Protein Evolution with Variational Auto-Encoder (PEVAE)

Requirements

Operation System: Linux (CentOS release 6.9)
Programming language: Python 3.5
Python Package: PyTorch 1.0.0, Numpy 1.15, ete2 3.1.1

Note: Although the souce code in this repository has only been tested on a Linux system, it is expected to be able to run on other operation systems (Windows or Mac) as long as both Python and required packages are installed. To install both Python and required Python packages, we highly recommend readers to first install Anaconda and then install required packages via conda install:

conda install pytorch torchvision -c pytorch
conda install numpy
conda install ete3

Depending on your computer, installing Anaconda can take several minutes to an hour. It should take less than 20 minutes to install pytorch, numpy and ete3 once Anaconda is installed.

Installation

In order to run the following demo, the source code in this repository needs to be downloaded onto your local computer. You can download all the source code via git clone https://github.com/xqding/PEVAE_Paper.git. If the command runs successfully, you should be able to find a new dictory called PEVAE_Paper under the directory where you run the git clone command. You can find all the source code in the directory PEVAE_Paper.

Demo and Reproduction Instructions

The following is a step-by-step instruction to repreduce the results presented in the manuscript. It also serves as a demonstration on how to use the provide script on data of your interest.

Learn a VAE model on a simulated multiple sequence alignment

Steps to run in order

Note: Becuase running the following command, please change your working direcotry to the directory PEVAE_Paper/simulated_msa/.

1. Simulate a multiple sequence alignment.
   Run python ./script/gene_random_tree.py to generate a random phylogenetic tree ./output/random_tree.newick.
   Run python ./script/read_LG_matrix.py to generate the LG amino acid substitute matrix ./output/LG_matrix.pkl
   Run python ./script/simulate_msa.py to simulate a multiple sequence alignment ./output/simulated_msa.pkl based on the phlogenetic tree and LG_matrix generated above.

2. Train a VAE model using the simulated multiple sequence alignment.
   Run python ./script/proc_msa.py to process the multiple sequence alignment into a binary matrix ./output/msa_binary.pkl.
   Run python ./script/train.py to train a VAE model using the binary representation of the multiple sequence alignment. Run python ./script/compute_elbo.py to compute the elbo (approximation of \log p(x)) of training sequence. This script can be used for cross validation.

3. Project sequences into the VAE latent space.
   Run python ./script/analyze_model.py to calculate the latent space coordinates of all the sequences in the multiple sequence alignment.
   Run python ./script/cluster.py to color sequences in the latent space based on their phlogenetic relationships
   Run python ./script/analyze_ancestors.py to ancestral relationship between sequences in latent space.
   Run python ./script/calc_R2_ancestor.py to calculate Pearson correlation coefficient between evolutionary time and positions of sequences in latent space.
   Run python ./script/plot_R2.py to plot the Pearson correlation coefficient calculated above.

Expected output

After running above commands, you shoud be able to get similar figures as the figure 2(E and F) and the figure 3 presented in the manuscript.

Running time

The most time consuming step is step 2 which train a VAE model. It takes about an hour to finish if it is run on a graphical process unit (GPU). It can take several hour to finish it runs on a central processing units (CPUs). Step 1 and 3 only takes minutes.

Learn a VAE model on a multiple sequence alignment of a protein family from Pfam

Steps to run in order

Note: Becuase running the following command, please change your working direcotry to the directory PEVAE_Paper/pfam_msa/.

1. Download the multiple sequence alignment given a Pfam id
   You can either run python ./script/download_MSA.py --Pfam_id PF00041 or go to Pfam website to download the sequence alignment.

2. Train a VAE model using the simulated multiple sequence alignment.
   Run python ./script/proc_msa.py to process the alignment
   Run python ./script/train.py --num_epoch 10000 --weight_decay 0.01 to train a VAE model of the multiple sequence alignment.

3. Project sequences into the VAE latent space.
   Run python ./script/analyze_model.py to project sequences into latent space.

Expected output

After running above commands, you shoud be able to get similar figures as the figure 2(A and B) and the figure 4(A and B) presented in the manuscript.

Running time

The most time consuming step is step 2 which train a VAE model. It takes about an hour to finish if it is run on a graphical process unit (GPU). It can take several hour to finish it runs on a central processing units (CPUs). Step 1 and 3 only takes minutes.