1
|
Alavi SF, Chen Y, Hou YF, Ge F, Zheng P, Dral PO. ANI-1ccx-gelu Universal Interatomic Potential and Its Fine-Tuning: Toward Accurate and Efficient Anharmonic Vibrational Frequencies. J Phys Chem Lett 2025; 16:483-493. [PMID: 39748511 DOI: 10.1021/acs.jpclett.4c03031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
Abstract
Calculating anharmonic vibrational modes of molecules for interpreting experimental spectra is one of the most interesting challenges of contemporary computational chemistry. However, the traditional QM methods are costly for this application. Machine learning techniques have emerged as a powerful tool for substituting the traditional QM methods. Universal interatomic potentials (UIPs) hold a particular promise to deliver accurate results at a fraction of the cost of the traditional QM methods, but the performance of UIPs for calculating anharmonic vibrational frequencies remains hitherto unknown. Here we show that despite a known excellent performance of the representative UIP ANI-1ccx for thermochemical properties, it fails for the anharmonic frequencies due to the original unfortunate choice of the activation function. Hence, we recommend evaluating new UIPs on anharmonic frequencies as an additional important quality test. To remedy the shortcomings of ANI-1ccx, we introduce its reformulation ANI-1ccx-gelu with the GELU activation function, which is capable of calculating IR anharmonic frequencies with reasonable accuracy (close to B3LYP/6-31G*). We also show that our new UIP can be fine-tuned to obtain very accurate anharmonic frequencies for some specific molecules but more effort is needed to improve the overall quality of UIP and its capability for fine-tuning. The new UIP will be included as part of our universal and updatable AI-enhanced QM methods (UAIQM) platform and is available together with usage and fine-tuning tutorials in open-source MLatom at https://github.com/dralgroup/mlatom. The calculations can also be performed via a web browser at https://XACScloud.com.
Collapse
Affiliation(s)
- Seyedeh Fatemeh Alavi
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yuxinxin Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yi-Fan Hou
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Fuchun Ge
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Peikun Zheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Pavlo O Dral
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Torun, ul. Grudziądzka 5, 87-100 Torun, Poland
| |
Collapse
|
2
|
Xu X, Li D, Bi J, Moeckel M. AutoML based workflow for design of experiments (DOE) selection and benchmarking data acquisition strategies with simulation models. Sci Rep 2024; 14:32170. [PMID: 39741203 DOI: 10.1038/s41598-024-83581-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Accepted: 12/16/2024] [Indexed: 01/02/2025] Open
Abstract
Design of experiments (DOE) is an established method to allocate resources for efficient parameter space exploration. Model based active learning (AL) data sampling strategies have shown potential for further optimization. This paper introduces a workflow for conducting DOE comparative studies using automated machine learning. Based on a practical definition of model complexity in the context of machine learning, the interplay of systematic data generation and model performance is examined considering various sources of uncertainty: this includes uncertainties caused by stochastic sampling strategies, imprecise data, suboptimal modeling, and model evaluation. Results obtained from electrical circuit models with varying complexity show that not all AL sampling strategies outperform conventional DOE strategies, depending on the available data volume, the complexity of the dataset, and data uncertainties. Trade-offs in resource allocation strategies, in particular between identical replication of data points for statistical noise reduction and broad sampling for maximum parameter space exploration, and their impact on subsequent machine learning analysis are systematically investigated. Results indicate that replication oriented strategies should not be dismissed but may prove advantageous for cases with non-negligible noise impact and intermediate resource availability. The provided workflow can be used to simulate practical experimental conditions for DOE testing and DOE selection.
