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<h1 class="title">Bilan semaine 16 2025</h1>
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<div class="quarto-category">colBiSBM</div>
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<div class="quarto-title-meta-heading">Affiliation</div>
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<p class="author">Louis Lacoste <a href="mailto:louis.lacoste@agroparistech.fr" class="quarto-title-author-email"><i class="bi bi-envelope"></i></a> <a href="https://orcid.org/0009-0004-0178-9821" class="quarto-title-author-orcid"> <img src="data:image/png;base64,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"></a></p>
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</div>
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<div class="quarto-title-meta-contents">
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<p class="affiliation">
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MIA Paris-Saclay, INRAE, AgroParisTech, Université Paris-Saclay
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</p>
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<div class="quarto-title-meta">
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<div class="quarto-title-meta-heading">Date de publication</div>
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<div class="quarto-title-meta-contents">
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<p class="date">18 avril 2025</p>
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<div class="quarto-title-meta-heading">Modifié</div>
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<p class="date-modified">17 août 2025</p>
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<h2 id="toc-title">Sur cette page</h2>
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<ul>
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<li><a href="#a-faire" id="toc-a-faire" class="nav-link active" data-scroll-target="#a-faire">A faire</a></li>
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<li><a href="#jai-fait" id="toc-jai-fait" class="nav-link" data-scroll-target="#jai-fait">J’ai fait</a></li>
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<li><a href="#a-continuer" id="toc-a-continuer" class="nav-link" data-scroll-target="#a-continuer">A continuer</a></li>
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<h2 class="anchored" data-anchor-id="a-faire">A faire</h2>
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<ul>
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<li><p>Relire intro St Clair</p></li>
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<li><p>S’inspirer structure pour mon intro</p></li>
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<li><p>Trouver biblio intro</p></li>
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<li><p>Rédiger l’intro</p></li>
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<li><p>Lire les papiers de Baldock Traveset Souza Cordeniz Trojelsgaard et Gibson</p></li>
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<li><p>Corriger structure de simus :</p>
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<ul>
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<li>Pour noisy <span class="math inline">\alpha</span> :
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<ul>
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<li>Logit pour envoyer la gaussienne vers (0,1)</li>
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<li>Beta contrainte dans (0,1)</li>
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</ul></li>
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<li>Pour noisy links : Générer <code>nb_clustering</code> collections de taille M puis prélever <span class="math inline">\epsilon_{max}n_r n_c</span> liens à inverser puis pour les <span class="math inline">\epsilon < \epsilon_{max}</span> prélever dans la liste des indices afin d’avoir des perturbations emboitées.</li>
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</ul></li>
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<li><p>Idée Sophie: Regarder clustering de données plantes-pollinisateur selon gradient d’urbanisation</p></li>
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<li><p>Idée Pierre : Regarder la contribution au BICL de la collection des réseaux et comparer au sep BICL pour essayer de repérer les outliers.</p></li>
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</ul>
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</section>
