
34
|
+
* @return {Coordinates} A two-dimensional filled with the value given.
|
|
35
|
+
* @todo Might be slow since used Array.map. Probably needs performance revision.
|
|
36
|
+
*/
|
|
37
|
+
function initCoordinates(dimension1: number, dimension2: number, fill: number = 0): Coordinates {
|
|
38
|
+
return new Array(dimension1).fill(fill).map(() => (new Vector(dimension2).fill(fill)));
|
|
39
|
+
}
|
|
40
|
+
|
|
41
|
+
/**
|
|
42
|
+
* Transpose matrix.
|
|
43
|
+
*
|
|
44
|
+
* @export
|
|
45
|
+
* @param {Matrix} matrix The matrix to be transposed.
|
|
46
|
+
* @return {Matrix} Transposed matrix.
|
|
47
|
+
* @todo Might be slow since used Array.map. Probably needs performance revision.
|
|
48
|
+
*/
|
|
49
|
+
export function transposeMatrix(matrix: Matrix): Matrix {
|
|
50
|
+
return new Array(matrix[0].length).fill(0).map((_, i) => (new Vector(matrix.length).fill(0).map((_, j) => (matrix[j][i]))));
|
|
51
|
+
}
|
|
52
|
+
|
|
53
|
+
/**
|
|
54
|
+
* Adds two vectors with the second one to be multiplied by the given ratio.
|
|
55
|
+
*
|
|
56
|
+
* @export
|
|
57
|
+
* @param {Vector} p The first vector to add.
|
|
58
|
+
* @param {Vector} q The second vector to add.
|
|
59
|
+
* @param {number} [multiplier=1] A multiplier to be used before the second vector is added.
|
|
60
|
+
* @return {Vector} New vector contained the result of operation p+multiplier*q.
|
|
61
|
+
*/
|
|
62
|
+
export function vectorAdd(p: Vector, q: Vector, multiplier: number = 1): Vector {
|
|
63
|
+
const nItems = p.length;
|
|
64
|
+
|
|
65
|
+
assert(nItems == q.length, 'Vector lengths do not match.')
|
|
66
|
+
|
|
67
|
+
let total = new Vector(nItems);
|
|
68
|
+
|
|
69
|
+
for (let i = 0; i < p.length; ++i) {
|
|
70
|
+
total[i] = p[i]+multiplier*q[i];
|
|
71
|
+
}
|
|
72
|
+
return total;
|
|
73
|
+
}
|
|
74
|
+
|
|
75
|
+
/**
|
|
76
|
+
* Sums the vector's items.
|
|
77
|
+
*
|
|
78
|
+
* @param {Vector} v The vector to be summed.
|
|
79
|
+
* @return {number} The vector's items sum.
|
|
80
|
+
*/
|
|
81
|
+
function itemsSum(v: Vector): number {
|
|
82
|
+
let total = 0;
|
|
83
|
+
|
|
84
|
+
for (let i = 0; i < v.length; ++i) {
|
|
85
|
+
total += v[i];
|
|
86
|
+
}
|
|
87
|
+
return total;
|
|
88
|
+
}
|
|
89
|
+
|
|
90
|
+
/**
|
|
91
|
+
* Suqares the vector's items.
|
|
92
|
+
*
|
|
93
|
+
* @param {Vector} v The vector to square.
|
|
94
|
+
* @return {Vector} A new vector containing the original's items squared.
|
|
95
|
+
*/
|
|
96
|
+
function vectorSquare(v: Vector): Vector {
|
|
97
|
+
const nItems = v.length;
|
|
98
|
+
let total = new Vector(nItems);
|
|
99
|
+
|
|
100
|
+
for (let i = 0; i < v.length; ++i) {
|
|
101
|
+
total[i] = v[i]*v[i];
|
|
102
|
+
}
|
|
103
|
+
return total;
|
|
104
|
+
}
|
|
105
|
+
|
|
106
|
+
/**
|
|
107
|
+
* Creates a matrix filled with random floating point values.
|
|
108
|
+
*
|
|
109
|
+
* @export
|
|
110
|
+
* @param {number} dimension1 The first dimension of the matrix.
|
|
111
|
+
* @param {number} dimension2 The second dimension of the matrix.
|
|
112
|
+
* @param {number} [scale=1.] Max value given by random generator.
|
|
113
|
+
* @return {Matrix} A new matrix filled with random floating point values.
|
|
114
|
+
*/
|
|
115
|
+
export function fillRandomMatrix(dimension1: number, dimension2: number, scale: number = 1.): Matrix {
|
|
116
|
+
let matrix = initCoordinates(dimension1, dimension2);
|
|
117
|
+
|
|
118
|
+
for (let i = 0; i < dimension1; ++i) {
|
|
119
|
+
for (let j = 0; j < dimension2; ++j) {
|
|
120
|
+
matrix[i][j] = Math.random() * scale;
|
|
121
|
+
}
|
|
122
|
+
}
|
|
123
|
+
return matrix;
|
|
124
|
+
}
|
|
125
|
+
|
|
126
|
+
/**
|
|
127
|
+
* Calculates Euclidean distance between two vectors.
