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In this paper, we investigated the relationship of t-SNE perplexity and graph layout evaluation metrics including graph stress, preserved neighborhood information and visual inspection. As we found that a small perplexity is correlated with a relative higher normalized stress while preserving neighborhood information with a higher precision but less global structure information, we proposed our method to estimate appropriate perplexity either based on a modified standard t-SNE or the sklearn Barnes\u2013Hut TSNE. Experimental results demonstrate effectiveness and ease of use of our approach when tested on a set of benchmark datasets.<\/jats:p>","DOI":"10.1007\/s41060-022-00348-7","type":"journal-article","created":{"date-parts":[[2022,7,30]],"date-time":"2022-07-30T21:02:32Z","timestamp":1659214952000},"page":"159-171","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Optimizing graph layout by t-SNE perplexity estimation"],"prefix":"10.1007","volume":"15","author":[{"given":"Chun","family":"Xiao","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Seokhee","family":"Hong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weidong","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,7,30]]},"reference":[{"key":"348_CR1","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1007\/978-3-319-13572-4_17","volume":"334","author":"T Buri\u00e1nek","year":"2015","unstructured":"Buri\u00e1nek, T., Zaor\u00e1lek, L., Sn\u00e1\u0161el, V., Peterek, T.: Graph drawing using dimension reduction methods. 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