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<section id="jai-fait" class="level2">
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<h2 class="anchored" data-anchor-id="jai-fait">J’ai fait</h2>
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<ul>
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<li><p>J’ai lancé le clustering iid ascendant sur données sub-Doré. Résultats stables mais 27 collections formées donc pas de mise en commun des structures…</p></li>
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<li><p>Rédiger et modifier les cadres de simulations dans le papier pour qu’ils soient raccord avec les données obtenues.</p></li>
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<li><p>Étoffer la partie simulations studies en mettant plusieurs points pour présenter les simus et les résultats succintement.</p></li>
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</ul>
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<blockquote class="blockquote">
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<p>je pense qu’il faudrait étoffer en mettrant plusieurs points répartis en paragraphe. genre vérif selection de modèle verif clustering réseau, verif transfer leraning et de dire les résultats en qq mots</p>
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</blockquote>
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<ul>
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<li>Comment faire pour l’inscription JdS (paiement, coldem …) : voir avec Christelle</li>
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<li>CSI : St Clair, Sonia ou Elisa et Pierre Gérard</li>
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</ul>
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</section>
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<h2 class="anchored" data-anchor-id="a-continuer">A continuer</h2>
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<ul>
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<li><p>Résultats simus NA <strong>Erreur pour certaines conditions</strong> : Pour NA robustness générer <code>nb_rep</code> collections de taille <span class="math inline">M=2</span> et prélever <span class="math inline">\epsilon_{max}n_r n_c</span> liens à retirer puis pour les <span class="math inline">\epsilon < \epsilon_{max}</span> prélever dans la liste des indices afin d’avoir des perturbations emboitées. Il faut que j’ajoute un mécanisme pour reprendre des conditions qui ont plantés et que je skip dans le future_lapply les conditions déjà traitées (pour avoir la même seed quand je vais exécuter le code). Implémenté les missing steps <em>en attente des résultats MIGALE</em>.</p></li>
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<li><p>Lire Biological Networks - François Képès</p></li>
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<li><p>J’ai esquissé des bouts d’intro</p></li>
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||
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
|
||
var mailtoRegex = new RegExp(/^mailto:/);
|
||
var filterRegex = new RegExp('/' + window.location.host + '/');
|
||
var isInternal = (href) => {
|
||
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
|
||
}
|
||
// Inspect non-navigation links and adorn them if external
|
||
var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)');
|
||
for (var i=0; i<links.length; i++) {
|
||
const link = links[i];
|
||
if (!isInternal(link.href)) {
|
||
// undo the damage that might have been done by quarto-nav.js in the case of
|
||
// links that we want to consider external
|
||
if (link.dataset.originalHref !== undefined) {
|
||
link.href = link.dataset.originalHref;
|
||
}
|
||
}
|
||
}
|
||
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
|
||
const config = {
|
||
allowHTML: true,
|
||
maxWidth: 500,
|
||
delay: 100,
|
||
arrow: false,
|
||
appendTo: function(el) {
|
||
return el.parentElement;
|
||
},
|
||
interactive: true,
|
||
interactiveBorder: 10,
|
||
theme: 'quarto',
|
||
placement: 'bottom-start',
|
||
};
|
||
if (contentFn) {
|
||
config.content = contentFn;
|
||
}
|
||
if (onTriggerFn) {
|
||
config.onTrigger = onTriggerFn;
|
||
}
|
||
if (onUntriggerFn) {
|
||
config.onUntrigger = onUntriggerFn;
|
||
}
|
||
window.tippy(el, config);
|
||
}
|
||
const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
|
||
for (var i=0; i<noterefs.length; i++) {
|
||
const ref = noterefs[i];
|
||
tippyHover(ref, function() {
|
||
// use id or data attribute instead here