Collapse
Affiliation(s)
- Xukuan Xu
- Aschaffenburg University of Applied Sciences, Faculty of Engineering, Aschaffenburg, 63743, Germany.
| | - Donghui Li
- Aschaffenburg University of Applied Sciences, Faculty of Engineering, Aschaffenburg, 63743, Germany
| | - Jinghou Bi
- Dresden University of Technology DE, Faculty of Engineering, Dresden, 01069, Germany
| | - Michael Moeckel
- Aschaffenburg University of Applied Sciences, Faculty of Engineering, Aschaffenburg, 63743, Germany
| |
Collapse
|
3
|
Bemporad A. Active Learning for Regression by Inverse Distance Weighting. Inf Sci (N Y) 2023. [DOI: 10.1016/j.ins.2023.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
4
|
Active Learning Query Strategies for Linear Regression Based on Efficient Global Optimization. JOURNAL OF ELECTRICAL AND COMPUTER ENGINEERING 2022. [DOI: 10.1155/2022/2891463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Active learning, a subfield of machine learning, can train a good model by selecting a minimum number of labeled samples. In many machine learning scenarios, needed information (such as the best value in unlabeled datasets) is acquired by prediction. When there is too little data in the training model, the prediction accuracy would obviously affect the accuracy of the results. To establish a high-performance regression model for a small dataset while accelerating the search for the best sample, a new active learning query strategy, EGO-ALR, that combines efficient global optimization (EGO) and active learning for regression (ALR) was proposed. It was found that the performance of EGO-ALR was significantly better than the original ALR query strategies in terms of the root mean square error (RMSE), correlation coefficient (CC), and opportunity cost (Oppo Cost). Specifically, EGO-ALR increased the Oppo Cost by an average of 25.27% when the RMSE and CC values were not more than 1.07% different from the original ALR. This study validated the efficiency and robustness of EGO-ALR approaches using 19 datasets from various domains and three distinct linear regression models (Ridge regression, Lasso, and Elastic network).
Collapse
|
5
|
|
6
|
Schrum M, Connolly MJ, Cole E, Ghetiya M, Gross R, Gombolay MC. Meta-Active Learning in Probabilistically Safe Optimization. IEEE Robot Autom Lett 2022. [DOI: 10.1109/lra.2022.3193497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mariah Schrum
- Institute for Robotics and Intelligent Machines, Georgia Institute of Technology, Atlanta, GA, Georgia
| | - Mark J Connolly
- Department of Bioengineering, Emory University, Atlanta, GA, USA
| | - Eric Cole
- Department of Bioengineering, Emory University, Atlanta, GA, USA
| | - Mihir Ghetiya
- Department of Bioengineering, Emory University, Atlanta, GA, USA
| | - Robert Gross
- Department of Bioengineering, Emory University, Atlanta, GA, USA
| | - Matthew C. Gombolay
- Institute for Robotics and Intelligent Machines, Georgia Institute of Technology, Atlanta, GA, Georgia
| |
Collapse
|
7
|
Abstract
The proliferation of renewable energy sources distributed generation (RES-DG) into the grid results in time-varying inertia constant. To ensure the security of the grid under varying inertia, techniques for fast security assessment are required. In addition, considering the high penetration of RES-DG units into the modern grids, security prediction using varying grid features is crucial. The computation burden concerns of conventional time-domain security assessment techniques make it unsuitable for real-time security prediction. This paper, therefore, proposes a fast security monitoring model that includes security prediction and load shedding for security control. The attributes considered in this paper include the load level, inertia constant, fault location, and power dispatched from the renewable energy sources generator. An incremental Naïve Bayes algorithm is applied on the training dataset developed from the responses of the grid to transient stability simulations. An additive Gaussian process regression (GPR) model is proposed to estimate the load shedding required for the predicted insecure states. Finally, an algorithm based on the nodes’ security margin is proposed to determine the optimal node (s) for the load shedding. The average security prediction and load shedding estimation model training times are 1.2 s and 3 s, respectively. The result shows that the proposed model can predict the security of the grid, estimate the amount of load shed required, and determine the specific node for load shedding operation.
