wilds 1.2.2

WILDS distribution shift benchmark

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Overview

WILDS is a benchmark of in-the-wild distribution shifts spanning diverse data modalities and applications, from tumor identification to wildlife monitoring to poverty mapping.

The WILDS package contains:

1. Data loaders that automatically handle data downloading, processing, and splitting, and
2. Dataset evaluators that standardize model evaluation for each dataset.

In addition, the example scripts contain default models, allowing new algorithms to be easily added and run on all of the WILDS datasets.

For more information, please read our paper or visit our website. For questions and feedback, please post on the discussion board.

Installation

We recommend using pip to install WILDS:

pip install wilds

If you have already installed it, please check that you have the latest version:

python -c "import wilds; print(wilds.__version__)"
# This should print "1.2.2". If it doesn't, update by running:
pip install -U wilds

If you plan to edit or contribute to WILDS, you should install from source:

git clone [e-mail]:p-lambda/wilds.git
cd wilds
pip install -e .

Requirements

• numpy>=1.19.1
• ogb>=1.2.6
• outdated>=0.2.0
• pandas>=1.1.0
• pillow>=7.2.0
• pytz>=2020.4
• torch>=1.7.0
• torch-scatter>=2.0.5
• torch-geometric>=1.6.1
• torchvision>=0.8.2
• tqdm>=4.53.0
• scikit-learn>=0.20.0
• scipy>=1.5.4

Running pip install wilds or pip install -e . will automatically check for and install all of these requirements except for the torch-scatter and torch-geometric packages, which require a quick manual install.

Default models

After installing the WILDS package, you can use the scripts in examples/ to train default models on the WILDS datasets. These scripts are not part of the installed WILDS package. To use them, you should clone the repo (assuming you did not install from source):

git clone [e-mail]:p-lambda/wilds.git

To run these scripts, you will also need to install this additional dependency:

• transformers>=3.5.0

All baseline experiments in the paper were run on Python 3.8.5 and CUDA 10.1.

Using the example scripts

In the examples/ folder, we provide a set of scripts that can be used to download WILDS datasets and train models on them. These scripts are configured with the default models and hyperparameters that we used for all of the baselines described in our paper. All baseline results in the paper can be easily replicated with commands like:

python examples/run_expt.py --dataset iwildcam --algorithm ERM --root_dir data
python examples/run_expt.py --dataset civilcomments --algorithm groupDRO --root_dir data

The scripts are set up to facilitate general-purpose algorithm development: new algorithms can be added to examples/algorithms and then run on all of the WILDS datasets using the default models.

Downloading and training on the WILDS datasets

The first time you run these scripts, you might need to download the datasets. You can do so with the --download argument, for example:

python examples/run_expt.py --dataset civilcomments --algorithm groupDRO --root_dir data --download

Alternatively, you can use the standalone wilds/download_datasets.py script to download the datasets, for example:

python wilds/download_datasets.py --root_dir data

This will download all datasets to the specified data folder. You can also use the --datasets argument to download particular datasets.

These are the sizes of each of our datasets, as well as their approximate time taken to train and evaluate the default model for a single ERM run using a NVIDIA V100 GPU.

Dataset command	Modality	Download size (GB)	Size on disk (GB)	Train+eval time (Hours)
iwildcam	Image	11	25	7
camelyon17	Image	10	15	2
rxrx1	Image	7	7	11
ogb-molpcba	Graph	0.04	2	15
globalwheat	Image	10	10	2
civilcomments	Text	0.1	0.3	4.5
fmow	Image	50	55	6
poverty	Image	12	14	5
amazon	Text	7	7	5
py150	Text	0.1	0.8	9.5

While the camelyon17 dataset is small and fast to train on, we advise against using it as the only dataset to prototype methods on, as the test performance of models trained on this dataset tend to exhibit a large degree of variability over random seeds.

The image datasets (iwildcam, camelyon17, rxrx1, globalwheat, fmow, and poverty) tend to have high disk I/O usage. If training time is much slower for you than the approximate times listed above, consider checking if I/O is a bottleneck (e.g., by moving to a local disk if you are using a network drive, or by increasing the number of data loader workers). To speed up training, you could also disable evaluation at each epoch or for all splits by toggling --evaluate_all_splits and related arguments.

Evaluating trained models

We also provide an evaluation script that aggregates prediction CSV files for different replicates and reports on their combined evaluation. To use this, run:

python examples/evaluate.py <predictions_dir> <output_dir> --root-dir <root_dir>

where <predictions_dir> is the path to your predictions directory, <output_dir> is where the results JSON will be writte, and <root_dir> is the dataset root directory. The predictions directory should have a subdirectory for each dataset (e.g. iwildcam) containing prediction CSV files to evaluate; see our submission guidelines for the format. The evaluation script will skip over any datasets that has missing prediction files. Any dataset not in <root_dir> will be downloaded to <root_dir>.

Reproducibility

We have an executable version of our paper on CodaLab that contains the exact commands, code, and data for the experiments reported in our paper, which rely on these scripts. Trained model weights for all datasets can also be found there. All configurations and hyperparameters can also be found in the examples/configs folder of this repo, and dataset-specific parameters are in examples/configs/datasets.py.

