Bacillus amyloliquefaciens G1: A Potential Antagonistic Bacterium against Eel-Pathogenic Aeromonas hydrophila

Recent studies have revealed that the use of probiotics is an alternative to control marine aeromonas. However, few probiotics are available against Aeromonas hydrophila infections in eels. In the present study, a potential antagonistic strain G1 against the eel-pathogenic A. hydrophila was isolated from sediment underlying brackish water. Its extracellular products with antibacterial activities were shown to be stable under wide range of pH, temperature, and proteinase K. It was initially identified as Bacillus amyloliquefaciens using API identification kits and confirmed to be B. amyloliquefaciens strain (GenBank accession number DQ422953) by phylogenetic analysis. In addition, it was shown to be safe for mammalians, had a wide anti-A. hydrophila spectrum, and exhibited significant effects on inhibiting the growth of the eel-pathogenic A. hydrophila both in vitro and in vivo. To the best of our knowledge, this is the first report on a promising antagonistic Bacillus amyloliquefaciens strain from brackish water sediment against eel-pathogenic A. hydrophila

Super-resolution reconstruction of digital rock CT images based on residual attention mechanism

Computer tomography technology is widely used in geological exploration because it is a nondestructive and three-dimensional imaging method that can be integrated with computer simulation. However, the large-scale application of the computer tomography technique is limited by economic costs and time consumption. Therefore, it is challenging and intractable to indicate the pore structure characteristics of rock. To address this issue, a super-resolution reconstruction algorithm based on convolutional neural networks, residual learning, and attention mechanism was proposed to generate super-resolution images in this study. This algorithm was applied to the reconstruction of carbonate rock and sandstone. The performance of two-dimensional image reconstruction was evaluated by quantitative extraction and qualitative visualization. The results from experiments indicate that the built model performs well on different upscaling factors and is superior to the existing super-resolution approaches based on convolutional neural network.Cited as: Shan, L., Bai, X., Liu, C., Feng, Y., Liu, Y., Qi, Y. Super-resolution reconstruction of digital rock CT images based on residual attention mechanism. Advances in Geo-Energy Research, 2022, 6(2): 157-168. https://doi.org/10.46690/ager.2022.02.0

Physics-informed machine learning for solving partial differential equations in porous media

Physical phenomenon in nature is generally simulated by partial differential equations. Among different sorts of partial differential equations, the problem of two-phase flow in porous media has been paid intense attention. As a promising direction, physics-informed neural networks shed new light on the solution of partial differential equations. However, current physics-informed neural networks’ ability to learn partial differential equations relies on adding artificial diffusion or using prior knowledge to increase the number of training points along the shock trajectory, or adaptive activation functions. To address these issues, this study proposes a physics-informed neural network with long short-term memory and attention mechanism, an ingenious method to solve the Buckley-Leverett partial differential equations representing two-phase flow in porous media. The designed network structure overcomes the dependency on artificial diffusion terms and enhances the importance of shallow features. The experimental results show that the proposed method is in good agreement with analytical solutions. Accurate approximations are shown even when encountering shock points in saturated fields of porous media. Furthermore, experiments show our innovative method outperforms existing traditional physics-informed machine learning approaches.Cited as: Shan, L., Liu, C., Liu, Y., Tu, Y., Dong, L., Hei, X. Physics-informed machine learning for solving partial differential equations in porous media. Advances in Geo-Energy Research, 2023, 8(1): 37-44. https://doi.org/10.46690/ager.2023.04.0

Facebook Report on Privacy of fNIRS data

The primary goal of this project is to develop privacy-preserving machine learning model training techniques for fNIRS data. This project will build a local model in a centralized setting with both differential privacy (DP) and certified robustness. It will also explore collaborative federated learning to train a shared model between multiple clients without sharing local fNIRS datasets. To prevent unintentional private information leakage of such clients' private datasets, we will also implement DP in the federated learning setting.Comment: 15 pages, 5 figures, 3 table

Auto DP-SGD: Dual Improvements of Privacy and Accuracy via Automatic Clipping Threshold and Noise Multiplier Estimation

DP-SGD has emerged as a popular method to protect personally identifiable information in deep learning applications. Unfortunately, DP-SGD's per-sample gradient clipping and uniform noise addition during training can significantly degrade model utility. To enhance the model's utility, researchers proposed various adaptive DP-SGD methods. However, we examine and discover that these techniques result in greater privacy leakage or lower accuracy than the traditional DP-SGD method, or a lack of evaluation on a complex data set such as CIFAR100. To address these limitations, we propose an Auto DP-SGD. Our method automates clipping threshold estimation based on the DL model's gradient norm and scales the gradients of each training sample without losing gradient information. This helps to improve the algorithm's utility while using a less privacy budget. To further improve accuracy, we introduce automatic noise multiplier decay mechanisms to decrease the noise multiplier after every epoch. Finally, we develop closed-form mathematical expressions using tCDP accountant for automatic noise multiplier and automatic clipping threshold estimation. Through extensive experimentation, we demonstrate that Auto DP-SGD outperforms existing SOTA DP-SGD methods in privacy and accuracy on various benchmark datasets. We also show that privacy can be improved by lowering the scale factor and using learning rate schedulers without significantly reducing accuracy. Specifically, Auto DP-SGD, when used with a step noise multiplier, improves accuracy by 3.20, 1.57, 6.73, and 1.42 for the MNIST, CIFAR10, CIFAR100, and AG News Corpus datasets, respectively. Furthermore, it obtains a substantial reduction in the privacy budget of 94.9, 79.16, 67.36, and 53.37 for the corresponding data sets.Comment: 25 pages single column, 2 figure

TencentPretrain: A Scalable and Flexible Toolkit for Pre-training Models of Different Modalities

Recently, the success of pre-training in text domain has been fully extended to vision, audio, and cross-modal scenarios. The proposed pre-training models of different modalities are showing a rising trend of homogeneity in their model structures, which brings the opportunity to implement different pre-training models within a uniform framework. In this paper, we present TencentPretrain, a toolkit supporting pre-training models of different modalities. The core feature of TencentPretrain is the modular design. The toolkit uniformly divides pre-training models into 5 components: embedding, encoder, target embedding, decoder, and target. As almost all of common modules are provided in each component, users can choose the desired modules from different components to build a complete pre-training model. The modular design enables users to efficiently reproduce existing pre-training models or build brand-new one. We test the toolkit on text, vision, and audio benchmarks and show that it can match the performance of the original implementations