Collapse
|
8
|
Data set quality in Machine Learning: Consistency measure based on Group Decision Making. Appl Soft Comput 2021. [DOI: 10.1016/j.asoc.2021.107366] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
9
|
A nearest neighbor-based active learning method and its application to time series classification. Pattern Recognit Lett 2021. [DOI: 10.1016/j.patrec.2021.03.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
10
|
Liu Z, Jiang X, Luo H, Fang W, Liu J, Wu D. Pool-based unsupervised active learning for regression using iterative representativeness-diversity maximization (iRDM). Pattern Recognit Lett 2021. [DOI: 10.1016/j.patrec.2020.11.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
11
|
Yang Y, Li G, Du D, Huang Q, Sebe N. Embedding Perspective Analysis Into Multi-Column Convolutional Neural Network for Crowd Counting. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2020; 30:1395-1407. [PMID: 33315562 DOI: 10.1109/tip.2020.3043122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The crowd counting is challenging for deep networks due to several factors. For instance, the networks can not efficiently analyze the perspective information of arbitrary scenes, and they are naturally inefficient to handle the scale variations. In this work, we deliver a simple yet efficient multi-column network, which integrates the perspective analysis method with the counting network. The proposed method explicitly excavates the perspective information and drives the counting network to analyze the scenes. More concretely, we explore the perspective information from the estimated density maps and quantify the perspective space into several separate scenes. We then embed the perspective analysis into the multi-column framework with a recurrent connection. Therefore, the proposed network matches various scales with the different receptive fields efficiently. Secondly, we share the parameters of the branches with various receptive fields. This strategy drives the convolutional kernels to be sensitive to the instances with various scales. Furthermore, to improve the evaluation accuracy of the column with a large receptive field, we propose a transform dilated convolution. The transform dilated convolution breaks the fixed sampling structure of the deep network. Moreover, it needs no extra parameters and training, and the offsets are constrained in a local region, which is designed for the congested scenes. The proposed method achieves state-of-the-art performance on five datasets (ShanghaiTech, UCF CC 50, WorldEXPO'10, UCSD, and TRANCOS).
Collapse
|
12
|
Fazakis N, Kostopoulos G, Karlos S, Kotsiantis S, Sgarbas K. An active learning ensemble method for regression tasks. INTELL DATA ANAL 2020. [DOI: 10.3233/ida-194608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Nikos Fazakis
- Department of Electrical and Computer Engineering, University of Patras, Patras, Greece
| | - Georgios Kostopoulos
- Educational Software Development Laboratory, Department of Mathematics, University of Patras, Patras, Greece
| | - Stamatis Karlos
- Department of Mathematics, University of Patras, Patras, Greece
| | - Sotiris Kotsiantis
- Educational Software Development Laboratory, Department of Mathematics, University of Patras, Patras, Greece
| | - Kyriakos Sgarbas
- Department of Electrical and Computer Engineering, University of Patras, Patras, Greece
| |
Collapse
|
13
|
Schrum ML, Gombolay MC. When Your Robot Breaks: Active Learning During Plant Failure. IEEE Robot Autom Lett 2020. [DOI: 10.1109/lra.2019.2961598] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
14
|
|
15
|
Haghighatlari M, Vishwakarma G, Altarawy D, Subramanian R, Kota BU, Sonpal A, Setlur S, Hachmann J. ChemML
: A machine learning and informatics program package for the analysis, mining, and modeling of chemical and materials data. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1458] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mojtaba Haghighatlari
- Department of Chemical and Biological Engineering University at Buffalo, The State University of New York Buffalo New York
| | - Gaurav Vishwakarma
- Department of Chemical and Biological Engineering University at Buffalo, The State University of New York Buffalo New York
| | - Doaa Altarawy
- The Molecular Sciences Software Institute, Virginia Tech Blacksburg Virginia
- Computer and Systems Engineering Department Alexandria University Alexandria Egypt
| | - Ramachandran Subramanian
- Department of Computer Science and Engineering University at Buffalo, The State University of New York Buffalo New York
- Center for Unified Biometrics and Sensors University at Buffalo, The State University of New York Buffalo New York
