mlatom 3.0.1

A Package for Atomistic Simulations with Machine Learning

Brief Introduction

A Package for Atomistic Simulations with Machine Learning

manual: http://mlatom.com/manual/
tutorial: http://mlatom.com/tutorial/

Tasks Performed by MLatom

A brief overview of MLatom capabilities (see above links for more up-to-date version). See sections below for more details.

Tasks

• Estimating accuracy of ML models.
• Creating ML model and saving it to a file.
• Loading existing ML model from a file and performing ML calculations with this model.
• ML-accelerated calculation of absorption spectra within nuclear ensemble approach
• Learning curves
• ML-two photon absorption

Data Set Operations

• Converting XYZ coordinates into an input vector (molecular descriptor) for ML.
• Sampling subsets from a data set.

Sampling

• none: simply splitting the data set into the training, test, and, if necessary, training set into the subtraining and validation sets (in this order) without changing the order of indices.
• random sampling.
• user-defined: requests MLatom to read indices for the training, test, and, if necessary, for the subtraining and validation sets from files.
• structure-based sampling
  • from unsliced and sliced data
• farthest-point traversal iterative procedure , which starts from two points farthest apart.

ML Algorithm

Kernel ridge regression with the following kernels:

• Gaussian .
• Laplacian .
• exponential.
• Matérn ( details of implementation ). Permutationally invariant kernel and self-correction are also supported.

Hybrid QM/ML Approaches

Δ-machine learning .

Molecular Descriptors

• Coulomb matrix
  • sorted by norms of its rows ;
  • unsorted;
  • permuted.
• Normalized inverse internuclear distances (RE descriptor)
  • sorted for user-defined atoms by the sum of their nuclear repulsions to all other atoms;
  • unsorted;
  • permuted.

ML models

The KREG (Kernel-ridge-regression using RE descriptor and the Gaussian kernel function ) model is the default ML method.

General-purpose ML models

• AIQM1 (requires interfaces to other programs as described in http://MLatom.com/AIQM1)
• Models available via interface to TorchANI
  • ANI-1x
  • ANI-1ccx
  • ANI-2x

Model Validation

ML model can be validated (generalization error can be estimated) in several ways:

• on a hold-out test set not used for training. Both training and test sets can be sampled in one of the ways described above;
• by performing N-fold cross-validation. User can define the number of folds N. If N is equal to the number of data points, leave-one-out cross-validation is performed. Only random or no sampling can be used for cross-validation.
• by performing leave-one-out cross-validation (special case of N-fold cross-validation). MLatom prints out mean absolute error (MAE), mean signed error (MSE), root-mean-squared error (RMSE), mean values of reference and estimated values, largest positive and negative outliers, correlation coefficient and its squared value R2 as well as coefficients of linear regression and corresponding standard deviations.

Hyperparameter Tuning

Gaussian, Laplacian, and Matérn kernels have σ and λ tunable hyperparameters. MLatom can determine them by performing user-defined number of iterations of hyperparameter optimization on a logarithmic grid. User can adjust number of grid points, starting and finishing points on the grid. Hyperparameter are tuned to minimize either mean absolute error or root-mean-square error as defined by the user. Hyperparameters can be tuned to minimize

• the error of the ML model trained on the subtraining set in a hold-out validation set. Both subtraining and validation sets are parts of the training set, which can be used at the end with optimal parameters for training the final ML model. These sets ideally should not overlap and can be sampled from the training set in one of the ways described above;
• N-fold cross-validation error. User can define the number of folds N. If N is equal to the number of data points, leave-one-out cross-validation is performed. Only random or no sampling can be used for cross-validation.

Note that hyperparameter tuning can be performed together with model validation. This means that for example one can perform outer loop of the cross-validation for model validation and tune hyperparameters via inner loop of the cross-validation.

Apart from natively implemented logarithmic grid search for hyperparameters, MLatom also provides the interface to the hyperopt package implementing hyperparameter optimization using Bayesian methods with Tree-structured Parzen Estimator (TPE).

First Derivatives

MLatom can be also used to estimate first derivatives from an ML model. Two scenarios are possible:

• partial derivatives are calculated for each dimension of given input vectors (analytical derivatives for Gaussian and Matern kernels);
• first derivatives are calculated in XYZ coordinates for input files containing molecular XYZ coordinates (analytical derivatives for the RE and Coulomb matrix descriptors).
• derivatives for interfaced models

UV/vis spectra

MLatom can significantly accelerate the calculation of cross-section with the Nuclear Ensemble Approach (NEA).

In brief, this feature uses fewer QC calculation to achieve higher precision and reduce computational cost. You can find more detail on this paper (please cite it when using this feature):

Bao-Xin Xue, Mario Barbatti, Pavlo O. Dral, Machine Learning for Absorption Cross Sections , J. Phys. Chem. A 2020, 124, 7199–7210. DOI: 10.1021/acs.jpca.0c05310.

