ترغب بنشر مسار تعليمي؟ اضغط هنا

Molecular modeling with machine-learned universal potential functions

127   0   0.0 ( 0 )
 نشر من قبل Junqiu Wu
 تاريخ النشر 2021
والبحث باللغة English




اسأل ChatGPT حول البحث

Molecular modeling is an important topic in drug discovery. Decades of research have led to the development of high quality scalable molecular force fields. In this paper, we show that neural networks can be used to train a universal approximator for energy potential functions. By incorporating a fully automated training process we have been able to train smooth, differentiable, and predictive potential functions on large-scale crystal structures. A variety of tests have also been performed to show the superiority and versatility of the machine-learned model.



قيم البحث

اقرأ أيضاً

72 - Kuan Lee , Ann Yang , Yen-Chu Lin 2021
Biological screens are plagued by false positive hits resulting from aggregation. Thus, methods to triage small colloidally aggregating molecules (SCAMs) are in high demand. Herein, we disclose a bespoke machine-learning tool to confidently and intel ligibly flag such entities. Our data demonstrate an unprecedented utility of machine learning for predicting SCAMs, achieving 80% of correct predictions in a challenging out-of-sample validation. The tool outperformed a panel of expert chemists, who correctly predicted 61 +/- 7% of the same test molecules in a Turing-like test. Further, the computational routine provided insight into molecular features governing aggregation that had remained hidden to expert intuition. Leveraging our tool, we quantify that up to 15-20% of ligands in publicly available chemogenomic databases have the high potential to aggregate at typical screening concentrations, imposing caution in systems biology and drug design programs. Our approach provides a means to augment human intuition, mitigate attrition and a pathway to accelerate future molecular medicine.
Current methods for viral discovery target evolutionarily conserved proteins that accurately identify virus families but remain unable to distinguish the zoonotic potential of newly discovered viruses. Here, we apply an attention-enhanced long-short- term memory (LSTM) deep neural net classifier to a highly conserved viral protein target to predict zoonotic potential across betacoronaviruses. The classifier performs with a 94% accuracy. Analysis and visualization of attention at the sequence and structure-level features indicate possible association between important protein-protein interactions governing viral replication in zoonotic betacoronaviruses and zoonotic transmission.
Solving the wave equation is one of the most (if not the most) fundamental problems we face as we try to illuminate the Earth using recorded seismic data. The Helmholtz equation provides wavefield solutions that are dimensionally reduced, per frequen cy, compared to the time domain, which is useful for many applications, like full waveform inversion (FWI). However, our ability to attain such wavefield solutions depends often on the size of the model and the complexity of the wave equation. Thus, we use here a recently introduced framework based on neural networks to predict functional solutions through setting the underlying physical equation as a loss function to optimize the neural network parameters. For an input given by a location in the model space, the network learns to predict the wavefield value at that location, and its partial derivatives using a concept referred to as automatic differentiation, to fit, in our case, a form of the Helmholtz equation. We specifically seek the solution of the scattered wavefield considering a simple homogeneous background model that allows for analytical solutions of the background wavefield. Providing the neural network (NN) a reasonable number of random points from the model space will ultimately train a fully connected deep NN to predict the scattered wavefield function. The size of the network depends mainly on the complexity of the desired wavefield, with such complexity increasing with increasing frequency and increasing model complexity. However, smaller networks can provide smoother wavefields that might be useful for inversion applications. Preliminary tests on a two-box-shaped scatterer model with a source in the middle, as well as, the Marmousi model with a source on the surface demonstrate the potential of the NN for this application. Additional tests on a 3D model demonstrate the potential versatility of the approach.
Machine-learning models that learn from data to predict how protein sequence encodes function are emerging as a useful protein engineering tool. However, when using these models to suggest new protein designs, one must deal with the vast combinatoria l complexity of protein sequences. Here, we review how to use a sequence-to-function machine-learning surrogate model to select sequences for experimental measurement. First, we discuss how to select sequences through a single round of machine-learning optimization. Then, we discuss sequential optimization, where the goal is to discover optimized sequences and improve the model across multiple rounds of training, optimization, and experimental measurement.
We propose a generalization of neural network sequence models. Instead of predicting one symbol at a time, our multi-scale model makes predictions over multiple, potentially overlapping multi-symbol tokens. A variation of the byte-pair encoding (BPE) compression algorithm is used to learn the dictionary of tokens that the model is trained with. When applied to language modelling, our model has the flexibility of character-level models while maintaining many of the performance benefits of word-level models. Our experiments show that this model performs better than a regular LSTM on language modeling tasks, especially for smaller models.

الأسئلة المقترحة

التعليقات
جاري جلب التعليقات جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
mircosoft-partner

هل ترغب بارسال اشعارات عن اخر التحديثات في شمرا-اكاديميا