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Rob Patro

@robp.bsky.social

Professor of CS @ University of Maryland. Proud Rust advocate! I ♥ science & compiled, statically-typed programming languages! Views are my own. Tech stack: https://github.com/rob-p/tech-stack.

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Rob Patro@robp.bsky.social · 20h ago

Thanks @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 - Blog

COMBINE-lab develops algorithms, data structures, and software for high-throughput genomics.

combine-lab.github.io

Niema Moshiri@niema.net · 20h ago

Definitely check out @robp.bsky.social's threads about his uses! For programming, if you're already an expert, it can be useful for getting an initial draft of an implementation of an idea you have: there's a lot of boilerplate code that it can help fill out quickly so you can focus on core details

Rob Patro@robp.bsky.social · yesterday

Opus 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.

Rob Patro@robp.bsky.social · 3d ago

blog.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!

Gemini 4 Argon: our next era of frontier intelligence

Announcing Gemini 4 Argon, our frontier model for real-world coding, enterprise knowledge work, and cyber defense, rolling out soon.

blog.google

Stephanie Hicks@stephaniehicks.bsky.social · 4d ago

Excited 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! 🎉

Johns Hopkins Dept of Biostatistics@jhubiostat.bsky.social · 2w ago

Come work with the Johns Hopkins Dept. of Biostatistics! We are currently hiring two open positions: Postdoctoral Fellow (Data Science and AI in Health & Medicine) and Assistant Professor (tenure track). Learn more online: publichealth.jhu.edu/departments/...

We Are HIRING Join Our Department Open Positions: Assistant Professor Postdoc: Data Science and AI in Health & Medicine
Rob Patro@robp.bsky.social · 6d ago

Tangentially, @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

Rob Patro@robp.bsky.social · last wk.

Ok comp. bio / bioinformatics / genomics friends. Let's talk about @recombconf.bsky.social and, specifically, the way in which the "proceedings" have evolved. This seems like something that we, as a community, should address. RECOMB now has no "published" proceedings in the classic sense.

Rob Patro@robp.bsky.social · last wk.

@richardsever.bsky.social : what are the potential impediments to having the ability to collect manuscripts (at specific "versions") into approved/signed "Volumes" in the context of @biorxivpreprint.bsky.social ? For context: bsky.app/profile/robp...

Rob Patro@robp.bsky.social · last wk.

Ok comp. bio / bioinformatics / genomics friends. Let's talk about @recombconf.bsky.social and, specifically, the way in which the "proceedings" have evolved. This seems like something that we, as a community, should address. RECOMB now has no "published" proceedings in the classic sense.

Rob Patro@robp.bsky.social · last wk.

Ok comp. bio / bioinformatics / genomics friends. Let's talk about @recombconf.bsky.social and, specifically, the way in which the "proceedings" have evolved. This seems like something that we, as a community, should address. RECOMB now has no "published" proceedings in the classic sense.

Rob Patro@robp.bsky.social · last wk.

Cuttlefish 3.0.3 is out! github.com/COMBINE-lab/... Fun little jaunt with Opus 5.5 to substantially reduce the memory requirement (especially at moderate thread counts). Now it's both non-trivially faster *and* more memory-frugal than the initial C++ implementation!

Release 3.0.3 · COMBINE-lab/cuttlefish

Release Notes Colored builds use far less memory at low and moderate thread counts. On 149,998 Salmonella assemblies at 16 threads, peak RSS falls from 22.4 GB to 8.9 GB (C++ Cuttlefish 3: 11.5 GB...

github.com

Steven Salzberg@stevensalzberg.bsky.social · last wk.

Check our new @biorxiv-genomic.bsky.social preprint on a method for masking low-complexity regions in genome databases, led by Yuchin (Peter) Ge in my lab. Also includes a new release of a very large, pre-masked microbial database: www.biorxiv.org/content/10.6...

Improving Metagenomics Classification with Kmask: Entropy-Based Masking of Low-Complexity Regions

Abstract Accurate taxonomic classification in metagenomics is often compromised by low-complexity sequences, which lead to chance matches that in turn cause sequences to be misclassified. Here we pres...

biorxiv.org

Rob Patro@robp.bsky.social · last wk.

What is "thought", how do you *know* there is none? Is it only thought if humans do it? Only if neurons are the substrate? We shouldn't anthropomorphize machines, of course, but we also should accept that we'll eventually have to grapple with hard questions, like what are thought & intelligence.

AP Stylebook@apstylebook.com · last wk.

Artificial intelligence systems do not think, feel, want or understand. Avoid language that gives them human characteristics.

Rob Patro@robp.bsky.social · 2w ago

What excites me most about gravlax is that it breaks the dichotomy between tiny but *very limited* count matrix data that is shared and reanalyzed on a near constant basis and huge and compute intensive raw read/bam artifacts that are often too inconvenient for people to routinely reuse.

Rob Patro@robp.bsky.social · 2w ago

It's here! new preprint: Gravlax, an annotation-independent molecular evidence archive for scRNA-seq. A count matrix freezes one annotation. Molecules never change. Instead, gravlax keeps the evidence. Requantify, query, and discover under any annotation. 🧵 www.biorxiv.org/content/10.6...