- Last 7 days
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P recisions
In this case does
sdenote tuning to how results are classified when calling true and false positives and negatives? Or weight terms in the F-measure score it self? -
x−i,j (t), which is the expression of gene j (the expres-sion of all other genes is masked)
Is this a vector with only a value at position j? So a vector of size N with only position j having a value set, hence being different than x_{j}(t)?
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- May 2024
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www.biorxiv.org www.biorxiv.org
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The black arrow highlights the longest barcode.
It might be easier to see if the longest barcode was in a different color or had a dashed line overlayed on top of it.
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e green and light blue clusters are on one side, and the other colors(especially the dark blue and magenta) are on the other side of the hole.
It's hard to tell exactly which part of the structure is being referenced (at least for me). It might be helpful to add an annotation like a circle to show which area is being discussed.
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xi,j − ̃x
The indexing of
x_{ij}doesn't seem to be a unique element but a pair(u_{ij}, s_{ij}). Is this loss function calculating the difference between the spliced and unspliced differences combined?
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- Feb 2024
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arxiv.org arxiv.org
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if di is equal to 1984-01-01, then U encompasses all papers published after diuntil 1989-01-01
This part is assuming that t has been set to 5, correct?
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scGPT v1 outperformed the scGPT model overall, raising the issue146of the need for increasing the size of pre-training datasets for this task
Wasn't scGPT v1 which out performed scGPT trained on a smaller pre-training data set?
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The fact that thisnarrative captured so much attention despite a complete lack of supporting evidence promptsus to reflect on how our biases shape our interpretation of data, and how extreme differencesin believing people based on where they work can lead to incorrect and harmful conclusions.Here, we are reflecting on our experiences, and we invite readers to do the same.
Really interesting article!
Given the impact this had do you feel there are changes or criticisms needed around the review and publication process of the Bloom results? I'm also curious if you have any thoughts on how pre-print and open science can do a better job with contentious results and discussions around them.
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- Oct 2023
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www.biorxiv.org www.biorxiv.org
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e also found associations top53, telomere maintenance, and cell fate within 1 Mbp of our top 25 loci of interest. Ourtop 25 loci also have links to cancer and height or body size, though these prevalent diseasesand biomarkers are of course heavily studied and consequently commonly annotated, and sowe cannot know whether their appearance is simply due to their frequency
Is this 1Mbp in either direction of a loci of interest? Just binning the human genome by 25 points gives about 1.7% of the genome within 1Mbp of these uniform bins. Depending on what percent of genes are associated with the traits of interest that could be very rare, or fairly common. Is there a way of viewing how impactful this result is in comparison to the size of the genome annotated as relevant to these traits?
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