# Getting started#

## Featurizing a MOF#

from mofdscribe.chemistry.racs import RACS
from pymatgen.core import Structure

s = Structure.from_file(<my_cif>)
featurizer = RACS()
features = featurizer.featurize(s)


mofdscribe base classes

Most featurizers in mofdscribe inherit from MOFBaseFeaturizer. This class can also handle the conversion to primitive cells if you pass primitive=True to the constructor. This can be useful to save computational time but also make it possible to, e.g., use the sum aggregation.

To avoid re-computation of the primitive cell, you should use the MOFMultipleFeaturizer for combining multiple featurizers. This will accept a keyword argument primitive=True in the constructor and then compute the primitive cell once and use it for all the featurizers.

It is also easy to combine multiple featurizers into a single pipeline:

from mofdscribe.chemistry.racs import RACS
from mofdscribe.pore.geometric_properties import PoreDiameters
from pymatgen.core import Structure
from mofdscribe.featurizers.base import MOFMultipleFeaturizer

s = Structure.from_file(<my_cif>)
featurizer = MOFMultipleFeaturizer([RACS(), PoreDiameters()])
features = featurizer.featurize(s)


You can, of course, also pass multiple structures to the featurizer (and the featurization is automatically parallelized via matminer):

s = Structure.from_file(<my_cif>)
s2 = Structure.from_file(<my_cif2>)
features = featurizer.featurize_many([s, s2])


And, clearly, you can also use the mofdscribe featurizers alongside ones from matminer:

from matminer.featurizers.structure import LocalStructuralOrderParams
from mofdscribe.chemistry.racs import RACS

featurizer = MOFMultipleFeaturizer([RACS(), LocalStructuralOrderParams()])
features = featurizer.featurize_many([s, s2])


If you use the zeo++ or raspa2 packages, you can customize the temporary directory used by the featurizers by exporting MOFDSCRIBE_TEMPDIR. If you do not specify the temporary directory, the default is the current working directory.

More examples

You can find more examples of how to featurize MOFs in the featurize.ipynb and notebook in the examples folder.

## Using a reference dataset#

mofdscribe contains some de-duplicated structure datasets (with labels) that can be useful to make machine learning studies more comparable. To use a reference dataset, you simply need to instantiate the corresponding object.

from mofdscribe.datasets import CoRE, QMOF
qmof = QMOF() # will use no labels and the latest version of the dataset


Upon first use this will download the datasets into a folder ~/.data/mofdscribe in your home directory. In case of corruption or problems you hence can also try removing the subfolders. The package should automatically download the missing files. Note that the currently implemented datasets are loaded completely into memory. On modern machines this should not be a problem, but it might be if you are resource constrained.

You get also get a specific entry with

qmof.get_structure(1)


mofdscribe tries to reduce the potential for data leakage by dropping duplicates. However, it is not trivial to define what is a duplicate. See Addressing data leakage in digital reticular chemistry for more information.

## Using splitters#

For model validation it is important to use stringent splits into folds. In many cases, a random split is not ideal for materials discovery application, where extrapolation is often more relevant than interpolation. To model extrapolative behavior, one can some splitting strategies implemented in mofdscribe. They all assume StructureDataset() as input.

from mofdscribe.splitters import TimeSplitter, HashSplitter
from mofdscribe.datasets import CoRE

ds = CoRE()

splitter = TimeSplitter(ds)

train_idx, valid_idx, test_idx = splitter.train_valid_test_split(train_frac=0.7, valid_frac=0.1)


All splitters are implemented based on BaseSplitter(). If you want to implement a custom grouping or stratification strategy, you’ll need to implement the

• _get_stratification_col: Should return an ArrayLike object of floats, categories, or ints.

If it is categorical data, the BaseSplitter will handle the discretization.

• _get_groups: Should return an ArrayLike object of categories (integers or strings)

methods.

## Using metrics#

For making machine learning comparable, it is important to report reliable metrics. mofdscribe implements some helpers to make this easier.

One interesting metric is the adversarial validation score, which can be a surrogate for how different two datasets, e.g. a train and a test set, are. Under the hood, this is implemented as a classifier that attempts to learn to distinguish the two datasets. If the two datasets are indistinguishable, the classifier will have a ROC-AUC of 0.5.

from mofdscribe.metrics import AdverserialValidator
from mofdscribe.datasets import CoRE
from mofdscribe.splitters import RandomSplitter

ds = CoRE()

FEATURES = list(ds.available_features)

train_idx, test_idx = RandomSplitter(ds).train_test_split(fract_train=0.8)

ds._df.iloc[test_idx][FEATURES])



However, you cannot only measure how different two datasets are, but also quantify how well your model does. A handy helper function is get_regression_metrics().

from mofdscribe.metrics import get_regression_metrics

metrics = get_regression_metrics(predictions, labels)


Which returns an object with the most relevant regression metrics.

## Running a benchmark#

The benchmarks will run k=5-fold cross validation on the dataset. We chose this over a single split, because this is more robust to randomness (and gives at least some indication of the variance of the estimate).

