Yu Shi

Yanyun Liu, Xiumeng Hua, Shouping Zhu et al.

This study aims to develop a new computational pathology approach that automates the identification and quantification of myocardial inflammatory infiltration in digital HE-stained images to provide a quantitative histological diagnosis of myocarditis.898 HE-stained whole slide images (WSIs) of myocardium from 154 heart transplant patients diagnosed with myocarditis or dilated cardiomyopathy (DCM) were included in this study. An automated DL-based computational pathology approach was developed to identify nuclei and detect myocardial inflammatory infiltration, enabling the quantification of the lymphocyte nuclear density (LND) on myocardial WSIs. A cutoff value based on the quantification of LND was proposed to determine if the myocardial inflammatory infiltration was present. The performance of our approach was evaluated with a five-fold cross-validation experiment, tested with an internal test set from the myocarditis group, and confirmed by an external test from a double-blind trial group. An LND of 1.02/mm2 could distinguish WSIs with myocarditis from those without. The accuracy, sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) in the five-fold cross-validation experiment were 0.899 plus or minus 0.035, 0.971 plus or minus 0.017, 0.728 plus or minus 0.073 and 0.849 plus or minus 0.044, respectively. For the internal test set, the accuracy, sensitivity, specificity, and AUC were 0.887, 0.971, 0.737, and 0.854, respectively. The accuracy, sensitivity, specificity, and AUC for the external test set reached 0.853, 0.846, 0.858, and 0.852, respectively. Our new approach provides accurate and reliable quantification of the LND of myocardial WSIs, facilitating automated quantitative diagnosis of myocarditis with HE-stained images.

Yu-Zhe Shi, Mingchen Liu, Fanxu Meng et al.

Self-driving laboratories have begun to replace human experimenters in performing single experimental skills or predetermined experimental protocols. However, as the pace of idea iteration in scientific research has been intensified by Artificial Intelligence, the demand for rapid design of new protocols for new discoveries become evident. Efforts to automate protocol design have been initiated, but the capabilities of knowledge-based machine designers, such as Large Language Models, have not been fully elicited, probably for the absence of a systematic representation of experimental knowledge, as opposed to isolated, flatten pieces of information. To tackle this issue, we propose a multi-faceted, multi-scale representation, where instance actions, generalized operations, and product flow models are hierarchically encapsulated using Domain-Specific Languages. We further develop a data-driven algorithm based on non-parametric modeling that autonomously customizes these representations for specific domains. The proposed representation is equipped with various machine designers to manage protocol design tasks, including planning, modification, and adjustment. The results demonstrate that the proposed method could effectively complement Large Language Models in the protocol design process, serving as an auxiliary module in the realm of machine-assisted scientific exploration.