Fast implementation of the MuyGPs Gaussian process hyperparameter estimation algorithm
MuyGPs is a GP estimation method that affords fast hyperparameter optimization by way of performing leave-one-out cross-validation. MuyGPs achieves best-in-class speed and scalability by limiting inference to the information contained in k nearest neighborhoods for prediction locations for both hyperparameter optimization and tuning. This feature affords the optimization of hyperparameters by way of leave-one-out cross-validation, as opposed to the more expensive loglikelihood evaluations requires by similar sparse methods.
Installation
Pip installation instructions:
$ pip install muygpys
To install from source, follow these instructions:
$ git clone [email protected]:LLNL/MuyGPyS.git
$ pip install -e MuyGPyS
Building Docs
Automatically-generated documentation can be found at readthedocs.io.
Doc building instructions:
$ cd /path/to/this/repo/docs
$ pip install -r requirements.txt
$ sphinx-build -b html docs docs/_build/html
Then open the file docs/_build/html/index.html in your browser of choice.
The Basics
Data format
MuyGPyS expects that each train or test observation corresponds to a row index in feature and response matrices. In our examples we assume that train data is bundled into a (train_count, feature_count) feature matrix train_features and a (train_count, response_count) response matrix train_responses. In classification examples we will instead refer to a (train_count, class_count) label matrix train_labels whose rows are one-hot encodings. Our examples will assume that the data is accessible via imaginary getter functions.
Constructing Nearest Neighbor Lookups
MuyGPyS.neighbors.NN_Wrapper is an api for tasking several KNN libraries with the construction of lookup indexes that empower fast training and inference. The wrapper constructor expects the training features, the number of nearest neighbors, and a method string specifying which algorithm to use, as well as any additional kwargs used by the methods. Currently supported implementations include exact KNN using sklearn ("exact") and approximate KNN using hnsw ("hnsw").
Construct exact and approximate KNN data example with k = 10
>>> from MuyGPyS.neighors import NN_Wrapper
>>> train_features = load_train_features() # imaginary getter
>>> nn_count = 10
>>> exact_nbrs_lookup = NN_Wrapper(train_features, nn_count, nn_method="exact", algorithm="ball_tree")
>>> approx_nbrs_lookup = NN_Wrapper(train_features, nn_count, nn_method="hnsw", space="l2", M=16)
These lookup data structures are then usable to find nearest neighbors of queries in the training data.
Sampling Batches of Data
MuyGPyS includes convenience functions for sampling batches of data from existing datasets. These batches are returned in the form of row indices, both of the sampled data as well as their nearest neighbors. Also included is the ability to sample "balanced" batches, where the data is partitioned by class and we attempt to sample as close to an equal number of items from each class as is possible.
Sampling random and balanced (for classification) batches of 100 elements:
>>> from MuyGPyS.optimize.batch import sample_batch, get_balanced_batch
>>> train_labels = load_train_labels() # imaginary getter
>>> batch_count = 200
>>> train_count, _ = train_features.shape
>>> batch_indices, batch_nn_indices = sample_batch(
... exact_nbrs_lookup, batch_count, train_count
... )
>>> train_lookup = np.argmax(train["output"], axis=1)
>>> balanced_indices, balanced_nn_indices = get_balanced_batch(
... exact_nbrs_lookup, train_lookup, batch_count
... ) # Classification only!
These indices and nn_indices arrays are the basic operating blocks of MuyGPyS linear algebraic inference. The elements of indices.shape == (batch_count,) lists all of the row indices into train's matrices corresponding to the sampled data. The rows of nn_indices.shape == (batch_count, nn_count) list the row indices into train's matrices corresponding to the nearest neighbors of the sampled data. While the user need not use MuyGPyS sampling tools to construct these data, they will need to construct similar indices into their data in order to use MuyGPyS.
Setting and Optimizing Hyperparameters
One initializes a MuyGPS object by indicating the kernel, as well as optionally specifying hyperparameters.
