Ethan Armand
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ethan-armand.bsky.social
Ethan Armand
@ethan-armand.bsky.social
200 followers 490 following 72 posts
Bioinformatics PhD Student in the Ren lab at UCSD. Modeling gene regulation across species.
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ethan-armand.bsky.social
@anshulkundaje.bsky.social has a point. Training lots of enformer-type models on psuedobulk there's generally a log-linear sampling depth-> performance relationship that is unsaturated. Even with gold standard sc epigenomes. Both data and models will keep improving.
For example Basenji from BICCN:
A scatter plot titled "Zu et al atlas test set performance". The X axis is labeled "number of cells in subtype" and is plotted in a log scale. the X axis ranges from ~80 to ~500 thousand. The Y axis is labled pearson corr and ranges from ~0.5 to ~0.9. The scatter plot has 275 points. The scatter points are in three colors, corresponding to cell class (Gabergic in blue, glutamatergic in yellow, and non-neuronal in gray). The points form roughly an arc with a low density region of cells in the bottom left (low cell number low accuracy), quickly climbing to a region of higher density, with cells ranging from 500-10,000 and with average correlation close to .85 (~.89 highest, ~.7 lowest, with a outlier at .6). Beyond ~10k cells the accuracy flatlines near 0.825, with lower performing non-neuronal cells as low as .75, and neuronal types between .8 and .85. On the bottom right, and area absent any points is the text "pearsonr =0.41"
January 29, 2025 at 8:55 PM
ethan-armand.bsky.social
Me with data
A six panel comic of a cute woodland creature (somewhere in between a chipmunk, cat, and raccoon) by Amy Revies. The creature is has large eyes, large cheeks, a striped tail, and is colored in dark shades of orange. Panel 1 (top left) The creature is holding a ball labeled "hobby" with a smile and perked up ears. The creatures says "This is fun!". Panel 2 (top right): With an inquisitive glance the creature's attention is drawn to another ball labeled hobby in the bottom left corner. Panel 3 (middle left): With a smile the creature reaches to the bottom left to grab the second ball labeled hobby. The creature says "This looks fun too!: Panel 4 (middle right): The creature now holding two balls labeled hobby smiles and looks down with adoration towards the two balls. The text says "Alrigh-" not completing the though". Barely visible In the bottom right corner is another ball labeled hobby. Panel 5 (bottom left): The creature looks conspicuously, almost guiltily towards the ball at the bottom right. A large ellipsis is shown to the right of the creatures head. Panel 6 (bottom right): The creature is consumed by mania laughing while surrounded by balls labeled "hobby" as if fallen into a giant ball pit. The creatures mania is reflected by an asymmetrical smile and misshapen irises pointing in different directions. The creatures laugh is written as large text at a 30 degree angle "AHAHAHA"
December 5, 2024 at 7:58 PM