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Update README.md
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ejohnson643 authored Dec 17, 2021
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Expand Up @@ -65,16 +65,16 @@ 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.

```python
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

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