CloudBrain-NMR: An Intelligent Cloud Computing Platform for NMR Spectroscopy Processing, Reconstruction and Analysis

Nuclear Magnetic Resonance (NMR) spectroscopy has served as a powerful analytical tool for studying molecular structure and dynamics in chemistry and biology. However, the processing of raw data acquired from NMR spectrometers and subsequent quantitative analysis involves various specialized tools, which necessitates comprehensive knowledge in programming and NMR. Particularly, the emerging deep learning tools is hard to be widely used in NMR due to the sophisticated setup of computation. Thus, NMR processing is not an easy task for chemist and biologists. In this work, we present CloudBrain-NMR, an intelligent online cloud computing platform designed for NMR data reading, processing, reconstruction, and quantitative analysis. The platform is conveniently accessed through a web browser, eliminating the need for any program installation on the user side. CloudBrain-NMR uses parallel computing with graphics processing units and central processing units, resulting in significantly shortened computation time. Furthermore, it incorporates state-of-the-art deep learning-based algorithms offering comprehensive functionalities that allow users to complete the entire processing procedure without relying on additional software. This platform has empowered NMR applications with advanced artificial intelligence processing. CloudBrain-NMR is openly accessible for free usage at https://csrc.xmu.edu.cn/CloudBrain.html

Resolution enhancement of NMR by decoupling with low-rank Hankel model

Nuclear magnetic resonance (NMR) spectroscopy has become a formidable tool for biochemistry and medicine. Although J-coupling carries essential structural information it may also limit the spectral resolution. Homonuclear decoupling remains a challenging problem. In this work, we introduce a new approach that uses a specific coupling value as prior knowledge, and Hankel property of exponential NMR signal to achieve the broadband heteronuclear decoupling using the low-rank method. Our results on synthetic and realistic HMQC spectra demonstrate that the proposed method not only effectively enhances resolution by decoupling, but also maintains sensitivity and suppresses spectral artefacts. The approach can be combined with the non-uniform sampling, which means that the resolution can be further improved without any extra acquisition time

On the Effectiveness of Sampled Softmax Loss for Item Recommendation

Learning objectives of recommender models remain largely unexplored. Most methods routinely adopt either pointwise or pairwise loss to train the model parameters, while rarely pay attention to softmax loss due to the high computational cost. Sampled softmax loss emerges as an efficient substitute for softmax loss. Its special case, InfoNCE loss, has been widely used in self-supervised learning and exhibited remarkable performance for contrastive learning. Nonetheless, limited studies use sampled softmax loss as the learning objective to train the recommender. Worse still, none of them explore its properties and answer "Does sampled softmax loss suit for item recommendation?" and "What are the conceptual advantages of sampled softmax loss, as compared with the prevalent losses?", to the best of our knowledge. In this work, we aim to better understand sampled softmax loss for item recommendation. Specifically, we first theoretically reveal three model-agnostic advantages: (1) mitigating popularity bias, which is beneficial to long-tail recommendation; (2) mining hard negative samples, which offers informative gradients to optimize model parameters; and (3) maximizing the ranking metric, which facilitates top-K performance. Moreover, we probe the model-specific characteristics on the top of various recommenders. Experimental results suggest that sampled softmax loss is more friendly to history and graph-based recommenders (e.g., SVD++ and LightGCN), but performs poorly for ID-based models (e.g., MF). We ascribe this to its shortcoming in learning representation magnitude, making the combination with the models that are also incapable of adjusting representation magnitude learn poor representations. In contrast, the history- and graph-based models, which naturally adjust representation magnitude according to node degree, are able to compensate for the shortcoming of sampled softmax loss.

Denoising Single Voxel Magnetic Resonance Spectroscopy with Deep Learning on Repeatedly Sampled In Vivo Data

Objective: Magnetic Resonance Spectroscopy (MRS) is a noninvasive tool to reveal metabolic information. One challenge of MRS is the relatively low Signal-Noise Ratio (SNR) due to low concentrations of metabolites. To improve the SNR, the most common approach is to average signals that are acquired in multiple times. The data acquisition time, however, is increased by multiple times accordingly, resulting in the scanned objects uncomfortable or even unbearable. Methods: By exploring the multiple sampled data, a deep learning denoising approach is proposed to learn a mapping from the low SNR signal to the high SNR one. Results: Results on simulated and in vivo data show that the proposed method significantly reduces the data acquisition time with slightly compromised metabolic accuracy. Conclusion: A deep learning denoising method was proposed to significantly shorten the time of data acquisition, while maintaining signal accuracy and reliability. Significance: Provide a solution of the fundamental low SNR problem in MRS with artificial intelligence.

Accelerated Nuclear Magnetic Resonance Spectroscopy with Deep Learning

Nuclear magnetic resonance (NMR) spectroscopy serves as an indispensable tool in chemistry and biology but often suffers from long experimental time. We present a proof-of-concept of application of deep learning and neural network for high-quality, reliable, and very fast NMR spectra reconstruction from limited experimental data. We show that the neural network training can be achieved using solely synthetic NMR signal, which lifts the prohibiting demand for a large volume of realistic training data usually required in the deep learning approach.