Interfaces to 3^rd-party software

MLatom also provides interfaces to some third-party software where extra ML model types are natively implemented. It allows users to access other popular ML model types within MLatom's workflow. Currently available third-party model types are:

• ANI (through TorchANI)
• DeepPot-SE and DPMD (through DeePMD-kit)
• GAP-SOAP (through GAP suite and QUIP)
• PhysNet (through PhysNet)
• sGDML (through sGDML)

About Program

MLatom: a Package for Atomistic Simulations with Machine Learning

Version 3.0.1

Official website: http://mlatom.com/
Manual: http://mlatom.com/manual/
Tutorial: http://mlatom.com/tutorial/

Copyright (c) 2013- Pavlo O. Dral
http://dr-dral.com/

MLatom is a software platform that enables AI-enhanced computational chemistry in a user-friendly manner as it was written by computational chemists for computational chemists. MLatom allows to perform a wide range of simulation tasks with a variety of machine learning and quantum mechanical models and their combinations, through simple and intuitive input files, command line options, and Python API. The platform can be used both as a ready-to-use tool for common computational chemistry simulations and as a Python library for developing custom workflows. More information about MLatom and its developers is on MLatom.com. MLatom can be also used on the XACS cloud computing platform.

License and citations

License

MLatom is an open-source software under the MIT license (modified to request proper citations).

Copyright (c) 2013- Pavlo O. Dral (http://dr-dral.com/)

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. When this Software or its derivatives are used in scientific publications, it shall be cited as:

• Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Mario Barbatti, Olexandr Isayev, Cheng Wang, Bao-Xin Xue, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Lina Zhang, Shuang Zhang, Arif Ullah, Quanhao Zhang, Yanchi Ou. MLatom 3: Platform for machine learning-enhanced computational chemistry simulations and workflows, submitted. Pre-print on arXiv: arXiv:2310.20155v1 [physics.chem-ph]. Check MLatom.com for citation updates.
• Pavlo O. Dral, Fuchun Ge, Bao-Xin Xue, Yi-Fan Hou, Max Pinheiro Jr, Jianxing Huang, Mario Barbatti. MLatom 2: An Integrative Platform for Atomistic Machine Learning. Top. Curr. Chem. 2021, 379, 27.
• Pavlo O. Dral. MLatom: A Program Package for Quantum Chemical Research Assisted by Machine Learning. J. Comput. Chem. 2019, 40, 2339--2347.
• Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Bao-Xin Xue, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Lina Zhang, Arif Ullah, Yanchi Ou, MLatom: A Package for Atomistic Simulations with Machine Learning, version [add version number], Xiamen University, Xiamen, China, 2013-2023. MLatom.com.

The citations for MLatom's interfaces and features shall be eventually included too. See program output, header.py, ref.json, and MLatom.com.

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.

Citations

Citations mentioned above should be included. For convenience, below we provide the citations in the Bibtex format.

@article{MLatom 3,
author = {Dral, Pavlo O. and Ge, Fuchun and Hou, Yi-Fan and Zheng, Peikun and Chen, Yuxinxin and Barbatti, Mario and Isayev, Olexandr and Wang, Cheng and Xue, Bao-Xin and Pinheiro Jr, Max and Su, Yuming and Dai, Yiheng and Chen, Yangtao and Zhang, Shuang and Zhang, Lina and Ullah, Arif and Zhang, Quanhao and Ou, Yanchi},
title = {MLatom 3: Platform for machine learning-enhanced computational chemistry simulations and workflows},
volume = {submitted, Pre-print on arXiv: arXiv:2310.20155v1 [physics.chem-ph]},
type = {Journal Article}
}

@article{MLatom2,
author = {Dral, Pavlo O. and Ge, Fuchun and Xue, Bao-Xin and Hou, Yi-Fan and Pinheiro Jr, Max and Huang, Jianxing and Barbatti, Mario},
title = {MLatom 2: An Integrative Platform for Atomistic Machine Learning},
journal = {Top. Curr. Chem.},
volume = {379},
number = {4},
pages = {27},
DOI = {10.1007/s41061-021-00339-5},
year = {2021},
type = {Journal Article}
}

@article{MLatom1,
author = {Dral, Pavlo O.},
title = {MLatom: A Program Package for Quantum Chemical Research Assisted by Machine Learning},
journal = {J. Comput. Chem.},
volume = {40},
number = {26},
pages = {2339--2347},
DOI = {10.1002/jcc.26004},
year = {2019},
type = {Journal Article}
}

@misc{MLatomProg,
author = {Dral, Pavlo O. and Ge, Fuchun and Hou, Yi-Fan and Zheng, Peikun and Chen, Yuxinxin and Xue, Bao-Xin and Pinheiro Jr, Max and Su, Yuming and Dai, Yiheng and Chen, Yangtao and Zhang, Shuang and Zhang, Lina and Ullah, Arif and Ou, Yanchi},
title = {MLatom: A Package for Atomistic Simulations with Machine Learning},
year = {2013--2023},
type = {Computer Program}
}