iiinova — where your digital self keeps evolving

A few hours of work x thousands of researchers = tens of thousands of hours of work.

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PaperPush — PaperPush 0.1.1

Full documentation is here: paperpush.readthedocs.io/en/latest/ 6/6

paperpush.readthedocs.io

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If you'd like to add a journal or conference, instructions are here: github.com/pachterlab/p... 5/

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This was not easy to build- it required a bunch of Joe's wizardry along with Playwright. But it's done in a way that is literally one-click-and-submitted! I just submitted my first paper with it. This is going to save many, many hours of pain. 3/

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Just clone the repo, and use an LLM of your choice, put the files to be uploaded in a directory, and use an LLM to create a .sub file which will have everything needed for the submission. PaperPush already has templates for 20+ journals. Easy to add more. 2/

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One of the major pains of academia is having to click through labyrinths of webpages to submit papers. Now, thanks to Joe Rich (and AI), problem solved! His tool is called PaperPush and is available at github.com/pachterlab/p... It's super easy to use! 1/🧵

GitHub - pachterlab/paperpush

Contribute to pachterlab/paperpush development by creating an account on GitHub.

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Reposted by Lior Pachter

Yasin Dagdas @plantophagy.bsky.social · 26/06/2026

I wonder what @elife.bsky.social board and behrenstimb.bsky.social thinks about the 1% list and their coll/ with @qedscience.bsky.social now? They’re facilitating the innovation of a system that will be bought by #Elsevier & #Springer w/funds from a charity.

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Lior Pachter @lpachter.bsky.social · 26/06/2026

Looks like Lior Pachter got better impact metrics on his post than you got on yours.

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Lior Pachter @lpachter.bsky.social · 26/06/2026

Can you share the code used to generate the scores?

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Lior Pachter @lpachter.bsky.social · 25/06/2026

FWIW when writing www.biorxiv.org/content/10.6... we selected eLife papers specifically because of their CC BY license and we cited every preprint we used: "The papers below were analyzed by OpenEval. They are distributed by eLife under the CC-BY license." www.biorxiv.org/content/bior...

Science should be machine-readable

We develop a machine-automated approach for extracting results from papers, which we assess via a comprehensive review of the entire eLife corpus. Our method facilitates a direct comparison of machine...

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Lior Pachter @lpachter.bsky.social · 01/06/2026

I have not but @pmelsted.bsky.social has. See, e.g. www.biorxiv.org/content/10.6...

William DeWitt @wsdewitt.github.io · 29/04/2026

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Reposted by Lior Pachter

Arc Institute’s “MULTI-evolve” learns a classical additive model, not epistasis. Preprint (w/ Gian Marco Visani and Aayush Verma): www.biorxiv.org/content/10.6... Blog: dewitt-lab.github.io/posts/2026-0...

dewitt-lab.github.io

Additivity is all you need?

Arc Institute’s “MULTI-evolve” learns a classical additive model, not epistasis.

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Lior Pachter @lpachter.bsky.social · 11/05/2026

Sorry if this doesn't fit your narrative. But of course feel free to continue to fantasize about the boogeyman!

static.klipy.com

Michael Myers: Dark Gaze

ALT: Michael Myers: Dark Gaze

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Lior Pachter @lpachter.bsky.social · 11/05/2026

In fact when we worked on applying splits networks to political data (see preprints.apsanet.org/engage/apsa/...) we also experimented with building splits networks from single-cell data and it was quite effective.

preprints.apsanet.org

The Split Senate

The theory of split systems provides a mathematical formalism for understanding and visualizing collections of partitions of sets into two parts. In particular, split networks, which generalize phylog...

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Lior Pachter @lpachter.bsky.social · 11/05/2026

I finally got around to looking at the Bonsai paper which proposes to approximate single-cell dissimilarity maps with tree metrics, which is a perfectly reasonable thing to do. Seems consistent with what we wrote in our "Specious art" paper.

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Lior Pachter @lpachter.bsky.social · 04/05/2026

Vito Volterra (of the Lotka-Volterra model) was born on this day (May 3rd) in 1860. Volterra was in the 1%. That is, he was one of only 12 out of ~1,200 Italian professors who refused to sign the compulsory oath of allegiance to Mussolini's Fascist government in 1931.

