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Lior Pachter Profile picture
@lpachter
Sep 18, 2020 • 8 tweets • 3 min read • Read on X
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There is something deeply flawed with SciPy. The recent @numpy_team paper just published with 26 male authors and 0 women is a symptom. 1/
There have been complaints about lack of diversity for years. 2/ ilovesymposia.com/2015/04/03/cal…
Does diversity matter? It sure does. Just one consequence: by shutting out women, the SciPy team arguably bears considerable responsibility for driving women to R. 3/ reshamas.github.io/why-women-are-…
A debate about R vs. Python can be settled elsewhere, but it doesn’t seem too much to insist that programming language choices should not be influenced by sexism. 4/
I’ve also been disheartened that funding agencies talking about emphasizing diversity, equity and inclusion turn a blind eye. 5/
As a result, the @numpy_team gets away with always promising the future. Every year it’s the same refrain: “wait till next year, we're doing much better now.” 6/
That’s how you end up with 26/26 male authors on a paper. 7/7

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More from @lpachter

Lior Pachter Profile picture
Jun 10
Arguably the most boring step in genomics is the first one: normalization. Settled science. Scale + log. Move on.

Except that here's been a huge blind spot in the field. And it matters for AIxBio. A 🧵about what I think may be one of the most important papers I've written. 1/
The standard normalization is log(x/s*K+1) w/ K=10,000 in Seurat and Scanpy. It's been used in hundreds of thousands of studies. AI agents nowadays run it routinely.

In an expansive benchmark in @naturemethods, Ahlmann-Eltze & Huber conclude it's pretty much best in class. 2/ Image
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Except it isn't. Not even close. In a project that is four years in the making, we show that another transformation massively outperforms existing methods on the Ahlmann-Eltze & Huber benchmarks (red dots below). Moreover, it's optimal. What is this new method? How can it be? 3/ Image
Read 25 tweets
Lior Pachter Profile picture
Dec 22, 2025
Exhibit 290 in the Epstein files raises some questions about whether he was truly a "source of intellectual exchange and stimulation."

The document is here:

Thread on what is in this document below: 1/🧵justice.gov/multimedia/Cou…
Epstein the racist:

"they [top mathematicians] don't exist in China because you need a bit of a creative person as opposed to simply a copy cat."

Also this take is not only racist but also so so so stupid. Hua Luogeng literally rolling in his grave.

2/🧵 Image
Epstein's embarrassing advice:

"Algebra is not as important as it used to be. Programming is important."

This has aged about as well as milk.

3/🧵 Image
Read 13 tweets
Lior Pachter Profile picture
Jul 1, 2025
This week in academia, a not so short🧵...

1. Staff reductions and other cost cutting measures coming to Brown University highereddive.com/news/brown-uni…
2. Michigan State University staff cuts lansingstatejournal.com/story/news/loc…
3. Indiana University eliminating or suspending academic programs
bloomingtonian.com/2025/06/30/ind…
Read 17 tweets
Lior Pachter Profile picture
Sep 10, 2024
So this plagiarism thing has happened to our lab.. again. This time it's plagiarism of our poseidon syringe pump paper @booeshaghi et al., 2019 in @SciReports:
Text has been plagiarized, as well as figures copied directly here: 1/🧵nature.com/articles/s4159…
ijirset.com/upload/2024/ma…
Here is figure 1 from our paper (LHS) and figure 1 in the plagiarized paper (RHS) published in the "International Journal of Innovative Research" 2/ ijirset.com/upload/2024/ma…

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The text seems to have been rewritten with an LLM. Our introduction (LHS) vs. the plagiarized version (RHS): 3/
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Read 11 tweets
Lior Pachter Profile picture
Aug 16, 2024
I've checked this paper out, as instructed. I was also interested in the main result for personal reasons: I'm 51 years old. Is it true that I've just gone through a major change? And that another one awaits me in just a few years?

Some comments on the paper in this thread 1/🧵
The main result about major changes in the mid 40s and 60s is shown in this plot (Fig. 4a). First, I redrew it with axes that start at 0, so the scale of change here was clearer. Not as impressive, but maybe it's a thing? 2/
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The authors say that this finding is even corroborated in another study (ref 14). But that's not true. I looked it up, and it shows something totally different (see RHS Fig 3c from ref 14). No change in mid 40s, but a change in the mid 30s, and the real change in the 80s 😕 3/
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Read 17 tweets
Lior Pachter Profile picture
Aug 10, 2024
I recently posted on @bound_to_love's work quantifying long-read RNA-seq. In response, a scientist acting in bad faith (Rob Patro @nomad421) trashed our work. This kind of mold in science's bathroom is extremely damaging so here's a bit of bleach. 1/🧵
At issue are benchmarking results we performed comparing our tool, lr-kallisto, to other programs including Patro's Oarfish. Shortly after we posted our preprint Patro started subtweeting our work, claiming we'd run an "appallingly wrong benchmark" and that we're "bullies". 2/
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This was followed, within days, by Patro posting a hastily written preprint disguised as research work on benchmarking, but really just misusing @biorxivpreprint to broadcast the lie that our work "... may be repeatable, but it appears neither replicable nor reproducible." 3/ Image
Read 25 tweets

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