100 citations · 176 across the 15 of their papers we have counts for
8 papers · 1 filter
Generating Developable 3D Molecules via Pocket-Conditioned Diffusion and Property-Aware Optimization
Ruoxi Gao, Jiangweizhi Peng, Ziqi Chen +10
Drug discovery and development is time-consuming and resource-intensive, motivating computational approaches such as diffusion models for de novo drug design. Many such models foll…
PACEvolve++: Improving Test-time Learning for Evolutionary Search Agents
Minghao Yan, Bo Peng, Benjamin Coleman +11
Large language models have become drivers of evolutionary search, but most systems rely on a fixed, prompt-elicited policy to sample next candidates. This limits adaptation in prac…
DiffER: Categorical Diffusion for Chemical Retrosynthesis
Sean Current, Ziqi Chen, Daniel Adu-Ampratwum +2
Methods for automatic chemical retrosynthesis have found recent success through the application of models traditionally built for natural language processing, primarily through tra…
Generating 3D Binding Molecules Using Shape-Conditioned Diffusion Models with Guidance
Ziqi Chen, Bo Peng, Tianhua Zhai +2
Drug development is a critical but notoriously resource- and time-consuming process. In this manuscript, we develop a novel generative artificial intelligence (genAI) method DiffSM…
RLSynC: Offline-Online Reinforcement Learning for Synthon Completion
Frazier N. Baker, Ziqi Chen, Daniel Adu-Ampratwum +1
Retrosynthesis is the process of determining the set of reactant molecules that can react to form a desired product. Semi-template-based retrosynthesis methods, which imitate the r…
Shape-conditioned 3D Molecule Generation via Equivariant Diffusion Models
Ziqi Chen, Bo Peng, Srinivasan Parthasarathy +1
Ligand-based drug design aims to identify novel drug candidates of similar shapes with known active molecules. In this paper, we formulated an in silico shape-conditioned molecule…
as a Two-Step Graph Generative Models for Retrosynthesis Prediction
Ziqi Chen, Oluwatosin R. Ayinde, James R. Fuchs +2
Retrosynthesis is a procedure where a target molecule is transformed into potential reactants and thus the synthesis routes can be identified. Recently, computational approaches ha…
A Deep Generative Model for Molecule Optimization via One Fragment Modification
Ziqi Chen, Martin Renqiang Min, Srinivasan Parthasarathy +1
Molecule optimization is a critical step in drug development to improve desired properties of drug candidates through chemical modification. We developed a novel deep generative mo…