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Xiao-Hui Yang

Publications and source records attributed to Xiao-Hui Yang.

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Ai2-Kit: Streamlining AI-Accelerated Ab Initio Workflows for Complex Chemical Systems

Molecular simulations of complex chemical systems, such as catalysis, electrochemistry, and energy storage, often need to capture the interplay of effects such as electronic structure, finite-temperature fluctuations, and electric-field response. Such complexity is difficult to address with traditional ab initio calculations, which are limited by the time and length scales they can reach. AI-accelerated ab initio (AI2) methods use machine learning potentials trained on first-principles data to replace expensive electronic-structure calculations, extending ab initio accuracy to these regimes, but their routine application requires reliable workflows that connect first-principles calculations, model training, molecular dynamics, enhanced sampling, trajectory analysis, and HPC orchestration. Here we present ai2-kit, a software toolkit for developing accessible, reproducible, and extensible AI2 workflows. ai2-kit provides high-semantic-density command-line interfaces and Python APIs for structure and dataset conversion, batch task generation, active-learning screening, job orchestration, and workflow recovery. We demonstrate ai2-kit in four representative applications: active-learning-based machine learning potential construction, free-energy perturbation for redox and acid-base processes, electrochemical machine learning potentials for electrified interfaces, and spectroscopies from machine learning molecular dynamics. ai2-kit also provides AI-agent skills that help users adapt these use cases into customized workflows for their own chemical systems and computational software stacks. Together, ai2-kit helps turn AI2 methods from bespoke computational protocols into reusable and extensible workflows for complex chemical systems, from model construction to property prediction.

physics.chem-ph

Inverse Projection Representation and Category Contribution Rate for Robust Tumor Recognition

Sparse representation based classification (SRC) methods have achieved remarkable results. SRC, however, still suffer from requiring enough training samples, insufficient use of test samples and instability of representation. In this paper, a stable inverse projection representation based classification (IPRC) is presented to tackle these problems by effectively using test samples. An IPR is firstly proposed and its feasibility and stability are analyzed. A classification criterion named category contribution rate is constructed to match the IPR and complete classification. Moreover, a statistical measure is introduced to quantify the stability of representation-based classification methods. Based on the IPRC technique, a robust tumor recognition framework is presented by interpreting microarray gene expression data, where a two-stage hybrid gene selection method is introduced to select informative genes. Finally, the functional analysis of candidate's pathogenicity-related genes is given. Extensive experiments on six public tumor microarray gene expression datasets demonstrate the proposed technique is competitive with state-of-the-art methods.

q-bio.QM