For those using WDL for their bioinformatic workflows: I wrote an extension for the @zed.dev code editor enabling syntax highlighting and integration with wdl-lsp. It also supports bash highlighting in command blocks.

Installable through the Zed extensions pane!

github.com/broadinstitu...

A printed thesis! Did not expect it would feel so good to have the final version physically in your hands 🙌

Found ChatGPT in Fallout New Vegas:

"Are you some kind of AI?"
"Regrettably not, sir. All modules in this habitat are synthetic personalities atop a mundane operating system. There is no intelligence here, sir."

www.youtube.com/watch?v=4XJw...

I think Philip Eng deserves a statue in the Boston common

Working through Prince's excellent "Understanding Deep Learning" book. Full of great insights like these: by optimizing using SGD we implicitly regularize the weights towards values where the gradients are similar across batches 🤯

For those interested in the technical details, POASTA achieves its performance through three techniques: 1) its minimum remaining gap heuristic, 2) depth-first greedy alignment of matches and 3) superbubble topology-informed pruning.

In low-diversity settings, POASTA's memory-scaling characteristics also enable alignment of much longer sequences, and we constructed megabase-length alignments of 342 M. tuberculosis sequences. This would require terabytes of memory with SPOA.