Rob Patro @robp.bsky.social · 04/10/2026The NFL is a damned joke. That call against Hamilton was complete nonsense. So no sacks allowed? 000
Rob Patro @robp.bsky.social · 04/10/2026Is there a new fish coming to the COMBINE-lab github.com/COMBINE-lab family? It seems likely :). Spearfish, soon!github.com 041
Rob Patro @robp.bsky.social · 04/10/2026It's at least several days at this point. I've heard they have a log of many hundred of papers... 121
Rob Patro @robp.bsky.social · 03/10/2026Yea, I don't think it's UB (compiler defined, perhaps), but leads to tricky semantics :). 000
Rob Patro @robp.bsky.social · 03/10/2026But the keys are equivalent, right? At least via hash and the equality traits. That's a requirement for it to be the same key (value). Are you changing something in the key upon which equality doesn't depend? 100
Rob Patro @robp.bsky.social · 03/10/2026Also, whole-body emergence is still physicalist emergence, just with a wider boundary. The content of our conscious experience is clearly shaped by our body, the mainstream working view is that consciousness depends on and arises from neural activity. 100
Rob Patro @robp.bsky.social · 03/10/2026Also, the clinical dissociations point the other way. For example, high spinal cord injury and locked-in syndrome remove most bodily input and output, yet people stay fully conscious. Brainstem or thalamocortical damage, or anesthetics, abolish it. The brain looks necessary in a way muscles aren't. 200
Rob Patro @robp.bsky.social · 03/10/2026I agree that the body matters. Interoception, inflammation, and gut signaling clearly shape mood, emotion, and sense of self. However, "demonstrates" overstates it. Influencing the contents of experience isn't the same as constituting consciousness. 210
Rob Patro @robp.bsky.social · 02/10/2026I'm much more in favor of weighting "good" exposition in submissions than a blanket per-month cap. Of course, evaluating that (especially at scale), is hard. So it's not clear how to filter based on the quality of the exposition of the paper (or the quality of the paper itself). 100
Rob Patro @robp.bsky.social · 02/10/2026There are. There are plenty of people who use AI as e.g. massively overpowered spell checkers. There is a range of "uses" of AI and they are not all the same nor are their impacts on the final product all the same. Either way... 100
Rob Patro @robp.bsky.social · 02/10/2026Thanks @niema.net! If @melodyschreiber.com is interested, I've also written about it in a bit more length on my / my lab's blog combine-lab.github.io/blog/.combine-lab.github.ioCOMBINE-lab - BlogCOMBINE-lab develops algorithms, data structures, and software for high-throughput genomics. 020
Rob Patro @robp.bsky.social · 02/10/2026Let's just hope that we figure out how to actually solve the problem in a long-term way 🤞 000
Rob Patro @robp.bsky.social · 02/10/2026I mean, you can disagree, of course. But I don't think it does. I've certainly had students with 3 conference papers ready at the same time, and my lab definitely does not paper-max. This is *especially* true if their limit applies to "updates" (they haven't specified). 100
Rob Patro @robp.bsky.social · 02/10/2026In a journal centric world (bio), a single author is unlikely to have 3 papers “ready” at once. In CS, in a conference heavy culture with maybe 2-3 conferences a year, a student may have truly bursty completion. I’d rather they be able to preprint that work when they submit, rather than delay it. 110
Rob Patro @robp.bsky.social · 02/10/2026Perhaps both. For example, I think separating mainly human from mainly non human submissions is a better approach. Rate limiting can help stem the bleed though. But I think it must be done in a way that doesn’t punish the way things are done in one field more than the other. 110
Rob Patro @robp.bsky.social · 02/10/2026Yes. I agree that this is MUCH less bad in the contex of how bio publications work. My biggest concern is if "updates" count against the limits. This the makes it difficult to keep preprints updates as one submits to subsequent conferences. 000
Rob Patro @robp.bsky.social · 02/10/2026I don't see arXiv having an account here. I would actually like to know how updates of existing preprints are counted. 100
