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Added 'noinit' results to elbo plots for nips data.
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pcarbo committed Aug 21, 2024
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148 changes: 132 additions & 16 deletions docs/assess_fits_nips.html
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Expand Up @@ -300,7 +300,7 @@ <h4 class="author">Peter Carbonetto</h4>
<div class="tab-content">
<div id="summary" class="tab-pane fade in active">
<p>
<strong>Last updated:</strong> 2024-07-29
<strong>Last updated:</strong> 2024-08-21
</p>
<p>
<strong>Checks:</strong> <span
Expand Down Expand Up @@ -432,15 +432,15 @@ <h4 class="author">Peter Carbonetto</h4>
<div class="panel panel-default">
<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgithubcomstephenslabfastTopicsexperimentstreef14aa4dee29c1a9b4f449840abd0d02e4ce046b3targetblankf14aa4da">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgithubcomstephenslabfastTopicsexperimentstreea482257f7c3f5a15f3c42b01287ed710b1de5522targetblanka482257a">
<span class="glyphicon glyphicon-ok text-success"
aria-hidden="true"></span> <strong>Repository version:</strong>
<a href="https://github.com/stephenslab/fastTopics-experiments/tree/f14aa4dee29c1a9b4f449840abd0d02e4ce046b3" target="_blank">f14aa4d</a>
<a href="https://github.com/stephenslab/fastTopics-experiments/tree/a482257f7c3f5a15f3c42b01287ed710b1de5522" target="_blank">a482257</a>
</a>
</p>
</div>
<div
id="strongRepositoryversionstrongahrefhttpsgithubcomstephenslabfastTopicsexperimentstreef14aa4dee29c1a9b4f449840abd0d02e4ce046b3targetblankf14aa4da"
id="strongRepositoryversionstrongahrefhttpsgithubcomstephenslabfastTopicsexperimentstreea482257f7c3f5a15f3c42b01287ed710b1de5522targetblanka482257a"
class="panel-collapse collapse">
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<p>
Expand All @@ -450,7 +450,7 @@ <h4 class="author">Peter Carbonetto</h4>
</p>
<p>
The results in this page were generated with repository version
<a href="https://github.com/stephenslab/fastTopics-experiments/tree/f14aa4dee29c1a9b4f449840abd0d02e4ce046b3" target="_blank">f14aa4d</a>.
<a href="https://github.com/stephenslab/fastTopics-experiments/tree/a482257f7c3f5a15f3c42b01287ed710b1de5522" target="_blank">a482257</a>.
See the <em>Past versions</em> tab to see a history of the changes made
to the R Markdown and HTML files.
</p>
Expand All @@ -470,28 +470,26 @@ <h4 class="author">Peter Carbonetto</h4>
Ignored: data/droplet.RData
Ignored: data/nips_1-17.mat
Ignored: data/pbmc_68k.RData
Ignored: output/droplet/fits-droplet.RData
Ignored: output/newsgroups/de-newsgroups.RData
Ignored: output/newsgroups/fits-newsgroups.RData
Ignored: output/newsgroups/lda-newsgroups.RData
Ignored: output/newsgroups/rds/
Ignored: output/nips/fits-nips.RData
Ignored: output/nips/lda-nips.RData
Ignored: output/pbmc68k/fits-pbmc68k.RData
Ignored: output/pbmc68k/rds/

Untracked files:
Untracked: .DS_Store
Untracked: analysis/lda-eb-newsgroups-em-k=10.rds
Untracked: analysis/lda-eb-newsgroups-scd-ex-k=10.rds
Untracked: analysis/lda-newsgroups-em-k=10.rds
Untracked: analysis/lda-newsgroups-scd-ex-k=10.rds
Untracked: analysis/maptpx-newsgroups-em-k=10.rds
Untracked: analysis/maptpx-newsgroups-scd-ex-k=10.rds
Untracked: analysis/smallsim_elbo.pdf
Untracked: analysis/smallsim_lda_structure_plots.pdf
Untracked: analysis/smallsim_progress.pdf
Untracked: analysis/smallsim_structure_plots.pdf
Untracked: output/newsgroups/lda-newsgroups.RData
Untracked: output/nips/lda-nips.RData
Untracked: plots/

