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Jiangtao Ma

Publications and source records attributed to Jiangtao Ma.

2 recordsLinked to original sources

PDEAgent-Bench: A Multi-Metric, Multi-Library Benchmark for PDE Solver Generation

PDE-to-solver code generation aims to automatically synthesize executable numerical solvers from partial differential equation (PDE) specifications. This task requires not only understanding the mathematical structure of PDEs, but also selecting appropriate discretization schemes and solver configurations, and correctly implementing the resulting formulations in finite-element method (FEM) libraries. Existing code generation benchmarks mainly evaluate syntactic correctness, or success on predefined test cases. To our knowledge, there is currently no publicly available benchmark specifically for PDE-to-solver code generation, and general-purpose code benchmarks do not fully capture the unique challenges of numerical PDE solution, such as ensuring solver accuracy, efficiency, and compatibility with professional FEM libraries. We introduce PDEAgent-Bench, to the best of our knowledge, the first multi-metric, multi-library benchmark for PDE-to-solver code generation. PDEAgent-Bench contains 645 instances across 6 mathematical categories and 11 PDE families, with common FEM libraries for DOLFINx, Firedrake, and deal.II. Each instance provides an agent-facing problem specification, a reference solution on a prescribed evaluation grid, and case-specific accuracy and runtime targets. PDEAgent-Bench adopts a staged evaluation framework in which generated solvers must sequentially pass executability, numerical accuracy, and computational efficiency checks. Experiments with representative LLMs and code agents show that models can often produce runnable code, but their pass rate drops substantially once accuracy and efficiency requirements are enforced. These results indicate that current agents remain limited in producing numerically reliable and efficient PDE solvers, and that PDEAgent-Bench provides a reproducible testbed grounded in the practical requirements of numerical PDE solving.

cs.AI

Inferring cell-specific lncRNA regulation with single-cell RNA-sequencing data in the developing human neocortex

Long non-coding RNAs (lncRNAs) are important regulators to modulate gene expression and cell proliferation in the developing human brain. Previous methods mainly use bulk lncRNA and mRNA expression data to study lncRNA regulation. However, to analyze lncRNA regulation regarding individual cells, we focus on single-cell RNA-sequencing (scRNA-seq) data instead of bulk data. Recent advance in scRNA-seq has provided a way to investigate lncRNA regulation at single-cell level. We will propose a novel computational method, CSlncR (cell-specific lncRNA regulation), which combines putative lncRNA-mRNA binding information with scRNA-seq data including lncRNAs and mRNAs to identify cell-specific lncRNA-mRNA regulation networks at individual cells. To understand lncRNA regulation at different development stages, we apply CSlncR to the scRNA-seq data of human neocortex. Network analysis shows that the lncRNA regulation is unique in each cell from the different human neocortex development stages. The comparison results indicate that CSlncR is also an effective tool for predicting cell-specific lncRNA targets and clustering single cells, which helps understand cell-cell communication.

q-bio.MN