Update information on GAUCHE (#437)

* update GAUCHE information * Update README.md Co-authored-by: Aaron Osburg <[email protected]> --------- Co-authored-by: Aaron Osburg <[email protected]>
experimental-design · Sep 6, 2024 · 6d7e065 · 6d7e065
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diff --git a/README.md b/README.md
@@ -122,6 +122,36 @@ We would love for you to use BoFire in your work! If you do, please cite [our pa
       url={https://arxiv.org/abs/2408.05040}, 
     }
 
+Bayesian optimization in BoFire is based on META's [BoTorch library](https://botorch.org/). For BoTorch, please cite also the [botorch paper](https://proceedings.neurips.cc/paper_files/paper/2020/hash/f5b1b89d98b7286673128a5fb112cb9a-Abstract.html):
+
+    @inproceedings{NEURIPS2020_f5b1b89d,
+        author = {Balandat, Maximilian and Karrer, Brian and Jiang, Daniel and Daulton, Samuel and Letham, Ben and Wilson, Andrew G and Bakshy, Eytan},
+        booktitle = {Advances in Neural Information Processing Systems},
+        editor = {H. Larochelle and M. Ranzato and R. Hadsell and M.F. Balcan and H. Lin},
+        pages = {21524--21538},
+        publisher = {Curran Associates, Inc.},
+        title = {BoTorch: A Framework for Efficient Monte-Carlo Bayesian Optimization},
+        url = {https://proceedings.neurips.cc/paper_files/paper/2020/file/f5b1b89d98b7286673128a5fb112cb9a-Paper.pdf},
+        volume = {33},
+        year = {2020}
+    }
+
+For molecular optimizations, BoFire uses the molecular kernels from the [Gauche library](https://github.com/leojklarner/gauche). If you use the molecular kernels in BoFire please cite also the [gauche paper](https://proceedings.neurips.cc/paper_files/paper/2023/hash/f2b1b2e974fa5ea622dd87f22815f423-Abstract-Conference.html):
+
+    @inproceedings{NEURIPS2023_f2b1b2e9,
+        author = {Griffiths, Ryan-Rhys and Klarner, Leo and Moss, Henry and Ravuri, Aditya and Truong, Sang and Du, Yuanqi and Stanton, Samuel and Tom, Gary and Rankovic, Bojana and Jamasb, Arian and Deshwal, Aryan and Schwartz, Julius and Tripp, Austin and Kell, Gregory and Frieder, Simon and Bourached, Anthony and Chan, Alex and Moss, Jacob and Guo, Chengzhi and D\"{u}rholt, Johannes Peter and Chaurasia, Saudamini and Park, Ji Won and Strieth-Kalthoff, Felix and Lee, Alpha and Cheng, Bingqing and Aspuru-Guzik, Alan and Schwaller, Philippe and Tang, Jian},
+        booktitle = {Advances in Neural Information Processing Systems},
+        editor = {A. Oh and T. Naumann and A. Globerson and K. Saenko and M. Hardt and S. Levine},
+        pages = {76923--76946},
+        publisher = {Curran Associates, Inc.},
+        title = {GAUCHE: A Library for Gaussian Processes in Chemistry},
+        url = {https://proceedings.neurips.cc/paper_files/paper/2023/file/f2b1b2e974fa5ea622dd87f22815f423-Paper-Conference.pdf},
+        volume = {36},
+        year = {2023}
+    }
+
+
+
 ## Contributing
 
 See our [Contributing](./CONTRIBUTING.md) guidelines. If you are not sure about something or find bugs, feel free to create an issue.

diff --git a/bofire/kernels/fingerprint_kernels/base_fingerprint_kernel.py b/bofire/kernels/fingerprint_kernels/base_fingerprint_kernel.py
@@ -1,9 +1,30 @@
 """
-Module for test_kernels that operate on fingerprint representations (bit vectors or count vectors).
-Author: Ryan-Rhys Griffiths and Austin Tripp 2022
-"""
+This module was copied from the GAUCHE library(https://github.com/leojklarner/gauche/blob/main/gauche/kernels/fingerprint_kernels/base_fingerprint_kernel.py).
+
+GAUCHE was published under the following license (https://github.com/leojklarner/gauche/blob/main/LICENSE):
+
+MIT License
+
+Copyright (c) 2021 Anonymous Authors
 
-# This code was copied from GAUCHE: https://github.com/leojklarner/gauche/blob/main/gauche/kernels/fingerprint_kernels/base_fingerprint_kernel.py
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+"""
 
 import torch
 from gpytorch.kernels import Kernel

diff --git a/bofire/kernels/fingerprint_kernels/tanimoto_kernel.py b/bofire/kernels/fingerprint_kernels/tanimoto_kernel.py
@@ -1,9 +1,30 @@
 """
-Tanimoto Kernel. Operates on representations including bit vectors e.g. Morgan/ECFP6 fingerprints count vectors e.g.
-RDKit fragment features.
-"""
+This module was copied from the GAUCHE library(https://github.com/leojklarner/gauche/blob/main/gauche/kernels/fingerprint_kernels/tanimoto_kernel.py).
+
+GAUCHE was published under the following license (https://github.com/leojklarner/gauche/blob/main/LICENSE):
+
+MIT License
+
+Copyright (c) 2021 Anonymous Authors
 
-# This code was copied from GAUCHE: https://github.com/leojklarner/gauche/blob/main/gauche/kernels/fingerprint_kernels/tanimoto_kernel.py
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+"""
 
 import torch