|
|
128
|
+
*
|
|
129
|
+
* @export
|
|
130
|
+
* @param {Vector} p The first vector.
|
|
131
|
+
* @param {Vector} q The second vector.
|
|
132
|
+
* @return {number} Euclidean distance between the given vectors.
|
|
133
|
+
*/
|
|
134
|
+
export function calculateEuclideanDistance(p: Vector, q: Vector): number {
|
|
135
|
+
const diff = vectorAdd(p, q, -1);
|
|
136
|
+
const sqdiff = vectorSquare(diff);
|
|
137
|
+
const sqdiffSumm = itemsSum(sqdiff);
|
|
138
|
+
return Math.sqrt(sqdiffSumm);
|
|
139
|
+
}
|
|
140
|
+
|
|
141
|
+
/**
|
|
142
|
+
* Creates a distance matrix using a custom distance function.
|
|
143
|
+
*
|
|
144
|
+
* @export
|
|
145
|
+
* @param {Vectors} data Input vectors to calculate distances.
|
|
146
|
+
* @param {DistanceMetric} distance Custom distance function.
|
|
147
|
+
* @return {Matrix} Calculated custom distance matrix.
|
|
148
|
+
*/
|
|
149
|
+
export function calcDistanceMatrix(data: Vectors, distance: DistanceMetric): Matrix {
|
|
150
|
+
const nItems = data.length;
|
|
151
|
+
let matrix = initCoordinates(nItems, nItems, 0);
|
|
152
|
+
|
|
153
|
+
for (let i = 0; i < nItems; ++i) {
|
|
154
|
+
for (let j = i+1; j < nItems; ++j) {
|
|
155
|
+
const d: number = (data[i] == null) || (data[j] == null) ? 0 : distance(data[i], data[j]);
|
|
156
|
+
matrix[i][j] = matrix[j][i] = d;
|
|
157
|
+
}
|
|
158
|
+
}
|
|
159
|
+
return matrix;
|
|
160
|
+
}
|
|
@@ -0,0 +1,233 @@
|
|
|
1
|
+
import * as umj from 'umap-js';
|
|
2
|
+
import { TSNE } from '@keckelt/tsne';
|
|
3
|
+
import { Vector } from './type_declarations';
|
|
4
|
+
import { calcDistanceMatrix, transposeMatrix } from './operations';
|
|
5
|
+
import { SPEBase, PSPEBase } from './spe';
|
|
6
|
+
import { Measurer } from './string-measure';
|
|
7
|
+
import { AlignedSequenceEncoder } from './sequence-encoder';
|
|
8
|
+
import { assert } from './operations';
|
|
9
|
+
/**
|
|
10
|
+
* Abstract dimensionality reducer.
|
|
11
|
+
*
|
|
12
|
+
* @abstract
|
|
13
|
+
* @class Reducer
|
|
14
|
+
*/
|
|
15
|
+
class Reducer {
|
|
16
|
+
/**
|
|
17
|
+
* Creates an instance of Reducer.
|
|
18
|
+
* @param {Options} options Options to pass to the constructor.
|
|
19
|
+
* @memberof Reducer
|
|
20
|
+
*/
|
|
21
|
+
constructor(options) {
|
|
22
|
+
this.data = options.data;
|
|
23
|
+
}
|
|
24
|
+
}
|
|
25
|
+
/**
|
|
26
|
+
* Implements t-SNE dimensionality reduction.
|
|
27
|
+
*
|
|
28
|
+
* @class TSNEReducer
|
|
29
|
+
* @extends {Reducer}
|
|
30
|
+
*/
|
|
31
|
+
class TSNEReducer extends Reducer {
|
|
32
|
+
/**
|
|
33
|
+
* Creates an instance of TSNEReducer.
|
|
34
|
+
* @param {Options} options Options to pass to the constructor.
|
|
35
|
+
* @memberof TSNEReducer
|
|
36
|
+
*/
|
|
37
|
+
constructor(options) {
|
|
38
|
+
var _a;
|
|
39
|
+
super(options);
|
|
40
|
+
this.reducer = new TSNE(options);
|
|
41
|
+
this.iterations = (_a = options === null || options === void 0 ? void 0 : options.iterations) !== null && _a !== void 0 ? _a : 100;
|
|
42
|
+
this.distance = options.distance;
|
|
43
|
+
}
|
|
44
|
+
/**
|
|
45
|
+
* Embeds the data given into the two-dimensional space using t-SNE method.
