Lior Pachter
@lpachter.bsky.social
Bren Professor of Computational Biology @Caltech.edu. Blog at http://liorpachter.wordpress.com. Posts represent my views, not my employer's. #methodsmatter
he underlying optimization problems are NP-hard, but for many visualization tasks can probably be solved optimally. It was fun returning to Bryant and Huson's NeighborNet as a good heuristic, but there is certainly room for improvement.
September 5, 2025 at 12:20 PM
he underlying optimization problems are NP-hard, but for many visualization tasks can probably be solved optimally. It was fun returning to Bryant and Huson's NeighborNet as a good heuristic, but there is certainly room for improvement.
The advantage of organizing with wompwomp is evident in the clarity one sees when tracing, say, the Lannisters vs. Westeros
September 5, 2025 at 12:20 PM
The advantage of organizing with wompwomp is evident in the clarity one sees when tracing, say, the Lannisters vs. Westeros
The improvements produced by wompwomp are evident in the Game of Thrones dataset displayed at the opening of this thread. To the left is the alluvial plot without wompwomp, to the right with wompwomp.
September 5, 2025 at 12:20 PM
The improvements produced by wompwomp are evident in the Game of Thrones dataset displayed at the opening of this thread. To the left is the alluvial plot without wompwomp, to the right with wompwomp.
wompwomp sorts columns and blocks within columns to best reveal structure in data. For instance, this is a comparison of clustering algorithms viewed in a randomly organized alluvial plot, fixed columns (only blocks sorted), and fully optimized with wompwomp.
September 5, 2025 at 12:20 PM
wompwomp sorts columns and blocks within columns to best reveal structure in data. For instance, this is a comparison of clustering algorithms viewed in a randomly organized alluvial plot, fixed columns (only blocks sorted), and fully optimized with wompwomp.
In a new work with Joseph Rich and Conrad Oakes we tackle the problem of how to best organize alluvial plots. We formalize two optimization problems and develop a solution for them based on the neighbornet algorithm, implemented in the program wompwomp: github.com/pachterlab/w...
September 5, 2025 at 12:20 PM
In a new work with Joseph Rich and Conrad Oakes we tackle the problem of how to best organize alluvial plots. We formalize two optimization problems and develop a solution for them based on the neighbornet algorithm, implemented in the program wompwomp: github.com/pachterlab/w...
Glacial area reduced by 41.6% from 1896 to 1921. Between 2015 and 2021, the rate at which Mount Rainier glaciers were losing area was more than two times faster than the rate estimated for the period of 2009 to 2015.
irma.nps.gov/DataStore/Do...
I took this photo on July 26, 2025.
irma.nps.gov/DataStore/Do...
I took this photo on July 26, 2025.
August 3, 2025 at 10:49 PM
Glacial area reduced by 41.6% from 1896 to 1921. Between 2015 and 2021, the rate at which Mount Rainier glaciers were losing area was more than two times faster than the rate estimated for the period of 2009 to 2015.
irma.nps.gov/DataStore/Do...
I took this photo on July 26, 2025.
irma.nps.gov/DataStore/Do...
I took this photo on July 26, 2025.
The confiscation of cell phones from children at schools & summer camps is largely the result of a national campaign by
@jonathanhaidt.bsky.social
But cell phones are safety devices used for notification & early warnings of active shooters, earthquakes, floods, tornados, tsunamis, wildfires, ..
@jonathanhaidt.bsky.social
But cell phones are safety devices used for notification & early warnings of active shooters, earthquakes, floods, tornados, tsunamis, wildfires, ..
July 6, 2025 at 3:22 PM
The confiscation of cell phones from children at schools & summer camps is largely the result of a national campaign by
@jonathanhaidt.bsky.social
But cell phones are safety devices used for notification & early warnings of active shooters, earthquakes, floods, tornados, tsunamis, wildfires, ..
@jonathanhaidt.bsky.social
But cell phones are safety devices used for notification & early warnings of active shooters, earthquakes, floods, tornados, tsunamis, wildfires, ..
Congratulations to @delaneyksull.bsky.social on successfully defending his PhD (photo below with his committee: Barbara Wold, @mitchguttman.bsky.social, and another of my former students @hjp.bsky.social).
His thesis is on software, tools, and methods development for single-cell transcriptomics.
His thesis is on software, tools, and methods development for single-cell transcriptomics.
May 5, 2025 at 12:14 AM
Congratulations to @delaneyksull.bsky.social on successfully defending his PhD (photo below with his committee: Barbara Wold, @mitchguttman.bsky.social, and another of my former students @hjp.bsky.social).
His thesis is on software, tools, and methods development for single-cell transcriptomics.
His thesis is on software, tools, and methods development for single-cell transcriptomics.
Congratulations to Anne Kil on successful defense of her PhD! Her thesis focused on engineering solutions for saliva as a biomedical diagnostic, from improved collection asmedigitalcollection.asme.org/medicaldevic... to assessing the potential of saliva multiomics www.biorxiv.org/content/10.1...