Creating a Matern kernel:
>>> from MuyGPyS.gp.muygps import MuyGPS
>>> k_kwargs = {
... "kern": "rbf",
... "metric": "F2",
... "eps": {"val": 1e-5},
... "nu": {"val": 0.38, "bounds": (0.1, 2.5)},
... "length_scale": {"val": 7.2},
... }
>>> muygps = MuyGPS(**k_kwarg)
Hyperparameters can be initialized or reset using dictionary arguments containing the optional "val" and "bounds" keys. "val" sets the hyperparameter to the given value, and "bounds" determines the upper and lower bounds to be used for optimization. If "bounds" is set, "val" can also take the arguments "sample" and "log_sample" to generate a uniform or log uniform sample, respectively. If "bounds" is set to "fixed", the hyperparameter will remain fixed during any optimization. This is the default behavior for all hyperparameters if "bounds" is unset by the user.
One sets hyperparameters such as eps, sigma_sq, as well as kernel-specific hyperparameters, e.g. nu and length_scale for the Matern kernel, at initialization as above. All hyperparameters other than sigma_sq are assumed to be fixed unless otherwise specified.
MuyGPyS depends upon linear operations on specially-constructed tensors in order to efficiently estimate GP realizations. Constructing these tensors depends upon the nearest neighbor index matrices that we described above. We can construct a distance tensor coalescing all of the square pairwise distance matrices of the nearest neighbors of a batch of points. This snippet constructs a Euclidean distance tensor.
>>> from MuyGPyS.gp.distance import pairwise_distances
>>> pairwise_dists = pairwise_distances(
... train_features, batch_nn_indices, metric="l2"
... )
We can similarly construct a matrix coalescing all of the distance vectors between the same batch of points and their nearest neighbors.
>>> from MuyGPyS.gp.distance import crosswise_distances
>>> crosswise_dists = crosswise_distances(
... train_features,
... train_features,
... batch_indices,
... batch_nn_indices,
... metric='l2',
... )
We can easily realize kernel tensors using a MuyGPS object's kernel functor:
>>> K = muygps.kernel(pairwise_dists)
>>> Kcross = muygps.kernel(crosswise_dists)
We supply a convenient leave-one-out cross-validation utility that internally realizes kernel tensors in this manner.
>>> from MuyGPyS.optimize.chassis.scipy_optimize_from_tensors
>>> scipy_optimize_from_tensors(
... muygps,
... batch_indices,
... batch_nn_indices,
... crosswise_dists,
... pairwise_dists,
... train_labels,
... loss_method="mse",
... verbose=True,
... )
parameters to be optimized: ['nu']
bounds: [[0.1 1. ]]
sampled x0: [0.8858425]
optimizer results:
fun: 0.4797763813693626
hess_inv: <1x1 LbfgsInvHessProduct with dtype=float64>
jac: array([-3.06976666e-06])
message: b'CONVERGENCE: NORM_OF_PROJECTED_GRADIENT_<=_PGTOL'
nfev: 16
nit: 5
njev: 8
status: 0
success: True
x: array([0.39963594])
If you do not need to keep the distance tensors around for reference, you can use a related function:
>>> from MuyGPyS.optimize.chassis.scipy_optimize_from_indices
>>> scipy_optimize_from_indices(
... muygps,
... batch_indices,
... batch_nn_indices,
... train_features,
... test_features,
... train_labels,
... loss_method="mse",
... verbose=False,
... )
One-line model creation
The library also provides one-line APIs for creating MuyGPs models intended for regression and classification. The functions are MuyGPyS.examples.regress.make_regressor and MuyGPyS.examples.classify.make_classifier, respectively. These functions provide convenient mechanisms for specifying and optimizing models if you have no need to later reference their intermediate data structures (such as the training batches or their distance tensors). They return only the trained MuyGPyS.gp.muygps.MuyGPS model and the MuyGPyS.neighbors.NN_Wrapper neighbors lookup data structure.