|
|
46
|
+
* @return {Coordinates} Cartesian coordinate of this embedding.
|
|
47
|
+
*/
|
|
48
|
+
transform() {
|
|
49
|
+
this.reducer.initDataDist(calcDistanceMatrix(this.data, this.distance));
|
|
50
|
+
for (let i = 0; i < this.iterations; ++i) {
|
|
51
|
+
this.reducer.step(); // every time you call this, solution gets better
|
|
52
|
+
}
|
|
53
|
+
return this.reducer.getSolution();
|
|
54
|
+
}
|
|
55
|
+
}
|
|
56
|
+
/**
|
|
57
|
+
* Implements UMAP dimensionality reduction.
|
|
58
|
+
*
|
|
59
|
+
* @class UMAPReducer
|
|
60
|
+
* @extends {Reducer}
|
|
61
|
+
*/
|
|
62
|
+
class UMAPReducer extends Reducer {
|
|
63
|
+
/**
|
|
64
|
+
* Creates an instance of UMAPReducer.
|
|
65
|
+
* @param {Options} options Options to pass to the constructor.
|
|
66
|
+
* @memberof UMAPReducer
|
|
67
|
+
*/
|
|
68
|
+
constructor(options) {
|
|
69
|
+
super(options);
|
|
70
|
+
assert('distanceFn' in options);
|
|
71
|
+
this.encoder = new AlignedSequenceEncoder();
|
|
72
|
+
this.distanceFn = options.distanceFn;
|
|
73
|
+
this.vectors = [];
|
|
74
|
+
options.distanceFn = this._encodedDistance.bind(this);
|
|
75
|
+
this.reducer = new umj.UMAP(options);
|
|
76
|
+
}
|
|
77
|
+
/**
|
|
78
|
+
* Custom distance wrapper to have numeric inputs instead of string ones.
|
|
79
|
+
*
|
|
80
|
+
* @protected
|
|
81
|
+
* @param {number[]} a The first item.
|
|
82
|
+
* @param {number[]} b The first item.
|
|
83
|
+
* @return {number} Distance metric.
|
|
84
|
+
* @memberof UMAPReducer
|
|
85
|
+
*/
|
|
86
|
+
_encodedDistance(a, b) {
|
|
87
|
+
return this.distanceFn(this.data[a[0]], this.data[b[0]]);
|
|
88
|
+
}
|
|
89
|
+
/**
|
|
90
|
+
* Encodes the input data as a vector of indices.
|
|
91
|
+
*
|
|
92
|
+
* @protected
|
|
93
|
+
* @memberof UMAPReducer
|
|
94
|
+
*/
|
|
95
|
+
_encode() {
|
|
96
|
+
for (let i = 0; i < this.data.length; ++i) {
|
|
97
|
+
this.vectors.push([i]);
|
|
98
|
+
}
|
|
99
|
+
}
|
|
100
|
+
/**
|
|
101
|
+
* Embeds the data given into the two-dimensional space using UMAP method.
|
|
102
|
+
* @return {Coordinates} Cartesian coordinate of this embedding.
|
|
103
|
+
*/
|
|
104
|
+
transform() {
|
|
105
|
+
this._encode();
|
|
106
|
+
const embedding = this.reducer.fit(this.vectors);
|
|
107
|
+
function arrayCast2Coordinates(data) {
|
|
108
|
+
return new Array(data.length).fill(0).map((_, i) => (Vector.from(data[i])));
|
|
109
|
+
}
|
|
110
|
+
return arrayCast2Coordinates(embedding);
|
|
111
|
+
}
|
|
112
|
+
}
|
|
113
|
+
/**
|
|
114
|
+
* Implements original SPE dimensionality reduction.
|
|
115
|
+
*
|
|
116
|
+
* @class SPEReducer
|
|
117
|
+
* @extends {Reducer}
|
|
118
|
+
*/
|
|
119
|
+
class SPEReducer extends Reducer {
|
|
120
|
+
/**
|
|
121
|
+
* Creates an instance of SPEReducer.
|
|
122
|
+
* @param {Options} options Options to pass to the constructor.
|
|
123
|
+
* @memberof SPEReducer
|
|
124
|
+
*/
|
|
125
|
+
constructor(options) {
|
|
126
|
+
super(options);
|
|
127
|
+
this.reducer = new SPEBase(options);
|
|
128
|
+
}
|
|
129
|
+
/**
|
|
130
|
+
* Embeds the data given into the two-dimensional space using the original SPE method.
|
|
131
|
+
* @return {Coordinates} Cartesian coordinate of this embedding.
|
|
132
|
+
*/
|
|
133
|
+
transform() {
|
|
134
|
+
return this.reducer.embed(this.data);
|
|
135
|
+
}
|
|
136
|
+
}
|
|
137
|
+
/**
|
|
138
|
+
* Implements modified SPE dimensionality reduction.