Rob Patro @robp.bsky.social · 02/10/2026But I think this blunt instrument is a bad fit to handle that. OTOH, as I said in another thread, I'd dislike this much less if it was a 12/year (or even 6/year) cap rather than a 2/month cap. The cadence is at odds with how things operate in conference heavy fields. 100
Rob Patro @robp.bsky.social · 02/10/2026A lot :). He does a lot of theory. He has many preprints that are a core idea, written up well, to get out for others to use and implement. This discourages those types of submissions, which I find valuable. IMO, the problem is tons of low quality submissions. That IS a problem! 210
Rob Patro @robp.bsky.social · 02/10/2026Preprints are often submitted concurrently with conference submission. In a field with very few large conferences, this yields a bursty cadence. It's not the pubs per year, it's that it's assumed to be uniform over the whole year. 12/year (or even 6) is *far* better than 2/month. 000
Rob Patro @robp.bsky.social · 02/10/2026Also, I don't see in the blog how they plan to handle updates to existing papers. Are those "free"? 110
Rob Patro @robp.bsky.social · 02/10/2026No. But CS submissions are super bursty. My field has only 2 large conferences each year. And often, papers that are really good but miss one get recycled for the next. So they may have saved up 3 papers for a conference. 310
Rob Patro @robp.bsky.social · 02/10/2026That's better than authors, but still a problem. What will authors like Travis Gagie or Gonzalo Navarro do when it's string algorithms conference season. Should they just not preprint their work? Should we move to blogs to disseminate results until they can fit in a submission cap limit? 110
Rob Patro @robp.bsky.social · 02/10/2026What are they trying to limit? AI submissions? Then attack that directly. This is particularly a relevant topic to me as I'm now arguing for preprint overlays as an alternative to traditional (non professional society) journals for peer reviewed conference proceeding. Timed caps break that. 400
Rob Patro @robp.bsky.social · 02/10/2026Longer term, I think we have to realize that we can't keep pretending that there exist numbers like number of papers, or citations, or h-index, or some other nonsense that are reasonable proxies for the "productivity" and "impact" of a scientist or researcher. 110
Rob Patro @robp.bsky.social · 02/10/2026I don't agree this is a pragmatic response. What about arXiv overlays for conferences? One of our only real alternatives to the journal racket (when not run by professional societies). Many labs have >2 students. I think from the perspective of the CS model, this response is irresponsible. 210
Rob Patro @robp.bsky.social · 02/10/2026This is a *bad* response. This is precisely how they usher in the end of the incredibly special thing they started. It is very disheartening to see this. 231
Rob Patro @robp.bsky.social · 02/10/2026"It will one day be admitted with shame that it might have been in error to say that AIDS is bad, but not quite as bad as condoms are bad, or as immoral in the same way." --Cristopher Hitchens 000
Rob Patro @robp.bsky.social · 02/10/2026I find its rust to be much better than its C++, all things considered. 100
Rob Patro @robp.bsky.social · 02/10/2026I mean. It's not beautiful, but I find that its Rust is often not so bad. Perhaps that's because Rust has some very strong idioms that somewhat flatten variation? 100
Rob Patro @robp.bsky.social · 02/10/20261000% : despite the pace of change, a main concern of mine is still the "widening gap" caveat I made in my post back in February combine-lab.github.io/blog/2026/02.... I think there is a very real risk that the better the models get, the larger the difference in how much previous experience matters.combine-lab.github.ioCOMBINE-lab - The skeptic’s guide to generative AI assisted codingCOMBINE-lab develops algorithms, data structures, and software for high-throughput genomics. 042
Rob Patro @robp.bsky.social · 02/10/2026Exactly. What would otherwise take weeks to iterate now takes minutes. I think that years of manually driving into walls (and seeing the subtlest of strange bugs) has prepared me to be sufficiently paranoid. Armed with that paranoia, the ability to iterate (and fix) fast is like a super power. 130
