Semi-supervised sequence modeling

A collection of tools (daart) for analyzing behavioral data. This repo currently supports fitting the following types of models on behavioral time series data:

• Dense MLP network with initial 1D convolutional layer
• RNNs - both LSTMs and GRUs
• Temporal Convolutional Networks (TCNs)

Installation

First you'll have to install the git package in order to access the code on github. Follow the directions here for your specific OS. Then, in the command line, navigate to where you'd like to install the semi-supervised-sequence-modeling package and move into that directory:

$: git clone /~https://github.com/neelimishra/semi-supervised-sequence-modeling
$: cd semi-supervised-sequence-modeling

Next, follow the directions here to install the conda package for managing development environments. Then, create a conda environment:

$: conda create --name=semi-supervised-sequence-modeling python=3.6
$: conda activate semi-supervised-sequence-modeling
(semi-supervised-sequence-modeling) $: pip install -r requirements.txt 

To make the package modules visible to the python interpreter, locally run pip install from inside the main semi-supervised-sequence-modeling directory:

(semi-supervised-sequence-modeling) $: pip install -e .

To be able to use this environment for jupyter notebooks:

(semi-supervised-sequence-modeling) $: python -m ipykernel install --user --name semi-supervised-sequence-modeling

Getting started

To fit models from the command line using test-tube for hyperparameter searching and model fitting, see fit_models.py in the examples directory. This script fits one or more models based on three yaml configuration files: one describing the data, one describing the model, and one describing the training procedure. Example configuration files can be found in the configs directory.

Note: Test-tube will automatically perform a hyperparameter search over any field that is provided as a list; for example, in the model.yaml file, change n_hid_layers: 1 to n_hid_layers: [1, 2, 3] to search over the number of hidden layers in the model.

Once you have set the desired parameters in these files (see comment on data paths below), you can then fit models like so:

(semi-supervised-sequence-modeling) $: python fit_models.py --data_config /path/to/data.yaml 
       --model_config /path/to/model.yaml --train_config /path/to/train.yaml

Data paths

The data.yaml file has a field for listing experiment/session/video ids (expt_ids), as well as a data_dir field. The fit_models.py script assumes data is stored in the following way, though this can easily be adapted by changing the appropriate lines in a copy of the fit_example.py script:

• markers: data_dir/[expt_id]_markers.csv or data_dir/[expt_id]_markers.h5; the standard file formats used by DLC/DGP are currently supported.

• hand labels: data_dir/[expt_id]_labels-hand.csv; a binary matrix of shape (T, n_classes + 1), where the first column represents the background class; the gradients contributed by these time points are zeroed out during training.

• heuristic labels: data_dir/[expt_id]_labels-heuristic.csv; an array of shape (T,) that contains the single discrete state assigned to each time point; 0 corresponds to background class.