initial
This commit is contained in:
Lucas Tadeu Marculino
commit
fb20596fba
36 changed files with 8679 additions and 0 deletions
559
www/src/search.js
Normal file
559
www/src/search.js
Normal file
|
|
@ -0,0 +1,559 @@
|
|||
import { PSO } from "./PSO.js";
|
||||
import { RK4, RK4getvalue } from "./runge-kutta.js";
|
||||
import { Objective } from "./Objective.js";
|
||||
import {
|
||||
monod,
|
||||
moser,
|
||||
contois,
|
||||
bergter,
|
||||
tessier,
|
||||
andrews,
|
||||
aiba,
|
||||
pirt,
|
||||
} from "./conhecidos.js";
|
||||
import "https://cdn.plot.ly/plotly-2.29.1.min.js";
|
||||
|
||||
const parameterCatalog = {
|
||||
K_S: {
|
||||
latex: "K_S",
|
||||
unitText: "g/L",
|
||||
unitLatex: "\\mathrm{g\\,L^{-1}}",
|
||||
overrides: {
|
||||
contois: {
|
||||
unitText: "g_S/g_X",
|
||||
unitLatex: "\\frac{\\mathrm{g}_{S}}{\\mathrm{g}_{X}}",
|
||||
},
|
||||
},
|
||||
},
|
||||
mu_max: {
|
||||
latex: "\\mu_{max}",
|
||||
unitText: "h⁻¹",
|
||||
unitLatex: "\\mathrm{h^{-1}}",
|
||||
},
|
||||
K_I: {
|
||||
latex: "K_I",
|
||||
unitText: "g/L",
|
||||
unitLatex: "\\mathrm{g\\,L^{-1}}",
|
||||
overrides: {
|
||||
aiba: {
|
||||
unitText: "L/g",
|
||||
unitLatex: "\\mathrm{L\\,g^{-1}}",
|
||||
},
|
||||
},
|
||||
},
|
||||
m_S: {
|
||||
latex: "m_S",
|
||||
unitText: "g_S/(g_X·h)",
|
||||
unitLatex: "\\frac{\\mathrm{g}_{S}}{\\mathrm{g}_{X}\\,\\mathrm{h}}",
|
||||
},
|
||||
Y_XS: {
|
||||
latex: "Y_{XS}",
|
||||
unitText: "g_X/g_S",
|
||||
unitLatex: "\\frac{\\mathrm{g}_{X}}{\\mathrm{g}_{S}}",
|
||||
},
|
||||
T: {
|
||||
latex: "T",
|
||||
unitText: "h",
|
||||
unitLatex: "\\mathrm{h}",
|
||||
},
|
||||
n: {
|
||||
latex: "n",
|
||||
unitText: null,
|
||||
unitLatex: null,
|
||||
},
|
||||
};
|
||||
|
||||
const modelParameters = {
|
||||
aiba: [
|
||||
{ key: "K_S", bounds: [0.005, 2] },
|
||||
{ key: "mu_max", bounds: [0.05, 0.9] },
|
||||
{ key: "K_I", bounds: [0.01, 1] },
|
||||
{ key: "m_S", bounds: [0.0015, 0.05] },
|
||||
{ key: "Y_XS", bounds: [0.3, 0.7] },
|
||||
],
|
||||
andrews: [
|
||||
{ key: "K_S", bounds: [0.005, 2] },
|
||||
{ key: "mu_max", bounds: [0.05, 0.9] },
|
||||
{ key: "K_I", bounds: [5, 150] },
|
||||
{ key: "m_S", bounds: [0.0015, 0.05] },
|
||||
{ key: "Y_XS", bounds: [0.3, 0.7] },
|
||||
],
|
||||
bergter: [
|
||||
{ key: "K_S", bounds: [0.005, 2] },
|
||||
{ key: "mu_max", bounds: [0.05, 0.9] },
|
||||
{ key: "T", bounds: [5, 80] },
|
||||
{ key: "m_S", bounds: [0.0015, 0.05] },
|
||||
{ key: "Y_XS", bounds: [0.3, 0.7] },
|
||||
],
|
||||
contois: [
|
||||
{ key: "K_S", bounds: [0.005, 2] },
|
||||
{ key: "mu_max", bounds: [0.05, 0.9] },
|
||||
{ key: "m_S", bounds: [0.0015, 0.05] },
|
||||
{ key: "Y_XS", bounds: [0.3, 0.7] },
|
||||
],
|
||||
monod: [
|
||||
{ key: "K_S", bounds: [0.005, 2] },
|
||||
{ key: "mu_max", bounds: [0.05, 0.9] },
|
||||
{ key: "m_S", bounds: [0.0015, 0.05] },
|
||||
{ key: "Y_XS", bounds: [0.3, 0.7] },
|
||||
],
|
||||
moser: [
|
||||
{ key: "K_S", bounds: [0.005, 2] },
|
||||
{ key: "mu_max", bounds: [0.05, 0.9] },
|
||||
{ key: "n", bounds: [0.8, 2.5] },
|
||||
{ key: "m_S", bounds: [0.0015, 0.05] },
|
||||
{ key: "Y_XS", bounds: [0.3, 0.7] },
|
||||
],
|
||||
tessier: [
|
||||
