Jie Hua

Ali Anaissi, Seid Miad Zandavi, Weidong Huang et al.

Single-cell data analysis has the potential to revolutionize personalized medicine by characterizing disease-associated molecular changes at the single-cell level. Advanced single-cell multimodal assays can now simultaneously measure various molecules (e.g., DNA, RNA, Protein) across hundreds of thousands of individual cells, providing a comprehensive molecular readout. A significant analytical challenge is integrating single-cell measurements across different modalities. Various methods have been developed to address this challenge, but there has been no systematic evaluation of these techniques with different preprocessing strategies. This study examines a general pipeline for single-cell data analysis, which includes normalization, data integration, and dimensionality reduction. The performance of different algorithm combinations often depends on the dataset sizes and characteristics. We evaluate six datasets across diverse modalities, tissues, and organisms using three metrics: Silhouette Coefficient Score, Adjusted Rand Index, and Calinski-Harabasz Index. Our experiments involve combinations of seven normalization methods, four dimensional reduction methods, and five integration methods. The results show that Seurat and Harmony excel in data integration, with Harmony being more time-efficient, especially for large datasets. UMAP is the most compatible dimensionality reduction method with the integration techniques, and the choice of normalization method varies depending on the integration method used.

Sangsu Lee, Xi Zheng, Jie Hua et al.

Pervasive computing applications commonly involve user's personal smartphones collecting data to influence application behavior. Applications are often backed by models that learn from the user's experiences to provide personalized and responsive behavior. While models are often pre-trained on massive datasets, federated learning has gained attention for its ability to train globally shared models on users' private data without requiring the users to share their data directly. However, federated learning requires devices to collaborate via a central server, under the assumption that all users desire to learn the same model. We define a new approach, opportunistic federated learning, in which individual devices belonging to different users seek to learn robust models that are personalized to their user's own experiences. However, instead of learning in isolation, these models opportunistically incorporate the learned experiences of other devices they encounter opportunistically. In this paper, we explore the feasibility and limits of such an approach, culminating in a framework that supports encounter-based pairwise collaborative learning. The use of our opportunistic encounter-based learning amplifies the performance of personalized learning while resisting overfitting to encountered data.