physbo 2.0.0__cp310-cp310-macosx_12_0_arm64.whl

physbo/variable.py

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+# SPDX-License-Identifier: MPL-2.0
+# Copyright (C) 2020- The University of Tokyo
+#
+# This Source Code Form is subject to the terms of the Mozilla Public
+# License, v. 2.0. If a copy of the MPL was not distributed with this
+# file, You can obtain one at https://mozilla.org/MPL/2.0/.
+
+import numpy as np
+
+
+class variable(object):
+    def __init__(self, X=None, t=None, Z=None):
+        """
+
+        Parameters
+        ----------
+        X:  numpy array
+            N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of each search candidate.
+        t:  numpy array
+            N dimensional array. The negative energy of each search candidate (value of the objective function to be optimized).
+        Z:
+
+        """
+        self.X = X
+        self.Z = Z
+        self.t = t
+
+    def get_subset(self, index):
+        """
+        Getting subset of variables.
+
+        Parameters
+        ----------
+        index: int or array of int
+            Index of selected action.
+        Returns
+        -------
+        variable: physbo.variable
+        """
+        temp_X = self.X[index, :] if self.X is not None else None
+        temp_t = self.t[index] if self.t is not None else None
+        temp_Z = self.Z[index, :] if self.Z is not None else None
+
+        return variable(X=temp_X, t=temp_t, Z=temp_Z)
+
+    def delete(self, num_row):
+        """
+        Deleting variables of X, t, Z whose indexes are specified by num_row.
+
+        Parameters
+        ----------
+        num_row: numpy array
+            Index array to be deleted.
+
+        Returns
+        -------
+
+        """
+        self.delete_X(num_row)
+        self.delete_t(num_row)
+        self.delete_Z(num_row)
+
+    def add(self, X=None, t=None, Z=None):
+        """
+        Adding variables of X, t, Z.
+
+        Parameters
+        ----------
+        X:  numpy array
+            N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of each search candidate.
+        t:  numpy array
+            N dimensional array. The negative energy of each search candidate (value of the objective function to be optimized).
+        Z
+
+        Returns
+        -------
+
+        """
+        self.add_X(X)
+        self.add_t(t)
+        self.add_Z(Z)
+
+    def delete_X(self, num_row):
+        """
+        Deleting variables of X whose indexes are specified by num_row.
+
+
+        Parameters
+        ----------
+        num_row: numpy array
+            Index array to be deleted.
+
+        Returns
+        -------
+
+        """
+        if self.X is not None:
+            self.X = np.delete(self.X, num_row, 0)
+
+    def delete_t(self, num_row):
+        """
+        Deleting variables of t whose indexes are specified by num_row.
+
+        Parameters
+        ----------
+        num_row: numpy array
+            Index array to be deleted.
+
+        Returns
+        -------
+
+        """
+        if self.t is not None:
+            self.t = np.delete(self.t, num_row)
+
+    def delete_Z(self, num_row):
+        """
+        Deleting variables of Z whose indexes are specified by num_row.
+
+        Parameters
+        ----------
+        num_row: numpy array
+            Index array to be deleted.
+
+        Returns
+        -------
+
+        """
+        if self.Z is not None:
+            self.Z = np.delete(self.Z, num_row, 0)
+
+    def add_X(self, X=None):
+        """
+        Adding variable X. If self.X is None, self.X is set as X.
+
+        Parameters
+        ----------
+        X:  numpy array
+            N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of each search candidate.
+
+        Returns
+        -------
+
+        """
+        if X is not None:
+            if self.X is not None:
+                self.X = np.vstack((self.X, X))
+            else:
+                self.X = X
+
+    def add_t(self, t=None):
+        """
+        Adding variable t. If self.t is None, self.t is set as t.
+
+        Parameters
+        ----------
+        t:  numpy array
+            N dimensional array. The negative energy of each search candidate (value of the objective function to be optimized).
+
+        Returns
+        -------
+
+        """
+        if not isinstance(t, np.ndarray):
+            t = np.array([t])
+
+        if t is not None:
+            if self.t is not None:
+                self.t = np.hstack((self.t, t))
+            else:
+                self.t = t
+
+    def add_Z(self, Z=None):
+        """
+        Adding variable Z. If self.Z is None, self.Z is set as Z.
+
+        Parameters
+        ----------
+        Z
+
+        Returns
+        -------
+
+        """
+        if Z is not None:
+            if self.Z is None:
+                self.Z = Z
+            else:
+                self.Z = np.vstack((self.Z, Z))
+
+    def save(self, file_name):
+        """
+        Saving variables X, t, Z to the file.
+
+        Parameters
+        ----------
+        file_name: str
+            A file name for saving variables X, t, Z using numpy.savez_compressed.
+
+        Returns
+        -------
+
+        """
+        np.savez_compressed(file_name, X=self.X, t=self.t, Z=self.Z)
+
+    def load(self, file_name):
+        """
+        Loading variables X, t, Z from the file.
+
+        Parameters
+        ----------
+        file_name: str
+            A file name for loading variables X, t, Z using numpy.load.
+
+        Returns
+        -------
+
+        """
+        data = np.load(file_name, allow_pickle=True)
+        self.X = data["X"]
+        self.t = data["t"]
+        self.Z = data["Z"]