|
|
139
|
+
*
|
|
140
|
+
* @class PSPEReducer
|
|
141
|
+
* @extends {Reducer}
|
|
142
|
+
*/
|
|
143
|
+
class PSPEReducer extends Reducer {
|
|
144
|
+
/**
|
|
145
|
+
* Creates an instance of PSPEReducer.
|
|
146
|
+
* @param {Options} options Options to pass to the constructor.
|
|
147
|
+
* @memberof PSPEReducer
|
|
148
|
+
*/
|
|
149
|
+
constructor(options) {
|
|
150
|
+
super(options);
|
|
151
|
+
this.reducer = new PSPEBase(options);
|
|
152
|
+
}
|
|
153
|
+
/**
|
|
154
|
+
* Embeds the data given into the two-dimensional space using the modified SPE method.
|
|
155
|
+
* @return {Coordinates} Cartesian coordinate of this embedding.
|
|
156
|
+
*/
|
|
157
|
+
transform() {
|
|
158
|
+
return this.reducer.embed(this.data);
|
|
159
|
+
}
|
|
160
|
+
}
|
|
161
|
+
/**
|
|
162
|
+
* Unified class implementing different dimensionality reduction methods.
|
|
163
|
+
*
|
|
164
|
+
* @export
|
|
165
|
+
* @class DimensionalityReducer
|
|
166
|
+
*/
|
|
167
|
+
export class DimensionalityReducer {
|
|
168
|
+
/**
|
|
169
|
+
* Creates an instance of DimensionalityReducer.
|
|
170
|
+
* @param {any[]} data Vectors to embed.
|
|
171
|
+
* @param {string} method Embedding method to be applied
|
|
172
|
+
* @param {string} metric Distance metric to be computed between each of the vectors.
|
|
173
|
+
* @param {Options} [options] Options to pass to the implementing embedders.
|
|
174
|
+
* @memberof DimensionalityReducer
|
|
175
|
+
*/
|
|
176
|
+
constructor(data, method, metric, options) {
|
|
177
|
+
var _a;
|
|
178
|
+
assert(DimensionalityReducer.availableMethods.includes(method), `The method '${method}' is not supported`);
|
|
179
|
+
this.measurer = new Measurer(metric);
|
|
180
|
+
const measure = this.measurer.getMeasure();
|
|
181
|
+
if (method == 'UMAP') {
|
|
182
|
+
this.reducer = new UMAPReducer({
|
|
183
|
+
...{ data: data },
|
|
184
|
+
...{ distanceFn: measure },
|
|
185
|
+
...{ nEpochs: options === null || options === void 0 ? void 0 : options.cycles },
|
|
186
|
+
...options
|
|
187
|
+
});
|
|
188
|
+
}
|
|
189
|
+
else if (method == 't-SNE') {
|
|
190
|
+
this.reducer = new TSNEReducer({
|
|
191
|
+
...{ data: data },
|
|
192
|
+
...{ distance: measure },
|
|
193
|
+
...{ iterations: (_a = options === null || options === void 0 ? void 0 : options.cycles) !== null && _a !== void 0 ? _a : undefined },
|
|
194
|
+
...options,
|
|
195
|
+
});
|
|
196
|
+
}
|
|
197
|
+
else if (method == 'SPE') {
|
|
198
|
+
this.reducer = new SPEReducer({ ...{ data: data }, ...{ distance: measure }, ...options });
|
|
199
|
+
}
|
|
200
|
+
else {
|
|
201
|
+
this.reducer = new PSPEReducer({ ...{ data: data }, ...{ distance: measure }, ...options });
|
|
202
|
+
}
|
|
203
|
+
}
|
|
204
|
+
/**
|
|
205
|
+
* Embeds the data given into the two-dimensional space using the chosen method.
|
|
206
|
+
*
|
|
207
|
+
* @param {boolean} transpose Whether to transform coordinates to have columns-first orientation.
|
|
208
|
+
* @throws {Error} If the embedding method was not found.
|
|
209
|
+
* @return {Coordinates} Cartesian coordinate of this embedding.
|
|
210
|
+
* @memberof DimensionalityReducer
|
|
211
|
+
*/
|
|
212
|
+
transform(transpose = false) {
|
|
213
|
+
if (this.reducer == undefined) {
|
|
214
|
+
throw new Error('Reducer was not defined.');
|
|
215
|
+
}
|
|
216
|
+
let embedding = this.reducer.transform();
|
|
217
|
+
if (transpose) {
|
|
218
|
+
embedding = transposeMatrix(embedding);
|
|
219
|
+
}
|
|
220
|
+
return embedding;
|
|
221
|
+
}
|
|
222
|
+
/**
|
|
223
|
+
* Returns dimensionality reduction methods available.
