MOTIVATION: The advent of single-cell RNA sequencing (scRNA-seq) technology has allowed researchers to measure gene expression profiles at the single-cell level, providing valuable insights into cellular heterogeneity. However, due to the limitations of current sequencing platforms, scRNA-seq data often contain significant noise, particularly severe dropout events, which pose major challenges for subsequent analyses. RESULTS: In this study, we developed a new method called topology-aware contrastive learning (scTACL). This approach uses contrastive learning between a cell similarity graph and a cell embedding similarity graph, employing a zero-inflated negative binomial (ZINB) distribution to model the reconstructed data. This alignment helps the processed data better reflect true biological signals. It delivers superior results in key tasks such as data imputation, clustering, batch effect correction, and cell-cell interaction. Additionally, scTACL successfully identified two distinct subtypes of epithelial cells in lung adenocarcinoma tissues, further demonstrating its effectiveness and usefulness in complex biological settings. Notably, without relying on spatial location information, scTACL still effectively distinguished the epithelial and mesenchymal regions in the spatial transcriptome data of liver cancer and identified the COLLAGEN signaling pathway, which plays a crucial role in the epithelial-mesenchymal transition process through intercellular communication analysis.

OBJECTIVES: To provide balanced consideration of the opportunities and challenges associated with integrating Large Language Models (LLMs) throughout the medical school continuum. PROCESS: Narrative review of published literature contextualized by current reports of LLM application in medical education. CONCLUSIONS: LLMs like OpenAI's ChatGPT can potentially revolutionize traditional teaching methodologies. LLMs offer several potential advantages to students, including direct access to vast information, facilitation of personalized learning experiences, and enhancement of clinical skills development. For faculty and instructors, LLMs can facilitate innovative approaches to teaching complex medical concepts and fostering student engagement. Notable challenges of LLMs integration include the risk of fostering academic misconduct, inadvertent overreliance on AI, potential dilution of critical thinking skills, concerns regarding the accuracy and reliability of LLM-generated content, and the possible implications on teaching staff.