An example regressor. In order to automatically train sigma_sq, set k_kwargs["sigma_sq"] = "learn". Note that this is the default behavior, and sigma_sq is the only hyperparameter assumed to be a training target by default.
>>> from MuyGPyS.examples.regress import make_regressor
>>> train_features, train_responses = load_train() # imaginary train getter
>>> test_features, test_responses = load_test() # imaginary test getter
>>> nn_kwargs = {"nn_method": "exact", "algorithm": "ball_tree"}
>>> k_kwargs = {
... "kern": "rbf",
... "metric": "F2",
... "eps": {"val": 1e-5},
... "nu": {"val": 0.38, "bounds": (0.1, 2.5)},
... "length_scale": {"val": 7.2},
... "sigma_sq": "learn",
... }
>>> muygps, nbrs_lookup = make_regressor(
... train_features,
... train_responses,
... nn_count=40,
... batch_size=500,
... loss_method="mse",
... k_kwargs=k_kwargs,
... nn_kwargs=nn_kwargs,
... verbose=False,
... )
An example surrogate classifier.
>>> from MuyGPyS.examples.classify import make_classifier
>>> train_features, train_labels = load_train() # imaginary train getter
>>> nn_kwargs = {"nn_method": "exact", "algorithm": "ball_tree"}
>>> k_kwargs = {
... "kern": "rbf",
... "metric": "F2",
... "eps": {"val": 1e-5},
... "nu": {"val": 0.38, "bounds": (0.1, 2.5)},
... "length_scale": {"val": 7.2},
... }
>>> muygps, nbrs_lookup = make_classifier(
... train_features,
... train_labels,
... nn_count=40,
... batch_size=500,
... loss_method="log",
... k_kwargs=k_kwargs,
... nn_kwargs=nn_kwargs,
... verbose=False,
... )
Multivariate Models
MuyGPyS also supports multivariate models via the MuyGPyS.gp.muygps.MultivariateMuyGPS class, which maintains a separte kernel function for each response dimension. This class is similar in interface to MuyGPyS.gp.muygps.MuyGPS, but requires a list of hyperparameter dicts at initialization. See the following example:
>>> from MuyGPyS.gp.muygps import MultivariateMuyGPS as MMuyGPS
>>> k_args = [
... {
... "eps": {"val": 1e-5},
... "nu": {"val": 0.38, "bounds": (0.1, 2.5)},
... "length_scale": {"val": 7.2},
... },
... {
... "eps": {"val": 1e-5},
... "nu": {"val": 0.67, "bounds": (0.1, 2.5)},
... "length_scale": {"val": 7.2},
... },
... ]
>>> mmuygps = MMuyGPS("matern", **k_args)
Training is similar, and depends upon the same neighbors index datastructures as the singular models. In order to train, one need only loop over the models contained within the multivariate object.
>>> from MuyGPyS.optimize.chassis.scipy_optimize_from_indices
>>> for i, model in mmuygps.models:
>>> scipy_optimize_from_indices(
... model,
... batch_indices,
... batch_nn_indices,
... train_features,
... test_features,
... train_responses[:, i].reshape(train_count, 1),
... loss_method="mse",
... verbose=False,
... )
We also support one-line make functions for regression and classification:
>>> from MuyGPyS.examples.regress import make_multivariate_regressor
>>> train_features, train_responses = load_train() # imaginary train getter
>>> nn_kwargs = {"nn_method": "exact", "algorithm": "ball_tree"}
>>> k_args = [
... {
... "eps": {"val": 1e-5},
... "nu": {"val": 0.38, "bounds": (0.1, 2.5)},
... "length_scale": {"val": 7.2},
... },
... {
... "eps": {"val": 1e-5},
... "nu": {"val": 0.67, "bounds": (0.1, 2.5)},
... "length_scale": {"val": 7.2},
... },
... ]
>>> muygps, nbrs_lookup = make_multivariate_regressor(
... train_features,
... train_responses,
... nn_count=40,
... batch_size=500,
... loss_method="mse",
... kern="matern",
... k_args=k_args,
... nn_kwargs=nn_kwargs,
... verbose=False,
... )
Inference
With set hyperparameters, we are able to use the muygps object to predict the response of test data. Several workflows are supported. See below a simple regression workflow, using the data structures built up in this example:
>>> indices = np.arange(test_count)
>>> nn_indices = train_nbrs_lookup.get_nns(test["input"])
>>> pairwise_dists = pairwise_distances(
... train_features, batch_nn_indices, metric="l2"
... )
>>> crosswise_dists = crosswise_distances(
... test_features,
... train_features,
... indices,
... nn_indices,
... metric='l2',
... )
>>> K = muygps.kernel(pairwise_dists)
>>> Kcross = muygps.kernel(crosswise_dists)
>>> predictions = muygps.regress(K, Kcross, train_responses[nn_indices, :])
Again if you do not want to reuse your tensors, you can run the more compact:
>>> indices = np.arange(test_count)
>>> nn_indices = train_nbrs_lookup.get_nns(test["input"])
>>> muygps.regress_from_indices(
... indices,
... nn_indices,
... test_features,
... train_features,
... train_responses,
... )
Multivariate models support the same functions.
