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cheminfo-botcheminfo-bot
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Release v0.13.6
1 parent ba51985 commit f40ac93

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3 files changed

+82
-63
lines changed

3 files changed

+82
-63
lines changed

‎bower.json‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
{
22
"name": "ml",
3-
"version": "0.13.4",
3+
"version": "0.13.6",
44
"main": [
55
"dist/ml.js",
66
"dist/ml.min.js"

‎dist/ml.js‎

Lines changed: 80 additions & 61 deletions
Original file line numberDiff line numberDiff line change
@@ -5741,6 +5741,9 @@ return /******/ (function(modules) { // webpackBootstrap
57415741
this.r = y.r;
57425742
this.r2 = y.r2;
57435743
}
5744+
if(y.chi2){
5745+
this.chi2 = y.chi2;
5746+
}
57445747
}
57455748
else{
57465749
var n = x.length;
@@ -5769,9 +5772,8 @@ return /******/ (function(modules) { // webpackBootstrap
57695772
this.slope = numerator / (n * xSquared - xSum * xSum);
57705773
this.intercept = (1 / n) * ySum - this.slope * (1 / n) * xSum;
57715774
this.coefficients = [this.intercept, this.slope];
5772-
if(options.computeCoefficient){
5773-
this.r = this.rCoefficient(x,y);
5774-
this.r2 = this.r*this.r;
5775+
if(options.computeQuality){
5776+
this.quality = this.modelQuality(x,y);
57755777
}
57765778
}
57775779

@@ -5783,9 +5785,8 @@ return /******/ (function(modules) { // webpackBootstrap
57835785
slope: this.slope,
57845786
intercept: this.intercept
57855787
}
5786-
if (this.r) {
5787-
out. r=this.r;
5788-
out.r2 = this.r2;
5788+
if(this.quality){
5789+
out.quality = this.quality;
57895790
}
57905791

57915792
return out;
@@ -5882,20 +5883,21 @@ return /******/ (function(modules) { // webpackBootstrap
58825883
}
58835884

58845885
/**
5885-
* Return the correlation coefficient of determination (r).
5886+
* Return the correlation coefficient of determination (r) and chi-square.
58865887
* @param x
58875888
* @param y
58885889
* @returns {number}
58895890
*/
5890-
rCoefficient(x, y) {
5891+
modelQuality(x, y) {
58915892
let n = x.length;
58925893
var y2 = new Array(n);
58935894
for (var i = 0; i < n; i++) {
58945895
y2[i]=this._predict(x[i]);
58955896
}
58965897
var xSum = 0;
58975898
var ySum = 0;
5898-
5899+
var chi2 = 0;
5900+
var rmsd = 0;
58995901
var xSquared = 0;
59005902
var ySquared = 0;
59015903
var xY = 0;
@@ -5906,10 +5908,16 @@ return /******/ (function(modules) { // webpackBootstrap
59065908
xSquared += y2[i] * y2[i];
59075909
ySquared += y[i] * y[i];
59085910
xY += y2[i] * y[i];
5911+
if(y[i]!=0)
5912+
chi2 += (y[i]-y2[i])*(y[i]-y2[i])/y[i];
5913+
rmsd = (y[i]-y2[i])*(y[i]-y2[i]);
59095914
}
59105915

5911-
return (n*xY-xSum*ySum)/Math.sqrt((n*xSquared-xSum*xSum)*(n*ySquared-ySum*ySum));
5916+
var r = (n*xY-xSum*ySum)/Math.sqrt((n*xSquared-xSum*xSum)*(n*ySquared-ySum*ySum));
5917+
5918+
return {r:r, r2:r*r, chi2:chi2, rmsd:rmsd*rmsd/n};
59125919
}
5920+
59135921
}
59145922

