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<h1 class="title">Bilan semaine 44 2025 : 27 octobre - 31 octobre</h1>
<div class="quarto-categories">
<div class="quarto-category">colBiSBM</div>
<div class="quarto-category">inférence</div>
<div class="quarto-category">GNN</div>
</div>
</div>
</div>
<div class="quarto-title-meta-author">
<div class="quarto-title-meta-heading">Auteur·rice</div>
<div class="quarto-title-meta-heading">Affiliation</div>
<div class="quarto-title-meta-contents">
<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>
</div>
<div class="quarto-title-meta-contents">
<p class="affiliation">
MIA Paris-Saclay, INRAE, AgroParisTech, Université Paris-Saclay
</p>
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<div class="quarto-title-meta">
<div>
<div class="quarto-title-meta-heading">Date de publication</div>
<div class="quarto-title-meta-contents">
<p class="date">27 octobre 2025</p>
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</div>
<div>
<div class="quarto-title-meta-heading">Modifié</div>
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<p class="date-modified">6 mai 2026</p>
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<h2 id="toc-title">Sur cette page</h2>
<ul>
<li><a href="#todo-list" id="toc-todo-list" class="nav-link active" data-scroll-target="#todo-list">TODO List</a>
<ul class="collapse">
<li><a href="#inférence-et-microbes" id="toc-inférence-et-microbes" class="nav-link" data-scroll-target="#inférence-et-microbes">Inférence et microbes</a></li>
</ul></li>
<li><a href="#a-discuter" id="toc-a-discuter" class="nav-link" data-scroll-target="#a-discuter">A discuter</a></li>
<li><a href="#biblio-à-faire" id="toc-biblio-à-faire" class="nav-link" data-scroll-target="#biblio-à-faire">Biblio à faire</a></li>
<li><a href="#lectures-en-cours" id="toc-lectures-en-cours" class="nav-link" data-scroll-target="#lectures-en-cours">Lectures en cours 📚</a>
<ul class="collapse">
<li><a href="#hdr-vincent-brault" id="toc-hdr-vincent-brault" class="nav-link" data-scroll-target="#hdr-vincent-brault">HDR Vincent Brault</a></li>
<li><a href="#ot" id="toc-ot" class="nav-link" data-scroll-target="#ot">OT</a></li>
<li><a href="#inférence-de-graphes" id="toc-inférence-de-graphes" class="nav-link" data-scroll-target="#inférence-de-graphes">Inférence de graphes</a></li>
<li><a href="#causalité-1" id="toc-causalité-1" class="nav-link" data-scroll-target="#causalité-1">Causalité</a></li>
<li><a href="#largest-gaps" id="toc-largest-gaps" class="nav-link" data-scroll-target="#largest-gaps">Largest Gaps</a></li>
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<section id="todo-list" class="level2">
<h2 class="anchored" data-anchor-id="todo-list">TODO List</h2>
<ul>
<li><p>Finir le papier :</p>
<ul>
<li><p>Re-structurer le plan, mon plan, Donnet et Barbillon, échelle méso et comparaison inter réseau et noeuds non partagés.</p></li>
<li><p>Partie Baldock: Ajouter lordre des modèles préférés</p></li>
<li><p>Envoyer Info transfer en annexe et remplacer par Network partitioning</p></li>
<li><p>✅ Fusionner VGAE et information transfer (missing links seulement) donc refaire tourner sur même données quen R. A adapter pour Python et pouvoir intégrer dans la figure. (raccourcit).</p></li>
<li><p>✅ Faire sep-VGAE (seulement sur le réseaux avec missing links) et VGAE avec les 4 réseaux. En train de reproduire les résultats, AUC stable autour de 0.7</p></li>
<li><p>Remplacer <em>Information tranfer on simu</em> par Network partitioning.</p></li>
<li><p>✅ Écrire le poster avec un titre aguicheur “Are my pollinators your pollinators: …”:</p></li>
</ul></li>
