neheller / labels18

The code associated with our submission to the 3rd Workshop on Large Scale Annotation of Biomedical data and Expert Label Synthesis

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

LABELS 2018 Code

A study of how erroneous training data affects the performance of deep learning systems for semantic segmentation

Usage

usage: model_runner.py [-h] [-n NEW] [-e EXISTING] [-b BATCH_SIZE]
                       [-d DATASET] [-p PERTURBATION] [-g GPU_INDEX]
                       [-m MODEL] [-t [TESTING]] [-v [VISUALIZE]]

Run a training or testing round for our Labels 2018 Submission

optional arguments:
  -h, --help            show this help message and exit
  -n NEW, --new NEW     A name for a new training session from random
                        initialization
  -e EXISTING, --existing EXISTING
                        A name for an existing training session to continue
  -b BATCH_SIZE, --batch_size BATCH_SIZE
                        The batch size to use during training
  -d DATASET, --dataset DATASET
                        The dataset to train/test on either lis or psd
  -p PERTURBATION, --perturbation PERTURBATION
                        The type of perturbations to do to the training data
  -g GPU_INDEX, --gpu GPU_INDEX
                        The GPU to limit this training run to.
  -m MODEL, --model MODEL
                        The architecture to use for this round
  -t [TESTING], --testing [TESTING]
                        Whether this round will be a testing round
  -v [VISUALIZE], --visualize [VISUALIZE]
                        Whether to visualize

Directory Structure

callbacks

A directory of callbacks used during training

  • TopNSaver: Saves top N models during training according to specified metric
  • VizPreds: Visualizes predictions made by model during training

Models

A directory of files which define and compile the models for training

viz

Put an x,y .npy pair here and it will visualize predictions on this data during training

Acknowledgements

About

The code associated with our submission to the 3rd Workshop on Large Scale Annotation of Biomedical data and Expert Label Synthesis


Languages

Language:Python 66.2%Language:Shell 33.8%