Friday, May 5, 2017

SageMath GSoC 2017 Projects

6 GSoC SageMath Projects

During the past couple of summers, SageMath successfully managed many Google Summer of Code projects. This year we are again happy to have six projects:


Implementing matroid classes and plotting improvements

(Zachary Gershkoff / Stefan van Zwam)
This project seeks to implement several common matroid classes in SageMath, along with algorithms for their display and relevant computations. The graphic matroid class in particular will be implemented with a representative graph with methods for Whitney switching and minor operations. This will be accompanied by improvements to the graph theory library, with methods relevant to matroids enabled to support multigraphs. Other modules for this project include improved plotting of rank 3 matroids to eliminate false colinearities, computation of a matroid's automorphism group using SageMath's group theory libraries, and faster minor testing based on an existing trac ticket.

Expanding the Functionality of Dynamical Systems

(Rebecca Lauren Miller / Paul Fili and Ben Hutz)

As a member of the sage-dynamics community, researchers have compiled a wishlist for algorithms and functionality they would like added. I would like to shorten the wish list for us.For my project I will be completing some desired additions to SAGE from the Sage Dynamics Wiki. I will implement Well’s Algorithm, strengthen the numerical precision in cannonical_height, as well as implement reduced_form for higher dimensions.

Improvement of Complex Dynamics in Sage

(Ben Barros / Adam Towsley and Ben Hutz)
There are three major things that I would like to implement to improve the functionality of Sage in the area Complex Dynamics. The details of the project are summarized in the following list:
  • Complex Dynamics Graphical package: Integrate or implement a complex dynamics software such as Mandel into Sage. This will be done by creating an optional package for Sage. If there is enough demand, the package may become a standard package for Sage at some point.
  • Spider Algorithm: The object of the Spider Algorithm is to construct polynomials with assigned combinatorics. For example, we may want to find a polynomial that has a periodic orbit of period 7. The Spider Algorithm provides a way for us to compute this polynomial efficiently. I plan to implement this algorithm into Sage.
  • Coercion: If you have a map defined over Q, you should be able to take the image of a point over C (i.e. somewhere you have a well-defined embedding) without having to use the command "change_ring()". Something similar works for polynomials in Sage but it does not work for morphisms/schemes.

Linear-time Implementation of Modular Decomposition of Undirected and Directed Graphs

(Lokesh Jain / Dima Pasechnik)
This project is aimed at providing linear time implementation for modular decomposition of graphs and digraphs. Modular decomposition is decomposition of graph into modules. A module is a subset of vertices and it is a generalization of connected component in graph. Let us take for example a module X. For any vertex v ∉ X it is either connected or not connected to every vertex of X. Another property of module is that a module can be subset of another module. There are various algorithms which have been published for modular decomposition of graphs. The focus in this project is on linear time complexity algorithms which can be practically implemented. The project further aims to use the modules developed for modular decomposition to implement other functionality like skew partitions. Skew partition is partition of graph into two sets of vertices such that induced graph formed by one set is disconnected and induced graph formed by other set is complement of the first. Modular decomposition is a very important concept in Graph Theory and it has a number of use cases. For instance it has been an important tool for solving optimization and combinatorics problems.

Modular Decomposition of graphs and digraphs

(Maria Ioanna Spyrakoy / Dima Pasechnik)
Modular decomposition of (di)graphs is a generalization of the concept of the decomposition of (di)graphs into connected components. Its current implementation in Sage relies on badly broken abandoned C code, and badly needs to be replaced by something that works and is not too slow. However, the only open-source implementations of some of these procedures are either in Java or in Perl, and thus aren't really useful for Sage.

Note: A attentive reader might notice the similarity between those projects. They will be split regarding the type of graph and be coordinated to not overlap but to augment each other.

Visualizing constructs in cluster algebras and quiver representations

(Bryan Wang / Travis Scrimshaw)
I aim to implement visualizations of several key constructs in cluster algebras and quiver representations. The first is Auslander-Reiten quivers, for at least the A_n and D_n cases. The second is labelled endomorphism quivers and mutations within a cluster category, focusing on the A_n case. The third is posets of down-mutations for the A_n case. These features will be useful not only for research purposes, but also as nice examples to play around with and learn from. Aside from these features, I am interested in implementing features for the Quantum Cluster Algebras project.

All the best for this summer, thank you to Google for making this possible, and sorry to all those candidates who didn't make it ...

