Search for: All records

The constant emergence of COVID-19 variants reduces the effectiveness of existing vaccines and test kits. Therefore, it is critical to identify conserved structures in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes as potential targets for variant-proof diagnostics and therapeutics. However, the algorithms to predict these conserved structures, which simultaneously fold and align multiple RNA homologs, scale at best cubically with sequence length and are thus infeasible for coronaviruses, which possess the longest genomes (∼30,000 nt) among RNA viruses. As a result, existing efforts on modeling SARS-CoV-2 structures resort to single-sequence folding as well as local folding methods with short window sizes, which inevitably neglect long-range interactions that are crucial in RNA functions. Here we present LinearTurboFold, an efficient algorithm for folding RNA homologs that scales linearly with sequence length, enabling unprecedented global structural analysis on SARS-CoV-2. Surprisingly, on a group of SARS-CoV-2 and SARS-related genomes, LinearTurboFold’s purely in silico prediction not only is close to experimentally guided models for local structures, but also goes far beyond them by capturing the end-to-end pairs between 5 ′ and 3 ′ untranslated regions (UTRs) (∼29,800 nt apart) that match perfectly with a purely experimental work. Furthermore, LinearTurboFold identifies undiscovered conserved structures and conserved accessible regions as potential targets for designing efficient and mutation-insensitive small-molecule drugs, antisense oligonucleotides, small interfering RNAs (siRNAs), CRISPR-Cas13 guide RNAs, and RT-PCR primers. LinearTurboFold is a general technique that can also be applied to other RNA viruses and full-length genome studies and will be a useful tool in fighting the current and future pandemics. 

The present work concerns the transferability of coarse-grained (CG) modeling in reproducing the dynamic properties of the reference atomistic systems across a range of parameters. In particular, we focus on implicit-solvent CG modeling of polymer solutions. The CG model is based on the generalized Langevin equation, where the memory kernel plays the critical role in determining the dynamics in all time scales. Thus, we propose methods for transfer learning of memory kernels. The key ingredient of our methods is Gaussian process regression. By integration with the model order reduction via proper orthogonal decomposition and the active learning technique, the transfer learning can be practically efficient and requires minimum training data. Through two example polymer solution systems, we demonstrate the accuracy and efficiency of the proposed transfer learning methods in the construction of transferable memory kernels. The transferability allows for out-of-sample predictions, even in the extrapolated domain of parameters. Built on the transferable memory kernels, the CG models can reproduce the dynamic properties of polymers in all time scales at different thermodynamic conditions (such as temperature and solvent viscosity) and for different systems with varying concentrations and lengths of polymers. 

Thermal fields exist widely in engineering systems and are critical for engineering operation, product quality and system safety in many industries. An accurate prediction of thermal field distribution, that is, acquiring any location of interest in a thermal field at the present and future time, is essential to provide useful information for the surveillance, maintenance, and improvement of a system. However, thermal field prediction using data acquired from sensor networks is challenging due to data sparsity and missing data problems. To address this issue, we propose a field spatiotemporal prediction approach based on transfer learning techniques by studying the dynamics of a 3D thermal field from multiple homogeneous fields. Our model characterizes the spatiotemporal dynamics of the local thermal field variations by considering the spatiotemporal correlation of the fields and harnessing the information from homogeneous fields to acquire an accurate thermal field distribution in the future. A real case study of thermal fields during grain storage is conducted to validate our proposed approach. Grain thermal field prediction results provide a deep insight of grain quality during storage, which is helpful for the manager of grain storage to make further decisions about grain quality control and maintenance. 

Simultaneous translation has many important application scenarios and attracts much attention from both academia and industry recently. Most existing frameworks, however, have difficulties in balancing between the translation quality and latency, i.e., the decoding policy is usually either too aggressive or too conservative. We propose an opportunistic decoding technique with timely correction ability, which always (over-)generates a certain mount of extra words at each step to keep the audience on track with the latest information. At the same time, it also corrects, in a timely fashion, the mistakes in the former overgenerated words when observing more source context to ensure high translation quality. Experiments show our technique achieves substantial reduction in latency and up to +3.1 increase in BLEU, with revision rate under 8% in Chinese-to-English and English-to-Chinese translation. 

The state-space models (SSMs) are widely used in a variety of areas where a set of observable variables are used to track some latent variables. While most existing works focus on the statistical modeling of the relationship between the latent variables and observable variables or statistical inferences of the latent variables based on the observable variables, it comes to our awareness that an important problem has been largely neglected. In many applications, although the latent variables cannot be routinely acquired, they can be occasionally acquired to enhance the monitoring of the state-space system. Therefore, in this paper, novel dynamic inspection (DI) methods under a general framework of SSMs are developed to identify and inspect the latent variables that are most uncertain. Extensive numeric studies are conducted to demonstrate the effectiveness of the proposed methods.