| | - Bhargava U. Kota
- Department of Computer Science and Engineering University at Buffalo, The State University of New York Buffalo New York
- Center for Unified Biometrics and Sensors University at Buffalo, The State University of New York Buffalo New York
| | - Aditya Sonpal
- Department of Chemical and Biological Engineering University at Buffalo, The State University of New York Buffalo New York
| | - Srirangaraj Setlur
- Department of Computer Science and Engineering University at Buffalo, The State University of New York Buffalo New York
- Center for Unified Biometrics and Sensors University at Buffalo, The State University of New York Buffalo New York
- Center of Excellence for Document Analysis and Recognition, University at Buffalo The State University of New York Buffalo New York
| | - Johannes Hachmann
- Department of Chemical and Biological Engineering University at Buffalo, The State University of New York Buffalo New York
- Computational and Data‐Enabled Science and Engineering Graduate Program University at Buffalo, The State University of New York Buffalo New York
- New York State Center of Excellence in Materials Informatics Buffalo New York
| |
Collapse
|
16
|
Javid M, Hamidzadeh J. An active multi-class classification using privileged information and belief function. INT J MACH LEARN CYB 2019. [DOI: 10.1007/s13042-019-00991-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
17
|
Kazllarof V, Karlos S, Kotsiantis S. Active learning Rotation Forest for multiclass classification. Comput Intell 2019. [DOI: 10.1111/coin.12217] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Stamatis Karlos
- Department of MathematicsUniversity of Patras Rio Patras Greece
| | | |
Collapse
|
18
|
Wu D. Pool-Based Sequential Active Learning for Regression. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2019; 30:1348-1359. [PMID: 30281482 DOI: 10.1109/tnnls.2018.2868649] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Active learning (AL) is a machine-learning approach for reducing the data labeling effort. Given a pool of unlabeled samples, it tries to select the most useful ones to label so that a model built from them can achieve the best possible performance. This paper focuses on pool-based sequential AL for regression (ALR). We first propose three essential criteria that an ALR approach should consider in selecting the most useful unlabeled samples: informativeness, representativeness, and diversity, and compare four existing ALR approaches against them. We then propose a new ALR approach using passive sampling, which considers both the representativeness and the diversity in both the initialization and subsequent iterations. Remarkably, this approach can also be integrated with other existing ALR approaches in the literature to further improve the performance. Extensive experiments on 11 University of California, Irvine, Carnegie Mellon University StatLib, and University of Florida Media Core data sets from various domains verified the effectiveness of our proposed ALR approaches.
Collapse
|
19
|
|
20
|
|
21
|
Zhang Y, Cai W, Wang W, Zhang Y. Stopping Criterion for Active Learning with Model Stability. ACM T INTEL SYST TEC 2018. [DOI: 10.1145/3125645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Active learning selectively labels the most informative instances, aiming to reduce the cost of data annotation. While much effort has been devoted to active sampling functions, relatively limited attention has been paid to when the learning process should stop. In this article, we focus on the stopping criterion of active learning and propose a model stability--based criterion, that is, when a model does not change with inclusion of additional training instances. The challenge lies in how to measure the model change without labeling additional instances and training new models. Inspired by the stochastic gradient update rule, we use the gradient of the loss function at each candidate example to measure its effect on model change. We propose to stop active learning when the model change brought by any of the remaining unlabeled examples is lower than a given threshold. We apply the proposed stopping criterion to two popular classifiers: logistic regression (LR) and support vector machines (SVMs). In addition, we theoretically analyze the stability and generalization ability of the model obtained by our stopping criterion. Substantial experiments on various UCI benchmark datasets and ImageNet datasets have demonstrated that the proposed approach is highly effective.
Collapse
Affiliation(s)
- Yexun Zhang
- Shanghai Jiao Tong University, Shanghai, China
| | | | | | - Ya Zhang
- Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|