diff --git a/README.md b/README.md index 014c669..c45ec3f 100644 --- a/README.md +++ b/README.md @@ -65,7 +65,7 @@ sweepObj.fit(X) sweepObj.plot_embedding(embed_2_show=1, param_2_plot=250) ``` -![Embedding of MNIST from sweep](EasyUseExample_SweepEmbedding) +![Embedding of MNIST from sweep](EasyUseExample_SweepEmbedding.png) In this example, at `perplexity` = 25, 100, and 250, we embedded the data 3 times, each with a different random initialization, and we embedded the null data once. We can then plot any of the embeddings at any of the values of `perplexity` using the `plot_embedding` method shown above. We can also visualize the entire sweep using the `sweep_boxplot` and `sweep_lineplot` functions, as shown below. @@ -73,8 +73,8 @@ In this example, at `perplexity` = 25, 100, and 250, we embedded the data 3 time sweepObj.sweep_boxplot() sweepObj.sweep_lineplot() ``` -![EMBEDR *p*-values at several values of perplexity](EasyUseExample_SweepBoxes) -![EMBEDR *p*-values at several values of perplexity](EasyUseExample_SweepLines) +![EMBEDR *p*-values at several values of perplexity](EasyUseExample_SweepBoxes.png) +![EMBEDR *p*-values at several values of perplexity](EasyUseExample_SweepLines.png) Using these figures, we can summarize the quality of t-SNE as the `perplexity` hyperparameter is varied. Using these figures, as shown in our paper, we can determine optimal values for `perplexity` (or `n_neighbors` in UMAP), find characteristic scales and neighborhood sizes for different samples, and detect robust features in embeddings. We can also determine the optimal `perplexity` for each sample individually and use this `perplexity` to