Rob Patro
@robp
Professor of CS @ University of Maryland. Proud Rust advocate! I ♥ science & compiled, statically-typed programming languages! Views are my own. Tech stack:
It's unusable. I asked it about a purely theoretical CS problem and it immediately flagged and bailed.
Got my copies (one for me and one for the lab) of Carl's new string algorithms book!
Some professional news: After adding use MoreResearch as _; use MoreMentoring as _; use MoreTeaching as _; use MoreService as _; the UMD trait solver has accepted the where-clause where Rob: Professor On this occasion, some thanks and some thoughts are in order! 1/5
This dismissal of community discussion in the r/bioinformatics community does not sit well with me. I (disagree with, but) understand policies related to not allowing self-promotion. However, disallowing tool posts all together, and applying the policy inconsistently, feels wrong.
The recently-released rammap from Jeremy Wang and @lh3lh3.bsky.social is, indeed, looking like a strong contender to replace minimap2-rs in oarfish!
TFW you're reading a brand new preprint, and you know it's about to get real (arxiv.org/pdf/2606.03929).
Let me be clear, I can only infer bad motives from his post denigrating the treatment providing an extra 6 months of life for people dying from metastatic pancreatic adenocarcinoma.
This disingenuous, sour-grapes, ex-Academic is over on Twitter complaining about his posts being "dragged" on BlueSky, but he blocks everyone on Twitter who calls him on his dishonest and manipulative posts. What did you imagine would happen, Jason?
For the curious; this is the comic originally from : cs.colby.edu/courses/S24/...
A very interesting new paper sent me down an optimization rabbit hole for piscem v0.20. Long-story-short - I thought I'd done a decent job squeezing optimizations in piscem-rs (the Rust port of piscem based on sshash-rs). It turns out, there were some non-trivial opportunities left on the table!
My older son finally got the last of the parts for his build for his bday. It's been a while since I've put one of these together!
New lab server is accessible! Now, I have to decide on the drive/volume layout. I'm working with ~92TB of NVMe gen5 storage. Any suggestions on setups for such storage that has worked well for folks in the past?
Made some updates to the generality of multi-sample probe quant (i.e. previously flex-quant, now multiplex-quant) in simpleaf/alevin-fry. The correlations on the Flex v1 data look... pretty convincing. New stack needs piscem 0.18, alevin-fry 0.13 & simpleaf 0.22 (last one still waiting on bioconda).
I was very impressed by what it could do with the ability to introspect, benchmark, look at assembly, etc. Below is the latest state (across both AVX2 and Neon). One idea it suggested that was quite nice & clever was cache coloring to reduce L1 pressure / interference :).
Ok guys; it turns out that Claude is kind of a gangsta at optimization. Some further gains when also benchmarking & optimizing on AVX2. Now, all modes in Rust are faster than their C alternative under Neon & most are under AVX2, some substantially so:
Less than 48 hours later and here is where we stand. It started as a simple experiment, but, honestly, if I were doing something in Rust now, I think I'd use this rather than any of the bindings for the C implementation ;P.
The (native) Rust version of wfa2-lib isn't all *safe* Rust, but damn it's fast! Currently, only the Affine2p (specifically with CIGAR) really lags behind the C impl, several others are considerably *faster*.