More complex workflows are of course available. See the MuyGPyS.examples high-level API functions for examples.
API Examples
Listed below are several examples using the high-level APIs located in MuyGPyS.examples.classify and MuyGPyS.examples.regress. Note that one need not go through these APIs to use MuyGPyS, but they condense many basic workflows into a single function call. In all of these examples, note that if all of the hyperparameters are fixed in k_kwargs (i.e. you supply no optimization bounds), the API will perform no optimization and will instead simply predict on the data problem using the provided kernel. While these examples all use a single model, one can modify those with multivariate responses to use multivariate models by supplying the additional keyword argument kern=kernel_name, for kernel_name in ['rbf', 'matern'] and providing a list of hyperparameter dicts to the keyword argument k_kwargs as above.
Regression
The following example performs GP regression on the Heaton spatial statistics case study dataset. In the example, load_heaton is a unspecified function that reads in the dataset in the specified dict format. In practice, a user can use any conforming dataset. If one wants to predict on a univariate response as in this example, one must ensure the data is stored as a matrix rather than as a vector, i.e. that train['output'].shape = (train_count, 1). The regression API adds a sigma_sq scale parameter for the variance. One can set sigma_sq using the hyper_dict kwarg like other hyperparameters. The API expects that sigma_sq is a numpy.ndarray with a value associated with each dimension of the response, i.e. that train['output'].shape[1] == len(sigma_sq). In general, one should only manually set sigma_sq if they are certain they know what they are doing.
Regress on Heaton data with no variance
>>> import numpy as np
>>> from MuyGPyS.examples.regress import do_regress
>>> from MuyGPyS.optimize.objective import mse_fn
>>> train_features, train_responses = load_heaton_train() # imaginary train getter
>>> test_features, test_responses = load_heaton_test() # imaginary test getter
>>> nn_kwargs = {"nn_method": "exact", "algorithm": "ball_tree"}
>>> k_kwargs = {
... "kern": "rbf",
... "metric": "F2",
... "eps": {"val": 1e-5},
... "nu": {"val": 0.38, "bounds": (0.1, 2.5)},
... "length_scale": {"val": 7.2},
... }
>>> muygps, nbrs_lookup, predictions = do_regress(
... test_features,
... train_features,
... train_responses,
... nn_count=30,
... batch_size=200,
... loss_method="mse",
... variance_mode=None,
... k_kwargs=k_kwargs,
... nn_kwargs=nn_kwargs,
... verbose=True,
... )
parameters to be optimized: ['nu']
bounds: [[0.1 1. ]]
sampled x0: [0.8858425]
optimizer results:
fun: 0.4797763813693626
hess_inv: <1x1 LbfgsInvHessProduct with dtype=float64>
jac: array([-3.06976666e-06])
message: b'CONVERGENCE: NORM_OF_PROJECTED_GRADIENT_<=_PGTOL'
nfev: 16
nit: 5
njev: 8
status: 0
success: True
x: array([0.39963594])
NN lookup creation time: 0.04974837500000007s
batch sampling time: 0.017116840000000022s
tensor creation time: 0.14439213699999998s
hyper opt time: 2.742181974s
sigma_sq opt time: 5.359999999399179e-07s
