Qiang Liu

Haisong Gong, Qiang Liu, Shu Wu et al.

Text-guided molecule generation is a task where molecules are generated to match specific textual descriptions. Recently, most existing SMILES-based molecule generation methods rely on an autoregressive architecture. In this work, we propose the Text-Guided Molecule Generation with Diffusion Language Model (TGM-DLM), a novel approach that leverages diffusion models to address the limitations of autoregressive methods. TGM-DLM updates token embeddings within the SMILES string collectively and iteratively, using a two-phase diffusion generation process. The first phase optimizes embeddings from random noise, guided by the text description, while the second phase corrects invalid SMILES strings to form valid molecular representations. We demonstrate that TGM-DLM outperforms MolT5-Base, an autoregressive model, without the need for additional data resources. Our findings underscore the remarkable effectiveness of TGM-DLM in generating coherent and precise molecules with specific properties, opening new avenues in drug discovery and related scientific domains. Code will be released at: https://github.com/Deno-V/tgm-dlm.

Mao Ye, Tongzheng Ren, Qiang Liu

We propose a new Stein self-repulsive dynamics for obtaining diversified samples from intractable un-normalized distributions. Our idea is to introduce Stein variational gradient as a repulsive force to push the samples of Langevin dynamics away from the past trajectories. This simple idea allows us to significantly decrease the auto-correlation in Langevin dynamics and hence increase the effective sample size. Importantly, as we establish in our theoretical analysis, the asymptotic stationary distribution remains correct even with the addition of the repulsive force, thanks to the special properties of the Stein variational gradient. We perform extensive empirical studies of our new algorithm, showing that our method yields much higher sample efficiency and better uncertainty estimation than vanilla Langevin dynamics.

Qiang Liu

Stein variational gradient descent (SVGD) is a deterministic sampling algorithm that iteratively transports a set of particles to approximate given distributions, based on an efficient gradient-based update that guarantees to optimally decrease the KL divergence within a function space. This paper develops the first theoretical analysis on SVGD, discussing its weak convergence properties and showing that its asymptotic behavior is captured by a gradient flow of the KL divergence functional under a new metric structure induced by Stein operator. We also provide a number of results on Stein operator and Stein's identity using the notion of weak derivative, including a new proof of the distinguishability of Stein discrepancy under weak conditions.