Yi Liu

Yi Liu, Limei Wang, Meng Liu et al.

We consider representation learning of 3D molecular graphs in which each atom is associated with a spatial position in 3D. This is an under-explored area of research, and a principled message passing framework is currently lacking. In this work, we conduct analyses in the spherical coordinate system (SCS) for the complete identification of 3D graph structures. Based on such observations, we propose the spherical message passing (SMP) as a novel and powerful scheme for 3D molecular learning. SMP dramatically reduces training complexity, enabling it to perform efficiently on large-scale molecules. In addition, SMP is capable of distinguishing almost all molecular structures, and the uncovered cases may not exist in practice. Based on meaningful physically-based representations of 3D information, we further propose the SphereNet for 3D molecular learning. Experimental results demonstrate that the use of meaningful 3D information in SphereNet leads to significant performance improvements in prediction tasks. Our results also demonstrate the advantages of SphereNet in terms of capability, efficiency, and scalability. Our code is publicly available as part of the DIG library (https://github.com/divelab/DIG).

Wei W. Xing, Xiang Jin, Yi Liu et al.

One of the greatest challenges in IC design is the repeated executions of computationally expensive SPICE simulations, particularly when highly complex chip testing/verification is involved. Recently, pseudo transient analysis (PTA) has shown to be one of the most promising continuation SPICE solver. However, the PTA efficiency is highly influenced by the inserted pseudo-parameters. In this work, we proposed BoA-PTA, a Bayesian optimization accelerated PTA that can substantially accelerate simulations and improve convergence performance without introducing extra errors. Furthermore, our method does not require any pre-computation data or offline training. The acceleration framework can either be implemented to speed up ongoing repeated simulations immediately or to improve new simulations of completely different circuits. BoA-PTA is equipped with cutting-edge machine learning techniques, e.g., deep learning, Gaussian process, Bayesian optimization, non-stationary monotonic transformation, and variational inference via parameterization. We assess BoA-PTA in 43 benchmark circuits against other SOTA SPICE solvers and demonstrate an average 2.3x (maximum 3.5x) speed-up over the original CEPTA.

Yi Liu, Lihong Li

The rich body of Bandit literature not only offers a diverse toolbox of algorithms, but also makes it hard for a practitioner to find the right solution to solve the problem at hand. Typical textbooks on Bandits focus on designing and analyzing algorithms, and surveys on applications often present a list of individual applications. While these are valuable resources, there exists a gap in mapping applications to appropriate Bandit algorithms. In this paper, we aim to reduce this gap with a structured map of Bandits to help practitioners navigate to find relevant and practical Bandit algorithms. Instead of providing a comprehensive overview, we focus on a small number of key decision points related to reward, action, and features, which often affect how Bandit algorithms are chosen in practice.

Yi Liu, Veronika Rockova

Thompson sampling is a heuristic algorithm for the multi-armed bandit problem which has a long tradition in machine learning. The algorithm has a Bayesian spirit in the sense that it selects arms based on posterior samples of reward probabilities of each arm. By forging a connection between combinatorial binary bandits and spike-and-slab variable selection, we propose a stochastic optimization approach to subset selection called Thompson Variable Selection (TVS). TVS is a framework for interpretable machine learning which does not rely on the underlying model to be linear. TVS brings together Bayesian reinforcement and machine learning in order to extend the reach of Bayesian subset selection to non-parametric models and large datasets with very many predictors and/or very many observations. Depending on the choice of a reward, TVS can be deployed in offline as well as online setups with streaming data batches. Tailoring multiplay bandits to variable selection, we provide regret bounds without necessarily assuming that the arm mean rewards be unrelated. We show a very strong empirical performance on both simulated and real data. Unlike deterministic optimization methods for spike-and-slab variable selection, the stochastic nature makes TVS less prone to local convergence and thereby more robust.