|
||
let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href');
|
||
try { href = new URL(href).hash; } catch {}
|
||
const id = href.replace(/^#\/?/, "");
|
||
const note = window.document.getElementById(id);
|
||
if (note) {
|
||
return note.innerHTML;
|
||
} else {
|
||
return "";
|
||
}
|
||
});
|
||
}
|
||
const xrefs = window.document.querySelectorAll('a.quarto-xref');
|
||
const processXRef = (id, note) => {
|
||
// Strip column container classes
|
||
const stripColumnClz = (el) => {
|
||
el.classList.remove("page-full", "page-columns");
|
||
if (el.children) {
|
||
for (const child of el.children) {
|
||
stripColumnClz(child);
|
||
}
|
||
}
|
||
}
|
||
stripColumnClz(note)
|
||
if (id === null || id.startsWith('sec-')) {
|
||
// Special case sections, only their first couple elements
|
||
const container = document.createElement("div");
|
||
if (note.children && note.children.length > 2) {
|
||
container.appendChild(note.children[0].cloneNode(true));
|
||
for (let i = 1; i < note.children.length; i++) {
|
||
const child = note.children[i];
|
||
if (child.tagName === "P" && child.innerText === "") {
|
||
continue;
|
||
} else {
|
||
container.appendChild(child.cloneNode(true));
|
||
break;
|
||
}
|
||
}
|
||
if (window.Quarto?.typesetMath) {
|
||
window.Quarto.typesetMath(container);
|
||
}
|
||
return container.innerHTML
|
||
} else {
|
||
if (window.Quarto?.typesetMath) {
|
||
window.Quarto.typesetMath(note);
|
||
}
|
||
return note.innerHTML;
|
||
}
|
||
} else {
|
||
// Remove any anchor links if they are present
|
||
const anchorLink = note.querySelector('a.anchorjs-link');
|
||
if (anchorLink) {
|
||
anchorLink.remove();
|
||
}
|
||
if (window.Quarto?.typesetMath) {
|
||
window.Quarto.typesetMath(note);
|
||
}
|
||
if (note.classList.contains("callout")) {
|
||
return note.outerHTML;
|
||
} else {
|
||
return note.innerHTML;
|
||
}
|
||
}
|
||
}
|
||
for (var i=0; i<xrefs.length; i++) {
|
||
const xref = xrefs[i];
|
||
tippyHover(xref, undefined, function(instance) {
|
||
instance.disable();
|
||
let url = xref.getAttribute('href');
|
||
let hash = undefined;
|
||
if (url.startsWith('#')) {
|
||
hash = url;
|
||
} else {
|
||
try { hash = new URL(url).hash; } catch {}
|
||
}
|
||
if (hash) {
|
||
const id = hash.replace(/^#\/?/, "");
|
||
const note = window.document.getElementById(id);
|
||
if (note !== null) {
|
||
try {
|
||
const html = processXRef(id, note.cloneNode(true));
|
||
instance.setContent(html);
|
||
} finally {
|
||
instance.enable();
|
||
instance.show();
|
||
}
|
||
} else {
|
||
// See if we can fetch this
|
||
fetch(url.split('#')[0])
|
||
.then(res => res.text())
|
||
.then(html => {
|
||
const parser = new DOMParser();
|
||
const htmlDoc = parser.parseFromString(html, "text/html");
|
||
const note = htmlDoc.getElementById(id);
|
||
if (note !== null) {
|
||
const html = processXRef(id, note);
|
||
instance.setContent(html);
|
||
}
|
||
}).finally(() => {
|
||
instance.enable();
|
||
instance.show();
|
||
});
|
||
}
|
||
} else {
|
||
// See if we can fetch a full url (with no hash to target)
|
||
// This is a special case and we should probably do some content thinning / targeting
|
||
fetch(url)
|
||
.then(res => res.text())
|
||
.then(html => {
|
||
const parser = new DOMParser();
|
||
const htmlDoc = parser.parseFromString(html, "text/html");
|
||
const note = htmlDoc.querySelector('main.content');
|
||
if (note !== null) {
|
||
// This should only happen for chapter cross references
|
||
// (since there is no id in the URL)
|
||
// remove the first header
|
||
if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
|
||
note.children[0].remove();
|
||
}
|
||
const html = processXRef(null, note);
|
||
instance.setContent(html);
|
||
}
|
||
}).finally(() => {
|
||
instance.enable();
|
||
instance.show();
|
||
});
|
||
}
|
||
}, function(instance) {
|
||
});
|
||
}
|
||
let selectedAnnoteEl;
|
||
const selectorForAnnotation = ( cell, annotation) => {
|
||
let cellAttr = 'data-code-cell="' + cell + '"';
|
||
let lineAttr = 'data-code-annotation="' + annotation + '"';
|
||
const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
|
||
return selector;
|
||
}
|
||
const selectCodeLines = (annoteEl) => {
|
||
const doc = window.document;
|
||
const targetCell = annoteEl.getAttribute("data-target-cell");
|
||
const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
|
||
const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
|
||
const lines = annoteSpan.getAttribute("data-code-lines").split(",");
