Pattern or Artifact? Interactively Exploring Embedding Quality with TRACE

This paper presents TRACE, a tool to analyze the quality of 2D embeddings generated through dimensionality reduction techniques. Dimensionality reduction methods often prioritize preserving either local neighborhoods or global distances, but insights from visual structures can be misleading if the objective has not been achieved uniformly. TRACE addresses this challenge by providing a scalable and extensible pipeline for computing both local and global quality measures. The interactive browser-based interface allows users to explore various embeddings while visually assessing the pointwise embedding quality. The interface also facilitates in-depth analysis by highlighting high-dimensional nearest neighbors for any group of points and displaying high-dimensional distances between points. TRACE enables analysts to make informed decisions regarding the most suitable dimensionality reduction method for their specific use case, by showing the degree and location where structure is preserved in the reduced space.

Revised Conditional t-SNE: Looking Beyond the Nearest Neighbors

Conditional t-SNE (ct-SNE) is a recent extension to t-SNE that allows removal of known cluster information from the embedding, to obtain a visualization revealing structure beyond label information. This is useful, for example, when one wants to factor out unwanted differences between a set of classes. We show that ct-SNE fails in many realistic settings, namely if the data is well clustered over the labels in the original high-dimensional space. We introduce a revised method by conditioning the high-dimensional similarities instead of the low-dimensional similarities and storing within- and across-label nearest neighbors separately. This also enables the use of recently proposed speedups for t-SNE, improving the scalability. From experiments on synthetic data, we find that our proposed method resolves the considered problems and improves the embedding quality. On real data containing batch effects, the expected improvement is not always there. We argue revised ct-SNE is preferable overall, given its improved scalability. The results also highlight new open questions, such as how to handle distance variations between clusters.