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Lior Pachter @lpachter.bsky.social · 28/04/2026

Donald Knuth gave up on email in 1990. www-cs-faculty.stanford.edu/~knuth/email...

www-cs-faculty.stanford.edu

Knuth versus Email

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Moreover, I think the data analogy is on point. "Research parasites" are on the whole fantastic, driving forward tons of science. Even if on occasion there is noise. I bristle at the idea that certain groups start to dictate what is and is not acceptable. That's gatekeeping, not community building.

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... mathematicians (e.g. Terence Tao), have focused on the (half) full portion of the glass. Individuals who previously had less knowledge in an area, can potentially meaningfully contribute now in ways not possible before. The same is true for software. And that should be encouraged.

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There is an interesting point here that I agree with: there is one difference between data and software that makes software more akin to math: rapidly generated "proofs" in math are noise for the community, and can be time consuming to check. However...

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Sorry for the confusion. I linked to that issue because "tilting at windmills" suggests I'm wasting my time on a pointless matter, but the fact is that there is active debate on this matter. My position is that the attempt of Longo and Drazen to police the reuse of published data was misguided.

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I have no idea whether their code is slop nor whether it's poorly attended. I haven't looked at it.

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Maybe. Maybe not. github.com/henriksson-l...

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Of course people can do problematic things with open source software. That's been the case for a long time, and certainly now the ability to be malicious is expanded with LLMs. However, trying to codify problematic scenarios is just an exercise in restricting freedom for others to benefit from OSS.

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The Research Parasite Awards

To paraphrase @iddux.bsky.social, "I propose to extend the research parasite award to those who used someone else's code to do some really cool sh*t". Their permission or collaboration is absolutely not required. researchparasite.com

researchparasite.com

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The aerial view of the concept of data sharing is beautiful. What could be better than having high-quality information carefully reexamined for the possibility that new nuggets of useful data are l...

"Setting out principles" just sounds like drafting a code of conduct to restrict the use of open source software in much the same way that Longo & Drazen advocated for restricting the use of published data in 2016: www.nejm.org/doi/full/10....

nejm.org

Data Sharing | NEJM

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It's possible that more restrictive licensing can help but I doubt that will matter in practice (who will enforce academic licensing terms?)

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So the specific versioning v10.0 would not work because the version number tracks my birthday (currently 0.52). But your point is well taken, and yes, that would be annoying but I think something like it is likely to happen (also I've seen much worse in academia).

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If someone writes a paper pretending they discovered pseudoalignment without attributing the discovery to the kallisto authors, and then copies the kallisto software (algorithm, parameters, etc.) to showcase it but gives the software a new name... that's plagiarism and not ok.

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I have no problem with either Callisto or rullisto. Of course rullisto is more valuable, but people are free to do poor work if they wish. kallisto is BSD-2 and the license allows for that. BUT....

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I brought nf-core into the conversation because it's yours, and it's MIT, and so nothing in rewrite.bio matters. Anyone can port or modify it, period. And that's not only ok it should be encouraged. If you think "emulate exactly" matters you should change the license.

rewrite.bio

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Isabel, booonyavirus wonk @isabelott.bsky.social · 13/04/2026

rewrite.bio mentions licensing only in section 5.3 in the context of advocating for open source and compliance. At the same time the remaining four sections are a call for onerous requirements which are completely irrelevant under most licensing (e.g. section 2.2 "emulate exactly").

rewrite.bio

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Reposted by Lior Pachter

Behind every extrernally lauded ‘disruptor’, there seems to be a half dozen (minimum) actual subject matter experts shaking their heads “no” and grimacing dramatically. Good to keep in mind, for those of us prone to a bit of epistemic…moseying.

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Within my lab edgePython made possible XgenePy which in turn is facilitating another lab to incorporate the method in another tool: github.com/pachterlab/X... Together these examples make clear to me that porting with LLMs is immediately useful.

GitHub - pachterlab/XgenePy

Contribute to pachterlab/XgenePy development by creating an account on GitHub.

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Moreover, the idea (not software) described in the preprint is discussed in the dreampy paper (which provides an alternate approach): www.biorxiv.org/content/10.6...

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4. edgePython has already been used for multiple other projects (single-cell, because it's in Python). For example for Allos: www.biorxiv.org/content/10.6...

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The relevance of single-cell is that I also ported large parts of NEBULA and combined with edgeR into edgePython to create a new single-cell tool. 3. Regarding a pull request in the original language, that's an interesting thought but a lot of extra work. I'm also less comfortable in R than Python.

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