{ key: "K_S", bounds: [0.005, 2] },
|
||||
{ key: "mu_max", bounds: [0.2, 0.9] },
|
||||
{ key: "m_S", bounds: [0.005, 0.05] },
|
||||
{ key: "Y_XS", bounds: [0.3, 0.7] },
|
||||
],
|
||||
};
|
||||
|
||||
function getParamDisplayInfo(paramKey, modelKey) {
|
||||
const baseInfo = parameterCatalog[paramKey];
|
||||
if (!baseInfo) {
|
||||
throw new Error(`Unknown parameter: ${paramKey}`);
|
||||
}
|
||||
const override = baseInfo.overrides?.[modelKey];
|
||||
if (!override) {
|
||||
return baseInfo;
|
||||
}
|
||||
return { ...baseInfo, ...override };
|
||||
}
|
||||
|
||||
function getDefaultBounds(modelKey) {
|
||||
return modelParameters[modelKey].map((param) => param.bounds.slice());
|
||||
}
|
||||
|
||||
function getParamDetails(modelKey) {
|
||||
return modelParameters[modelKey].map((param) => {
|
||||
const { latex, unitText, unitLatex } = getParamDisplayInfo(
|
||||
param.key,
|
||||
modelKey,
|
||||
);
|
||||
return {
|
||||
key: param.key,
|
||||
latex,
|
||||
unitText,
|
||||
unitLatex,
|
||||
};
|
||||
});
|
||||
}
|
||||
|
||||
function monodPirt(_, y, params) {
|
||||
let K_S = params[0];
|
||||
let mu_max = params[1];
|
||||
//pirt:
|
||||
let m_S = params[2];
|
||||
let Y_XS = params[3];
|
||||
let X = y[0];
|
||||
let S = y[1];
|
||||
let dmu = monod(S, mu_max, K_S);
|
||||
let dX = X * dmu;
|
||||
const qS = pirt(dmu, Y_XS, m_S);
|
||||
let dS = -qS * X;
|
||||
return [dX, dS];
|
||||
}
|
||||
|
||||
function moserPirt(_, y, params) {
|
||||
let K_S = params[0];
|
||||
let mu_max = params[1];
|
||||
let n = params[2];
|
||||
//pirt:
|
||||
let m_S = params[3];
|
||||
let Y_XS = params[4];
|
||||
let X = y[0];
|
||||
let S = y[1];
|
||||
let dmu = moser(S, mu_max, K_S, n);
|
||||
let dX = X * dmu;
|
||||
const qS = pirt(dmu, Y_XS, m_S);
|
||||
let dS = -qS * X;
|
||||
return [dX, dS];
|
||||
}
|
||||
|
||||
function contoisPirt(_, y, params) {
|
||||
let K_S = params[0];
|
||||
let mu_max = params[1];
|
||||
let m_S = params[2];
|
||||
let Y_XS = params[3];
|
||||
let X = y[0];
|
||||
let S = y[1];
|
||||
let dmu = contois(S, X, mu_max, K_S);
|
||||
let dX = X * dmu;
|
||||
const qS = pirt(dmu, Y_XS, m_S);
|
||||
let dS = -qS * X;
|
||||
return [dX, dS];
|
||||
}
|
||||
|
||||
function bergterPirt(time, y, params) {
|
||||
let K_S = params[0];
|
||||
let mu_max = params[1];
|
||||
let T = params[2];
|
||||
// pirt:
|
||||
let m_S = params[3];
|
||||
let Y_XS = params[4];
|
||||
let X = y[0];
|
||||
let S = y[1];
|
||||
let dmu = bergter(S, time, mu_max, K_S, T);
|
||||
let dX = X * dmu;
|
||||
const qS = pirt(dmu, Y_XS, m_S);
|
||||
let dS = -qS * X;
|
||||
return [dX, dS];
|
||||
}
|
||||
|
||||
function tessierPirt(_, y, params) {
|
||||
let K_S = params[0];
|
||||
let mu_max = params[1];
|
||||
// pirt:
|
||||
let m_S = params[2];
|
||||
let Y_XS = params[3];
|
||||
let X = y[0];
|
||||
let S = y[1];
|
||||
let dmu = tessier(S, mu_max, K_S);
|
||||
let dX = X * dmu;
|
||||
const qS = pirt(dmu, Y_XS, m_S);
|
||||
let dS = -qS * X;
|
||||
return [dX, dS];
|
||||
}
|
||||
|
||||
function andrewsPirt(_, y, params) {
|
||||
let K_S = params[0];
|
||||
let mu_max = params[1];
|
||||
let K_I = params[2];
|
||||
// pirt:
|
||||
let m_S = params[3];
|