|
||
const lineIds = lines.map((line) => {
|
||
return targetCell + "-" + line;
|
||
})
|
||
let top = null;
|
||
let height = null;
|
||
let parent = null;
|
||
if (lineIds.length > 0) {
|
||
//compute the position of the single el (top and bottom and make a div)
|
||
const el = window.document.getElementById(lineIds[0]);
|
||
top = el.offsetTop;
|
||
height = el.offsetHeight;
|
||
parent = el.parentElement.parentElement;
|
||
if (lineIds.length > 1) {
|
||
const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
|
||
const bottom = lastEl.offsetTop + lastEl.offsetHeight;
|
||
height = bottom - top;
|
||
}
|
||
if (top !== null && height !== null && parent !== null) {
|
||
// cook up a div (if necessary) and position it
|
||
let div = window.document.getElementById("code-annotation-line-highlight");
|
||
if (div === null) {
|
||
div = window.document.createElement("div");
|
||
div.setAttribute("id", "code-annotation-line-highlight");
|
||
div.style.position = 'absolute';
|
||
parent.appendChild(div);
|
||
}
|
||
div.style.top = top - 2 + "px";
|
||
div.style.height = height + 4 + "px";
|
||
div.style.left = 0;
|
||
let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
|
||
if (gutterDiv === null) {
|
||
gutterDiv = window.document.createElement("div");
|
||
gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
|
||
gutterDiv.style.position = 'absolute';
|
||
const codeCell = window.document.getElementById(targetCell);
|
||
const gutter = codeCell.querySelector('.code-annotation-gutter');
|
||
gutter.appendChild(gutterDiv);
|
||
}
|
||
gutterDiv.style.top = top - 2 + "px";
|
||
gutterDiv.style.height = height + 4 + "px";
|
||
}
|
||
selectedAnnoteEl = annoteEl;
|
||
}
|
||
};
|
||
const unselectCodeLines = () => {
|
||
const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
|
||
elementsIds.forEach((elId) => {
|
||
const div = window.document.getElementById(elId);
|
||
if (div) {
|
||
div.remove();
|
||
}
|
||
});
|
||
selectedAnnoteEl = undefined;
|
||
};
|
||
// Handle positioning of the toggle
|
||
window.addEventListener(
|
||
"resize",
|
||
throttle(() => {
|
||
elRect = undefined;
|
||
if (selectedAnnoteEl) {
|
||
selectCodeLines(selectedAnnoteEl);
|
||
}
|
||
}, 10)
|
||
);
|
||
function throttle(fn, ms) {
|
||
let throttle = false;
|
||
let timer;
|
||
return (...args) => {
|
||
if(!throttle) { // first call gets through
|
||
fn.apply(this, args);
|
||
throttle = true;
|
||
} else { // all the others get throttled
|
||
if(timer) clearTimeout(timer); // cancel #2
|
||
timer = setTimeout(() => {
|
||
fn.apply(this, args);
|
||
timer = throttle = false;
|
||
}, ms);
|
||
}
|
||
};
|
||
}
|
||
// Attach click handler to the DT
|
||
const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
|
||
for (const annoteDlNode of annoteDls) {
|
||
annoteDlNode.addEventListener('click', (event) => {
|
||
const clickedEl = event.target;
|
||
if (clickedEl !== selectedAnnoteEl) {
|
||
unselectCodeLines();
|
||
const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
|
||
if (activeEl) {
|
||
activeEl.classList.remove('code-annotation-active');
|
||
}
|
||
selectCodeLines(clickedEl);
|
||
clickedEl.classList.add('code-annotation-active');
|
||
} else {
|
||
// Unselect the line
|
||
unselectCodeLines();
|
||
clickedEl.classList.remove('code-annotation-active');
|
||
}
|
||
});
|
||
}
|
||
const findCites = (el) => {
|
||
const parentEl = el.parentElement;
|
||
if (parentEl) {
|
||
const cites = parentEl.dataset.cites;
|
||
if (cites) {
|
||
return {
|
||
el,
|
||
cites: cites.split(' ')
|
||
};
|
||
} else {
|
||
return findCites(el.parentElement)
|
||
}
|
||
} else {
|
||
return undefined;
|
||
}
|
||
};
|
||
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
|
||
for (var i=0; i<bibliorefs.length; i++) {
|
||
const ref = bibliorefs[i];
|
||
const citeInfo = findCites(ref);
|
||
if (citeInfo) {
|
||
tippyHover(citeInfo.el, function() {
|
||
var popup = window.document.createElement('div');
|
||
citeInfo.cites.forEach(function(cite) {
|
||
var citeDiv = window.document.createElement('div');
|
||
citeDiv.classList.add('hanging-indent');
|
||
citeDiv.classList.add('csl-entry');
|
||
var biblioDiv = window.document.getElementById('ref-' + cite);
|
||
if (biblioDiv) {
|
||
citeDiv.innerHTML = biblioDiv.innerHTML;
|
||
}
|
||
popup.appendChild(citeDiv);
|
||
});
|
||
return popup.innerHTML;
|
||
});
|
||
}
|
||
}
|
||
});
|
||
</script>
|
||
</div> <!-- /content -->
|
||
|
||
|
||
|
||
|
||
</body></html> |