|
|
224
|
+
*
|
|
225
|
+
* @readonly
|
|
226
|
+
* @memberof DimensionalityReducer
|
|
227
|
+
*/
|
|
228
|
+
static get availableMethods() {
|
|
229
|
+
return DimensionalityReducer.methods;
|
|
230
|
+
}
|
|
231
|
+
}
|
|
232
|
+
DimensionalityReducer.methods = ['UMAP', 't-SNE', 'SPE', 'pSPE'];
|
|
233
|
+
//# sourceMappingURL=data:application/json;base64,{"version":3,"file":"reduce-dimensionality.js","sourceRoot":"","sources":["reduce-dimensionality.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,GAAG,MAAM,SAAS,CAAC;AAC/B,OAAO,EAAC,IAAI,EAAC,MAAM,eAAe,CAAC;AAEnC,OAAO,EAAuC,MAAM,EAAkB,MAAM,qBAAqB,CAAC;AAClG,OAAO,EAAC,kBAAkB,EAAE,eAAe,EAAC,MAAM,cAAc,CAAC;AACjE,OAAO,EAAC,OAAO,EAAE,QAAQ,EAAC,MAAM,OAAO,CAAC;AACxC,OAAO,EAAC,QAAQ,EAAC,MAAM,kBAAkB,CAAC;AAC1C,OAAO,EAAC,sBAAsB,EAAC,MAAM,oBAAoB,CAAC;AAC1D,OAAO,EAAC,MAAM,EAAC,MAAM,cAAc,CAAC;AAEpC;;;;;GAKG;AACH,MAAe,OAAO;IAGpB;;;;OAIG;IACH,YAAY,OAAgB;QAC1B,IAAI,CAAC,IAAI,GAAG,OAAO,CAAC,IAAI,CAAC;IAC3B,CAAC;CAUF;AAED;;;;;GAKG;AACH,MAAM,WAAY,SAAQ,OAAO;IAK/B;;;;OAIG;IACH,YAAY,OAAgB;;QAC1B,KAAK,CAAC,OAAO,CAAC,CAAC;QACf,IAAI,CAAC,OAAO,GAAG,IAAI,IAAI,CAAC,OAAO,CAAC,CAAC;QACjC,IAAI,CAAC,UAAU,GAAG,MAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,UAAU,mCAAI,GAAG,CAAC;QAC7C,IAAI,CAAC,QAAQ,GAAG,OAAO,CAAC,QAAQ,CAAC;IACnC,CAAC;IAED;;;OAGG;IACI,SAAS;QACd,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,kBAAkB,CAAC,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC;QAExE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,UAAU,EAAE,EAAE,CAAC,EAAE;YACxC,IAAI,CAAC,OAAO,CAAC,IAAI,EAAE,CAAC,CAAC,iDAAiD;SACvE;QACD,OAAO,IAAI,CAAC,OAAO,CAAC,WAAW,EAAE,CAAC;IACpC,CAAC;CACF;AAED;;;;;GAKG;AACH,MAAM,WAAY,SAAQ,OAAO;IAM/B;;;;OAIG;IACH,YAAY,OAAgB;QAC1B,KAAK,CAAC,OAAO,CAAC,CAAC;QAEf,MAAM,CAAC,YAAY,IAAI,OAAO,CAAC,CAAC;QAEhC,IAAI,CAAC,OAAO,GAAG,IAAI,sBAAsB,EAAE,CAAC;QAC5C,IAAI,CAAC,UAAU,GAAG,OAAO,CAAC,UAAU,CAAC;QACrC,IAAI,CAAC,OAAO,GAAG,EAAE,CAAC;QAClB,OAAO,CAAC,UAAU,GAAG,IAAI,CAAC,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QACtD,IAAI,CAAC,OAAO,GAAG,IAAI,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IACvC,CAAC;IAED;;;;;;;;OAQG;IACO,gBAAgB,CAAC,CAAW,EAAE,CAAW;QACjD,OAAO,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAC3D,CAAC;IAED;;;;;OAKG;IACO,OAAO;QACf,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;YACzC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;SACxB;IACH,CAAC;IAED;;;OAGG;IACI,SAAS;QACd,IAAI,CAAC,OAAO,EAAE,CAAC;QAEf,MAAM,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;QAEjD,SAAS,qBAAqB,CAAC,IAAgB;YAC7C,OAAO,IAAI,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QAC9E,CAAC;QAED,OAAO,qBAAqB,CAAC,SAAS,CAAC,CAAC;IAC1C,CAAC;CACF;AAED;;;;;GAKG;AACH,MAAM,UAAW,SAAQ,OAAO;IAG9B;;;;OAIG;IACH,YAAY,OAAgB;QAC1B,KAAK,CAAC,OAAO,CAAC,CAAC;QACf,IAAI,CAAC,OAAO,GAAG,IAAI,OAAO,CAAC,OAAO,CAAC,CAAC;IACtC,CAAC;IAED;;;OAGG;IACI,SAAS;QACd,OAAO,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IACvC,CAAC;CACF;AAED;;;;;GAKG;AACH,MAAM,WAAY,SAAQ,OAAO;IAG/B;;;;OAIG;IACH,YAAY,OAAgB;QAC1B,KAAK,CAAC,OAAO,CAAC,CAAC;QACf,IAAI,CAAC,OAAO,GAAG,IAAI,QAAQ,CAAC,OAAO,CAAC,CAAC;IACvC,CAAC;IAED;;;OAGG;IACI,SAAS;QACd,OAAO,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IACvC,CAAC;CACF;AAED;;;;;GAKG;AACH,MAAM,OAAO,qBAAqB;IAKhC;;;;;;;OAOG;IACH,YAAY,IAAW,EAAE,MAAc,EAAE,MAAc,EAAE,OAAiB;;QACxE,MAAM,CAAC,qBAAqB,CAAC,gBAAgB,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE,eAAe,MAAM,oBAAoB,CAAC,CAAC;QAE3G,IAAI,CAAC,QAAQ,GAAG,IAAI,QAAQ,CAAC,MAAM,CAAC,CAAC;QACrC,MAAM,OAAO,GAAG,IAAI,CAAC,QAAQ,CAAC,UAAU,EAAE,CAAA;QAE1C,IAAI,MAAM,IAAI,MAAM,EAAE;YACpB,IAAI,CAAC,OAAO,GAAG,IAAI,WAAW,CAAC;gBAC7B,GAAG,EAAC,IAAI,EAAE,IAAI,EAAC;gBACf,GAAG,EAAC,UAAU,EAAE,OAAO,EAAC;gBACxB,GAAG,EAAC,OAAO,EAAE,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,MAAM,EAAC;gBAC7B,GAAG,OAAO;aACX,CAAC,CAAC;SACJ;aAAM,IAAI,MAAM,IAAI,OAAO,EAAE;YAC5B,IAAI,CAAC,OAAO,GAAG,IAAI,WAAW,CAAC;gBAC7B,GAAG,EAAC,IAAI,EAAE,IAAI,EAAC;gBACf,GAAG,EAAC,QAAQ,EAAE,OAAO,EAAC;gBACtB,GAAG,EAAC,UAAU,EAAE,MAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,MAAM,mCAAI,SAAS,EAAC;gBAC7C,GAAG,OAAO;aACX,CAAC,CAAC;SACJ;aAAM,IAAI,MAAM,IAAI,KAAK,EAAE;YAC1B,IAAI,CAAC,OAAO,GAAG,IAAI,UAAU,CAAC,EAAC,GAAG,EAAC,IAAI,EAAE,IAAI,EAAC,EAAE,GAAG,EAAC,QAAQ,EAAE,OAAO,EAAC,EAAE,GAAG,OAAO,EAAC,CAAC,CAAC;SACtF;aAAM;YACL,IAAI,CAAC,OAAO,GAAG,IAAI,WAAW,CAAC,EAAC,GAAG,EAAC,IAAI,EAAE,IAAI,EAAC,EAAE,GAAG,EAAC,QAAQ,EAAE,OAAO,EAAC,EAAE,GAAG,OAAO,EAAC,CAAC,CAAC;SACvF;IACH,CAAC;IAED;;;;;;;OAOG;IACI,SAAS,CAAC,YAAqB,KAAK;QACzC,IAAI,IAAI,CAAC,OAAO,IAAI,SAAS,EAAE;YAC7B,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAC;SAC7C;QACD,IAAI,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,EAAE,CAAC;QAEzC,IAAI,SAAS,EAAE;YACb,SAAS,GAAG,eAAe,CAAC,SAAS,CAAC,CAAC;SACxC;QACD,OAAO,SAAS,CAAC;IACnB,CAAC;IAED;;;;;OAKG;IACH,MAAM,KAAK,gBAAgB;QACzB,OAAO,qBAAqB,CAAC,OAAO,CAAC;IACvC,CAAC;;AAlEa,6BAAO,GAAa,CAAC,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC","sourcesContent":["import * as umj from 'umap-js';\r\nimport {TSNE} from '@keckelt/tsne';\r\n\r\nimport {Options, DistanceMetric, Coordinates, Vector, Vectors, Matrix} from './type_declarations';\r\nimport {calcDistanceMatrix, transposeMatrix} from './operations';\r\nimport {SPEBase, PSPEBase} from './spe';\r\nimport {Measurer} from './string-measure';\r\nimport {AlignedSequenceEncoder} from './sequence-encoder';\r\nimport {assert} from './operations';\r\n\r\n/**\r\n * Abstract dimensionality reducer.\r\n *\r\n * @abstract\r\n * @class Reducer\r\n */\r\nabstract class Reducer {\r\n  protected data: Vectors;\r\n\r\n  /**\r\n   * Creates an instance of Reducer.\r\n   * @param {Options} options Options to pass to the constructor.\r\n   * @memberof Reducer\r\n   */\r\n  constructor(options: Options) {\r\n    this.data = options.data;\r\n  }\r\n\r\n  /**\r\n   * Is to embed the data given into the two-dimensional space.\r\n   *\r\n   * @abstract\r\n   * @return {Coordinates} Cartesian coordinate of this embedding.\r\n   * @memberof Reducer\r\n   */\r\n  abstract transform(): Coordinates;\r\n}\r\n\r\n/**\r\n * Implements t-SNE dimensionality reduction.\r\n *\r\n * @class TSNEReducer\r\n * @extends {Reducer}\r\n */\r\nclass TSNEReducer extends Reducer {\r\n  protected reducer: TSNE;\r\n  protected iterations: number;\r\n  protected distance: DistanceMetric;\r\n\r\n  /**\r\n   * Creates an instance of TSNEReducer.\r\n   * @param {Options} options Options to pass to the constructor.\r\n   * @memberof TSNEReducer\r\n   */\r\n  constructor(options: Options) {\r\n    super(options);\r\n    this.reducer = new TSNE(options);\r\n    this.iterations = options?.iterations ?? 100;\r\n    this.distance = options.distance;\r\n  }\r\n\r\n  /**\r\n   * Embeds the data given into the two-dimensional space using t-SNE method.