Le 3/3/16 06:25, Hernán Morales Durand a écrit :
Hi Stef,
For bioinformatics research it would be **really** nice to have:
- Tree creation algorithms: UPGMA, WPGMA.
- MCMC methods: Metropolis-adjusted Langevin algorithm (MALA and
SMMALA), Metropolis-coupled MCMC (MC3) would enable Bayesian
inferences and to work with evolution of genes. I cannot tell how
important is to have such algorithms implemented in Smalltalk.
- Mahalanobis distance for analyzing bacterial plasmids.
- Random Forest is used a lot for gene expression, protein-protein
interaction predictions, genome-wide association studies, etc . For
the argument "let's use FFI for it" please remember many of these
methods are extended, like enriched random forest, for research with
specialized data.
Yes we need random forest for our untangler too.
There are implementations of naive Bayes classifier in
NaturalSmalltalk (which could be adapted to SciPharo)
http://smalltalkhub.com/#!/~hernan/NaturalSmalltalk
<http://smalltalkhub.com/#%21/%7Ehernan/NaturalSmalltalk>
Thanks!
First we should clean and move forward SciPharo
As a side note I found an interesting history report of SciPy.
From the slide 9 onwards:
http://sssslide.com/www.slideshare.net/shoheihido/sci-pyhistory
Yes this is really interesting. I was wondering what is the NumPy Array
exactly page 34
Do you think that this is something like WordArray
a kind of Array with typed elements?
Presentation shows SciPy history (credited contributors with pictures,
very nice!).
As you can se they even have a Foundation NumFOCUS for raising money.
Hernán
2016-03-02 10:17 GMT-03:00 stepharo <steph...@free.fr
<mailto:steph...@free.fr>>:
Hi guys
I met Didier Besset and we had a great hacking session and
discussions with Serge Stinckwich.
Didier would like to help Pharo and the numerical part of it.
***Big thanks*** Didier.
We would like to do several things:
- Work on "Hows to"
The numerical methods in Pharo is good but the gap between
us and the math is too large :)
so the idea is to have a series of "how to ..."
- histomgram (simple, based on distribution)
- Improve the SciPharo/NumPha (previously SciSmalltalk) library
This morning we started to implement a
ComponentPrincipalDecomposition by combining two of the
objects available in SciPharo.
Then we started to enhance the distributions to make sure
that we can plug other distribution for having
controlled random number.
- Do a public call to know what is missing for you: this is
this mail :)
Didier would like to work on concrete cases. I love that attitude
So tell us :)
Hernan ??
Alex: ?? pvalue? better distribution?
Vincent: covariance? CPA?
Philippe: times series
Serge R frames?
Sami: Better random number and various distributions?
- Organise a two day lectures with practices on concrete case
in September with a recording session.
Either at IRD Bondy or Lille.
- Make sure that the Numerical Method book will get on lulu :)
with a better cover and title :)
Stef