<li><p>Maitriser graphtools de Peixoto pour essayer dutiliser larbre taxonomique sur graphe de cooccurence inférer par SparCC</p></li>
<li><p>Maitriser SparCC</p></li>
<li><p>Faire LBM sur niveau taxonomique grossier, initialiser avec le résultat pour un niveau plus fin et ainsi de suite.</p></li>
<li><p>Clustering unipartite jai cassé une fonction de distance à vérifier et réparer</p></li>
</ul>
<!-- - Idée clustering unipartite graphes des métros
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<ul>
<li><p>Pour clustering de collections sur données <del>réelles</del> :<br>
→ Lintuition de Pierre semble être confirmé, les dissimilarités semblent arrêter de varier sensiblement pour de grandes valeurs <span class="math inline">(Q_1,Q_2)</span>.</p></li>
<li><p>👶 (délégué à stagiaire) Clustering sur Doré :</p>
<ul>
<li><p>Regarder pour les couples date+nom les études et le nombre de réseaux analysables (Possible demander à Élisa)</p>
<ul>
<li>⌛ Chamberlain et al semble intéressant à regarder ! Voir le Rmarkdown</li>
</ul></li>
<li><p>Clusteriser sur la base des noms et voir parmi les réseaux Européens (désagrégés ?)</p></li>
<li><p>Si M &gt; 10, alors voir si je retrouve les mêmes résultats que dans les études.</p></li>
<li><p>Regarder <em>Largest gap</em> sur réseaux Doré</p></li>
<li><p>Essayer <em>clustering</em> sur <code>supinfo</code></p></li>
</ul></li>
<li><p>✅ Homogénéiser notations dans les supplementaries</p></li>
</ul>
<section id="inférence-et-microbes" class="level3">
<h3 class="anchored" data-anchor-id="inférence-et-microbes">Inférence et microbes</h3>
<section id="bibliographie-à-lire-à-faire" class="level4">
<h4 class="anchored" data-anchor-id="bibliographie-à-lire-à-faire">Bibliographie: à lire, à faire</h4>
<ul>
<li>Lire article multi-niveaux Saint-Clair</li>
<li>🆕⌛ Papier Julie Negative Binomiale</li>
<li>🆕 🔎 Trouver des papiers:
<ul>
<li>LBM Negative Binomial</li>
<li>Network inference through sample comparison</li>
</ul></li>
</ul>
</section>
<section id="réflexion" class="level4">
<h4 class="anchored" data-anchor-id="réflexion">Réflexion</h4>
<ul>
<li>easy16s : se renseigner sur
<ul>
<li><span class="math inline">\alpha</span>, <span class="math inline">\beta</span> diversité</li>
<li>Heatmap</li>
</ul></li>
<li>Regarder <strong>SPARTA</strong> Rennes</li>
<li>Ecrire et étudier les modèles pour différents niveaux taxonomiques.</li>
<li>🆕 Regarder NetComi</li>
<li>🆕 Regarder OneNet car aggrégation plus robuste</li>
<li>🆕 Réfléchir sens daggréger les données ou de les diviser</li>
</ul>
</section>
<section id="écrire-et-faire-tourner" class="level4">
<h4 class="anchored" data-anchor-id="écrire-et-faire-tourner">Écrire et faire tourner</h4>
<ul>
<li>Lancer <em>colBiSBM</em> sur <span class="math inline">OTU\times Sample</span> → problème du chargement en mémoire des données à voir</li>
<li>Lancer <em>colSBM</em> sur <span class="math inline">OTU\times OTU</span></li>
<li>TabNet pratiquer les <a href="https://github.com/cregouby/Tutoriel_torch">exercices</a></li>
<li>🆕 SparCC à différent niveaux</li>
<li>🆕 SBM à différent niveaux</li>
<li>🆕⌛ Tree-PLN à différents niveaux</li>
</ul>
</section>
<section id="causalité" class="level4">
<h4 class="anchored" data-anchor-id="causalité">Causalité</h4>
<p>Plus sur le temps long, à regarder</p>
<ul>
<li>GT causalité</li>
<li>Daria Bystrova lire présentation <span class="citation" data-cites="bystrovaCausalDiscovery">Bystrova (<a href="#ref-bystrovaCausalDiscovery" role="doc-biblioref">s.&nbsp;d.</a>)</span> (Meek rules, V-structure)</li>
</ul>
</section>
</section>
</section>
<section id="a-discuter" class="level2">
<h2 class="anchored" data-anchor-id="a-discuter">A discuter</h2>
<ul>
<li>🆕 Voir pour des Réseaux / GDR ou aller</li>