Thursday, November 19, 2015

Saturday, April 4, 2015

R's sapply in Numpy

One quick blog entry about sapply and numpy:

Usually, sapply is equal to list comprehensions in Python.
i.e. [f(x) for x in range(1, 10)] is sapply(1:10, f).

But: When you want to apply a function (mapping a number to a vector!) to a vector, you get a matrix. R's sapply does raise the rank of the output to two, while in Numpy you have to push the vector to a higher rank via the magical vector[:, np.newaxis].

In [1]: import numpy as np

In [2]: def f(x):
   ...:     return np.array([4,2,3,9.1,-1]) * x
   ...: 

In [3]: f(9)
Out[3]: array([ 36. ,  18. ,  27. ,  81.9,  -9. ])

In [4]: vals = np.linspace(-1,1,20)

In [5]: np.apply_along_axis(f, 1, vals[:, np.newaxis])
Out[5]: 
array([[-4.        , -2.        , -3.        , -9.1       ,  1.        ],
       [-3.57894737, -1.78947368, -2.68421053, -8.14210526,  0.89473684],
       [-3.15789474, -1.57894737, -2.36842105, -7.18421053,  0.78947368],
       [-2.73684211, -1.36842105, -2.05263158, -6.22631579,  0.68421053],
       [-2.31578947, -1.15789474, -1.73684211, -5.26842105,  0.57894737],
       [-1.89473684, -0.94736842, -1.42105263, -4.31052632,  0.47368421],
       [-1.47368421, -0.73684211, -1.10526316, -3.35263158,  0.36842105],
       [-1.05263158, -0.52631579, -0.78947368, -2.39473684,  0.26315789],
       [-0.63157895, -0.31578947, -0.47368421, -1.43684211,  0.15789474],
       [-0.21052632, -0.10526316, -0.15789474, -0.47894737,  0.05263158],
       [ 0.21052632,  0.10526316,  0.15789474,  0.47894737, -0.05263158],
       [ 0.63157895,  0.31578947,  0.47368421,  1.43684211, -0.15789474],
       [ 1.05263158,  0.52631579,  0.78947368,  2.39473684, -0.26315789],
       [ 1.47368421,  0.73684211,  1.10526316,  3.35263158, -0.36842105],
       [ 1.89473684,  0.94736842,  1.42105263,  4.31052632, -0.47368421],
       [ 2.31578947,  1.15789474,  1.73684211,  5.26842105, -0.57894737],
       [ 2.73684211,  1.36842105,  2.05263158,  6.22631579, -0.68421053],
       [ 3.15789474,  1.57894737,  2.36842105,  7.18421053, -0.78947368],
       [ 3.57894737,  1.78947368,  2.68421053,  8.14210526, -0.89473684],
       [ 4.        ,  2.        ,  3.        ,  9.1       , -1.        ]])

It also works happily for an additional argument weights, which will be defined in the variable w.

In [6]: def f(x, weights):
    return weights * x
   ...: 

In [7]: w = np.array([-2,-1,5,1.1])

In [8]: np.apply_along_axis(f, 1, vals[:, np.newaxis], w)
Out[8]: 
array([[ 2.        ,  1.        , -5.        , -1.1       ],
       [ 1.78947368,  0.89473684, -4.47368421, -0.98421053],
       [ 1.57894737,  0.78947368, -3.94736842, -0.86842105],
       [ 1.36842105,  0.68421053, -3.42105263, -0.75263158],
       [ 1.15789474,  0.57894737, -2.89473684, -0.63684211],
       [ 0.94736842,  0.47368421, -2.36842105, -0.52105263],
       [ 0.73684211,  0.36842105, -1.84210526, -0.40526316],
       [ 0.52631579,  0.26315789, -1.31578947, -0.28947368],
       [ 0.31578947,  0.15789474, -0.78947368, -0.17368421],
       [ 0.10526316,  0.05263158, -0.26315789, -0.05789474],
       [-0.10526316, -0.05263158,  0.26315789,  0.05789474],
       [-0.31578947, -0.15789474,  0.78947368,  0.17368421],
       [-0.52631579, -0.26315789,  1.31578947,  0.28947368],
       [-0.73684211, -0.36842105,  1.84210526,  0.40526316],
       [-0.94736842, -0.47368421,  2.36842105,  0.52105263],
       [-1.15789474, -0.57894737,  2.89473684,  0.63684211],
       [-1.36842105, -0.68421053,  3.42105263,  0.75263158],
       [-1.57894737, -0.78947368,  3.94736842,  0.86842105],
       [-1.78947368, -0.89473684,  4.47368421,  0.98421053],
       [-2.        , -1.        ,  5.        ,  1.1       ]])

Wednesday, December 24, 2014

Convert several IPython Notebooks to one huge PDF

The IPython Notebook is a neat interactive document. It mixes headings, formatted text (markdown), formulas, images/pictures and interactive code. This is very neat for creating well-documented code examples.

