Xinyu Li

Lirong Wu, Junjie Wang, Zhifeng Gao et al.

Organic reaction, the foundation of modern chemical industry, is crucial for new material development and drug discovery. However, deciphering reaction mechanisms and modeling multi-molecular relationships remain formidable challenges due to the complexity of molecular dynamics. While several state-of-the-art models like Uni-Mol2 have revolutionized single-molecular representation learning, their extension to multi-molecular systems, where chemical reactions inherently occur, has been underexplored. This paper introduces Uni-Mol3, a novel deep learning framework that employs a hierarchical pipeline for multi-molecular reaction modeling. At its core, Uni-Mol3 adopts a multi-scale molecular tokenizer (Mol-Tokenizer) that encodes 3D structures of molecules and other features into discrete tokens, creating a 3D-aware molecular language. The framework innovatively combines two pre-training stages: molecular pre-training to learn the molecular grammars and reaction pre-training to capture fundamental reaction principles, forming a progressive learning paradigm from single- to multi-molecular systems. With prompt-aware downstream fine-tuning, Uni-Mol3 demonstrates exceptional performance in diverse organic reaction tasks and supports multi-task prediction with strong generalizability. Experimental results across 10 datasets spanning 4 downstream tasks show that Uni-Mol3 outperforms existing methods, validating its effectiveness in modeling complex organic reactions. This work not only ushers in an alternative paradigm for multi-molecular computational modeling but also charts a course for intelligent organic reaction by bridging molecular representation with reaction mechanism understanding.

Haotian Gu, Xin Guo, Timothy L. Jacobs et al.

Freight transportation marketplace rates are typically challenging to forecast accurately. In this work, we have developed a novel statistical technique based on signature transforms and have built a predictive and adaptive model to forecast these marketplace rates. Our technique is based on two key elements of the signature transform: one being its universal nonlinearity property, which linearizes the feature space and hence translates the forecasting problem into linear regression, and the other being the signature kernel, which allows for comparing computationally efficiently similarities between time series data. Combined, it allows for efficient feature generation and precise identification of seasonality and regime switching in the forecasting process. An algorithm based on our technique has been deployed by Amazon trucking operations, with far superior forecast accuracy and better interpretability versus commercially available industry models, even during the COVID-19 pandemic and the Ukraine conflict. Furthermore, our technique is able to capture the influence of business cycles and the heterogeneity of the marketplace, improving prediction accuracy by more than fivefold, with an estimated annualized saving of \$50MM.

Xinyu Li, Yang Xu, Xiaohu Zhang et al.

As an important task for the management of bike sharing systems, accurate forecast of travel demand could facilitate dispatch and relocation of bicycles to improve user satisfaction. In recent years, many deep learning algorithms have been introduced to improve bicycle usage forecast. A typical practice is to integrate convolutional (CNN) and recurrent neural network (RNN) to capture spatial-temporal dependency in historical travel demand. For typical CNN, the convolution operation is conducted through a kernel that moves across a "matrix-format" city to extract features over spatially adjacent urban areas. This practice assumes that areas close to each other could provide useful information that improves prediction accuracy. However, bicycle usage in neighboring areas might not always be similar, given spatial variations in built environment characteristics and travel behavior that affect cycling activities. Yet, areas that are far apart can be relatively more similar in temporal usage patterns. To utilize the hidden linkage among these distant urban areas, the study proposes an irregular convolutional Long-Short Term Memory model (IrConv+LSTM) to improve short-term bike sharing demand forecast. The model modifies traditional CNN with irregular convolutional architecture to extract dependency among "semantic neighbors". The proposed model is evaluated with a set of benchmark models in five study sites, which include one dockless bike sharing system in Singapore, and four station-based systems in Chicago, Washington, D.C., New York, and London. We find that IrConv+LSTM outperforms other benchmark models in the five cities. The model also achieves superior performance in areas with varying levels of bicycle usage and during peak periods. The findings suggest that "thinking beyond spatial neighbors" can further improve short-term travel demand prediction of urban bike sharing systems.