OOD vs ID

Most benchmarks come in OOD and ID versions. OOD indicates out-of-distribution, and typically involves grouping on a key feature (e.g. density). ID indicates in-distribution, and typically is stratified on the target variable.

Why k-fold CV?

For the benchmarks we decided to use k-fold cross validation. While this is clearly more expensive than a simple holdout split, splits need to be performed multiple times as ML models are unstable [Lones]. This is in particular the case for the relatively small datasets we work with in digital reticular chemistry (for larger datasets repeated holdout splits are less of a problem). One could add more rigor using repeated k-fold cross validation. However, this would result in a large computational overhead. Note that the choice of the k is not trivial, and k=5 is a pragmatic choice, for more details see [Raschka].

Also note that the errorbars one estimates via the standard error of k-fold crossvalidation are often too small. [Varoquaux] However, as [Varoquaux] writes

Cross-validation is not a silver bullet. However, it is the best tool available, because it is the only non-parametric method to test for model generalization.

For running a benchmark with your model, your model must be in the form of a class with fit(idx, structures, y) and predict(idx, structures) methods, for example

class MyDummyModel:
"""Dummy model."""

def __init__(self, lr_kwargs: Optional[Dict] = None):
"""Initialize the model.

Args:
lr_kwargs (Optional[Dict], optional): Keyword arguments
that are passed to the linear regressor.
Defaults to None.
"""
self.model = Pipeline(
[("scaler", StandardScaler()), ("lr", LinearRegression(**(lr_kwargs or {})))]
)

def featurize(self, s: Structure):
"""You might want to use a lookup in some dataframe instead.

Or use some mofdscribe featurizers.
"""
return s.density

def fit(self, idx, structures, y):
x = np.array([self.featurize(s) for s in structures]).reshape(-1, 1)
self.model.fit(x, y)

def predict(self, idx, structures):
x = np.array([self.featurize(s) for s in structures]).reshape(-1, 1)
return self.model.predict(x)


Use dataset in model

If you want to use the dataset in your model class, you might find the patch_in_ds keyword argument of the MOFBench class useful. This will make the dataset available to your model under the ds attribute.

If you want to log any additional information during the fitting process, for instance hyperparameters, you can do so using the log() method, that we also patch into your model.

That is, your model will have a log method to which you can pass a dictionary that will be appended to a list that will appear in the report. In this way, for instance, you can record hyperparameters or other information in each fold.

If you have a model in this form, you can use a bench class.

from mofdscribe.bench.logKHCO2 import LogkHCO2IDBench

bench = LogkHCO2IDBench(MyDummyModel(), name='My great model')
report = bench.bench()
report.save_json(<directory>)
report.save_rst(<directory>)


You can test this using some dummy models implemented in mofdscribe

from mofdscribe.bench.dummy_models import DensityRegressor

logkHCO2_interpolation_density = LogkHCO2IDBench(
DensityRegressor(),
version="v0.0.1",
name="linear density",
features="density",
model_type="linear regression /w polynomial features",
implementation="mofdscribe",
reference="mofdscribe",
)


Reference in BibTeX format

If you provide your reference in BibTeX format, it will appear in a copyable text box in the documentation. That is, it is super easy for others to cite you!

For testing purposes, you can set debug=True in the constructors of the benchmark classes.

Which will generate a report file that you can use to make a pull request for adding your model to the leaderboard.

For this:

1. Fork the repository.

2. Make a new branch (e.g. named add_{modelname}).

3. Add your .json and .rst files to the corresponding bench_results sub folder. Do not change the name of the file, it will be used as unique identifier.

4. Push your branch to the repository.

5. Make a pull request.

Upon your PR, a pull request will ask one of the maintainers for approval for a rebuild of the leaderboard. Once we checked that you include all the important parts and some additional context (e.g. link to an implementation), your model will appear on the leaderboard.

More examples

You can find more examples of how to build benchmarks in the hyperparameter_optimization_in_bench.ipynb and add_model_to_leaderboard.ipynb notebooks in the examples folder.

Do not look at the dataset!

Do not perform hyper-parameter optimization (or model selection) on the dataset used for the benchmark outside the bench loop. This is data leakage.

If you need to perform hyper-parameter optimization, use an approach such as nested-cross validation in the bench loop. Only this allows for fair comparison and only this allows others to reproduce the hyperparameter selection (and, hence, use “fair” hyperparameters when they compare their model with your model as a baseline).

## Referencing datasets and featurizers#

If you use a dataset or featurizers please cite all the references you find in the citations property of the featurizer/dataset.

## Logging#

mofdscribe uses the loguru for logging. By default, logging from mofdscribe is disabled to not interfere with your logs.

However, you can easily customize the logging:

import sys
from loguru import logger

# enable mofdscribe logging
logger.enable("mofdscribe")

# define the logging level
LEVEL = "INFO || DEBUG || WARNING || etc."

# set the handler
# for logging to stdout

In many cases, however, you might find it convenient to simply call enable_logging()
from mofdscribe.helpers import enable_logging

which will enable logging with sane defaults (i.e. logging to stderr for INFO and WARNING levels).