To make ordinary publishing possible, nbconvert converts this interactive json-based file format to ordinary static HTML or LaTeX. The nbviewer website is a well known example for such a repository of HTML-notebooks.

Converting to LaTeX is also very handy, because then you can compile them to static PDF files -- e.g. think of a proper report or article.

So far I know, each input document is converted to only one output document. For one of my projects, I wanted to merge a whole bunch of IPython Notebooks to one (very large) PDF document! To achieve this, I've looked into the various *.tplx template file and started to build on top of them two new templates: partial and master. As the names suggest, partial is the template for each partial document, and master is essentially empty, but combines all partial documents in an orderly fashion.

You can see this here: github:haraldschilly/python-fuer-mathematiker

In particular:
  • partial.tplx: This removes all the preamble and heading stuff and sets the document class to the wonderful subfiles LaTeX class.
  • master.tplx: This template contains the default header definitions (inherited from IPython's base template), adds some tweaks of my own (font family, margins, title, and subfiles master class) and an embedded Python script to magically gather all documents!
How it works: First, all partial IPython Notebook files are converted to LaTeX using the partial template. Then, the master.tplx contains a small embedded Python script, which iterates through all partial LaTeX files. They are named numerically as --chaptername. This script inserts all those subdocuments and if there is an  increments in the major-number, it inserts a \chapter{...} heading.

To orchestrate all this, a usual Makefile checks for dependencies and finally uses latexmk with the --shell-escape switch (which is necessary to run the embedded Python). Works like a charm!

I hope this is helpful for some of you.

Friday, October 3, 2014

Mein Email an den VAP

Habe soeben dies an vap1@aon.at gesendet:
Mit Entsetzen muss ich heute lesen, dass österreichweit eine Blokadeinfrastruktur für Netzzensur errichtet wird. Ihr Mitwirken an diesem Akt der Unmündigmachung aller Österreicher_innen ist eine Skandal. Legen Sie mir bitte dar, welche Gesetze beim bloßen Download exakt verletzt werden und in welcher Relation dies zu der angeprangerten Bundesbürger_innenbevormundung steht. Die alten Wirtschaftsmodelle haben ausgedient und Ihr VAP Verein ist eine reine Interessensvertreung für große, längst überholte internationale Konzerne und im Beamtenschimmel verfilzte österreichische Organisationen. Ich hoffe Sie bekommen in den nächsten Wochen und Monaten reichlich Gegenwind zu spüren. Willkommen im 21-ten Jahrhundert!

In Vollendung,
ein Bundesbürger

PS:

Als Wochenendlektüre empfehle ich den Barbara Streisand Effekt:
https://en.wikipedia.org/wiki/Streisand_effect

Wednesday, September 17, 2014

Netflix in Ubuntu - part 2347 of \infinity

Today, Netflix started in Austria. Well, I thought, give it a try. Too bad, it's really painful in my Linux box. So, if you also have Ubuntu 14.10:

  1. Get Chrome Beta 38 or higher
  2. Update libnss3 via running this in your terminal:

    for pkg in libnss3_3.17-1ubuntu1_amd64.deb libnss3-nssdb_3.17-1ubuntu1_all.deb libnss3-1d_3.17-1ubuntu1_amd64.deb
    do
       wget http://archive.ubuntu.com/ubuntu/pool/main/n/nss/${pkg}
    done
    Then install it:

    $ sudo dpkg -i libnss*.deb
  3. Install the User-Agent Switcher for Chrome
    In its options (right-click on the icon) you have to add a new entry (besides the "String", nothing else really matters):

    • Name: Netflix
    • String: Mozilla/5.0 (Windows NT 6.3; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/38.0.2114.2 Safari/537.36
    • Group: keep it empty
    • Indicator: FLX (for Net-Flix)

    After that, set it to be active on netflix.com automatically: On the left, in "Permanent Spoof List"...
  4. Restart chrome, ... cross your fingers ... and enjoy.
  5. Edit: you also have to set the profile properties in netflix to HTML5 (though, I think it still works without doing anything, because there is no silverlight anyways)

Monday, August 18, 2014

New combinatorial designs in Sage - by Nathann Cohen

This is a guest post by Nathann Cohen. 


