A Gradient-Based Forward Greedy Algorithm for Space Gaussian Process Regression

Author(s):  
Ping Sun ◽  
Xin Yao
Author(s):  
Shiyi Yang ◽  
Soo Jeon ◽  
Jongeun Choi

This paper proposes an efficient greedy algorithm to estimate the object shape within a limited number of sample data (i.e. the touch-down points). Specifically, we treat the object shape as an implicit surface which is defined as the zero level-set of an unknown function and apply Gaussian process to estimate the surface. The mutual information criteria is utilized to decide which point should be sampled in the next iteration. To expedite the estimation process, we implement sequential Gaussian process for computational efficiency and significantly reduce the computational cost by selecting search area based on the estimated level-set variance. We present some simulation results to compare the performance of the proposed algorithm with the random sampling algorithm and demonstrate the improvements in both speed and accuracy over the random sampling algorithm.


2020 ◽  
Author(s):  
Marc Philipp Bahlke ◽  
Natnael Mogos ◽  
Jonny Proppe ◽  
Carmen Herrmann

Heisenberg exchange spin coupling between metal centers is essential for describing and understanding the electronic structure of many molecular catalysts, metalloenzymes, and molecular magnets for potential application in information technology. We explore the machine-learnability of exchange spin coupling, which has not been studied yet. We employ Gaussian process regression since it can potentially deal with small training sets (as likely associated with the rather complex molecular structures required for exploring spin coupling) and since it provides uncertainty estimates (“error bars”) along with predicted values. We compare a range of descriptors and kernels for 257 small dicopper complexes and find that a simple descriptor based on chemical intuition, consisting only of copper-bridge angles and copper-copper distances, clearly outperforms several more sophisticated descriptors when it comes to extrapolating towards larger experimentally relevant complexes. Exchange spin coupling is similarly easy to learn as the polarizability, while learning dipole moments is much harder. The strength of the sophisticated descriptors lies in their ability to linearize structure-property relationships, to the point that a simple linear ridge regression performs just as well as the kernel-based machine-learning model for our small dicopper data set. The superior extrapolation performance of the simple descriptor is unique to exchange spin coupling, reinforcing the crucial role of choosing a suitable descriptor, and highlighting the interesting question of the role of chemical intuition vs. systematic or automated selection of features for machine learning in chemistry and material science.


2018 ◽  
Author(s):  
Caitlin C. Bannan ◽  
David Mobley ◽  
A. Geoff Skillman

<div>A variety of fields would benefit from accurate pK<sub>a</sub> predictions, especially drug design due to the affect a change in ionization state can have on a molecules physiochemical properties.</div><div>Participants in the recent SAMPL6 blind challenge were asked to submit predictions for microscopic and macroscopic pK<sub>a</sub>s of 24 drug like small molecules.</div><div>We recently built a general model for predicting pK<sub>a</sub>s using a Gaussian process regression trained using physical and chemical features of each ionizable group.</div><div>Our pipeline takes a molecular graph and uses the OpenEye Toolkits to calculate features describing the removal of a proton.</div><div>These features are fed into a Scikit-learn Gaussian process to predict microscopic pK<sub>a</sub>s which are then used to analytically determine macroscopic pK<sub>a</sub>s.</div><div>Our Gaussian process is trained on a set of 2,700 macroscopic pK<sub>a</sub>s from monoprotic and select diprotic molecules.</div><div>Here, we share our results for microscopic and macroscopic predictions in the SAMPL6 challenge.</div><div>Overall, we ranked in the middle of the pack compared to other participants, but our fairly good agreement with experiment is still promising considering the challenge molecules are chemically diverse and often polyprotic while our training set is predominately monoprotic.</div><div>Of particular importance to us when building this model was to include an uncertainty estimate based on the chemistry of the molecule that would reflect the likely accuracy of our prediction. </div><div>Our model reports large uncertainties for the molecules that appear to have chemistry outside our domain of applicability, along with good agreement in quantile-quantile plots, indicating it can predict its own accuracy.</div><div>The challenge highlighted a variety of means to improve our model, including adding more polyprotic molecules to our training set and more carefully considering what functional groups we do or do not identify as ionizable. </div>


2019 ◽  
Vol 150 (4) ◽  
pp. 041101 ◽  
Author(s):  
Iakov Polyak ◽  
Gareth W. Richings ◽  
Scott Habershon ◽  
Peter J. Knowles

2020 ◽  
Vol 53 (3) ◽  
pp. 348-353
Author(s):  
Maharshi Dhada ◽  
Georgios M. Hadjidemetriou ◽  
Ajith K. Parlikad

2021 ◽  
Vol 11 (9) ◽  
pp. 4055
Author(s):  
Mahdi S. Alajmi ◽  
Abdullah M. Almeshal

Machining process data can be utilized to predict cutting force and optimize process parameters. Cutting force is an essential parameter that has a significant impact on the metal turning process. In this study, a cutting force prediction model for turning AISI 4340 alloy steel was developed using Gaussian process regression (GPR), support vector machines (SVM), and artificial neural network (ANN) methods. The GPR simulations demonstrated a reliable prediction of surface roughness for the dry turning method with R2 = 0.9843, MAPE = 5.12%, and RMSE = 1.86%. Performance comparisons between GPR, SVM, and ANN show that GPR is an effective method that can ensure high predictive accuracy of the cutting force in the turning of AISI 4340.


2021 ◽  
Vol 15 (1) ◽  
pp. 1147-1158
Author(s):  
Shahab S. Band ◽  
Essam Heggy ◽  
Sayed M. Bateni ◽  
Hojat Karami ◽  
Mobina Rabiee ◽  
...  

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