Rob Patro @robp.bsky.social · 02/10/2026What a wild time to be developing new methods. The friction between having an idea and having a competent implementation of that idea (as long as you check the work!) has been brought down to almost 0. It's still kind of astonishing to see. 340
Rob Patro @robp.bsky.social · 02/10/2026Opus 5.5: This library looks excellent, but the API isn't a good fit. I'll implement Meyers' bitpacked DP myself (30 seconds pass). It's only 3x faster than the alternative, let me add banding & SIMD (30 more seconds). We beat the competition by 13.5x on runtime. We'll return to optimization later. 280
Rob Patro @robp.bsky.social · 02/10/2026LFG! www.courthousenews.com/ai-training-...courthousenews.comAI training of copyrighted material not fair use: Third CircuitUsing someone else's "creative spark" to start a competing business runs afoul of copyright law, the panel found. 094
Reposted by Rob PatroChildhood Cancer Data Lab @cancerdatalab.bsky.social · 01/10/2026Our Director, Jaclyn Taroni, is giving two talks on the Single-cell Pediatric Cancer Atlas (ScPCA) this month, each for a different audience. 🧵 121
Rob Patro @robp.bsky.social · 30/09/2026blog.google/innovation-a... "Large Scale Codebase Migrations and Optimizations: Argon agents are working on migrating C/C++ codebases to Rust across Google—scaling from tens of thousands of lines ... up to 800K+ lines for the Fuchsia OS Zircon kernel." You love to see it!blog.googleGemini 4 Argon: our next era of frontier intelligenceAnnouncing Gemini 4 Argon, our frontier model for real-world coding, enterprise knowledge work, and cyber defense, rolling out soon. 0101
Rob Patro @robp.bsky.social · 30/09/2026As a millennial, I can absolutely say that for US, it's "this is your brain on drugs". 110
Rob Patro @robp.bsky.social · 30/09/2026Yes. The problem with having a written policy that differs from what one actually does is, unfortunately, a microcosm of the US right now. My federal government is an illigitimate mess. I don't want the same of my reddit communities 😭. 010
Rob Patro @robp.bsky.social · 30/09/2026Yes: under "advertising" www.reddit.com/r/bioinforma.... But that's the stated not the actual policy. In reality it's a neat blanket ban on methods. I posted about @curiouscoding.nl's tool (not a coauthor/contributor) and rejected. People post recent papers that aren't theirs; removed. It's dumb.reddit.comFrom the bioinformatics community on RedditExplore this post and more from the bioinformatics community 100
Rob Patro @robp.bsky.social · 30/09/2026The mod decided it (IMO arbitrarily). The policy is also not enforced uniformly. Nonetheless, the mods point people at the meager bioinformaticstools as the proper place for such posts. IMO, this eliminates the most useful category of posts from r/bioinformatics 100
Rob Patro @robp.bsky.social · 30/09/2026Relatively niche problem, but worth discussing anyway. Reddit’s /r/bioinformatics doesn’t take posts about new tools or methods (?!?! again, WTAF), and /r/bioinformaticstools has measly throughput and community size. What do we do to address this problem? Cc @curiouscoding.nl @psy-fer.bsky.social 3101
Reposted by Rob PatroISCB News @iscb.bsky.social · 30/09/2026Hoping to present at #ISMBECCB2027 in July? Here's a sneak peek at the upcoming submission deadlines for the biggest bioinformatics and computational biology conference of the year! 033
Reposted by Rob PatroStephanie Hicks @stephaniehicks.bsky.social · 29/09/2026Excited to share that @jhubiostat.bsky.social is hiring for postdoctoral fellows and tenure-track Assistant Professors! Details below and committees will start reviewing for both on Oct 1! 🎉 1810
Rob Patro @robp.bsky.social · 28/09/2026Good riddance to the stupid training where we all know the answers but it won't let you fast-forward the videos. 170
Rob Patro @robp.bsky.social · 27/09/2026Tangentially, @jermp.bsky.social also points out @recombconf.bsky.social is listed as B tier in CORE portal.core.edu.au/conf-ranks/?.... This is something that we should figure out how to address. RECOMB is a premiere conference in comp bio, & it is highly selective. It is `A` tier without question.portal.core.edu.au 043