59155923
module.exports = BaseRegression;
@@ -5953,9 +5961,8 @@ return /******/ (function(modules) { // webpackBootstrap
59535961
this.coefficients = outputs.coefficients;
59545962
this.powers = outputs.powers;
59555963
this.M = outputs.M;
5956-
if(y.r){
5957-
this.r = y.r;
5958-
this.r2 = y.r2;
5964+
if(y.quality){
5965+
this.quality = y.quality;
59595966
}
59605967
} else {
59615968
var n = x.length;
@@ -5993,9 +6000,8 @@ return /******/ (function(modules) { // webpackBootstrap
59936000
this.coefficients = A.solve(B).to1DArray();
59946001
this.powers = powers;
59956002
this.M = M-1;
5996-
if(opt.computeCoefficient){
5997-
this.r = this.rCoefficient(x,y);
5998-
this.r2 = this.r*this.r;
6003+
if(opt.computeQuality){
6004+
this.quality = this.modelQuality(x,y);
59996005
}
60006006
}
60016007
}
@@ -6015,9 +6021,8 @@ return /******/ (function(modules) { // webpackBootstrap
60156021
M: this.M
60166022
};
60176023

6018-
if(this.r){
6019-
out.r = this.r;
6020-
out.r2=this.r2;
6024+
if(this.quality){
6025+
out.quality = this.quality;
60216026
}
60226027
return out;
60236028
}
@@ -6109,9 +6114,8 @@ return /******/ (function(modules) { // webpackBootstrap
61096114
if (x === true) { // reloading model
61106115
this.A = outputs.A;
61116116
this.M = outputs.M;
6112-
if(y.r){
6113-
this.r = y.r;
6114-
this.r2 = y.r2;
6117+
if(y.quality){
6118+
this.quality = y.quality;
61156119
}
61166120
} else {
61176121
var n = x.length;
@@ -6122,9 +6126,8 @@ return /******/ (function(modules) { // webpackBootstrap
61226126
var linear = new PolynomialRegression(x, y, [M] ,{computeCoefficient:true});
61236127
this.A = linear.coefficients[0];
61246128
this.M = M;
6125-
if(opt.computeCoefficient){
6126-
this.r = this.rCoefficient(x,y);
6127-
this.r2 = this.r*this.r;
6129+
if(opt.computeQuality){
6130+
this.quality = this.modelQuality(x,y);
61286131
}
61296132
}
61306133
}
@@ -6135,9 +6138,8 @@ return /******/ (function(modules) { // webpackBootstrap
61356138

61366139
toJSON() {
61376140
var out = {name: 'potentialRegression', A: this.A, M: this.M};
6138-
if(this.r){
6139-
out.r = this.r;
6140-
out.r2 = this.r2;
6141+
if(this.quality){
6142+
out.quality = this.quality;
61416143
}
61426144
return out;
61436145
}
@@ -6147,7 +6149,11 @@ return /******/ (function(modules) { // webpackBootstrap
61476149
}
61486150

61496151
toLaTeX(precision){
6150-
return "y = "+maybeToPrecision(this.A, precision)+"x^{"+this.M+"}";
6152+
6153+
if (this.M >= 0)
6154+
return "y = "+maybeToPrecision(this.A, precision)+"x^{"+this.M+"}";
6155+
else
6156+
return "y = \\frac{"+maybeToPrecision(this.A, precision)+"}{x^{"+(-this.M)+"}}";
61516157
}
61526158