||||
let Y_XS = params[4];
|
||||
let X = y[0];
|
||||
let S = y[1];
|
||||
let dmu = andrews(S, mu_max, K_S, K_I);
|
||||
let dX = X * dmu;
|
||||
const qS = pirt(dmu, Y_XS, m_S);
|
||||
let dS = -qS * X;
|
||||
return [dX, dS];
|
||||
}
|
||||
|
||||
function aibaPirt(_, y, params) {
|
||||
let K_S = params[0];
|
||||
let mu_max = params[1];
|
||||
let K_I = params[2];
|
||||
// pirt:
|
||||
let m_S = params[3];
|
||||
let Y_XS = params[4];
|
||||
let X = y[0];
|
||||
let S = y[1];
|
||||
let dmu = aiba(S, mu_max, K_S, K_I);
|
||||
let dX = X * dmu;
|
||||
const qS = pirt(dmu, Y_XS, m_S);
|
||||
let dS = -qS * X;
|
||||
return [dX, dS];
|
||||
}
|
||||
|
||||
export async function main(input, options = {}) {
|
||||
const alg = options.alg || {
|
||||
particles: 50,
|
||||
c1: 1.49618,
|
||||
c2: 1.49618,
|
||||
w: 0.7298,
|
||||
iterations: 150,
|
||||
};
|
||||
const boundsOpt = options.bounds || {};
|
||||
const onProgress = options.onProgress || (() => {});
|
||||
|
||||
const time = [];
|
||||
const subs = [];
|
||||
const cels = [];
|
||||
for (let i = 1; i < input.length; i++) {
|
||||
time[i] = input[i][0];
|
||||
subs[i] = input[i][1];
|
||||
cels[i] = input[i][2];
|
||||
}
|
||||
|
||||
const basePlot = [
|
||||
{
|
||||
x: time,
|
||||
y: subs,
|
||||
name: "Experimental substrate",
|
||||
mode: "markers",
|
||||
marker: { size: 10, color: "#4a90e2" },
|
||||
type: "scatter",
|
||||
},
|
||||
{
|
||||
x: time,
|
||||
y: cels,
|
||||
name: "Experimental cells",
|
||||
mode: "markers",
|
||||
marker: { size: 10, color: "#50e3c2" },
|
||||
type: "scatter",
|
||||
},
|
||||
];
|
||||
|
||||
function calculateAIC(obj, sol, params) {
|
||||
let sse = 0;
|
||||
let count = 0;
|
||||
|
||||
for (let i = 1; i < input.length; i++) {
|
||||
const timePoint = input[i][0];
|
||||
const prediction = RK4getvalue(
|
||||
sol,
|
||||
obj.timeArray,
|
||||
timePoint,
|
||||
obj.f,
|
||||
params,
|
||||
);
|
||||
|
||||
const cellResidual = prediction[0] - input[i][2];
|
||||
const substrateResidual = prediction[1] - input[i][1];
|
||||
|
||||
sse += cellResidual ** 2 + substrateResidual ** 2;
|
||||
count += 2;
|
||||
}
|
||||
|
||||
const n = count;
|
||||
const k = params.length;
|
||||
const meanSquaredError = n > 0 ? sse / n : 0;
|
||||
const safeMSE = Math.max(meanSquaredError, Number.EPSILON);
|
||||
|
||||
return {
|
||||
aic: 2 * k + n * Math.log(safeMSE),
|
||||
mse: meanSquaredError,
|
||||
};
|
||||
}
|
||||
|
||||
function runModel(cfg) {
|
||||
const obj = new Objective(input, cfg.ode, 500, 2);
|
||||
const optim = new PSO(obj, alg.particles, cfg.bounds);
|
||||
optim.run(alg.c1, alg.c2, alg.w, alg.iterations);
|
||||
|
||||
const sol = RK4(obj.f, obj.timeArray, obj.y0, optim.pos_best_g);
|
||||
const celsM = sol.map((row) => row[0]);
|
||||
const subsM = sol.map((row) => row[1]);
|
||||
|
||||
const { aic, mse } = calculateAIC(obj, sol, optim.pos_best_g);
|
||||
|
||||
let objectiveText = "MSE: N/A";
|
||||
if (Number.isFinite(mse)) {
|
||||
const absValue = Math.abs(mse);
|
||||
const formatted =
|
||||
absValue !== 0 && (absValue >= 1e3 || absValue < 1e-2)
|
||||
? mse.toExponential(4)
|
||||
: mse.toFixed(8);
|
||||
objectiveText = `MSE: ${formatted}`;
