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When visualizing a high-dimensional dataset, dimension reduction techniques are commonly employed which provide a single 2 dimensional view of the data. We describe ENS-t-SNE: an algorithm for Embedding Neighborhoods Simultaneously that generalizes the t-Stochastic Neighborhood Embedding approach. By using different viewpoints in ENS-t-SNE’s 3D embedding, one can visualize different types of clusters within the same high-dimensional dataset. This enables the viewer to see and keep track of the different types of clusters, which is harder to do when providing multiple 2D embeddings, where corresponding points cannot be easily identified. We illustrate the utility of ENS-t-SNE with real-world applications and provide an extensive quantitative evaluation with datasets of different types and sizes.
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This content will become publicly available on April 11, 2026
Dimension Reduction with Locally Adjusted Graphs
Dimension reduction (DR) algorithms have proven to be extremely useful for gaining insight into large-scale high-dimensional datasets, particularly finding clusters in transcriptomic data. The initial phase of these DR methods often involves converting the original high-dimensional data into a graph. In this graph, each edge represents the similarity or dissimilarity between pairs of data points. However, this graph is frequently suboptimal due to unreliable high-dimensional distances and the limited information extracted from the high-dimensional data. This problem is exacerbated as the dataset size increases. If we reduce the size of the dataset by selecting points for a specific sections of the embeddings, the clusters observed through DR are more separable since the extracted subgraphs are more reliable. In this paper, we introduce LocalMAP, a new dimensionality reduction algorithm that dynamically and locally adjusts the graph to address this challenge. By dynamically extracting subgraphs and updating the graph on-the-fly, LocalMAP is capable of identifying and separating real clusters within the data that other DR methods may overlook or combine. We demonstrate the benefits of LocalMAP through a case study on biological datasets, highlighting its utility in helping users more accurately identify clusters for real-world problems.
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- PAR ID:
- 10627567
- Publisher / Repository:
- Association for the Advancement of Artificial Intelligence
- Date Published:
- Journal Name:
- Proceedings of the AAAI Conference on Artificial Intelligence
- Volume:
- 39
- Issue:
- 20
- ISSN:
- 2159-5399
- Page Range / eLocation ID:
- 21357 to 21365
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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