prediction time breakdown:
nn time:0.1069446140000001s
agree time:1.9999999967268423e-07s
pred time:10.363597161000001s
finds hyperparameters:
nu : 0.8858424985399979
>>> print(f"mse : {mse_fn(predictions, test_responses)}")
obtains mse: 2.345136495565052
If one requires the (individual, independent) posterior variances for each of the predictions, one can pass variance_mode="diagonal". This mode assumes that each output dimension uses the same model, and so will output an additional vector variance with a scalar posterior variance associated with each test point. The API also returns a (possibly trained) MuyGPyS.gp.MuyGPS or MuyGPyS.gp.MultivariateMuyGPS instance, whose sigma_sq member reports an array of multiplicative scaling parameters associated with the variance of each dimension. Obtaining the tuned posterior variance implies multiplying the returned variance by the scaling parameter along each dimension.
Regress on Heaton data while estimating diagonal variance
>>> import numpy as np
>>> from MuyGPyS.examples.regress import do_regress
>>> from MuyGPyS.optimize.objective import mse_fn
>>> train_features, train_responses = load_heaton_train() # imaginary train getter
>>> test_features, test_responses = load_heaton_test() # imaginary test getter
>>> nn_kwargs = {"nn_method": "exact", "algorithm": "ball_tree"}
>>> k_kwargs = {
... "kern": "rbf",
... "metric": "F2",
... "eps": {"val": 1e-5},
... "nu": {"val": 0.38, "bounds": (0.1, 2.5)},
... "length_scale": {"val": 7.2},
... "sigma_sq": "learn",
... }
>>> muygps, nbrs_lookup, predictions, variance = do_regress(
... test_features,
... train_features,
... train_responses,
... nn_count=30,
... batch_size=200,
... loss_method="mse",
... variance_mode="diagonal",
... k_kwargs=k_kwargs,
... nn_kwargs=nn_kwargs,
... verbose=False,
... )
>>> print(f"mse : {mse_fn(predictions, test_responses)}")
obtains mse: 2.345136495565052
>>> print(f"diagonal posterior variance: {variance * muygps.sigma_sq()}")
diagonal posterior variance: [0.52199482 0.45934382 0.81381388 ... 0.64982631 0.45958342 0.68602048]
Independent diagonal variance for each test item is the only form of posterior variance supported for a single model, and independent diagonal variance for each test item along each response dimension is the only form of posterior variacne supported for a multivariate model. Computing the full posterior covariance between the dimensions of multivariate output is not currently supported, but is planned for a future release. Computing the full posterior covariance between all inputs is not and will not be supported for scalability reasons.
Classification
What follows is an example workflow performing two-class classification with uncertainty quantification. Specific outputs uses a star-galaxy image dataset, where stars are labeled [-1, +1] and galaxies are labeled [+1, -1]. Loading logic is encapsulated in the imaginary load_stargal function. The workflow suffices for any conforming 2-class dataset.
What follows is example code surrounding the invocation of MuyGPyS.examples.classify.do_classify_uq. This function returns GP predictions surrogate_predictions and a list of index masks masks.
