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  1. Machine learning represents a milestone in data-driven research, including material informatics, robotics, and computer-aided drug discovery. With the continuously growing virtual and synthetically available chemical space, efficient and robust quantitative structure–activity relationship (QSAR) methods are required to uncover molecules with desired properties. Herein, we propose variable-length-array SMILES-based (VLA-SMILES) structural descriptors that expand conventional SMILES descriptors widely used in machine learning. This structural representation extends the family of numerically coded SMILES, particularly binary SMILES, to expedite the discovery of new deep learning QSAR models with high predictive ability. VLA-SMILES descriptors were shown to speed up the training of QSAR models basedmore »on multilayer perceptron (MLP) with optimized backpropagation (ATransformedBP), resilient propagation (iRPROP‒), and Adam optimization learning algorithms featuring rational train–test splitting, while improving the predictive ability toward the more compute-intensive binary SMILES representation format. All the tested MLPs under the same length-array-based SMILES descriptors showed similar predictive ability and convergence rate of training in combination with the considered learning procedures. Validation with the Kennard–Stone train–test splitting based on the structural descriptor similarity metrics was found more effective than the partitioning with the ranking by activity based on biological activity values metrics for the entire set of VLA-SMILES featured QSAR. Robustness and the predictive ability of MLP models based on VLA-SMILES were assessed via the method of QSAR parametric model validation. In addition, the method of the statistical H0 hypothesis testing of the linear regression between real and observed activities based on the F2,n−2 -criteria was used for predictability estimation among VLA-SMILES featured QSAR-MLPs (with n being the volume of the testing set). Both approaches of QSAR parametric model validation and statistical hypothesis testing were found to correlate when used for the quantitative evaluation of predictabilities of the designed QSAR models with VLA-SMILES descriptors.« less
    Free, publicly-accessible full text available September 1, 2023
  2. Free, publicly-accessible full text available July 25, 2023
  3. Metal-fullerene compounds are characterized by significant electron transfer to the fullerene cage, giving rise to an electric dipole moment. We use the method of electrostatic beam deflection to verify whether such reactions take place within superfluid helium nanodroplets between an embedded C 60 molecule and either alkali (heliophobic) or rare-earth (heliophilic) atoms. The two cases lead to distinctly different outcomes: C 60 Na n ( n = 1–4) display no discernable dipole moment, while C 60 Yb is strongly polar. This suggests that the fullerene and small alkali clusters fail to form a charge-transfer bond in the helium matrix despitemore »their strong van der Waals attraction. The C 60 Yb dipole moment, on the other hand, is in agreement with the value expected for an ionic complex.« less
    Free, publicly-accessible full text available May 4, 2023
  4. We present sharpness-aware minimization (SAM) for fluid dynamics which can efficiently learn the plausible dynamics of liquid splashes. Due to its ability to achieve robust and generalizing solutions, SAM efficiently converges to a parameter set that predicts plausible dynamics of elusive liquid splashes. Our training scheme requires 6 times smaller number of epochs to converge and, 4 times shorter wall-clock time. Our result shows that sharpness of loss function has a close connection to the plausibility of fluid dynamics and suggests further applicability of SAM to machine learning based fluid simulation.
    Free, publicly-accessible full text available April 1, 2023