physbo-2.0.0.dist-info/METADATA

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+Metadata-Version: 2.1
+Name: physbo
+Version: 2.0.0
+Summary: optimization tool for PHYSics based on Bayesian Optimization
+Home-page: https://github.com/issp-center-dev/PHYSBO
+Author: PHYSBO developers
+Author-email: physbo-dev@issp.u-tokyo.ac.jp
+License: MPLv2
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+Requires-Dist: numpy <2.0
+Requires-Dist: scipy
+
+# optimization tools for PHYsics based on Bayesian Optimization ( PHYSBO )
+
+Bayesian optimization has been proven as an effective tool in accelerating scientific discovery.
+A standard implementation (e.g., scikit-learn), however, can accommodate only small training data.
+PHYSBO is highly scalable due to an efficient protocol that employs Thompson sampling, random feature maps, one-rank Cholesky update and automatic hyperparameter tuning. Technical features are described in [COMBO's document](https://github.com/tsudalab/combo/blob/master/docs/combo_document.pdf) and [PHYSBO's report](https://doi.org/10.1016/j.cpc.2022.108405) (open access).
+PHYSBO was developed based on [COMBO](https://github.com/tsudalab/combo) for academic use.
+
+## Document
+
+- Stable (master branch)
+    - [English](https://issp-center-dev.github.io/PHYSBO/manual/master/en/index.html)
+    - [日本語](https://issp-center-dev.github.io/PHYSBO/manual/master/ja/index.html)
+- Latest (develop branch)
+    - [English](https://issp-center-dev.github.io/PHYSBO/manual/develop/en/index.html)
+    - [日本語](https://issp-center-dev.github.io/PHYSBO/manual/develop/ja/index.html)
+
+## Required Packages
+
+- Python >= 3.6
+    - No longer tested with Python 3.6
+- NumPy < 2.0.0
+- SciPy
+
+## Install
+
+- From PyPI (recommended)
+
+```bash
+python3 -m pip install physbo
+```
+
+- From source (for developers)
+    1. Update pip (>= 19.0)
+
+        ```bash
+        python3 -m pip install -U pip
+        ```
+
+    1. Download or clone the github repository
+
+        ```
+        git clone https://github.com/issp-center-dev/PHYSBO
+        ```
+
+    1. Install via pip
+
+        ``` bash
+        # ./PHYSBO is the root directory of PHYSBO
+        # pip install options such as --user are avaiable
+
+        python3 -m pip install ./PHYSBO
+        ```
+
+    1. Note: Do not `import physbo` at the root directory of the repository because `import physbo` does not try to import the installed PHYSBO but one in the repository, which includes Cython codes not compiled.
+
+## Uninstall
+
+```bash
+python3 -m pip uninstall physbo
+```
+
+## Usage
+
+['examples/simple.py'](https://github.com/issp-center-dev/PHYSBO/examples/simple.py) is a simple example.
+
+## Data repository
+
+A tutorial and a dataset of a paper about PHYSBO can be found in [PHYSBO Gallery](http://isspns-container.issp.u-tokyo.ac.jp/repo/12).
+
+## License
+
+PHYSBO was developed based on [COMBO](https://github.com/tsudalab/COMBO) for academic use.
+PHYSBO v2 is distributed under Mozilla Public License version 2.0 (MPL v2).
+We hope that you cite the following reference when you publish the results using PHYSBO:
+
+[“Bayesian optimization package: PHYSBO”, Yuichi Motoyama, Ryo Tamura, Kazuyoshi Yoshimi, Kei Terayama, Tsuyoshi Ueno, Koji Tsuda, Computer Physics Communications Volume 278, September 2022, 108405.](https://doi.org/10.1016/j.cpc.2022.108405)
+
+Bibtex
+
+```
+@misc{@article{MOTOYAMA2022108405,
+title = {Bayesian optimization package: PHYSBO},
+journal = {Computer Physics Communications},
+volume = {278},
+pages = {108405},
+year = {2022},
+issn = {0010-4655},
+doi = {https://doi.org/10.1016/j.cpc.2022.108405},
+author = {Yuichi Motoyama and Ryo Tamura and Kazuyoshi Yoshimi and Kei Terayama and Tsuyoshi Ueno and Koji Tsuda},
+keywords = {Bayesian optimization, Multi-objective optimization, Materials screening, Effective model estimation}
+}
+```
+
+### Copyright
+
+© *2020- The University of Tokyo. All rights reserved.*
+This software was developed with the support of \"*Project for advancement of software usability in materials science*\" of The Institute for Solid State Physics, The University of Tokyo.

physbo-2.0.0.dist-info/RECORD

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physbo-2.0.0.dist-info/WHEEL

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+Generator: bdist_wheel (0.43.0)
+Root-Is-Purelib: false
+Tag: cp310-cp310-macosx_12_0_arm64
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physbo-2.0.0.dist-info/top_level.txt

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