From peter.ruckdeschel at itwm.fraunhofer.de  Fri Mar 20 20:04:01 2015
From: peter.ruckdeschel at itwm.fraunhofer.de (Dr. Peter Ruckdeschel)
Date: Fri, 20 Mar 2015 20:04:01 +0100
Subject: [Rd] RFC: Matrix package: Matrix products (%*%, crossprod,
 tcrossprod) involving "nsparseMatrix" aka sparse pattern matrices
In-Reply-To: <CAPRP4-ciBhLvJAEbiwdp+kZF3Sg4nr3NBohmV43P1gQF0pCA3Q@mail.gmail.com>
References: <CAPRP4-ciBhLvJAEbiwdp+kZF3Sg4nr3NBohmV43P1gQF0pCA3Q@mail.gmail.com>
Message-ID: <550C6F21.1090102@itwm.fraunhofer.de>

Hi Martin,

many thanks to you and Doug for providing the Matrix package
in the first place, and, second, for taking us into this decision.

I have only some minor comments to make:

+ wherever there is a usual function call involved, using an
   argument "boolean" as you proposed seems perfect to me

+ default behaviour and default values in function arguments
   should, even if bugous, stick to the old behaviour for backward
   compatibility right now, but you might still want to change this
   after a long enough announcement period

+ when it comes to arithmetic symbols, something like %&%
   certainly is nice to have, but the inadvertent user (like me,
   probably) would not know of this, unless this is documented
   at a prominent place

+ although this is against the functional paradigm of R, I would
   --exceptionally-- opt for a global option to change the behaviour
   (a) in function argument defaults and (b), more importantly, in
    binary arithmetic operators like %*%, *, +
    --- this way everybody can have the Matrix flavour he likes
 

just my 2c,
best regards,
Peter


Am 19.03.2015 um 23:02 schrieb Martin Maechler:
> This is a Request For Comment, also BCCed to 390 package maintainers
> of reverse dependencies of the Matrix package.
>
> Most users and package authors working with our 'Matrix' package will
> be using it for numerical computations, and so will be using
> "dMatrix" (d : double precision) matrix objects  M,   and indirectly, e.g., for
> M >= c  will also use "lMatrix" (l: logical i.e.  TRUE/FALSE/NA).
> All the following is  **not** affecting those numerical / logical
> computations.
>
> A few others will know that we also have "pattern" matrices (purely
> binary: TRUE/FALSE, no NA) notably sparse ones, those "ngCMatrix" etc,
> all starting with "n" (from ``patter[n]``) which do play a prominent
> role in the internal sparse matrix algorithms, notably of the
> (underlying C code) CHOLMOD library in the so-called "symbolic"
> cholesky decomposition and other such operations. Another reason you
> may use them because they are equivalent to incidence matrices of
> unweighted (directed or undirected) graphs.
>
> Now, as the subject says, I'm bringing up the topic of what should
> happen when these matrices appear in matrix multiplications.
> Somewhat by design, but also partly by coincidence,  the *sparse*
> pattern matrices multiplication in the Matrix package mostly builds on
> the CHOLMOD library `cholmod_ssmult()` function which implements
> "Boolean arithmetic" for them, instead of regular arithmetic:
>  "+" is logical "or"
>  "*" is  logical "and".
> Once we map  TRUE <-> 1  and  FALSE <-> 0, the only difference between
> boolean and regular arithmetic is that "1+1 = 1" in the (mapped)
> boolean arithmetic, because  "TRUE | TRUE" is TRUE in original logic.
>
> The drawback of using the boolean arithmetic here is the "clash" with
> the usual numeric arithmetic, and arithmetic in R where logical is
> coerced to integer (and that to "double") when certain numerical
> functions/operations are used.
>
> A more severe problem --- which I had not been aware of until
> relatively recently -- is the fact that  the CHOLMD function
> cholmod_ssdmult(A, B)
> treats *both* A and B as "pattern" as soon as one of them is a
> (sparse) pattern matrix.
> And this is - I say - in clear contrast to what R users would expect:
> If you multiply a numeric with a "kind of logical" matrix (a pattern
> one), you will expect that the
> TRUE/FALSE matrix will be treated as a 1/0 matrix because it is
> combined with a numeric matrix.
> So we could say that in this case, the Matrix package behavior is
> clearly bugous .... but still it has been the behavior for the last 10
> years or so.
>
> RFC 1: "Change 1":
> I currently propose to change this behavior for the upcoming release
> of Matrix (version 1.2-0),  though I have no idea if dependent
> packages would partly fail their checks or otherwise have changed
> behavior subsequently.
> The change seems sensible, since I think if your package relied on
> this behavior, it was inadvertent and accidental.
> Still you may differ in your opinion about this change nr.1
>
> RFC 2: "Change 2":
> This change would be more radical, and something I would not plan for
> the upcoming release of Matrix, but possibly for an update say one or
> two months later or so:  It concerns the matrix products when *both*
> matrices are pattern.  A situation where the boolean arithmetic may
> really make sense and where indeed packages may have depended on the
> current behavior  ("T + T  |--> T"). ... although that is currently
> only used for *sparse* pattern matrices, not for dense ones.
>
> Further, it may still seem surprising that matrix multiplication does
> not behave numerically for a pair of such matrices, and by the
> principle of "least surprise" we should provide the boolean arithmetic
> matrix products in another way than  by the   standard  %*%,
> crossprod()  and  tcrossprod() functions.
> So one possibility could be to change the standard functions to behave
> numerically,
> and e.g., use   %&%  (replace the numeric "*" by a logical "&")  and
> crossprod(A,B, boolean=TRUE),  tcrossprod(A,B, boolean=TRUE)
> for the three  boolean arithmetic  version of matrix multiplications.
>
> What do you think about this?   I'm particularly interested to hear
> from authors and users of  packages such as 'arules'  which IIRC
> explicitly work with sparse pattern matrices.
>
> Thank you for your thoughts and creative ideas,
> Martin Maechler, ETH Zurich


-- 
Dr. habil. Peter Ruckdeschel, Abteilung Finanzmathematik, F3.17
Fraunhofer ITWM, Fraunhofer Platz 1, 67663 Kaiserslautern
Telefon:  +49 631/31600-4699   Fax:  +49 631/31600-5699
E-Mail :  peter.ruckdeschel at itwm.fraunhofer.de
http://www.itwm.fraunhofer.de/abteilungen/finanzmathematik/mitarbeiterinnen/mitarbeiter/dr-peter-ruckdeschel.html



[Rd] RFC: Matrix package: Matrix products (%*%, crossprod, tcrossprod) involving "nsparseMatrix" aka sparse pattern matrices
Dr. Peter Ruckdeschel