<li>🆕 Chercher des cours à suivre</li>
</ul>
</section>
<section id="biblio-à-faire" class="level2">
<h2 class="anchored" data-anchor-id="biblio-à-faire">Biblio à faire</h2>
<ul>
<li>Regarder Transport optimal graphes bipartite.</li>
</ul>
</section>
<section id="lectures-en-cours" class="level2">
<h2 class="anchored" data-anchor-id="lectures-en-cours">Lectures en cours 📚</h2>
<section id="hdr-vincent-brault" class="level3">
<h3 class="anchored" data-anchor-id="hdr-vincent-brault">HDR Vincent Brault</h3>
<ul>
<li>⌛ Chap 2 : Creuser lidée de maximiser lénergie libre, très intéressant regarder le critère CARI et lire Robert et al 2021. Actuellement p32 du manuscrit</li>
<li>Chap 3</li>
</ul>
</section>
<section id="ot" class="level3">
<h3 class="anchored" data-anchor-id="ot">OT</h3>
<ul>
<li><span class="citation" data-cites="mazeletUnsupervisedLearningOptimal">Mazelet, Flamary, et Thirion (<a href="#ref-mazeletUnsupervisedLearningOptimal" role="doc-biblioref">s.&nbsp;d.</a>)</span> Intéressant pour le transport optimal entre graphes de tailles différentes | Regarder si regularization entropique ne marche pas bien pour le graphe.</li>
<li><span class="citation" data-cites="nennaLecture2Entropic">Nenna (<a href="#ref-nennaLecture2Entropic" role="doc-biblioref">s.&nbsp;d.b</a>)</span> Pour comprendre le problème dOT régularisé pour lentropie.</li>
<li><span class="citation" data-cites="nennaLecture1Monge">Nenna (<a href="#ref-nennaLecture1Monge" role="doc-biblioref">s.&nbsp;d.a</a>)</span></li>
</ul>
</section>
<section id="inférence-de-graphes" class="level3">
<h3 class="anchored" data-anchor-id="inférence-de-graphes">Inférence de graphes</h3>
<ul>
<li><p><span class="citation" data-cites="aitchisonStatisticalAnalysisCompositional1982a">Aitchison (<a href="#ref-aitchisonStatisticalAnalysisCompositional1982a" role="doc-biblioref">1982</a>)</span>, en cours</p></li>
<li><p>❗📖 <span class="citation" data-cites="payneFiniteMixturesMultivariate2023">Payne et al. (<a href="#ref-payneFiniteMixturesMultivariate2023" role="doc-biblioref">2023</a>)</span> sur MixMPLN</p></li>
</ul>
</section>
<section id="causalité-1" class="level3">
<h3 class="anchored" data-anchor-id="causalité-1">Causalité</h3>
<ul>
<li>❗📖 <span class="citation" data-cites="bystrovaCausalDiscovery">Bystrova (<a href="#ref-bystrovaCausalDiscovery" role="doc-biblioref">s.&nbsp;d.</a>)</span></li>
</ul>
</section>
<section id="largest-gaps" class="level3">
<h3 class="anchored" data-anchor-id="largest-gaps">Largest Gaps</h3>
<ul>
<li>❗📖 <span class="citation" data-cites="braultFastConsistentAlgorithm2023">Brault et Channarond (<a href="#ref-braultFastConsistentAlgorithm2023" role="doc-biblioref">2023</a>)</span></li>
<li>❗📖 <span class="citation" data-cites="channarondClassificationEstimationStochastic2012">Channarond, Daudin, et Robin (<a href="#ref-channarondClassificationEstimationStochastic2012" role="doc-biblioref">2012</a>)</span> le papier qui introduit le <em>Largest Gaps</em></li>
</ul>
</section>
</section>
<div id="quarto-appendix" class="default"><section class="quarto-appendix-contents" role="doc-bibliography" id="quarto-bibliography"><h2 class="anchored quarto-appendix-heading">Les références</h2><div id="refs" class="references csl-bib-body hanging-indent" data-entry-spacing="0" role="list">
<div id="ref-aitchisonStatisticalAnalysisCompositional1982a" class="csl-entry" role="listitem">
Aitchison, J. 1982. <span>«&nbsp;The <span>Statistical Analysis</span> of <span>Compositional Data</span>&nbsp;»</span>. <em>Journal of the Royal Statistical Society. Series B (Methodological)</em> 44 (2): 13977. <a href="https://www.jstor.org/stable/2345821">https://www.jstor.org/stable/2345821</a>.
