pveber

I think I'm hitting the same problem, namely that for many genes I obtained large and systematic differences between the EM estimate and all of the bootstrap EM estimates. Here...

I think I got it: see [Bootstrap::run_em](https://github.com/pachterlab/kallisto/blob/ae81a8620c5cc247eba2128866faefa6e3c6e03e/src/Bootstrap.cpp#L4) ```cpp EMAlgorithm Bootstrap::run_em() { auto counts = mult_.sample(); EMAlgorithm em(counts, index_, tc_, mean_fls_, opt); //em.set_start(em_start); em.run(10000, 50, false, false); /* em.compute_rho(); */ return...

It seems the page is still there, although not reachable anymore from the tutorial page. If there's an interest, I could translate it to `Seq`, but I'm not sure it's...

Gasp, I didn't expect you'd be eavesdropping here ;). More seriously, I understand and share your concerns (at least what I've read from you on the inclusion of `Seq` in...

I think there are much better alternatives nowadays, for example you can have a look at [angstrom](https://github.com/inhabitedtype/angstrom/), or [menhir](http://gallium.inria.fr/~fpottier/menhir/) for more complex parsers and better error messages in case of...

Thanks a lot for having a look at this. I'll gladly give it a try once available on the tree! Le 2 avr. 2014 00:01, "Calascibetta Romain" [email protected] a écrit...

@rizo Impressive summary, thanks! First, I like the idea of representing inner groups as simple lists rather than a stream. Second, while I followed Core's naming because the library is...

In order to make it easier to experiment, I created a branch in `owl` repository, see [there](/pveber/owl/tree/perf-vs-lacaml)

Actually the conversion (flattening) happens also when multiplying matrices, and AFAIU this is partly where the difference comes from for small matrices. I pushed a new commit on the branch...

Interesting, I didn't know `snap`. So up till now we have three typing levels: 1. none 2. order (as in tensor order, that is distinguish between scalar, vector and matrices)...