behaveml

BehaveML

Machine learning for animal behavior.

Interprets pose-tracking files (currently only from DLC) and behavior annotations (currently only from BORIS) to train a behavior classifier, perform unsupervised learning, and other common analysis tasks.

Installation

pip install behaveml

Can install optional extras with:

pip install numpy, cython
pip install behaveml[all]

This includes matplotlib, keras, and Linderman lab's state-space model package, ssm. Note that installing ssm requires cython and numpy for the build, so must be already present in the environment.

Quickstart

Import

from glob import glob 
from behaveml import VideosetDataFrame, clone_metadata
from behaveml import compute_dl_probability_features, compute_mars_features
from behaveml.io import get_sample_data_paths

Gather the DLC and BORIS tracking and annotation files

tracking_files, boris_files = get_sample_data_paths()

Setup some parameters

frame_width = 20                 # (float) length of entire horizontal shot
frame_width_units = 'in'         # (str) units frame_width is given in
fps = 30                         # (int) frames per second
resolution = (1200, 1600)        # (tuple) HxW in pixels

Create a parameter object and video dataset

metadata = clone_metadata(tracking_files, 
                          label_files = boris_files, 
                          frame_width = frame_width, 
                          fps = fps, 
                          frame_width_units = frame_width_units, 
                          resolution = resolution)

animal_renamer = {'adult': 'resident', 'juvenile':'intruder'}

dataset = VideosetDataFrame(metadata, animal_renamer=animal_renamer)

Now create features on this dataset

dataset.add_features(compute_dl_probability_features, 
                     featureset_name = '1dcnn', 
                     add_to_features = True)

dataset.add_features(compute_mars_features, 
                     featureset_name = 'MARS', 
                     add_to_features = True)

Now access a features table, labels, and groups for learning with dataset.features, dataset.labels, dataset.groups. From here it's easy to use some ML libraries to predict behavior. For example:

from sklearn.ensemble import ExtraTreesClassifier, RandomForestClassifier
from sklearn.model_selection import cross_val_predict
from sklearn.metrics import accuracy_score

model = RandomForestClassifier()
predictions = cross_val_predict(model, dataset.features, dataset.labels, dataset.groups)
score = accuracy_score(dataset.labels, predictions)

Features

• Quickly generate a movie