Dataset Information

Faster and More Accurate Geometrical-Optics Optical Force Calculation Using Neural Networks.

ABSTRACT: Optical forces are often calculated by discretizing the trapping light beam into a set of rays and using geometrical optics to compute the exchange of momentum. However, the number of rays sets a trade-off between calculation speed and accuracy. Here, we show that using neural networks permits overcoming this limitation, obtaining not only faster but also more accurate simulations. We demonstrate this using an optically trapped spherical particle for which we obtain an analytical solution to use as ground truth. Then, we take advantage of the acceleration provided by neural networks to study the dynamics of ellipsoidal particles in a double trap, which would be computationally impossible otherwise.

SUBMITTER: Bronte Ciriza D

PROVIDER: S-EPMC9853855 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature

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Faster and More Accurate Geometrical-Optics Optical Force Calculation Using Neural Networks.

Bronte Ciriza David D Magazzù Alessandro A Callegari Agnese A Barbosa Gunther G Neves Antonio A R AAR Iatì Maria Antonia MA Volpe Giovanni G Maragò Onofrio M OM

ACS photonics 20221219 1

Optical forces are often calculated by discretizing the trapping light beam into a set of rays and using geometrical optics to compute the exchange of momentum. However, the number of rays sets a trade-off between calculation speed and accuracy. Here, we show that using neural networks permits overcoming this limitation, obtaining not only faster but also more accurate simulations. We demonstrate this using an optically trapped spherical particle for which we obtain an analytical solution to use ...[more]

PMID: 36691426

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Project description:BackgroundThe prediction of potentially pathogenic variant combinations in patients remains a key task in the field of medical genetics for the understanding and detection of oligogenic/multilocus diseases. Models tailored towards such cases can help shorten the gap of missing diagnoses and can aid researchers in dealing with the high complexity of the derived data. The predictor VarCoPP (Variant Combinations Pathogenicity Predictor) that was published in 2019 and identified potentially pathogenic variant combinations in gene pairs (bilocus variant combinations), was the first important step in this direction. Despite its usefulness and applicability, several issues still remained that hindered a better performance, such as its False Positive (FP) rate, the quality of its training set and its complex architecture.ResultsWe present VarCoPP2.0: the successor of VarCoPP that is a simplified, faster and more accurate predictive model identifying potentially pathogenic bilocus variant combinations. Results from cross-validation and on independent data sets reveal that VarCoPP2.0 has improved in terms of both sensitivity (95% in cross-validation and 98% during testing) and specificity (5% FP rate). At the same time, its running time shows a significant 150-fold decrease due to the selection of a simpler Balanced Random Forest model. Its positive training set now consists of variant combinations that are more confidently linked with evidence of pathogenicity, based on the confidence scores present in OLIDA, the Oligogenic Diseases Database ( https://olida.ibsquare.be ). The improvement of its performance is also attributed to a more careful selection of up-to-date features identified via an original wrapper method. We show that the combination of different variant and gene pair features together is important for predictions, highlighting the usefulness of integrating biological information at different levels.ConclusionsThrough its improved performance and faster execution time, VarCoPP2.0 enables a more accurate analysis of larger data sets linked to oligogenic diseases. Users can access the ORVAL platform ( https://orval.ibsquare.be ) to apply VarCoPP2.0 on their data.

Dataset Information

Faster and More Accurate Geometrical-Optics Optical Force Calculation Using Neural Networks.

Publications

Faster and More Accurate Geometrical-Optics Optical Force Calculation Using Neural Networks.

Similar Datasets

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