zachcp

I am working on a translation of this pytorch code to Rust/Candle. Can you step through this code line by line and term by term. Please provide me the shapes of the tensors at each step and be sure to mention where there is implicit broadcasting.

for t_ in range(L):
               t = decoding_order[:, t_]  # [B]
               chain_mask_t = torch.gather(chain_mask, 1, t[:, None])[:, 0]  # [B]
               mask_t = torch.gather(mask, 1, t[:, None])[:, 0]  # [B]
               bias_t = torch.gather(bias, 1, t[:, None, None].repeat(1, 1, 21))[

Setup

Repo and Rust


# setup rust

	run:
	./cyber readfq.cy < test.fasta

	# 190 Mb
	downloadref:
	wget https://ftp.ncbi.nlm.nih.gov/genomes/genbank/metagenomes/human_skin_metagenome/latest_assembly_versions/GCA_013297495.1_ASM1329749v1/GCA_013297495.1_ASM1329749v1_genomic.fna.gz
	gunzip GCA_013297495.1_ASM1329749v1_genomic.fna.gz


	test_cy:

	<!DOCTYPE html>
	<html>
	<head>
	<script src="https://cdn.jsdelivr.net/pyodide/v0.21.3/full/pyodide.js"></script>
	</head>
	<body>
	Pyodide test page <br>
	Open your browser console to see Pyodide output

	<p>You can execute any Python code. Just enter something in the box below and click the button.</p>

	library(dplyr)
	library(depict)
	library(grid)
	library(ggplot2)
	library(svgparser)

	# SVG code to make background box transparent
	my_css = '
	rect {
	fill: none;

	# install.packages("microbenchmark")
	# install.packages("plyr")
	#
	# install.packages("rcdk")
	# install.packages("OrgMassSpecR")
	# install.packages("CHNOSZ")
	#
	# BiocManager::install("Rdisop")
	# BiocManager::install("MetaboCoreUtils")
	#

	select kcu.table_schema \|\| '.' \|\|kcu.table_name as foreign_table,
	'>-' as rel,
	rel_tco.table_schema \|\| '.' \|\| rel_tco.table_name as primary_table,
	string_agg(kcu.column_name, ', ') as fk_columns,
	kcu.constraint_name
	from information_schema.table_constraints tco
	join information_schema.key_column_usage kcu
	on tco.constraint_schema = kcu.constraint_schema
	and tco.constraint_name = kcu.constraint_name
	join information_schema.referential_constraints rco

	wget https://www.npatlas.org/custom/versions/np_atlas_2020_06/NPAtlas_download.json

	-- POCKET2DEVONTHINK
	-- script imports articles from a local Pocket for Mac app into the inbox of the current Devonthink database
	-- script comes with the use-it-like-you-want-to-and-dont-blame-me licence
	-- last changed on Jan 5, 2015
	-- recent changes: errorhandling; pdfs for pocket records without mime setting; conditional searches

	-- USER SETTINGS; please adopt to your needs
	--loop_min/max define the range of pocket articles to be imported
	-- 1/10 would, e.g., import the first ten articles you've ever stored in Pocket
	-- 1 and, say, 100000 would presumably move all of them into DT

	* using log directory ‘/private/var/folders/yc/53w8dbxx2hjg11_brr2pj5740000gn/T/RtmpWPpy1T/rcdk.Rcheck’
	* using R version 3.6.0 (2019-04-26)
	* using platform: x86_64-apple-darwin15.6.0 (64-bit)
	* using session charset: UTF-8
	* using options ‘--no-manual --as-cran’
	* checking for file ‘rcdk/DESCRIPTION’ ... OK
	* this is package ‘rcdk’ version ‘3.4.9.2’
	* checking package namespace information ... OK
	* checking package dependencies ... OK
	* checking if this is a source package ... OK