New combinatorial designs in Sage

Below, these graphs are a decomposition of a $K_{13}$ (i.e. the complete graph on 13 points) into copies of $K_4$. Pick two vertices you like: they appear exactly once together in one of the $K_4$.


The second graph shows a decomposition of a $K_{4,4,4}$ (i.e. the complete multipartite graph on $4\times 3$ points) into copies of $K_3$. Pick two vertices you like from different groups: they appear exactly once together in one of the $K_4$.




Sage has gotten quite good at building such decompositions (a specific kind of combinatorial designs) when they exist. This post is about them.

The first object belongs to a family called Balanced Incomplete Block Designs (or $(n,k)$-BIBD), which are defined as "a collection $\mathcal S$ of sets, all of them with size $k$ (here $k=4$), such that any pair of points of a set $X$ with $|X|=n$ (here $n=13$) appears in exactly one set of $\mathcal S$".

The second belongs to the family of Transversal Designs (or $TD(k,n)$) which have a similar definition: consider a set $X$ containing $k$ groups (here $k=3$) of $n$ vertices (here $n=4$). A collection $\mathcal S$ of sets, each of which contains one point from each group, is a $TD(k,n)$ if any two points from different groups appear together in exactly one set of $\mathcal S$.

The main problem with combinatorial designs is to know where they exist. And that is not obvious. Sage does what it can on about that:

  • If you want it to build a $(14,4)$-BIBD, it will tell you that none exists.
  • If you want it to build a $(16,4)$-BIBD, it will tell you that one exists.
  • If you want it to build a $(51,6)$-BIBD, it will tell you that it just not know if there is one (and nobody knows better at the moment)
Examples here:

sage: designs.balanced_incomplete_block_design(14,4,existence=True)
False
sage: designs.balanced_incomplete_block_design(16,4,existence=True)
True
sage: designs.balanced_incomplete_block_design(51,6,existence=True)
Unknown

For a developer (and design lover), the game consists in teaching Sage how to build all combinatorial designs that appear in some research paper. For BIBD as well as for Transversal Designs, on which a LOT of sweat was spent these last months.

For Transversal designs the game is a bit different, as we know that a $TD(k-1,n)$ exists whenever a $TD(k,n)$ exists. Thus, the game consists in finding the largest integer $k_n$ such that a $TD(k_n,n)$ exists. This game is hardly new, and hardly straightforward: In the Handbook of Combinatorial Designs, one can find the table of such $k$ up to $n=10000$ (see here).

The good thing about Sage is that it does not just claim that such a design exists: it also builds it, and there is no better existence proof than that (it is very very quick to check that a combinatorial design is valid). The other good thing is that there is no common database for such data (the Handbook is not updated/printed every night), and that by teaching Sage all new designs found by researchers we build such a database. And it already contains designs that were not known when the Handbook was printed.

Finally, the other other good thing about Sage is that it will soon be able to tell you where those designs come from. Indeed, the most powerful results in the field of Transversal Designs are of the shape "If there exists a $TD(k_1,n_1)$, and a $TD(k_2,n_2)$, ..., and a $TD(k_c,n_c)$, then you can combine them all to obtain a $TD(k,n)$ with $k=k(k_1,...,k_c)$ and $n=n(n_1,...,n_c)$". And it is never very clear how to inverse these functions: if you want to build a $TD(k,n)$, which integers $k_1,...,k_c,n_1,...,n_c$ should you pick ?

Sage knows. It must know it, in order to build these designs anyway. And you can find that data inside. And soon, we will teach it to give you the bibliographical references of the papers in which you can find the right construction to produce the $TD(k,n)$ that you want. And we will provide the right parameters. And the world will be at peace.

A couple of things before we part:

  • Transversal Designs (TD), Orthogonal Arrays (OA), and Mutually Orthogonal Latin Squares (MOLS) are all equivalent objects.
  • We write a LOT of Transversal Designs code these days, so expect all this to improve very fast.
  • You can learn what Sage knows of combinatorial designs right here.
Finally, there are far too many combinatorial designs for one man to learn. If you love combinatorial designs, come join us: Vincent Delecroix, you, and I have code to write together. And if you know a related mathematical results that Sage ignores, come tell us: we could not have gone so far without the mathematical knowledge of Julian Abel. And Sage does not know everything yet.

Have fuuuuuuuuuuuuuuuuuuun !

Nathann