Ruiyi Zhang

Youwei Liang, Ruiyi Zhang, Li Zhang et al.

A ChatGPT-like system for drug compounds could be a game-changer in pharmaceutical research, accelerating drug discovery, enhancing our understanding of structure-activity relationships, guiding lead optimization, aiding drug repurposing, reducing the failure rate, and streamlining clinical trials. In this work, we make an initial attempt towards enabling ChatGPT-like capabilities on drug molecule graphs, by developing a prototype system DrugChat. DrugChat works in a similar way as ChatGPT. Users upload a compound molecule graph and ask various questions about this compound. DrugChat will answer these questions in a multi-turn, interactive manner. The DrugChat system consists of a graph neural network (GNN), a large language model (LLM), and an adaptor. The GNN takes a compound molecule graph as input and learns a representation for this graph. The adaptor transforms the graph representation produced by the GNN into another representation that is acceptable to the LLM. The LLM takes the compound representation transformed by the adaptor and users' questions about this compound as inputs and generates answers. All these components are trained end-to-end. To train DrugChat, we collected instruction tuning datasets which contain 10,834 drug compounds and 143,517 question-answer pairs. The code and data is available at \url{https://github.com/UCSD-AI4H/drugchat}

Jianyi Zhang, Ruiyi Zhang, Lawrence Carin et al.

Particle-optimization-based sampling (POS) is a recently developed effective sampling technique that interactively updates a set of particles. A representative algorithm is the Stein variational gradient descent (SVGD). We prove, under certain conditions, SVGD experiences a theoretical pitfall, {\it i.e.}, particles tend to collapse. As a remedy, we generalize POS to a stochastic setting by injecting random noise into particle updates, thus yielding particle-optimization sampling (SPOS). Notably, for the first time, we develop {\em non-asymptotic convergence theory} for the SPOS framework (related to SVGD), characterizing algorithm convergence in terms of the 1-Wasserstein distance w.r.t.\! the numbers of particles and iterations. Somewhat surprisingly, with the same number of updates (not too large) for each particle, our theory suggests adopting more particles does not necessarily lead to a better approximation of a target distribution, due to limited computational budget and numerical errors. This phenomenon is also observed in SVGD and verified via an experiment on synthetic data. Extensive experimental results verify our theory and demonstrate the effectiveness of our proposed framework.

Changyou Chen, Ruiyi Zhang, Wenlin Wang et al.

There has been recent interest in developing scalable Bayesian sampling methods such as stochastic gradient MCMC (SG-MCMC) and Stein variational gradient descent (SVGD) for big-data analysis. A standard SG-MCMC algorithm simulates samples from a discrete-time Markov chain to approximate a target distribution, thus samples could be highly correlated, an undesired property for SG-MCMC. In contrary, SVGD directly optimizes a set of particles to approximate a target distribution, and thus is able to obtain good approximations with relatively much fewer samples. In this paper, we propose a principle particle-optimization framework based on Wasserstein gradient flows to unify SG-MCMC and SVGD, and to allow new algorithms to be developed. Our framework interprets SG-MCMC as particle optimization on the space of probability measures, revealing a strong connection between SG-MCMC and SVGD. The key component of our framework is several particle-approximate techniques to efficiently solve the original partial differential equations on the space of probability measures. Extensive experiments on both synthetic data and deep neural networks demonstrate the effectiveness and efficiency of our framework for scalable Bayesian sampling.

Changyou Chen, Ruiyi Zhang

Stochastic gradient Markov chain Monte Carlo (SG-MCMC) has been increasingly popular in Bayesian learning due to its ability to deal with large data. A standard SG-MCMC algorithm simulates samples from a discretized-time Markov chain to approximate a target distribution. However, the samples are typically highly correlated due to the sequential generation process, an undesired property in SG-MCMC. In contrary, Stein variational gradient descent (SVGD) directly optimizes a set of particles, and it is able to approximate a target distribution with much fewer samples. In this paper, we propose a novel method to directly optimize particles (or samples) in SG-MCMC from scratch. Specifically, we propose efficient methods to solve the corresponding Fokker-Planck equation on the space of probability distributions, whose solution (i.e., a distribution) is approximated by particles. Through our framework, we are able to show connections of SG-MCMC to SVGD, as well as the seemly unrelated generative-adversarial-net framework. Under certain relaxations, particle optimization in SG-MCMC can be interpreted as an extension of standard SVGD with momentum.