Managing Expectations and Imbalanced Training Data in Reactive Force Field Development: An Application to Water Adsorption on Alumina.

J Chem Theory Comput

Center for Molecular Modeling (CMM), Ghent University, Technologiepark-Zwijnaarde 46, Zwijnaarde, B-9052 Ghent, Belgium.

Published: May 2024

ReaxFF is a computationally efficient model for reactive molecular dynamics simulations that has been applied to a wide variety of chemical systems. When ReaxFF parameters are not yet available for a chemistry of interest, they must be (re)optimized, for which one defines a set of training data that the new ReaxFF parameters should reproduce. ReaxFF training sets typically contain diverse properties with different units, some of which are more abundant (by orders of magnitude) than others. To find the best parameters, one conventionally minimizes a weighted sum of squared errors over all of the data in the training set. One of the challenges in such numerical optimizations is to assign weights so that the optimized parameters represent a good compromise among all the requirements defined in the training set. This work introduces a new loss function, called Balanced Loss, and a workflow that replaces weight assignment with a more manageable procedure. The training data are divided into categories with corresponding "tolerances", , acceptable root-mean-square errors for the categories, which define the expectations for the optimized ReaxFF parameters. Through the Log-Sum-Exp form of Balanced Loss, the parameter optimization is also a validation of one's expectations, providing meaningful feedback that can be used to reconfigure the tolerances if needed. The new methodology is demonstrated with a nontrivial parametrization of ReaxFF for water adsorption on alumina. This results in a new force field that reproduces both the rare and frequent properties of a validation set not used for training. We also demonstrate the robustness of the new force field with a molecular dynamics simulation of water desorption from a γ-AlO slab model.

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jctc.3c01009DOI Listing

Publication Analysis

Top Keywords

training data
12
force field
12
reaxff parameters
12
water adsorption
8
adsorption alumina
8
molecular dynamics
8
set training
8
training set
8
balanced loss
8
training
7

Similar Publications

Introduction: Prostate cancer (PCa) is the second most common cancer in men worldwide, with significant incidence and mortality, particularly in Mexico, where diagnosis at advanced stages is common. Early detection through screening methods such as digital rectal examination and prostate-specific antigen testing is essential to improve outcomes. Despite current efforts, compliance with prostate screening (PS) remains low due to several barriers.

View Article and Find Full Text PDF

Food needs and health behaviors in the COVID-19 situation: a case study of quarantined communities in densely populated areas of Bangkok, Thailand.

J Health Popul Nutr

January 2025

Department of General Education, Faculty of Sciences and Health Technology, Navamindradhiraj University, 3 Khao Rd. Vajirapayaban Dusit, Bangkok, 10300, Thailand.

Background: The Thai government's initial response to the novel coronavirus disease 2019 (COVID-19) led to confusion and food insecurity in quarantined low-income communities. Although free food programs were initiated, no official assessment of their impact exists. The objective of this study was to evaluate the effectiveness of these food programs by surveying the food requirements, food needs, and health behaviors of quarantined, densely populated communities in Bangkok.

View Article and Find Full Text PDF

Background: The impact of public health measures against the coronavirus disease 2019 on the rate of childhood immunization has not yet been fully defined. Particularly, measures which directly affect health-seeking behaviors (e.g.

View Article and Find Full Text PDF

Background: Unplanned readmission, a measure of surgical quality, occurs after 4.8% of primary total knee arthroplasties (TKA). Although the prediction of individualized readmission risk may inform appropriate preoperative interventions, current predictive models, such as the American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP) surgical risk calculator (SRC), have limited utility.

View Article and Find Full Text PDF

Supervised machine learning statistical models for visual outcome prediction in macular hole surgery: a single-surgeon, standardized surgery study.

Int J Retina Vitreous

January 2025

Department of Retina and Vitreous, Narayana Nethralaya, #121/C, 1st R Block, Chord Road, Rajaji Nagar, Bengaluru, 560010, India.

Purpose: To evaluate the predictive accuracy of various machine learning (ML) statistical models in forecasting postoperative visual acuity (VA) outcomes following macular hole (MH) surgery using preoperative optical coherence tomography (OCT) parameters.

Methods: This retrospective study included 158 eyes (151 patients) with full-thickness MHs treated between 2017 and 2023 by the same surgeon and using the same intraoperative surgical technique. Data from electronic medical records and OCT scans were extracted, with OCT-derived qualitative and quantitative MH characteristics recorded.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!