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Yongjian He

Publications and source records attributed to Yongjian He.

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Third-order transitions in Ising and Potts models on Watts--Strogatz small-world networks

We study third-order transitions in the two-dimensional Ising and Potts model on regular lattices and Watts--Strogatz small-world networks. Cluster observables are used to track post-critical boundary reorganization and pre-critical cluster breakup. For the Ising model, the critical temperature $T_c$ is calibrated independently from Binder-cumulant crossings and susceptibility peaks, whereas for the Potts model on small-world networks it is identified operationally from the dominant critical peak of $\mathrm d\langle P\rangle/\mathrm dT$. The independent and dependent third-order transitions are identified from the isolated-spin peak and the post-critical structural extremum, respectively. For both lattice and small-world topologies, we find the robust ordering $T_{\mathrm{ind}}<T_c<T_{\mathrm{dep}}$. Increasing the rewiring probability shifts all three characteristic temperatures upward and enhances the visibility of the post-critical transition. The effect is especially clear in the Potts model, where perimeter-based observables are more sensitive to multistate boundary fluctuations. The systematic persistence of the characteristic temperature hierarchy across topologies and finite sizes argues against interpreting these features as incidental finite-size irregularities. Instead, our results support their interpretation as genuine third-order transitions whose structural detectability can be amplified by network topology.

cond-mat.stat-mech

Predicting cell-specific gene expression profile and knockout impact through deep learning

Gene expression data is essential for understanding how genes are regulated and interact within biological systems, providing insights into disease pathways and potential therapeutic targets. Gene knockout has proven to be a fundamental technique in molecular biology, allowing the investigation of the function of specific genes in an organism, as well as in specific cell types. However, gene expression patterns are quite heterogeneous in single-cell transcriptional data from a uniform environment, representing different cell states, which produce cell-type and cell-specific gene knockout impacts. A computational method that can predict the single-cell resolution knockout impact is still lacking. Here, we present a data-driven framework for learning the mapping between gene expression profiles derived from gene assemblages, enabling the accurate prediction of perturbed expression profiles following knockout (KO) for any cell, without relying on prior perturbed data. We systematically validated our framework using synthetic data generated from gene regulatory dynamics models, two mouse knockout single-cell datasets, and high-throughput in vitro CRISPRi Perturb-seq data. Our results demonstrate that the framework can accurately predict both expression profiles and KO effects at the single-cell level. Our approach provides a generalizable tool for inferring gene function at single-cell resolution, offering new opportunities to study genetic perturbations in contexts where large-scale experimental screens are infeasible.

q-bio.GN