Unstaged changes:
Modified: analysis/assess_fits_newsgroups.Rmd

</code></pre>
<p>
Note that any generated files, e.g. HTML, png, CSS, etc., are not
Expand Down Expand Up @@ -541,6 +539,40 @@ <h4 class="author">Peter Carbonetto</h4>
Rmd
</td>
<td>
<a href="https://github.com/stephenslab/fastTopics-experiments/blob/a482257f7c3f5a15f3c42b01287ed710b1de5522/analysis/assess_fits_nips.Rmd" target="_blank">a482257</a>
</td>
<td>
Peter Carbonetto
</td>
<td>
2024-08-21
</td>
<td>
workflowr::wflow_publish("assess_fits_nips.Rmd", verbose = TRUE)
</td>
</tr>
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<td>
html
</td>
<td>
<a href="https://rawcdn.githack.com/stephenslab/fastTopics-experiments/70d8b9632258163fa0a322b12ca20fdc3438b7f9/docs/assess_fits_nips.html" target="_blank">70d8b96</a>
</td>
<td>
Peter Carbonetto
</td>
<td>
2024-07-29
</td>
<td>
Added ELBO plots to the assess_fits_nips analysis.
</td>
</tr>
<tr>
<td>
Rmd
</td>
<td>
<a href="https://github.com/stephenslab/fastTopics-experiments/blob/f14aa4dee29c1a9b4f449840abd0d02e4ce046b3/analysis/assess_fits_nips.Rmd" target="_blank">f14aa4d</a>
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<td>
Expand Down Expand Up @@ -826,6 +858,17 @@ <h4 class="author">Peter Carbonetto</h4>
<tbody>
<tr>
<td>
<a href="https://github.com/stephenslab/fastTopics-experiments/blob/70d8b9632258163fa0a322b12ca20fdc3438b7f9/docs/figure/assess_fits_nips.Rmd/plot-loglik-vs-k-1.png" target="_blank">70d8b96</a>
</td>
<td>
Peter Carbonetto
</td>
<td>
2024-07-29
</td>
</tr>
<tr>
<td>
<a href="https://github.com/stephenslab/fastTopics-experiments/blob/269a77bd395aee274d4c10c67a236a32e510824e/docs/figure/assess_fits_nips.Rmd/plot-loglik-vs-k-1.png" target="_blank">269a77b</a>
</td>
<td>
Expand Down Expand Up @@ -894,6 +937,17 @@ <h4 class="author">Peter Carbonetto</h4>
<tbody>
<tr>
<td>
<a href="https://github.com/stephenslab/fastTopics-experiments/blob/70d8b9632258163fa0a322b12ca20fdc3438b7f9/docs/figure/assess_fits_nips.Rmd/plot-loglik-1.png" target="_blank">70d8b96</a>
</td>
<td>
Peter Carbonetto
</td>
<td>
2024-07-29
</td>
</tr>
<tr>
<td>
<a href="https://github.com/stephenslab/fastTopics-experiments/blob/b2fe08fa33f9dfcc62e1e6a6ef4baa5e001cf5be/docs/figure/assess_fits_nips.Rmd/plot-loglik-1.png" target="_blank">b2fe08f</a>
</td>
<td>
Expand Down Expand Up @@ -950,6 +1004,17 @@ <h4 class="author">Peter Carbonetto</h4>
<tbody>
<tr>
<td>
<a href="https://github.com/stephenslab/fastTopics-experiments/blob/70d8b9632258163fa0a322b12ca20fdc3438b7f9/docs/figure/assess_fits_nips.Rmd/plot-res-1.png" target="_blank">70d8b96</a>
</td>
<td>
Peter Carbonetto
</td>
<td>
2024-07-29
</td>
</tr>
<tr>
<td>
<a href="https://github.com/stephenslab/fastTopics-experiments/blob/b2fe08fa33f9dfcc62e1e6a6ef4baa5e001cf5be/docs/figure/assess_fits_nips.Rmd/plot-res-1.png" target="_blank">b2fe08f</a>
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Expand Down Expand Up @@ -1013,6 +1078,17 @@ <h4 class="author">Peter Carbonetto</h4>
<tbody>
<tr>
<td>
<a href="https://github.com/stephenslab/fastTopics-experiments/blob/70d8b9632258163fa0a322b12ca20fdc3438b7f9/docs/figure/assess_fits_nips.Rmd/loadings-scatterplot-1.png" target="_blank">70d8b96</a>
</td>
<td>
Peter Carbonetto
</td>
<td>
2024-07-29
</td>
</tr>
<tr>
<td>
<a href="https://github.com/stephenslab/fastTopics-experiments/blob/7149b0906c4df676131f1639ee5ea9c0050bc77b/docs/figure/assess_fits_nips.Rmd/loadings-scatterplot-1.png" target="_blank">7149b09</a>
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<td>
Expand Down Expand Up @@ -1041,15 +1117,55 @@ <h4 class="author">Peter Carbonetto</h4>
various initializations:</p>
<pre class="r"><code>load(&quot;../output/nips/lda-nips.RData&quot;)
p &lt;- vector(&quot;list&quot;,12)
runs &lt;- which(dat$k == 2)
p[[1]] &lt;- create_elbo_plot(fits[runs],dat[runs,&quot;runtime&quot;],2)
for (i in 2:12) {
runs &lt;- which(dat$k == i)
p[[i]] &lt;- create_elbo_plot(fits[runs],dat[runs,&quot;runtime&quot;],i)
p[[i]] &lt;- create_elbo_plot(fits[runs],dat[runs,&quot;runtime&quot;],i) +
guides(color = &quot;none&quot;,linetype = &quot;none&quot;)
}
plot_grid(p[[2]],p[[3]],p[[4]],p[[5]],
p[[6]],p[[7]],p[[8]],p[[9]],
p[[10]],p[[11]],p[[12]],
p[[10]],p[[11]],p[[12]],p[[1]],
nrow = 3,ncol = 4)</code></pre>
<p><img src="figure/assess_fits_nips.Rmd/elbo-plots-1.png" width="864" style="display: block; margin: auto;" /></p>
<p>
<button type="button" class="btn btn-default btn-xs btn-workflowr btn-workflowr-fig" data-toggle="collapse" data-target="#fig-elbo-plots-1">
Past versions of elbo-plots-1.png
</button>
</p>
<div id="fig-elbo-plots-1" class="collapse">
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<th>
Version
</th>
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Author
</th>
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Date
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<td>
<a href="https://github.com/stephenslab/fastTopics-experiments/blob/70d8b9632258163fa0a322b12ca20fdc3438b7f9/docs/figure/assess_fits_nips.Rmd/elbo-plots-1.png" target="_blank">70d8b96</a>
</td>
<td>
Peter Carbonetto
</td>
<td>
2024-07-29
</td>
</tr>
</tbody>
</table>
</div>
</div>
<br>
<p>
<button type="button" class="btn btn-default btn-workflowr btn-workflowr-sessioninfo" data-toggle="collapse" data-target="#workflowr-sessioninfo" style="display: block;">
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