|
||||
}
|
||||
|
||||
Plotly.newPlot(
|
||||
document.getElementById(cfg.plotId),
|
||||
[
|
||||
...basePlot,
|
||||
{
|
||||
x: obj.timeArray,
|
||||
y: subsM,
|
||||
name: "Model fit for the substrate",
|
||||
mode: "lines",
|
||||
line: { color: "#4a90e2" },
|
||||
},
|
||||
{
|
||||
x: obj.timeArray,
|
||||
y: celsM,
|
||||
name: "Model fit for the cells",
|
||||
mode: "lines",
|
||||
line: { color: "#50e3c2" },
|
||||
},
|
||||
],
|
||||
{
|
||||
margin: { t: 10, b: 30 },
|
||||
paper_bgcolor: "#f0f4f8",
|
||||
plot_bgcolor: "#f0f4f8",
|
||||
xaxis: {
|
||||
title: { text: "Time (h)" },
|
||||
},
|
||||
yaxis: {
|
||||
title: { text: "Concentration (g/L)" },
|
||||
},
|
||||
legend: {
|
||||
orientation: "h",
|
||||
yanchor: "top",
|
||||
y: -0.2,
|
||||
xanchor: "left",
|
||||
x: 0,
|
||||
font: { size: 10 },
|
||||
},
|
||||
annotations: [
|
||||
{
|
||||
text: objectiveText,
|
||||
x: 1,
|
||||
y: 1,
|
||||
xref: "paper",
|
||||
yref: "paper",
|
||||
xanchor: "right",
|
||||
yanchor: "top",
|
||||
showarrow: false,
|
||||
font: { size: 12, color: "#1f2933" },
|
||||
bordercolor: "#d9e2ef",
|
||||
borderwidth: 1,
|
||||
borderpad: 6,
|
||||
},
|
||||
],
|
||||
},
|
||||
);
|
||||
|
||||
const params = optim.pos_best_g.map((p) => p.toFixed(3));
|
||||
const paramContainer = document.getElementById(cfg.paramDiv);
|
||||
paramContainer.classList.add("model-params");
|
||||
paramContainer.innerHTML = "";
|
||||
|
||||
const label = document.createElement("div");
|
||||
label.className = "param-label";
|
||||
label.textContent = "Parameters:";
|
||||
paramContainer.appendChild(label);
|
||||
|
||||
const list = document.createElement("ul");
|
||||
list.className = "param-list";
|
||||
|
||||
params.forEach((value, i) => {
|
||||
const detail = cfg.paramDetails[i];
|
||||
const item = document.createElement("li");
|
||||
const mathSpan = document.createElement("span");
|
||||
const latexUnit = detail.unitLatex;
|
||||
const latexExpression = latexUnit
|
||||
? `${detail.latex} = ${value}\\,${latexUnit}`
|
||||
: `${detail.latex} = ${value}`;
|
||||
|
||||
if (typeof katex !== "undefined") {
|
||||
katex.render(latexExpression, mathSpan, { throwOnError: false });
|
||||
} else {
|
||||
mathSpan.textContent = latexUnit
|
||||
? `${detail.latex} = ${value} ${detail.unitText || ""}`
|
||||
: `${detail.latex} = ${value}`;
|
||||
}
|
||||
|
||||
item.appendChild(mathSpan);
|
||||
list.appendChild(item);
|
||||
});
|
||||
|
||||
paramContainer.appendChild(list);
|
||||
|
||||
return { title: cfg.title, aic, key: cfg.key };
|
||||
}
|
||||
|
||||
const models = [
|
||||
{
|
||||
key: "aiba",
|
||||
ode: aibaPirt,
|
||||
bounds: boundsOpt.aiba || getDefaultBounds("aiba"),
|
||||
plotId: "Plot1",
|
||||
paramDiv: "AibaParam",
|
||||
title: "Pirt-Aiba",
|
||||
paramDetails: getParamDetails("aiba"),
|
||||
container: document.getElementById("Plot1")?.closest(".box"),
|
||||
},
|
||||
{
|
||||
key: "andrews",
|
||||
ode: andrewsPirt,
|
||||
bounds: boundsOpt.andrews || getDefaultBounds("andrews"),
|
||||
plotId: "Plot2",
|
||||
paramDiv: "AndrewsParam",
|
||||
title: "Pirt-Andrews",
|
||||
paramDetails: getParamDetails("andrews"),
|
||||
