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Liying Zhang

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Published work

9 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.

preprint2016arXiv

Energy-conserving method for Stochastic Maxwell Equations with Multiplicative Noise

In this paper, it is shown that three-dimensional stochastic Maxwell equations with multiplicative noise are stochastic Hamiltonian partial differential equations possessing a geometric structure (i.e. stochastic mutli-symplectic conservation law), and the energy of system is a conservative quantity almost surely. We propose a stochastic multi-symplectic energy-conserving method for the equations by using the wavelet collocation method in space and stochastic symplectic method in time. Numerical experiments are performed to verify the excellent abilities of the proposed method in providing accurate solution and preserving energy. The mean square convergence result of the method in temporal direction is tested numerically, and numerical comparisons with finite difference method are also investigated.

preprint2016arXiv

Numerical Analysis on Ergodic Limit of Approximations for Stochastic NLS Equation via Multi-symplectic Scheme

We consider a finite dimensional approximation of the stochastic nonlinear Schrödinger equation driven by multiplicative noise, which is derived by applying a symplectic method to the original equation in spatial direction. Both the unique ergodicity and the charge conservation law for this finite dimensional approximation are obtained on the unit sphere. To simulate the ergodic limit over long time for the finite dimensional approximation, we discretize it further in temporal direction to obtain a fully discrete scheme, which inherits not only the stochastic multi-symplecticity and charge conservation law of the original equation but also the unique ergodicity of the finite dimensional approximation. The temporal average of the fully discrete numerical solution is proved to converge to the ergodic limit with order one with respect to the time step for a fixed spatial step. Numerical experiments verify our theoretical results on charge conservation, ergodicity and weak convergence.

preprint2016arXiv

Projection methods for stochastic differential equations with conserved quantities

In this paper, we consider the numerical methods preserving single or multiple conserved quantities, and these methods are able to reach high order of strong convergence simultaneously based on some kinds of projection methods. The mean-square convergence orders of these methods under certain conditions are given, which can reach order 1.5 or even 2 according to the supporting methods embedded in the projection step. Finally, three numerical experiments are taken into account to show the superiority of the projection methods.

preprint2015arXiv

Preservation of Physical Properties of Stochastic Maxwell Equations with Additive Noise via Stochastic Multi-symplectic Methods

Stochastic Maxwell equations with additive noise are a system of stochastic Hamiltonian partial differential equations intrinsically, possessing the stochastic multi-symplectic conservation law.It is shown that the averaged energy increases linearly with respect to the evolution of time and the flow of stochastic Maxwell equations with additive noise preserves the divergence in the sense of expectation. Moreover, we propose three novel stochastic multi-symplectic methods to discretize stochastic Maxwell equations in order to investigate the preservation of these properties numerically. We made theoretical discussions and comparisons on all of the three methods to observe that all of them preserve the corresponding discrete version of the averaged divergence. Meanwhile, we obtain the corresponding dissipative property of the discrete averaged energy satisfied by each method. Especially, the evolution rates of the averaged energies for all of the three methods are derived which are in accordance with the continuous case. Numerical experiments are performed to verify our theoretical results.

preprint2014arXiv

Multi-symplectic Preserving Integrator for the Schrödinger Equation with Wave Operator

In the article, we discuss the conservation laws for the nonlinear Schrödinger equation with wave operator under multisymplectic integrator (MI). First, the conservation laws of the continuous equation are presented and one of them is new. The multisymplectic structure and MI are constructed for the equation. The discrete conservation laws of the numerical method are analyzed. It is verified that the proposed MI can stably simulate the multisymplectic Hamiltonian system excellent over long-term. It is more accurate than some energy-preserving schemes though they are of the same accuracy. Moreover, the residual of mass is less than energy-preserving schemes under the same mesh partition over long-term.

preprint2014arXiv

Near Preservation of Quadratic Invariants by Stochastic Runge-Kutta Methods

Based on the combinatory theory of rooted colored trees, we investigate the conditions for the explicit stochastic Runge-Kutta (SRK) methods to preserve quadratic invariants (QI) up to certain orders of accuracy. These conditions can supply a practical approach of constructing explicit nearly conservative SRK methods. Meanwhile, we estimate errors in the preservation of QI resulting from iterative implementation of implicit conservative SRK methods with fixed-point and Newton's iterations. Finally, numerical experiments are performed to test the behavior of the methods in preserving QI.