Microbial Dynamic

Installation

The code is written for Python 3.6, all dependencies can be installed by

pip install -r requirements.txt

To Run

cd src
python runner_flag.py

Results will be store in src/rslts/clv_group/[datatype]_Dx[Dx] where [datatype] and [Dx] are flags in src/runner_flag.py

Data Format

a python 3 pickle file contains a dict with following items:

• Ytrain: (list of np.array) each np.array, named y_i, represents observations for a training trajectory. y_i has shape (n_observed_days, 1 + Dy), and y_i[:, 0] is the date when the observation is recorded. y_i[:, 1:] are absolute abundance of taxa.
• Ytest: (list of np.array) observations of test set.
• Vtrain: (list of np.array) each np.array, named v_i, represents perturbations for a training trajectory. Similar to observations, v_i has shape (n_perturbation_days, 1 + Dv), and v_i[:, 0] is the date when the perturbations is recorded. v_i[:, 1:] are absolute abundance of taxa. Currently, perturbations are either 1 or 0 (appear or not).
• Vtest: (list of np.array) perturbations of test set.
• counts_train: (list of np.array) each np.array, named c_i, represents total counts of each day for a training trajectory. c_i has shape (n_observed_days).
• counts_test: total counts of test set.

The following items are optional:

• Xtrain: (list of np.array) each np.array, named x_i, represents hidden states for a training trajectory. x_i has shape (n_total_days, Dx), and it's only know for simulation data.
• Xtest: (list of np.array) hidden states of test set.
• A, g, Wv: simulation parameters for interaction, growth rate, and perturbation matrix.
• k_var, k_len: simulation parameters for added gaussian process noise.

To add a new data file

1. prepare a dict meetings the above requirements and dump it to a python 3 pickle file.
2. add the file to src/utils/available_data.py
   • specifies its path, such as group_Dx_2_Dv_0_ntrain_300_Kvar_05_dir = "data/clv_gp/group_interaction/Dx_2_Dy_8_Dv_0_s_1_Kvar_0.3_ntrain_300.p"
   • add it to COUNT_DATA_DICT, such as group_Dx_2_Dv_0_ntrain_300_Kvar_05=group_Dx_2_Dv_0_ntrain_300_Kvar_05_dir