Xuan Zhang

Meng Liu, Cong Fu, Xuan Zhang et al.

Molecular property prediction is gaining increasing attention due to its diverse applications. One task of particular interests and importance is to predict quantum chemical properties without 3D equilibrium structures. This is practically favorable since obtaining 3D equilibrium structures requires extremely expensive calculations. In this work, we design a deep graph neural network to predict quantum properties by directly learning from 2D molecular graphs. In addition, we propose a 3D graph neural network to learn from low-cost conformer sets, which can be obtained with open-source tools using an affordable budget. We employ our methods to participate in the 2021 KDD Cup on OGB Large-Scale Challenge (OGB-LSC), which aims to predict the HOMO-LUMO energy gap of molecules. Final evaluation results reveal that we are one of the winners with a mean absolute error of 0.1235 on the holdout test set. Our implementation is available as part of the MoleculeX package (https://github.com/divelab/MoleculeX).

Meng Liu, Youzhi Luo, Limei Wang et al.

Although there exist several libraries for deep learning on graphs, they are aiming at implementing basic operations for graph deep learning. In the research community, implementing and benchmarking various advanced tasks are still painful and time-consuming with existing libraries. To facilitate graph deep learning research, we introduce DIG: Dive into Graphs, a turnkey library that provides a unified testbed for higher level, research-oriented graph deep learning tasks. Currently, we consider graph generation, self-supervised learning on graphs, explainability of graph neural networks, and deep learning on 3D graphs. For each direction, we provide unified implementations of data interfaces, common algorithms, and evaluation metrics. Altogether, DIG is an extensible, open-source, and turnkey library for researchers to develop new methods and effortlessly compare with common baselines using widely used datasets and evaluation metrics. Source code is available at https://github.com/divelab/DIG.

Yunlong Hou, Fengzhuo Zhang, Cunxiao Du et al.

Speculative decoding has emerged as a popular method to accelerate the inference of Large Language Models (LLMs) while retaining their superior text generation performance. Previous methods either adopt a fixed speculative decoding configuration regardless of the prefix tokens, or train draft models in an offline or online manner to align them with the context. This paper proposes a training-free online learning framework to adaptively choose the configuration of the hyperparameters for speculative decoding as text is being generated. We first formulate this hyperparameter selection problem as a Multi-Armed Bandit problem and provide a general speculative decoding framework BanditSpec. Furthermore, two bandit-based hyperparameter selection algorithms, UCBSpec and EXP3Spec, are designed and analyzed in terms of a novel quantity, the stopping time regret. We upper bound this regret under both stochastic and adversarial reward settings. By deriving an information-theoretic impossibility result, it is shown that the regret performance of UCBSpec is optimal up to universal constants. Finally, extensive empirical experiments with LLaMA3 and Qwen2 demonstrate that our algorithms are effective compared to existing methods, and the throughput is close to the oracle best hyperparameter in simulated real-life LLM serving scenarios with diverse input prompts.

Zhao Xu, Yaochen Xie, Youzhi Luo et al.

Ground-state 3D geometries of molecules are essential for many molecular analysis tasks. Modern quantum mechanical methods can compute accurate 3D geometries but are computationally prohibitive. Currently, an efficient alternative to computing ground-state 3D molecular geometries from 2D graphs is lacking. Here, we propose a novel deep learning framework to predict 3D geometries from molecular graphs. To this end, we develop an equilibrium message passing neural network (EMPNN) to better capture ground-state geometries from molecular graphs. To provide a testbed for 3D molecular geometry analysis, we develop a benchmark that includes a large-scale molecular geometry dataset, data splits, and evaluation protocols. Experimental results show that EMPNN can efficiently predict more accurate ground-state 3D geometries than RDKit and other deep learning methods. Results also show that the proposed framework outperforms self-supervised learning methods on property prediction tasks.