Using the WILDS package

Data

The WILDS package provides a simple, standardized interface for all datasets in the benchmark. This short Python snippet covers all of the steps of getting started with a WILDS dataset, including dataset download and initialization, accessing various splits, and preparing a user-customizable data loader. We discuss data loading in more detail in #Data loading.

>>> from wilds import get_dataset
>>> from wilds.common.data_loaders import get_train_loader
>>> import torchvision.transforms as transforms

# Load the full dataset, and download it if necessary
>>> dataset = get_dataset(dataset='iwildcam', download=True)

# Get the training set
>>> train_data = dataset.get_subset('train',
...                                 transform=transforms.Compose([transforms.Resize((448,448)),
...                                                               transforms.ToTensor()]))

# Prepare the standard data loader
>>> train_loader = get_train_loader('standard', train_data, batch_size=16)

# Train loop
>>> for x, y_true, metadata in train_loader:
...   ...

The metadata contains information like the domain identity, e.g., which camera a photo was taken from, or which hospital the patient's data came from, etc., as well as other metadata.

Domain information

To allow algorithms to leverage domain annotations as well as other groupings over the available metadata, the WILDS package provides Grouper objects. These Grouper objects are helper objects that extract group annotations from metadata, allowing users to specify the grouping scheme in a flexible fashion. They are used to initialize group-aware data loaders (as discussed in #Data loading) and to implement algorithms that rely on domain annotations (e.g., Group DRO). In the following code snippet, we initialize and use a Grouper that extracts the domain annotations on the iWildCam dataset, where the domain is location.

>>> from wilds.common.grouper import CombinatorialGrouper

# Initialize grouper, which extracts domain information
# In this example, we form domains based on location
>>> grouper = CombinatorialGrouper(dataset, ['location'])

# Train loop
>>> for x, y_true, metadata in train_loader:
...   z = grouper.metadata_to_group(metadata)
...   ...

Data loading

For training, the WILDS package provides two types of data loaders. The standard data loader shuffles examples in the training set, and is used for the standard approach of empirical risk minimization (ERM), where we minimize the average loss.

>>> from wilds.common.data_loaders import get_train_loader

# Prepare the standard data loader
>>> train_loader = get_train_loader('standard', train_data, batch_size=16)

To support other algorithms that rely on specific data loading schemes, we also provide the group data loader. In each minibatch, the group loader first samples a specified number of groups, and then samples a fixed number of examples from each of those groups. (By default, the groups are sampled uniformly at random, which upweights minority groups as a result. This can be toggled by the uniform_over_groups parameter.) We initialize group loaders as follows, using Grouper that specifies the grouping scheme.

# Prepare a group data loader that samples from user-specified groups
>>> train_loader = get_train_loader('group', train_data,
...                                 grouper=grouper,
...                                 n_groups_per_batch=2,
...                                 batch_size=16)

Lastly, we also provide a data loader for evaluation, which loads examples without shuffling (unlike the training loaders).

>>> from wilds.common.data_loaders import get_eval_loader

# Get the test set
>>> test_data = dataset.get_subset('test',
...                                 transform=transforms.Compose([transforms.Resize((224,224)),
...                                                               transforms.ToTensor()]))

# Prepare the evaluation data loader
>>> test_loader = get_eval_loader('standard', test_data, batch_size=16)

Evaluators

The WILDS package standardizes and automates evaluation for each dataset. Invoking the eval method of each dataset yields all metrics reported in the paper and on the leaderboard.

>>> from wilds.common.data_loaders import get_eval_loader

# Get the test set
>>> test_data = dataset.get_subset('test',
...                                 transform=transforms.Compose([transforms.Resize((224,224)),
...                                                               transforms.ToTensor()]))

# Prepare the data loader
>>> test_loader = get_eval_loader('standard', test_data, batch_size=16)

# Get predictions for the full test set
>>> for x, y_true, metadata in test_loader:
...   y_pred = model(x)
...   [accumulate y_true, y_pred, metadata]

# Evaluate
>>> dataset.eval(all_y_pred, all_y_true, all_metadata)
{'recall_macro_all': 0.66, ...}

Most eval methods take in predicted labels for all_y_pred by default, but the default inputs vary across datasets and are documented in the eval docstrings of the corresponding dataset class.

Leaderboard

If you are developing new training algorithms and/or models on WILDS, please consider submitting them to our public leaderboard.

Citing WILDS

If you use WILDS datasets in your work, please cite our paper (Bibtex):

• WILDS: A Benchmark of in-the-Wild Distribution Shifts. Pang Wei Koh*, Shiori Sagawa*, Henrik Marklund, Sang Michael Xie, Marvin Zhang, Akshay Balsubramani, Weihua Hu, Michihiro Yasunaga, Richard Lanas Phillips, Irena Gao, Tony Lee, Etienne David, Ian Stavness, Wei Guo, Berton A. Earnshaw, Imran S. Haque, Sara Beery, Jure Leskovec, Anshul Kundaje, Emma Pierson, Sergey Levine, Chelsea Finn, and Percy Liang. ICML 2021.

Please also cite the original papers that introduce the datasets, as listed on the datasets page.

Acknowledgements

The design of the WILDS benchmark was inspired by the Open Graph Benchmark, and we are grateful to the Open Graph Benchmark team for their advice and help in setting up WILDS.