\r\n   * @return {Coordinates} Cartesian coordinate of this embedding.\r\n   */\r\n  public transform(): Coordinates {\r\n    this.reducer.initDataDist(calcDistanceMatrix(this.data, this.distance));\r\n\r\n    for (let i = 0; i < this.iterations; ++i) {\r\n      this.reducer.step(); // every time you call this, solution gets better\r\n    }\r\n    return this.reducer.getSolution();\r\n  }\r\n}\r\n\r\n/**\r\n * Implements UMAP dimensionality reduction.\r\n *\r\n * @class UMAPReducer\r\n * @extends {Reducer}\r\n */\r\nclass UMAPReducer extends Reducer {\r\n  protected reducer: umj.UMAP;\r\n  protected encoder: AlignedSequenceEncoder;\r\n  protected distanceFn: Function;\r\n  protected vectors: number[][];\r\n\r\n  /**\r\n   * Creates an instance of UMAPReducer.\r\n   * @param {Options} options Options to pass to the constructor.\r\n   * @memberof UMAPReducer\r\n   */\r\n  constructor(options: Options) {\r\n    super(options);\r\n\r\n    assert('distanceFn' in options);\r\n\r\n    this.encoder = new AlignedSequenceEncoder();\r\n    this.distanceFn = options.distanceFn;\r\n    this.vectors = [];\r\n    options.distanceFn = this._encodedDistance.bind(this);\r\n    this.reducer = new umj.UMAP(options);\r\n  }\r\n\r\n  /**\r\n   * Custom distance wrapper to have numeric inputs instead of string ones.\r\n   *\r\n   * @protected\r\n   * @param {number[]} a The first item.\r\n   * @param {number[]} b The first item.\r\n   * @return {number} Distance metric.\r\n   * @memberof UMAPReducer\r\n   */\r\n  protected _encodedDistance(a: number[], b: number[]): number {\r\n    return this.distanceFn(this.data[a[0]], this.data[b[0]]);\r\n  }\r\n\r\n  /**\r\n   * Encodes the input data as a vector of indices.\r\n   *\r\n   * @protected\r\n   * @memberof UMAPReducer\r\n   */\r\n  protected _encode() {\r\n    for (let i = 0; i < this.data.length; ++i) {\r\n      this.vectors.push([i]);\r\n    }\r\n  }\r\n\r\n  /**\r\n   * Embeds the data given into the two-dimensional space using UMAP method.\r\n   * @return {Coordinates} Cartesian coordinate of this embedding.\r\n   */\r\n  public transform(): Coordinates {\r\n    this._encode();\r\n\r\n    const embedding = this.reducer.fit(this.vectors);\r\n\r\n    function arrayCast2Coordinates(data: number[][]): Coordinates {\r\n      return new Array(data.length).fill(0).map((_, i) => (Vector.from(data[i])));\r\n    }\r\n\r\n    return arrayCast2Coordinates(embedding);\r\n  }\r\n}\r\n\r\n/**\r\n * Implements original SPE dimensionality reduction.\r\n *\r\n * @class SPEReducer\r\n * @extends {Reducer}\r\n */\r\nclass SPEReducer extends Reducer {\r\n  protected reducer: SPEBase;\r\n\r\n  /**\r\n   * Creates an instance of SPEReducer.\r\n   * @param {Options} options Options to pass to the constructor.\r\n   * @memberof SPEReducer\r\n   */\r\n  constructor(options: Options) {\r\n    super(options);\r\n    this.reducer = new SPEBase(options);\r\n  }\r\n\r\n  /**\r\n   * Embeds the data given into the two-dimensional space using the original SPE method.\r\n   * @return {Coordinates} Cartesian coordinate of this embedding.\r\n   */\r\n  public transform(): Coordinates {\r\n    return this.reducer.embed(this.data);\r\n  }\r\n}\r\n\r\n/**\r\n * Implements modified SPE dimensionality reduction.