</div>
<div id="ref-braultFastConsistentAlgorithm2023" class="csl-entry" role="listitem">
Brault, Vincent, et Antoine Channarond. 2023. <span>«&nbsp;Fast and <span>Consistent Algorithm</span> for the <span>Latent Block Model</span>&nbsp;»</span>. 9 mars 2023. <a href="https://doi.org/10.48550/arXiv.1610.09005">https://doi.org/10.48550/arXiv.1610.09005</a>.
</div>
<div id="ref-bystrovaCausalDiscovery" class="csl-entry" role="listitem">
Bystrova, Daria. s.&nbsp;d. <span>«&nbsp;Causal Discovery&nbsp;»</span>.
</div>
<div id="ref-channarondClassificationEstimationStochastic2012" class="csl-entry" role="listitem">
Channarond, Antoine, Jean-Jacques Daudin, et Stéphane Robin. 2012. <span>«&nbsp;Classification and Estimation in the <span>Stochastic Blockmodel</span> Based on the Empirical Degrees&nbsp;»</span>. <em>Electronic Journal of Statistics</em> 6 (janvier). <a href="https://doi.org/10.1214/12-ejs753">https://doi.org/10.1214/12-ejs753</a>.
</div>
<div id="ref-mazeletUnsupervisedLearningOptimal" class="csl-entry" role="listitem">
Mazelet, Sonia, Rémi Flamary, et Bertrand Thirion. s.&nbsp;d. <span>«&nbsp;Unsupervised <span>Learning</span> for <span>Optimal Transport</span> Plan Prediction Between Unbalanced Graphs&nbsp;»</span>.
</div>
<div id="ref-nennaLecture1Monge" class="csl-entry" role="listitem">
Nenna, Luca. s.&nbsp;d.a. <span>«&nbsp;Lecture 1 <span>Monge</span> and <span>Kantorovich</span> Problems: From Primal to Dual&nbsp;»</span>.
</div>
<div id="ref-nennaLecture2Entropic" class="csl-entry" role="listitem">
———. s.&nbsp;d.b. <span>«&nbsp;Lecture 2: <span>Entropic Optimal Transport</span>&nbsp;»</span>.
</div>
<div id="ref-payneFiniteMixturesMultivariate2023" class="csl-entry" role="listitem">
Payne, Andrea, Anjali Silva, Steven J. Rothstein, Paul D. McNicholas, et Sanjeena Subedi. 2023. <span>«&nbsp;Finite <span>Mixtures</span> of <span>Multivariate Poisson-Log Normal Factor Analyzers</span> for <span>Clustering Count Data</span>&nbsp;»</span>. 13 novembre 2023. <a href="https://doi.org/10.48550/arXiv.2311.07762">https://doi.org/10.48550/arXiv.2311.07762</a>.
</div>
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