Run star-gal with UQ example instructions:
>>> import numpy as np
>>> from MuyGPyS.examples.two_class_classify_uq import do_classify_uq, do_uq, example_lambdas
>>> from MuyGPyS.optimize.objective import mse_fn
>>> train_features, train_labels = load_stargal_train() # imaginary train getter
>>> test_features, test_labels = load_stargal_test() # imaginary test getter
>>> nn_kwargs = {"nn_method": "exact", "algorithm": "ball_tree"}
>>> k_kwargs = {
... "kern": "rbf",
... "metric": "F2",
... "eps": {"val": 1e-5},
... "nu": {"val": 0.38, "bounds": (0.1, 2.5)},
... "length_scale": {"val": 7.2},
... }
>>> muygps, nbrs_lookup, surrogate_predictions, masks = do_classify_uq(
... test_features,
... train_features,
... train_labels,
... nn_count=30,
... opt_batch_size=200,
... uq_batch_size=500,
... loss_method="log",
... variance_mode=None,
... uq_objectives=example_lambdas,
... k_kwargs=k_kwargs,
... nn_kwargs=nn_kwargs,
... verbose=False,
... )
>>> accuracy, uq = do_uq(surrogate_predictions, test_labels, masks)
>>> print(f"obtained accuracy: {accuracy}")
obtained accuracy: 0.973...
>>> print(f"mask uq : \n{uq}")
mask uq :
[[8.21000000e+02 8.53836784e-01 9.87144569e-01]
[8.59000000e+02 8.55646100e-01 9.87528717e-01]
[1.03500000e+03 8.66666667e-01 9.88845510e-01]
[1.03500000e+03 8.66666667e-01 9.88845510e-01]
[5.80000000e+01 6.72413793e-01 9.77972239e-01]]
uq_objectives expects a list of functions of alpha, beta, correct_count, and incorrect_count, where alpha and beta are the number of type I and type II errors, respectively. MuyGPyS.examples.classify.example_lambdas lists some options, but you can supply your own.
If uncertainty quantification is not desired, or the classifcation problem in question involves more than two classes, see instead an example workflow like that in MuyGPyS.examples.classify.do_classify.
Run MNIST without UQ example instructions:
>>> import numpy as np
>>> from MuyGPyS.examples.classify import do_classify
>>> from MuyGPyS.optimize.objective import mse_fn
>>> train_features, train_labels = load_stargal_train() # imaginary train getter
>>> test_features, test_labels = load_stargal_test() # imaginary test getter
>>> nn_kwargs = {"nn_method": "exact", "algorithm": "ball_tree"}
>>> k_kwargs = {
... "kern": "rbf",
... "metric": "F2",
... "eps": {"val": 1e-5},
... "nu": {"val": 0.38, "bounds": (0.1, 2.5)},
... "length_scale": {"val": 7.2},
... }
>>> muygps, nbrs_lookup, surrogate_predictions = do_classify(
... test_features,
... train_features,
... train_labels,
... nn_count=30,
... batch_size=200,
... loss_method="log",
... variance_mode=None,
... k_kwargs=k_kwargs,
... nn_kwargs=nn_kwargs,
... verbose=False,
... )
>>> predicted_labels = np.argmax(surrogate_predictions, axis=1)
>>> true_labels = np.argmax(test_labels, axis=1)
>>> accuracy = np.mean(predicted_labels == true_labels)
>>> print(f"obtained accuracy: {accuracy}")
0.97634
About
Authors
- Benjamin W. Priest (priest2 at llnl dot gov)
- Amanada L. Muyskens (muyskens1 at llnl dot gov)
Papers
MuyGPyS has been used the in the following papers (newest first):
- Gaussian Process Classification fo Galaxy Blend Identification in LSST
- Star-Galaxy Image Separation with Computationally Efficient Gaussian Process Classification
- Star-Galaxy Separation via Gaussian Processes with Model Reduction
Citation
If you use MuyGPyS in a research paper, please reference our article:
@article{muygps2021,
title={MuyGPs: Scalable Gaussian Process Hyperparameter Estimation Using Local Cross-Validation},
author={Muyskens, Amanda and Priest, Benjamin W. and Goumiri, Im{\`e}ne and Schneider, Michael},
journal={arXiv preprint arXiv:2104.14581},
year={2021}
}
License
MuyGPyS is distributed under the terms of the MIT license. All new contributions must be made under the MIT license.
See LICENSE-MIT, NOTICE, and COPYRIGHT for details.
SPDX-License-Identifier: MIT
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