Stephen Zhang
Stephen Zhang
The semi-smooth Newton algorithm of [Lorenz et al. 2019] can be specialised to the case of symmetric inputs, much like the approach already used for symmetric Sinkhorn algorithm in the...
Recently came across a use case for this. Might be something worth implementing in the future. https://arxiv.org/pdf/1910.12958.pdf
Instead of using the `quadreg` function call for the quadratic regularisation, this PR provides a general set of functions `ot_reg_plan` and `ot_reg_cost` for computing OT with 'general' regularisations. Now `quadreg`...
Using `transform` in a bpipe script seems to yield an error when processing paired-end reads `*.R1.fastq.gz` and `*.R2.fastq.gz`. I've been able to replicate this simply (using latest version of bpipe...
Thanks for this package! At the moment, the Factored distribution only applies to UnivariateDistributions. Is there any reason currently the code does not support MultivariateDistribution? The reason I am interested...
Hi, I've been trying to get this QC package to work as part of an ATAC-seq pipeline I've been working on. I have followed the instructions from the ATACseqQC vignette...
Potential serious bug caused by marginalizing along incorrect axes. Example: https://github.com/Tchanders/InformationMeasures.jl/blob/64810f28917dd015429951ac9722ef2b79559acb/src/Measures.jl#L152 Should be instead `sum(probabilities_xy; dims = 1)` since we want to integrate out `x` (corresp. to 1st dim of...
Let `w, x` be vectors. I'm interested in computing `log(dot(w, exp.(x))`. The current `logsumexp` functions can be used to compute this, but one must take `log.(w)`which is troublesome when `w`...