Shuqing Sun | Searcharxiv

arXiv2025

Sleep Modulation: The Challenge of Transitioning from Open Loop to Closed Loop

Sleep disorders have emerged as a critical global health issue, highlighting the urgent need for effective and widely accessible intervention technologies. Non-invasive brain stimulation has garnered attention as it enables direct or indirect modulation of neural activity, thereby promoting sleep enhancement in a safe and unobtrusive manner. This class of approaches is collectively referred to as sleep modulation. To date, the majority of sleep modulation research relies on open-loop paradigms with empirically determined parameters, while achieving individual adaptation and modulation accuracy remains a distant objective. The paradigm-specific constraints inherent to open-loop designs represent a major obstacle to clinical translation and large-scale deployment in home environments. In this paper, we delineate fundamental paradigms of sleep modulation, critically examine the intrinsic limitations of open-loop approaches, and formally conceptualize sleep closed-loop modulation. We further provide a comprehensive synthesis of prior studies involving five commonly employed modulation techniques, evaluating their potential integration within a closed-loop framework. Finally, we identify three primary challenges in constructing an effective sleep closed-loop modulation system: sensor solution selection, monitoring model design, and modulation strategy design, while also proposing potential solutions. Collectively, this work aims to advance the paradigm shift of sleep modulation from open-loop toward closed-loop systems.

cs.HC↗

arXiv2024

Deep Learning in Single-Cell and Spatial Transcriptomics Data Analysis: Advances and Challenges from a Data Science Perspective

The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial contexts. However, the analysis of single-cell and spatial omics data remains challenging. First, single-cell sequencing data are high-dimensional and sparse, often contaminated by noise and uncertainty, obscuring the underlying biological signals. Second, these data often encompass multiple modalities, including gene expression, epigenetic modifications, and spatial locations. Integrating these diverse data modalities is crucial for enhancing prediction accuracy and biological interpretability. Third, while the scale of single-cell sequencing has expanded to millions of cells, high-quality annotated datasets are still limited. Fourth, the complex correlations of biological tissues make it difficult to accurately reconstruct cellular states and spatial contexts. Traditional feature engineering-based analysis methods struggle to deal with the various challenges presented by intricate biological networks. Deep learning has emerged as a powerful tool capable of handling high-dimensional complex data and automatically identifying meaningful patterns, offering significant promise in addressing these challenges. This review systematically analyzes these challenges and discusses related deep learning approaches. Moreover, we have curated 21 datasets from 9 benchmarks, encompassing 58 computational methods, and evaluated their performance on the respective modeling tasks. Finally, we highlight three areas for future development from a technical, dataset, and application perspective. This work will serve as a valuable resource for understanding how deep learning can be effectively utilized in single-cell and spatial transcriptomics analyses, while inspiring novel approaches to address emerging challenges.

q-bio.GN↗