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. 2022 Nov 11;18(12):7179–7192. doi: 10.1021/acs.jctc.2c00873

Table 1. Summary of Reweighted Stochastic Embedding Methods Used in (Section 3.2): mrse and stkea.

  mrse stke
reweighting factor r(xk, xl) Inline graphic [eq 29] Inline graphic [eq 31]
high-dim. prob. M(xk, xl) Gaussian mixture [eq 30] for perplexities ∈ {256, 128, 64, 32} Gaussian [eq 32] with ε = 0.12
low-dim. prob. Q(zk, zl) t-distribution [eq 26] Gaussian with ε = 0.12
landmark sampling weight-tempered random sampling for τ = 3 and 5000 landmarks minimal pairwise distance for rc = 1.2 and 97000 landmarks
activation functions ReLU (3 layers) hyperbolic tangent (3 layers)
optimizer Adam (μ = 0.001, β1 = 0.9, β2 = 0.999) Adam (μ = 0.001, β1 = 0.9, β2 = 0.999)
batch size 1000 256
a

Labels: reweighting factor r(xk, xl), high-dimensional Markov transition matrix M(xk, xl), and low-dimensional Markov transition matrix Q(zk, zl).