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Machine learning techniques, specifically gradient-enhanced Kriging (GEK), have been implemented for molecular geometry optimization. GEK-based optimization has many advantages compared to conventional-step-restricted second-order truncated expansion-molecular optimization methods. In particular, the surrogate model given by GEK can have multiple stationary points, will smoothly converge to the exact model as the number of sample points increases, and contains an explicit expression for the expected error of the model function at an arbitrary point. Machine learning is, however, associated with abundance of data, contrary to the situation desired for efficient geometry optimizations. In this paper, we demonstrate how the GEK procedure can be utilized in a fashion such that in the presence of few data points, the surrogate surface will in a robust way guide the optimization to a minimum of a potential energy surface. In this respect, the GEK procedure will be used to mimic the behavior of a conventional second-order scheme but retaining the flexibility of the superior machine learning approach. Moreover, the expected error will be used in the optimizations to facilitate restricted-variance optimizations. A procedure which relates the eigenvalues of the approximate guessed Hessian with the individual characteristic lengths, used in the GEK model, reduces the number of empirical parameters to optimize to two: the value of the trend function and the maximum allowed variance. These parameters are determined using the extended Baker (e-Baker) and part of the Baker transition-state (Baker-TS) test suites as a training set. The so-created optimization procedure is tested using the e-Baker, full Baker-TS, and S22 test suites, at the density functional theory and second-order Møller-Plesset levels of approximation. The results show that the new method is generally of similar or better performance than a state-of-the-art conventional method, even for cases where no significant improvement was expected.
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http://dx.doi.org/10.1021/acs.jctc.0c00257 | DOI Listing |
Stroke
September 2025
Department of Neurology, Yale School of Medicine, New Haven, CT (L.H.S.).
Preclinical stroke research faces a critical translational gap, with animal studies failing to reliably predict clinical efficacy. To address this, the field is moving toward rigorous, multicenter preclinical randomized controlled trials (mpRCTs) that mimic phase 3 clinical trials in several key components. This collective statement, derived from experts involved in mpRCTs, outlines considerations for designing and executing such trials.
View Article and Find Full Text PDFF1000Res
September 2025
Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK.
Background: Subcellular localisation is a determining factor of protein function. Mass spectrometry-based correlation profiling experiments facilitate the classification of protein subcellular localisation on a proteome-wide scale. In turn, static localisations can be compared across conditions to identify differential protein localisation events.
View Article and Find Full Text PDFAnal Methods
September 2025
College of Science, Kunming University of Science and Technology, Kunming, 650500, China.
To address the technical challenges associated with determining the chronological order of overlapping stamps and textual content in forensic document examination, this study proposes a novel non-destructive method that integrates hyperspectral imaging (HSI) with convolutional neural networks (CNNs). A multi-type cross-sequence dataset was constructed, comprising 60 samples of handwriting-stamp sequences and 20 samples of printed text-stamp sequences, all subjected to six months of natural aging. Spectral responses were collected across the 400-1000 nm range in the overlapping regions.
View Article and Find Full Text PDFPeriodontol 2000
September 2025
Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Oral cancer is a major global health burden, ranking sixth in prevalence, with oral squamous cell carcinoma (OSCC) being the most common type. Importantly, OSCC is often diagnosed at late stages, underscoring the need for innovative methods for early detection. The oral microbiome, an active microbial community within the oral cavity, holds promise as a biomarker for the prediction and progression of cancer.
View Article and Find Full Text PDFHum Brain Mapp
September 2025
Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany.
Postoperative aphasia (POA) is a common complication in patients undergoing surgery for language-eloquent lesions. This study aimed to enhance the prediction of POA by leveraging preoperative navigated transcranial magnetic stimulation (nTMS) language mapping and diffusion tensor imaging (DTI)-based tractography, incorporating deep learning (DL) algorithms. One hundred patients with left-hemispheric lesions were retrospectively enrolled (43 developed postoperative aphasia, as the POA group; 57 did not, as the non-aphasia (NA) group).
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