container: document.getElementById("Plot2")?.closest(".box"),
|
||||
},
|
||||
{
|
||||
key: "bergter",
|
||||
ode: bergterPirt,
|
||||
bounds: boundsOpt.bergter || getDefaultBounds("bergter"),
|
||||
plotId: "Plot3",
|
||||
paramDiv: "BergterParam",
|
||||
title: "Pirt-Bergter",
|
||||
paramDetails: getParamDetails("bergter"),
|
||||
container: document.getElementById("Plot3")?.closest(".box"),
|
||||
},
|
||||
{
|
||||
key: "contois",
|
||||
ode: contoisPirt,
|
||||
bounds: boundsOpt.contois || getDefaultBounds("contois"),
|
||||
plotId: "Plot4",
|
||||
paramDiv: "ContoisParam",
|
||||
title: "Pirt-Contois",
|
||||
paramDetails: getParamDetails("contois"),
|
||||
container: document.getElementById("Plot4")?.closest(".box"),
|
||||
},
|
||||
{
|
||||
key: "monod",
|
||||
ode: monodPirt,
|
||||
bounds: boundsOpt.monod || getDefaultBounds("monod"),
|
||||
plotId: "Plot5",
|
||||
paramDiv: "MonodParam",
|
||||
title: "Pirt-Monod",
|
||||
paramDetails: getParamDetails("monod"),
|
||||
container: document.getElementById("Plot5")?.closest(".box"),
|
||||
},
|
||||
{
|
||||
key: "moser",
|
||||
ode: moserPirt,
|
||||
bounds: boundsOpt.moser || getDefaultBounds("moser"),
|
||||
plotId: "Plot6",
|
||||
paramDiv: "MoserParam",
|
||||
title: "Pirt-Moser",
|
||||
paramDetails: getParamDetails("moser"),
|
||||
container: document.getElementById("Plot6")?.closest(".box"),
|
||||
},
|
||||
{
|
||||
key: "tessier",
|
||||
ode: tessierPirt,
|
||||
bounds: boundsOpt.tessier || getDefaultBounds("tessier"),
|
||||
plotId: "Plot7",
|
||||
paramDiv: "TessierParam",
|
||||
title: "Pirt-Tessier",
|
||||
paramDetails: getParamDetails("tessier"),
|
||||
container: document.getElementById("Plot7")?.closest(".box"),
|
||||
},
|
||||
];
|
||||
|
||||
const modelByKey = new Map(models.map((model) => [model.key, model]));
|
||||
|
||||
const results = [];
|
||||
for (let idx = 0; idx < models.length; idx++) {
|
||||
const cfg = models[idx];
|
||||
const res = runModel(cfg);
|
||||
results.push(res);
|
||||
onProgress(idx + 1, models.length);
|
||||
await new Promise((resolve) => setTimeout(resolve, 0));
|
||||
}
|
||||
|
||||
results.sort((a, b) => a.aic - b.aic);
|
||||
const comparisonBox = document.getElementById("comparison");
|
||||
const chartParent = models[0]?.container?.parentElement;
|
||||
|
||||
if (comparisonBox && chartParent) {
|
||||
results.forEach((result) => {
|
||||
const modelCfg = modelByKey.get(result.key);
|
||||
if (!modelCfg?.container) {
|
||||
return;
|
||||
}
|
||||
chartParent.insertBefore(modelCfg.container, comparisonBox);
|
||||
});
|
||||
}
|
||||
|
||||
const compDiv = document.getElementById("comparison");
|
||||
compDiv.innerHTML =
|
||||
`<h2>Model comparison</h2>
|
||||
<table class="abnt-table table-numbered">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>#</th>
|
||||
<th>Model</th>
|
||||
<th>Akaike Information Criterion</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>` +
|
||||
results
|
||||
.map((r, index) => {
|
||||
return `<tr><td>${index + 1}</td><td>${r.title}</td><td>${r.aic.toFixed(
|
||||
2,
|
||||
)}</td></tr>`;
|
||||
})
|
||||
.join("") +
|
||||
"</tbody></table>";
|
||||
}
|
||||
Loading…
Add table
Add a link
Reference in a new issue