latest
Content
Installation
API Guide
AggMap
AggMapNet
Useful Functions
Hyperparameters
AggMap HPs
The important hyperparameters in AggMap feature restructuring
Code example of AggMap feature restructuring.
AggMapNet HPs
The important hyperparameters in AggMapNet
Code example of AggMapNet modelling
AggMapNet Explainers
Code example of AggMapNet model explaination
Simply-explainer vs. Shapley-explainer
References
Examples
MNIST reconstruction from pixel random permutation
Introduction
Step0: Import AggMap and Orignal MNIST data
Step1: MNIST pixel random permutation
Step2: AggMap pre-fitting on training set
Step3: AggMap transformation on training and test test
Step4: AggMap visualization
Fashion-MNIST reconstruction from pixel random permutation
Introduction
Step1: MNIST pixel random permutation
Step2: AggMap pre-fitting on training set
Step3: AggMap transformation on training and test test
Pick up stage-specific genes in cell cycle data
Introduction
Read data and pre-fit on AggMap
Transform the data by AggMap
Multi-channel Fmaps
Single-channel Fmaps
Visulization
01.scatter plot
02.grid plot
03.tree plot
Metagenomic deep learning and biomarker discovery
1. Introduction
1.1 MEGMA introduction
1.2 Metagenomic cross nation datasets and tasks
1.3 MEGMA fitting and AggMapNet training strategy
2. MEGMA Training & Transformation
2.1 Fitting MEGMA on metagenomic abundance data of all countries
2.1.1 Read and preprocess data for MEGMA
2.1.2 MEGMA initialization, fitting and dump
2.1.3 MEGMA loading and 2D-microbiomeprints transformation
2.1.4 MEGMA 2D-microbiomeprints visulization
2.1.5 Well-trained MEGMA to transform the abundance data of each country
2.2 Fitting MEGMA on metagenomic abundance data of one country only
2.2.1 Read and preprocess data for MEGMA
2.2.2 MEGMA initialization & fitting
2.2.3 MEGMA 2D-microbiomeprints transformation
2.2.4 MEGMA Fmaps visulization
2.2.5 Transform the abandance data of the rest countries by country-specific MEGMA
2.2.6 Fitting country-specific megma for all countries
2.3 Discussions & conclusions on MEGMA 2D-microbiomeprints
3. Training the CRC detection models based on MEGMA Fmaps
3.1 Training and test AggMapNet on overall MEGMA Fmaps
3.2 Training and test AggMapNet on country specific MEGMA Fmaps
3.3 Comparing the STST performance and discussion
4. Important microbial marker identification
4.1 Calculate the global feature importance
4.1.1 GFI for model trained on overall MEGMA Fmaps
4.1.2 GFI for model trained on country specific MEGMA Fmaps
4.2 Generate the explaination saliency map
4.2.1 Saliency map for overall MEGMA Fmaps
4.2.2 Saliency map country specific MEGMA Fmaps
4.3 Global feature importance correlation
4.4 Discussions and conclusions on saliency map
5. Toplogical analyisis on the important microbes
5.1 Plotting the the embedded and arranged microbes
5.2 Plotting the linear assignment of the embedded microbes
5.3 Fetching the optimized toplogical graph and clustering
5.4 Exploring the toplogical relationship of the important microbes
6. Exploring the embedding & grouping in MEGMA
6.1 Microbial embedding
6.1.1 Manifold embedding
6.1.2 Ramdom embedding
6.2 Microbial grouping
6.2.1 Hierarchical clustering tree based grouping
6.2.2 Taxonomic tree based grouping
Performances
Modules
aggmap package
Subpackages
aggmap.aggmodel package
Submodules
aggmap.aggmodel.cbks module
aggmap.aggmodel.explain_dev module
aggmap.aggmodel.explainer module
aggmap.aggmodel.loss module
aggmap.aggmodel.net module
Module contents
aggmap.utils package
Submodules
aggmap.utils.calculator module
aggmap.utils.distances module
aggmap.utils.gen_nwk module
aggmap.utils.logtools module
aggmap.utils.matrixopt module
aggmap.utils.multiproc module
aggmap.utils.summary module
aggmap.utils.vismap module
Module contents
Submodules
aggmap.AggMapNet module
aggmap.map module
aggmap.show module
Module contents
aggmap.utils package
Submodules
aggmap.utils.calculator module
aggmap.utils.distances module
aggmap.utils.gen_nwk module
aggmap.utils.logtools module
aggmap.utils.matrixopt module
aggmap.utils.multiproc module
aggmap.utils.summary module
aggmap.utils.vismap module
Module contents
aggmap.aggmodel package
Submodules
aggmap.aggmodel.cbks module
aggmap.aggmodel.explain_dev module
aggmap.aggmodel.explainer module
aggmap.aggmodel.loss module
aggmap.aggmodel.net module
Module contents
aggmap
Performances
Edit on GitHub
Performances
Read the Docs
v: latest
Versions
master
latest
pip
Downloads
On Read the Docs
Project Home
Builds