Researcher profile

Liying Zhang

Liying Zhang contributes to research discovery and scholarly infrastructure.

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Published work

3 published item(s)

preprint2026arXiv

MolWorld: Molecule World Models for Actionable Molecular Optimization

Molecular optimization in drug discovery aims to discover molecules with improved target properties, but practical lead optimization often requires more than high predicted scores. A useful candidate should also be actionable: it should be reachable from known molecules through valid local structural transformations, so that it can be interpreted as a plausible revision within an evolving chemical series. Existing de novo and single-molecule optimization methods do not explicitly model such reachability, especially when both the target molecules and the intermediate molecules connecting them to known compounds are unknown. In this work, we formulate actionable molecular optimization as sequential expansion of a molecule-transfer graph, where nodes are molecules and edges encode valid local transformations. We propose MolWorld, a molecule world model-guided framework that treats the current molecule-transfer graph as an evolving search state. At each iteration, MolWorld selects local anchor contexts, generates candidate molecules conditioned on these contexts, evaluates their properties, and uses a learned world model to update the evolving molecule world by retaining admissible candidates and inserting them into the molecule-transfer graph. The expanded molecule world then guides subsequent optimization. Experiments on property optimization and docking-based tasks show that MolWorld discovers high-property molecules while maintaining substantially stronger structural connectivity, supporting actionable and sequential molecular design.

preprint2026arXiv

Transformer-Based Approach for Automated Functional Group Replacement in Chemical Compounds

Functional group replacement is a pivotal approach in cheminformatics to enable the design of novel chemical compounds with tailored properties. Traditional methods for functional group removal and replacement often rely on rule-based heuristics, which can be limited in their ability to generate diverse and novel chemical structures. Recently, transformer-based models have shown promise in improving the accuracy and efficiency of molecular transformations, but existing approaches typically focus on single-step modeling, lacking the guarantee of structural similarity. In this work, we seek to advance the state of the art by developing a novel two-stage transformer model for functional group removal and replacement. Unlike one-shot approaches that generate entire molecules in a single pass, our method generates the functional group to be removed and appended sequentially, ensuring strict substructure-level modifications. Using a matched molecular pairs (MMPs) dataset derived from ChEMBL, we trained an encoder-decoder transformer model with SMIRKS-based representations to capture transformation rules effectively. Extensive evaluations demonstrate our method's ability to generate chemically valid transformations, explore diverse chemical spaces, and maintain scalability across varying search sizes.

preprint2020arXiv

Measurement of the neutron beam profile of the Back-n white neutron facility at CSNS with a Micromegas detector

The Back-n white neutron beam line, which uses back-streaming white neutrons from the spallation target of the China Spallation Neutron Source, is used for nuclear data measurements. A Micromegas-based neutron detector with two variants was specially developed to measure the beam spot distribution for this beam line. In this article, the design, fabrication, and characterization of the detector are described. The results of the detector performance tests are presented, which include the relative electron transparency, the gain and the gain uniformity, and the neutron beam profile reconstruction capability. The result of the first measurement of the Back-n neutron beam spot distribution is also presented.