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Louis
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---
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title: "Bilan semaine 18 2025 : 28 avril - 2 mai"
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categories: [colBiSBM, inférence]
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date: 2025 05 02
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---
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## A faire
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### JdS
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- colDEM CSE
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### Stratégie suite : Inférence
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- Lire biblio fournie Julie, Inférence de réseaux : co-occurence
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@ -36,12 +33,6 @@ categories: [colBiSBM, inférence]
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### Simulations article
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- Relancer simus clustering avec VEM steps = 10 000 et plus nombreux init pour spectral
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- Ajouter simu clustering métriques nb sous-collections obtenues.
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Vérifier les résultats obtenus si ARI = 0. Et augmenter la taille $M = 30$ avec $M_1 = M_2 = M_3 = 10$.
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- Comparer sur clustering unipartite avec versions symétriser des par blocs des matrices d'adjacences.
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- Corriger structure de simus :
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@ -63,7 +54,19 @@ Car densités déséquilibrées.
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## J'ai fait
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### JdS
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- colDEM CSE
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### Clustering exhaustif Baldock
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- Le clustering de toutes les 52 partitions s'est fait en 5h30 ! (Mémoïsation)
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- Pour iid la meilleure partition avec $BICL=-9466.911$ contre $BICL_{algo} = -9466.873 \pm 0.02205$ trouvé avec l'algo
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- Pour $\pi\rho$ la meilleure partition avec $BICL = en cours$ contre $BICL_{algo} =-9497.92 \pm 0.00009$
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## A continuer
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@ -82,4 +85,10 @@ En attente résultats MIGALE
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- Idée Sophie: Regarder clustering de données plantes-pollinisateur selon gradient d'urbanisation
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> Sophie a fait une appli qui marche bien et va dans le sens de l'analyse faite
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(à savoir pas d'effet du gradien d'urbanisation). À continuer pour l'intégrer dans l'article !
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(à savoir pas d'effet du gradien d'urbanisation). À continuer pour l'intégrer dans l'article !
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### Simulations article
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- Relancer simulations de clustering avec $M = 30$ où $M_i = 10, \forall i$. En attente retour MIGALE
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Relancer simus clustering avec VEM steps = 10 000 et plus nombreux init pour spectral. Ajouter simu clustering métriques nb sous-collections obtenues.
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Vérifier les résultats obtenus si ARI = 0. Et augmenter la taille $M = 30$ avec $M_1 = M_2 = M_3 = 10$.
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suivi/2025-18/figs/partition-iid.svg
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89
suivi/2025-19/2025-19.qmd
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|||
---
|
||||
title: "Bilan semaine 19 2025 : 5 mai - 9 mai"
|
||||
categories: [colBiSBM, inférence]
|
||||
---
|
||||
|
||||
## A faire
|
||||
|
||||
### ML at Aussois
|
||||
|
||||
- Détails d'inscriptions
|
||||
|
||||
### Stratégie suite : Inférence
|
||||
|
||||
- Papier pour comprendre données
|
||||
|
||||
- pbs : variance, bcp de zero, covariables, offset et taxonomie (Reseaux arretes differents niveaux : Genre, OTU ...)
|
||||
|
||||
> Combine networks at different taxonomic levels
|
||||
|
||||
- Inférence + GREMLINS
|
||||
|
||||
### Rédaction article
|
||||
|
||||
- Relire intro St Clair
|
||||
- S'inspirer structure pour mon intro
|
||||
- Trouver biblio intro
|
||||
- Rédiger l'intro
|
||||
- Regarder les applications pour les collections de réseaux recommender system
|
||||
- Lire les papiers de Baldock Traveset Souza Cordeniz Trojelsgaard et Gibson
|
||||
|
||||
- Dire résultats nettement meilleurs et variabilités inférieures.
|
||||
|
||||
- Intégrer les retours de Sophie
|
||||
|
||||
### Simulations article
|
||||
|
||||
- Comparer sur clustering unipartite avec versions symétriser des par blocs des matrices d'adjacences.
|
||||
|
||||
- Corriger structure de simus :
|
||||
- Pour noisy $\alpha$ :
|
||||
- Logit pour envoyer la gaussienne vers (0,1)
|
||||
- Beta contrainte dans (0,1)
|
||||
- Pour noisy links : Générer `nb_clustering` collections de taille M puis prélever $\epsilon_{max}n_r n_c$ liens à inverser puis pour les $\epsilon < \epsilon_{max}$ prélever dans la liste des indices afin d'avoir des perturbations emboitées.
|
||||
|
||||
### Applications
|
||||
|
||||
- Kmeans sur la densité des réseaux subdoré pour pré-partitionner et *clusteriser*.
|
||||
Car densités déséquilibrées.
|
||||
|
||||
|
||||
|
||||
### Autour de l'article et du package
|
||||
|
||||
- Créer des vignettes illustrant par exemple des cas de simulations. **Possible de mettre l'exemple d'application de Sophie sur les réseaux avec gradient d'urbanisation**.
|
||||
|
||||
## J'ai fait
|
||||
|
||||
|
||||
## A continuer
|
||||
|
||||
- Résultats simus NA **Erreur pour certaines conditions** : Pour NA robustness générer `nb_rep` collections de taille $M=2$ et prélever
|
||||
$\epsilon_{max}n_r n_c$ liens à retirer puis pour les $\epsilon < \epsilon_{max}$ 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 *en attente des résultats MIGALE*.
|
||||
|
||||
- Lire Biological Networks - François Képès
|
||||
|
||||
- Relancer simus d'inférence avec n = 240 pour voir si la qualité augmenter (se rassurer). En fait on est déjà à 240, j'ai relancé avec M = 4 au lieu de M = 2.
|
||||
En attente résultats MIGALE
|
||||
|
||||
### Applications
|
||||
|
||||
- Idée Sophie: Regarder clustering de données plantes-pollinisateur selon gradient d'urbanisation
|
||||
|
||||
> Sophie a fait une appli qui marche bien et va dans le sens de l'analyse faite
|
||||
(à savoir pas d'effet du gradien d'urbanisation). À continuer pour l'intégrer dans l'article !
|
||||
|
||||
### Simulations article
|
||||
|
||||
- Relancer simulations de clustering avec $M = 30$ où $M_i = 10, \forall i$. En attente retour MIGALE
|
||||
Relancer simus clustering avec VEM steps = 10 000 et plus nombreux init pour spectral. Ajouter simu clustering métriques nb sous-collections obtenues.
|
||||
Vérifier les résultats obtenus si ARI = 0. Et augmenter la taille $M = 30$ avec $M_1 = M_2 = M_3 = 10$.
|
||||
|
||||
### Axe inférence
|
||||
|
||||
|
||||
- Lire biblio fournie Julie, Inférence de réseaux : co-occurence
|
||||
|
||||
> J'ai commencé à lire Faust et al.
|
||||
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