Metadata-Version: 2.1
Name: phylodeep
Version: 0.2.61
Summary: Phylodynamic paramater and model inference using pretrained deep neural networks.
Home-page: https://github.com/evolbioinfo/pastml
Author: Jakub Voznica
Author-email: jakub.voznica@pasteur.fr
Maintainer: Anna Zhukova
Maintainer-email: anna.zhukova@pasteur.fr
License: UNKNOWN
Description: # PhyloDeep
        
        PhyloDeep is a python library for parameter estimation and model selection from phylogenetic trees, based on deep learning.
        
        For more information on the method, including the covered parameter subspace, please refer to the preprint here: [bioRxiv](https://www.biorxiv.org/content/10.1101/2021.03.11.435006v1)
        
        Together with the phylodeep package code (in the folder phylodeep), we provide:
        - all data shown in the preprint (in the folder data_publication)
        - used simulators to train deep learners (in the folder simulators)
        - the tree analyzed in the study as a showcase application (in the folder test_tree_HIV_Zurich, for description and 
          original reference see below)
        
        The data are extensive (including 50.000 testing trees), we thus do not recommend copying the whole repository.
        
        The installation time of the package can be up to several minutes, including downloading dependencies. The run time 
        should be a couple of seconds. The package was tested in Linux (Ubuntu 18.08), Windows 10 and MacOS.
        
        ## Installation
        
        PhyloDeep is available for Python 3.6 on [pip](https://pypi.org/project/phylodeep).
        
        
        ### Windows
        For **Windows** users, we recommend installing __phylodeep__ via [Cygwin environment](https://www.cygwin.com/).
        First instal Python 3.6 and pip3 from the Cygwin packages. Then install __phylodeep__:
        ```bash
        pip3 install phylodeep
        ```
        
        ### All other platforms
        
        You can install __phylodeep__ for Python 3.6 with or without [conda](https://conda.io/docs/), following the procedures described below:
        
        #### Installing with conda
        
        Once you have conda installed, create an environment for __phylodeep__ with Python 3.6 (here we name it phyloenv):
        
        ```bash
        conda create --name phyloenv python=3.6
        ```
        
        Then activate it:
        ```bash
        conda activate phyloenv
        ```
        
        Then install __phylodeep__ in it:
        
        ```bash
        pip install phylodeep
        ```
        
        #### Installing without conda
        
        Make sure that Pyhon 3.6 and pip3 are installed, then install __phylodeep__:
        
        ```bash
        pip3 install phylodeep
        ```
        
        ## Usage 
        
        If you installed __phylodeep__ with conda, do not forget to activate the corresponding environment (e.g. phyloenv) before using PhyloDeep:
        ```bash
        conda activate phyloenv
        ```
        
        
        We recommend to perform a priori model adequacy first to assess whether the input data resembles well the 
        simulations on which the neural networks were trained.
        
        Here, we use an HIV tree reconstructed from 200 sequences, published in Phylodynamics on local sexual contact networks 
        by Rasmussen et al in PloS Computational Biology in 2017, and that you can find at [github](./test_tree_HIV_Zurich/Zurich.trees) 
        and in this [repository](https://github.com/evolbioinfo/phylodeep/blob/main/test_tree_HIV_Zurich/Zurich.trees). 
        
        ### Python
        
        ```python
        from phylodeep import BD, BDEI, BDSS, SUMSTATS, FULL
        from phylodeep.checkdeep import checkdeep
        from phylodeep.modeldeep import modeldeep
        from phylodeep.paramdeep import paramdeep
        
        
        path_to_tree = './Zurich.trees'
        
        # set presumed sampling probability
        sampling_proba = 0.25
        
        # a priori check for models BD, BDEI, BDSS
        checkdeep(path_to_tree, model=BD, outputfile_png='BD_a_priori_check.png')
        checkdeep(path_to_tree, model=BDEI, outputfile_png='BDEI_a_priori_check.png')
        checkdeep(path_to_tree, model=BDSS, outputfile_png='BDSS_a_priori_check.png')
        
