MIK改进了t-SNE的相似性计算,更好保留数据局部结构。
MIK: Modified Isolation Kernel for Biological Sequence Visualization, Classification, and Clustering
- 用自适应密度估计的MIK替代传统高斯核,提升局部结构捕捉能力。
- 在多个数据集上,MIK使嵌入空间的聚类和子聚类更清晰可辨。
- 适合生物序列等高维数据的可视化与分类分析,尤其关注局部特征。
t-SNE已成为高维数据可视化的主流降维技术,其默认使用RBF核与随机初始化,在捕捉整体结构方面表现良好,但对局部结构的保持效率不足。本文提出一种新型方法——改进的隔离核(Modified Isolation Kernel, MIK),作为高斯核的替代方案。MIK基于隔离核思想,采用自适应密度估计以更准确地捕获局部结构,并融入鲁棒性度量。该方法为邻近点赋予更高相似性值,远点则赋予更低值。通过对比标准高斯核、隔离核及多种初始化方式(随机、PCA、随机游走)进行评估,涵盖三种核与三种初始化方法的组合。实验结果表明,MIK在保持局部与全局结构方面表现更优,显著提升嵌入空间中簇与子簇的可视化效果。该研究推动了降维技术发展,为科研人员提供了一种高效的数据探索与分析工具。
原文摘要 · Abstract (English)
The t-Distributed Stochastic Neighbor Embedding (t-SNE) has emerged as a popular dimensionality reduction technique for visualizing high-dimensional data. It computes pairwise similarities between data points by default using an RBF kernel and random initialization (in low-dimensional space), which successfully captures the overall structure but may struggle to preserve the local structure efficiently. This research proposes a novel approach called the Modified Isolation Kernel (MIK) as an alternative to the Gaussian kernel, which is built upon the concept of the Isolation Kernel. MIK uses adaptive density estimation to capture local structures more accurately and integrates robustness measures. It also assigns higher similarity values to nearby points and lower values to distant points. Comparative research using the normal Gaussian kernel, the isolation kernel, and several initialization techniques, including random, PCA, and random walk initializations, are used to assess the proposed approach (MIK). Additionally, we compare the computational efficiency of all $3$ kernels with $3$ different initialization methods. Our experimental results demonstrate several advantages of the proposed kernel (MIK) and initialization method selection. It exhibits improved preservation of the local and global structure and enables better visualization of clusters and subclusters in the embedded space. These findings contribute to advancing dimensionality reduction techniques and provide researchers and practitioners with an effective tool for data exploration, visualization, and analysis in various domains.
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