61536159
static load(json) {
@@ -6194,9 +6200,8 @@ return /******/ (function(modules) { // webpackBootstrap
61946200
if (x === true) { // reloading model
61956201
this.A = outputs.A;
61966202
this.C = outputs.C;
6197-
if(y.r){
6198-
this.r = y.r;
6199-
this.r2 = y.r2;
6203+
if(y.quality){
6204+
this.quality = y.quality;
62006205
}
62016206
} else {
62026207
var n = x.length;
@@ -6211,9 +6216,8 @@ return /******/ (function(modules) { // webpackBootstrap
62116216
var linear = new SimpleLinearRegression(x, yl, {computeCoefficient:false});
62126217
this.A = linear.slope;
62136218
this.C = Math.exp(linear.intercept);
6214-
if(opt.computeCoefficient){
6215-
this.r = this.rCoefficient(x,y);
6216-
this.r2 = this.r*this.r;
6219+
if(opt.computeQuality){
6220+
this.quality = this.modelQuality(x,y);
62176221
}
62186222
}
62196223
}
@@ -6224,9 +6228,8 @@ return /******/ (function(modules) { // webpackBootstrap
62246228

62256229
toJSON() {
62266230
var out = {name: 'expRegression', A: this.A, C: this.C};
6227-
if(this.r){
6228-
out.r = this.r;
6229-
out.r2=this.r2;
6231+
if(this.quality){
6232+
out.quality = this.quality;
62306233
}
62316234
return out;
62326235
}
@@ -6236,7 +6239,11 @@ return /******/ (function(modules) { // webpackBootstrap
62366239
}
62376240

62386241
toLaTeX(precision){
6239-
return "y = "+maybeToPrecision(this.C, precision)+"e^{"+maybeToPrecision(this.A, precision)+"x}";
6242+
if(this.A>=0)
6243+
return "y = "+maybeToPrecision(this.C, precision)+"e^{"+maybeToPrecision(this.A, precision)+"x}";
6244+
else
6245+
return "y = \\frac{"+maybeToPrecision(this.C, precision)+"}{e^{"+maybeToPrecision(-this.A, precision)+"x}}";
6246+
62406247
}
62416248

62426249
static load(json) {
@@ -6283,6 +6290,9 @@ return /******/ (function(modules) { // webpackBootstrap
62836290
this.r = y.r;
62846291
this.r2 = y.r2;
62856292
}
6293+
if(y.chi2){
6294+
this.chi2 = y.chi2;
6295+
}
62866296
} else {
62876297
var n = x.length;
62886298
if (n !== y.length) {
@@ -6297,9 +6307,8 @@ return /******/ (function(modules) { // webpackBootstrap
62976307
var linear = new SimpleLinearRegression(xl, yl, {computeCoefficient:false});
62986308
this.A = Math.exp(linear.intercept);
62996309
this.B = linear.slope;
6300-
if(opt.computeCoefficient){
6301-
this.r = this.rCoefficient(x,y);
6302-
this.r2 = this.r*this.r;
6310+
if(opt.computeQuality){
6311+
this.quality = this.modelQuality(x,y);
63036312
}
63046313
}
63056314
}
@@ -6310,9 +6319,8 @@ return /******/ (function(modules) { // webpackBootstrap
63106319

63116320
toJSON() {
63126321
var out = {name: 'powerRegression', A: this.A, B: this.B};
6313-
if(this.r){
6314-
out.r = this.r;
6315-
out.r2=this.r2;
6322+
if(this.quality){
6323+
out.quality = this.quality;
63166324
}
63176325
return out;
63186326
}
@@ -6321,8 +6329,11 @@ return /******/ (function(modules) { // webpackBootstrap
63216329
return "y = "+maybeToPrecision(this.A, precision)+"*x^"+maybeToPrecision(this.B, precision);
63226330
}
63236331

6324-
toLaTeX(precision){
6325-
return "y = "+maybeToPrecision(this.A, precision)+"x^{"+maybeToPrecision(this.B, precision)+"}";
6332+
toLaTeX(precision) {
6333+
if (this.B >= 0)
6334+
return "y = " + maybeToPrecision(this.A, precision) + "x^{" + maybeToPrecision(this.B, precision) + "}";
6335+
else
6336+
return "y = \\frac{" + maybeToPrecision(this.A, precision) + "}{x^{" + maybeToPrecision(-this.B, precision) + "}}";
63266337
}
63276338