\r\n *\r\n * @class PSPEReducer\r\n * @extends {Reducer}\r\n */\r\nclass PSPEReducer extends Reducer {\r\n  protected reducer: PSPEBase;\r\n\r\n  /**\r\n   * Creates an instance of PSPEReducer.\r\n   * @param {Options} options Options to pass to the constructor.\r\n   * @memberof PSPEReducer\r\n   */\r\n  constructor(options: Options) {\r\n    super(options);\r\n    this.reducer = new PSPEBase(options);\r\n  }\r\n\r\n  /**\r\n   * Embeds the data given into the two-dimensional space using the modified SPE method.\r\n   * @return {Coordinates} Cartesian coordinate of this embedding.\r\n   */\r\n  public transform(): Coordinates {\r\n    return this.reducer.embed(this.data);\r\n  }\r\n}\r\n\r\n/**\r\n * Unified class implementing different dimensionality reduction methods.\r\n *\r\n * @export\r\n * @class DimensionalityReducer\r\n */\r\nexport class DimensionalityReducer {\r\n  private reducer: Reducer | undefined;\r\n  public static methods: string[] = ['UMAP', 't-SNE', 'SPE', 'pSPE'];\r\n  private measurer: Measurer;\r\n\r\n  /**\r\n   * Creates an instance of DimensionalityReducer.\r\n   * @param {any[]} data Vectors to embed.\r\n   * @param {string} method Embedding method to be applied\r\n   * @param {string} metric Distance metric to be computed between each of the vectors.\r\n   * @param {Options} [options] Options to pass to the implementing embedders.\r\n   * @memberof DimensionalityReducer\r\n   */\r\n  constructor(data: any[], method: string, metric: string, options?: Options) {\r\n    assert(DimensionalityReducer.availableMethods.includes(method), `The method '${method}' is not supported`);\r\n\r\n    this.measurer = new Measurer(metric);\r\n    const measure = this.measurer.getMeasure()\r\n\r\n    if (method == 'UMAP') {\r\n      this.reducer = new UMAPReducer({\r\n        ...{data: data}, \r\n        ...{distanceFn: measure}, \r\n        ...{nEpochs: options?.cycles},\r\n        ...options\r\n      });\r\n    } else if (method == 't-SNE') {\r\n      this.reducer = new TSNEReducer({\r\n        ...{data: data},\r\n        ...{distance: measure},\r\n        ...{iterations: options?.cycles ?? undefined},\r\n        ...options,\r\n      });\r\n    } else if (method == 'SPE') {\r\n      this.reducer = new SPEReducer({...{data: data}, ...{distance: measure}, ...options});\r\n    } else {\r\n      this.reducer = new PSPEReducer({...{data: data}, ...{distance: measure}, ...options});\r\n    }\r\n  }\r\n\r\n  /**\r\n   * Embeds the data given into the two-dimensional space using the chosen method.\r\n   *\r\n   * @param {boolean} transpose Whether to transform coordinates to have columns-first orientation.\r\n   * @throws {Error} If the embedding method was not found.\r\n   * @return {Coordinates} Cartesian coordinate of this embedding.\r\n   * @memberof DimensionalityReducer\r\n   */\r\n  public transform(transpose: boolean = false): Coordinates {\r\n    if (this.reducer == undefined) {\r\n      throw new Error('Reducer was not defined.');\r\n    }\r\n    let embedding = this.reducer.transform();\r\n\r\n    if (transpose) {\r\n      embedding = transposeMatrix(embedding);\r\n    }\r\n    return embedding;\r\n  }\r\n\r\n  /**\r\n   * Returns dimensionality reduction methods available.\r\n   *\r\n   * @readonly\r\n   * @memberof DimensionalityReducer\r\n   */\r\n  static get availableMethods() {\r\n    return DimensionalityReducer.methods;\r\n  }\r\n}\r\n"]}
|