Joint t-SNE for Comparable Projections of Multiple High-Dimensional Datasets

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. Despite this progress, the analysis of single-cell and spatial omics data remains challenging. First, single-cell sequencing data are high-dimensional and sparse, and are often contaminated by noise and uncertainty, obscuring the underlying biological signal. Second, these data often encompass multiple modalities, including gene expression, epigenetic modifications, metabolite levels, 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 approaches struggle with the complexity of biological networks, while deep learning, with its ability to handle high-dimensional data and automatically identify meaningful patterns, has shown great promise in overcoming these challenges. Besides systematically reviewing the strengths and weaknesses of advanced deep learning methods, we have curated 21 datasets from nine benchmarks to evaluate the performance of 58 computational methods. Our analysis reveals that model performance can vary significantly across different benchmark datasets and evaluation metrics, providing a useful perspective for selecting the most appropriate approach based on a specific application scenario. We highlight three key areas for future development, offering valuable insights into how deep learning can be effectively applied to transcriptomic data analysis in biological, medical, and clinical settings.

Single-cell omics: experimental workflow, data analyses and applications

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

DRAVA: Aligning Human Concepts with Machine Learning Latent Dimensions for the Visual Exploration of Small Multiples

Latent vectors extracted by machine learning (ML) are widely used in data exploration (e.g., t-SNE) but suffer from a lack of interpretability. While previous studies employed disentangled representation learning (DRL) to enable more interpretable exploration, they often overlooked the potential mismatches between the concepts of humans and the semantic dimensions learned by DRL. To address this issue, we propose Drava, a visual analytics system that supports users in 1) relating the concepts of humans with the semantic dimensions of DRL and identifying mismatches, 2) providing feedback to minimize the mismatches, and 3) obtaining data insights from concept-driven exploration. Drava provides a set of visualizations and interactions based on visual piles to help users understand and refine concepts and conduct concept-driven exploration. Meanwhile, Drava employs a concept adaptor model to fine-tune the semantic dimensions of DRL based on user refinement. The usefulness of Drava is demonstrated through application scenarios and experimental validation.

Research on E-Commerce Database Marketing Based on Machine Learning Algorithm

From simple commercial relations to complex online transactions at this stage, it not only highlights the progress of science and technology, but also indirectly explains the diversified evolution of marketing methods and means. In marketing, database marketing has been favored by more marketers with its low cost and high efficiency and has become the “rookie” in marketing in recent years. However, as a kind of prediction and ferry, database marketing tends to be applied after simple data analysis in unpredictable market and in practice. In contrast, database marketing combined with machine learning algorithms has always been a depression in the marketing field. Therefore, this paper takes e-commerce as the research object and carries out database marketing research based on machine learning algorithm from four stages: theoretical preparation, status analysis, model construction, and results application. Firstly, the connotation, advantages, and specific operation procedures of database marketing are discussed. At the same time, four excellent machine learning algorithms including logistic regression, random forest, support vector machine, and gradient boosted decision tree (GBDT) are selected to explain the basic principles and algorithm introduction, respectively, laying a theoretical foundation for the model training chapter. Secondly, it analyzes the current situation of e-commerce from the distribution of marketing objects, the proportion of marketing channels, and the composition of marketing methods and finds new marketing ideas based on the main problems existing at the present stage of database marketing using machine learning algorithm. Thirdly, on the premise of marketing ideas, data acquisition, data processing, and positive and negative sample setting. At the same time, four machine learning algorithms are used to combine features from the perspectives of consumers, stores, and the relationship between consumers and stores. Finally, by substituting the predicted sample into the model for testing, the crowd whose predicted score is between 80 and 99 is selected to be put into the market as the model predicted crowd, and it is proposed that e-commerce should mainly adopt the database marketing method of model prediction. On the one hand, machine learning algorithm can solve the problem of uneven distribution of marketing objects, and on the other hand, it can effectively prevent the loss of potential consumers. In addition, the application strategy of optimizing other database marketing methods and assisting model prediction to improve marketing effect is also put forward.