CosMAP combines cosine-similarity neighborhoods, a temperature-scaled affinity graph, and a two-phase embedding refinement to produce low-dimensional visualizations that the authors find clearer than UMAP, t-SNE, LocalMAP, and related methods on benchmark and omics data.
Node Embeddings via Neighbor Embeddings
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abstract
Node embeddings are a paradigm in non-parametric graph representation learning, where graph nodes are embedded into a given vector space to enable downstream processing. State-of-the-art node-embedding algorithms, such as DeepWalk and node2vec, are based on random-walk notions of node similarity and on contrastive learning. In this work, we introduce the graph neighbor-embedding (graph NE) framework that directly pulls together embedding vectors of adjacent nodes without relying on any random walks. We show that graph NE strongly outperforms state-of-the-art node-embedding algorithms in terms of local structure preservation. Furthermore, we apply graph NE to the 2D node-embedding problem, obtaining graph t-SNE layouts that also outperform existing graph-layout algorithms.
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CosMAP: Contrastive Manifold Approximation and Projection for Dimensionality Reduction of Omics and Genealogical Data
CosMAP combines cosine-similarity neighborhoods, a temperature-scaled affinity graph, and a two-phase embedding refinement to produce low-dimensional visualizations that the authors find clearer than UMAP, t-SNE, LocalMAP, and related methods on benchmark and omics data.