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updates css
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lucasbrambrink committed Sep 6, 2024
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Expand Up @@ -19,10 +19,15 @@ authors: ["msamman", "danielecook", "awcarroll", "lucasbrambrink"]
margin-left: -100px;
}
@media (min-width: 1200px) {
max-width: 1000px;
max-width: 1100px;
margin-left: -100px;
}
}
figcaption {
text-align: left;
margin: auto;
width: 90%;
}

</style>

Expand Down Expand Up @@ -69,21 +74,29 @@ In order to gain a better understanding of each channel's contribution to overal

<figure>
<img src="{{ site.baseurl }}/assets/images/2024-09-04/figure_2a.png" alt="Figure 2(a): A pileup image with the base_differs_from_ref channel ablated"/>
<figcaption style='text-align: center;'>Figure 2(a): A pileup image with the <code class="highlighter-rouge" style='font-size: 13px;'>base_differs_from_ref</code> channel ablated.</figcaption>
<figcaption style='text-align: center;'>
Figure 2(a): A pileup image with the <code class="highlighter-rouge" style='font-size: 13px;'>base_differs_from_ref</code> channel ablated.
</figcaption>
</figure>

The second set of models were trained on just a **single** channel chosen from the default channels. These experiments isolate the information contained in each of the channels separately. The following illustration is an example of isolating the `read_base` channel.

<figure>
<img src="{{ site.baseurl }}/assets/images/2024-09-04/figure_2b.png" alt="Figure 2(b): A single channel pileup image, showing only read_base information"/>
<figcaption style='text-align: center;'>A single channel pileup image, showing only <code class="highlighter-rouge" style='font-size: 13px;'>read_base</code> information.</figcaption>
<img src="{{ site.baseurl }}/assets/images/2024-09-04/figure_2b.png"
alt="Figure 2(b): A single channel pileup image, showing only read_base information"
style='width: 350px;'/>
<figcaption style='text-align: center;'>Figure 2(b): A single channel pileup image, showing only <code class="highlighter-rouge" style='font-size: 13px;'>read_base</code> information.
</figcaption>
</figure>

Included in our set of single channel experiments is a model trained on a completely blank channel (i.e. a black image). This model receives absolutely no information about any candidate and acts as a floor for expected performance.

<figure>
<img src="{{ site.baseurl }}/assets/images/2024-09-04/figure_2c.png" alt="Figure 2(b): An example of a blank channel, containing no information about reads or reference"/>
<figcaption style='text-align: center;'>An example of a <code class="highlighter-rouge" style='font-size: 13px;'>blank</code> channel, containing no information about reads or reference.</figcaption>
<img src="{{ site.baseurl }}/assets/images/2024-09-04/figure_2c.png"
alt="Figure 2(b): An example of a blank channel, containing no information about reads or reference"
style='width: 350px;'/>
<figcaption style='text-align: center;'>Figure 2(c): An example of a <code class="highlighter-rouge" style='font-size: 13px;'>blank</code> channel, containing no information about reads or reference.
</figcaption>
</figure>

All models were trained using our standard GIAB Illumina WGS dataset and evaluated on HG003.
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