        
        # model selection
        model_BDEI_vs_BD_vs_BDSS = modeldeep(path_to_tree, sampling_proba, vector_representation=FULL)
        
        # the selected model is BDSS
        
        # parameter inference
        param_BDSS = paramdeep(path_to_tree, sampling_proba, model=BDSS, vector_representation=FULL, 
                                         ci_computation=True)
        
        # for the interpretation of results, please see below
        ```
        
        ### Command line
        
        ```python
        
        # we use here a tree of 200 tips
        
        # a priori model adequacy check: highly recommended
        checkdeep -t ./Zurich.trees -m BD -o BD_model_adequacy.png
        checkdeep -t ./Zurich.trees -m BDEI -o BDEI_model_adequacy.png
        checkdeep -t ./Zurich.trees -m BDSS -o BDSS_model_adequacy.png
        
        # model selection
        modeldeep -t ./Zurich.trees -p 0.25 -v CNN_FULL_TREE -o model_selection.csv
        
        # parameter inference
        paramdeep -t ./Zurich.trees -p 0.25 -m BDSS -v CNN_FULL_TREE -o HIV_Zurich_BDSS_CNN.csv
        paramdeep -t ./Zurich.trees -p 0.25 -m BDSS -v FFNN_SUMSTATS -o HIV_Zurich_BDSS_FFNN_CI.csv -c
        ```
        
        ### Example of output and interpretations
        Here, we use an HIV tree reconstructed from 200 sequences, published in Phylodynamics on local sexual contact networks 
        by Rasmussen et al in PloS Computational Biology in 2017, and that you can find at [github](./test_tree_HIV_Zurich/Zurich.trees)
        
        The a priori model adequacy check results in the following figures:
        
        #### BD model adequacy test
        ![BD model adequacy](./phylodeep/test/BD_model_adequacy.png)
        
        #### BDEI model adequacy test
        ![BDEI model adequacy](./phylodeep/test/BDEI_model_adequacy.png)
        
        #### BDSS model adequacy test
        ![BDSS model adequacy](./phylodeep/test/BDSS_model_adequacy.png)
        
        For the three models (BD, BDEI and BDSS), HIV tree datapoint (represented by a red star) is well inside the data cloud
        of simulations, where warm colors correspond to high density of simulations. The simulations and HIV tree datapoint were
        in the form of summary statistics prior to applying PCA. All three models thus pass the model adequacy check.
        
        We then apply model selection using the full tree representation and obtain the following result:
        
        | Model | Probability BDEI | Probability BD | Probability BDSS |
        | -------- | ------------- | ------------- | ------------- |
        | __Predicted probability__ | 0.00 | 0.00 | 1.00 |
        
        The BDSS probability is by far the highest: it is the BDSS model that is confidently selected
        
        Finally, under the selected model BDSS, we predict parameter values together with 95% CIs:
        
        |  |  R naught  |  Infectious period  |  X transmission  |  Superspreading fraction  |
        | ------------- | ------------- | -------------  |  -------------  | ------- |
        | __predicted value__ | 1.69 |  9.78  | 9.34  |  0.079  |
        | __CI 2.5%__  |  1.40  |  8.12  |  6.65  |  0.050  |
        | __CI 97.5%__  |  2.08  |  12.26  |  10  |  0.133  |
        
        The point estimates for parameters that are no time related (R naught, X transmission and Superspreading fraction) are
        well inside the parameter ranges of simulations and thus seem valid (R naught between 1 and 5, x transmission between 3 
        and 10, superspreading fraction between 0.05 and 0.20). 
        
        
        The time related parameters (infectious and eventually incubation period for BDEI model) are in the same units as the 
        branches of input tree, here in years (9.78 years). The covered parameter space for time related parameters is large 
        due to internal rescaling of all input trees. It should apply to any tree.
        
        ## Preprint
        
        Voznica J, Zhukova A, Boskova V, Saulnier E, Lemoine F, Moslonka-Lefebvre M, Gascuel O (2021)
        __Deep learning from phylogenies to uncover the transmission dynamics of epidemics__. [bioRxiv](https://www.biorxiv.org/content/10.1101/2021.03.11.435006v1)
        
Keywords: phylodynamics,molecular epidemiology,phylogeny,model selection,paramdeep,phylodeep,deep learning,convolutional networks
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Programming Language :: Python :: 3
Description-Content-Type: text/markdown