63286339
static load(json) {
@@ -6364,9 +6375,9 @@ return /******/ (function(modules) { // webpackBootstrap
63646375
this.kernelType = outputs.kernelType;
63656376
this.kernelOptions = outputs.kernelOptions;
63666377
this.kernel = new Kernel(outputs.kernelType, outputs.kernelOptions);
6367-
if(outputs.r){
6368-
this.r = outputs.r;
6369-
this.r2 = outputs.r2;
6378+
6379+
if(outputs.quality){
6380+
this.quality = outputs.quality;
63706381
}
63716382
} else {
63726383
options = Object.assign({}, defaultOptions, options);
@@ -6382,9 +6393,8 @@ return /******/ (function(modules) { // webpackBootstrap
63826393
this.kernelOptions = options.kernelOptions;
63836394
this.kernel = kernelFunction;
63846395

6385-
if(options.computeCoefficient){
6386-
this.r = this.rCoefficient(inputs, outputs);
6387-
this.r2 = this.r*this.r;
6396+
if(options.computeQuality){
6397+
this.quality=this.modelQuality(inputs,outputs);
63886398
}
63896399
}
63906400
}
@@ -6394,13 +6404,17 @@ return /******/ (function(modules) { // webpackBootstrap
63946404
}
63956405

63966406
toJSON() {
6397-
return {
6407+
var out = {
63986408
name: 'kernelRidgeRegression',
63996409
alpha: this.alpha,
64006410
inputs: this.inputs,
64016411
kernelType: this.kernelType,
64026412
kernelOptions: this.kernelOptions
64036413
};
6414+
if(this.quality){
6415+
out.quality = this.quality;
6416+
}
6417+
return out;
64046418
}
64056419

64066420
static load(json) {
@@ -6588,6 +6602,9 @@ return /******/ (function(modules) { // webpackBootstrap
65886602
this.r = outputs.r;
65896603
this.r2 = outputs.r2;
65906604
}
6605+
if(outputs.chi2){
6606+
this.chi2 = outputs.chi2;
6607+
}
65916608
} else {
65926609
options = Object.assign({}, defaultOptions, options);
65936610
this.order = options.order;
@@ -6596,9 +6613,9 @@ return /******/ (function(modules) { // webpackBootstrap
65966613
this.y = outputs;
65976614

65986615
this.train(this.X,this.y,options);
6599-
if(options.computeCoefficient){
6600-
this.r = this.rCoefficient(inputs, outputs);
6601-
this.r2 = this.r*this.r;
6616+
6617+
if(options.computeQuality){
6618+
this.quality = this.modelQuality(inputs,outputs);
66026619
}
66036620
}
66046621
}
@@ -6695,9 +6712,7 @@ return /******/ (function(modules) { // webpackBootstrap
66956712

66966713
for(var i = 0; i <= this.order; i++) {
66976714
for(var j = 0; j <= this.order - i; j++) {
6698-
var value = Math.pow(x1, i)*(Math.pow(x2, j));
6699-
value*=this.coefficients[column][0];
6700-
y+=value;
6715+
y+= Math.pow(x1, i)*(Math.pow(x2, j))*this.coefficients[column][0];
67016716
column++;
67026717
}
67036718
}
@@ -6706,11 +6721,15 @@ return /******/ (function(modules) { // webpackBootstrap
67066721
}
67076722

67086723
toJSON() {
6709-
return {
6724+
var out = {
67106725
name: "polyfit2D",
67116726
order: this.order,
67126727
coefficients: this.coefficients
67136728
};
6729+
if(this.quality){
6730+
out.quality = this.quality;
6731+
}
6732+
return out;
67146733
};
67156734

67166735
static load(json) {

‎package.json‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
{
22
"name": "ml",
3-
"version": "0.13.5",
3+
"version": "0.13.6",
44
"description": "Machine learning tools",
55
"main": "src/index.js",
66
"scripts": {

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