May 4, 2025 at 11:56 PM
Congratulations to Anne Kil on successful defense of her PhD! Her thesis focused on engineering solutions for saliva as a biomedical diagnostic, from improved collection asmedigitalcollection.asme.org/medicaldevic... to assessing the potential of saliva multiomics www.biorxiv.org/content/10.1...
Huh? This is what the authors are detecting. This is what they are talking about in their abstract.
February 1, 2025 at 8:35 PM
Huh? This is what the authors are detecting. This is what they are talking about in their abstract.
Did you actually look at the data? It's clear what the abstract means.
February 1, 2025 at 8:25 PM
Did you actually look at the data? It's clear what the abstract means.
Apropos of nothing: less than 10% of pilots are women (5% for airline). And yet it's male pilots (specifically older & w/ experience) who are more likely to be involved in a fatal accident. www.sciencedirect.com/science/arti...
There's a pilot shortage. Shouldn't one try hard to recruit women?
There's a pilot shortage. Shouldn't one try hard to recruit women?
January 31, 2025 at 6:26 PM
Apropos of nothing: less than 10% of pilots are women (5% for airline). And yet it's male pilots (specifically older & w/ experience) who are more likely to be involved in a fatal accident. www.sciencedirect.com/science/arti...
There's a pilot shortage. Shouldn't one try hard to recruit women?
There's a pilot shortage. Shouldn't one try hard to recruit women?
Knights can be fierce warriors but are idle tools in the hands of fools.
January 29, 2025 at 8:06 AM
Knights can be fierce warriors but are idle tools in the hands of fools.
Even a pawn can checkmate a king.
January 29, 2025 at 7:45 AM
Even a pawn can checkmate a king.
I found this small charred fragment from Gray’s Anatomy in our backyard. 😢
January 15, 2025 at 12:39 AM
I found this small charred fragment from Gray’s Anatomy in our backyard. 😢
Looks like Gerver's sofa is optimal.
arxiv.org/pdf/2411.19826
arxiv.org/pdf/2411.19826
December 7, 2024 at 10:17 PM
Looks like Gerver's sofa is optimal.
arxiv.org/pdf/2411.19826
arxiv.org/pdf/2411.19826
This is very cool.
November 30, 2024 at 12:59 AM
This is very cool.
Another example of the different results one gets from a Scanpy vs. Seurat analysis, in this case a Visium HD dataset from academic.oup.com/bioinformati...
13 vs. 20 clusters. And qualitatively different results, corroborating what we saw in biorxiv.org/content/10.1...
13 vs. 20 clusters. And qualitatively different results, corroborating what we saw in biorxiv.org/content/10.1...
November 25, 2024 at 6:10 PM
Another example of the different results one gets from a Scanpy vs. Seurat analysis, in this case a Visium HD dataset from academic.oup.com/bioinformati...
13 vs. 20 clusters. And qualitatively different results, corroborating what we saw in biorxiv.org/content/10.1...
13 vs. 20 clusters. And qualitatively different results, corroborating what we saw in biorxiv.org/content/10.1...
Hope this helps. Of course it’s just for visualization, you will have to verify with follow up experiments.
November 18, 2024 at 1:45 PM
Hope this helps. Of course it’s just for visualization, you will have to verify with follow up experiments.
It's not so much an echo chamber as it is a sphere, although at a distance it appears to be a pale blue dot (credit NASA/JPL-Caltech February 14, 1990 photograph from Voyager I taken at a distance of 3.7 billion miles).
November 18, 2024 at 1:31 PM
It's not so much an echo chamber as it is a sphere, although at a distance it appears to be a pale blue dot (credit NASA/JPL-Caltech February 14, 1990 photograph from Voyager I taken at a distance of 3.7 billion miles).
A reminder that if you are reading a preprint and the data is not released but is available (privately) on Genbank, SRA, or GEO, you can email and ask for it to be released.
November 17, 2024 at 6:04 PM
A reminder that if you are reading a preprint and the data is not released but is available (privately) on Genbank, SRA, or GEO, you can email and ask for it to be released.
I can't really claim to be on this @bsky.app site if I'm not ever posting here about UMAPs...
...so here is a recent Science paper with contours on their UMAPs... 😱 How is this still a thing? www.science.org/doi/full/10....
...so here is a recent Science paper with contours on their UMAPs... 😱 How is this still a thing? www.science.org/doi/full/10....
November 13, 2024 at 1:35 AM
I can't really claim to be on this @bsky.app site if I'm not ever posting here about UMAPs...
...so here is a recent Science paper with contours on their UMAPs... 😱 How is this still a thing? www.science.org/doi/full/10....
...so here is a recent Science paper with contours on their UMAPs... 😱 How is this still a thing? www.science.org/doi/full/10....