Can't disable messages for pymc3.find_MAP() - pymc3

Sorry for the dumb question but I am unable to find any way to disable messages for pymc3.find_MAP(). As someone new to PyMC3 I think I've just learned to use the syntax properly (shakily) to do a single MAP estimate, given prior and likelihood functions. I'm about to try and scale this up to process a large number of variables but to so I'd like to eliminate messages of the type that I'm getting, e.g.:
Optimization terminated successfully.
Current function value: 1.889038
Iterations:2
Function evaluations: 4
Gradient evaluations: 4
but can't find anything in the documentation indicating how to do so. I figure I can turn them back on when I need to debug. Any suggestions ? Thanks in advance.

Extra arguments are passed into the optimization function, which by default is from scipy.optimize.*, so passing disp=False to pm.find_MAP will suppress messages.
As an aside, find_MAP is no longer recommended to initialize sampling.

Related

Piecewise function with variable values at domain breakpoints

In our model we need a set of equations
model.y[k] = model.F(model.x[k]) (where k is in a proper Set)
with piecewise function F(x) defined on a fixed set of domain variable (breakpoints), but with unknown, variable (!), values at these breakpoints.
I implemented the case via SOSConstraint(..., sos=2) and it works (I tested by SCIP solver).
Now we want to try other implementations of pw-functions (LOG, BIGM_BIN, DCC, DLOG, etc.) mentioned in Pyomo pyomo.core.base.piecewise.Piecewise code. But it seems that this class requires fixed numerical values for F(x) at all breakpoints. If a function passed by f_rule argument to Piecewise constructor returns Pyomo expression with variable, then I get the following error:
ERROR: evaluating object as numeric value: ...
Can somebody give an advice or an a reference to some example of a "variable" piecewise-function ?
E.g., regarding "LOG" representation (from Vielma etc.) I see the code of _LOGPiecewise function in pyomo/core/base/piecewise.py module. And I do not see any reasons to forbidden to use variables as "y"-values of pw-expression being constructed ...
Updated
I've succeeded to modify pyomo.core.base.piecewise module to use variables as values of pw-function. Frankly speaking, these "modifications" were just commenting of some fragments in piecewise.py...
But, for my problem, I did not get any speed up in comparison with SOSConstraint (for SCIP solver !).
Can anybody give the benefit of experience: what pw-models were faster SOSConstraint or LOG, BIGM_BIN, DCC, DLOG for other problems ?

Maxima: creating a function that acts on parts of a string

Context: I'm using Maxima on a platform that also uses KaTeX. For various reasons related to content management, this means that we are regularly using Maxima functions to generate the necessary KaTeX commands.
I'm currently trying to develop a group of functions that will facilitate generating different sets of strings corresponding to KaTeX commands for various symbols related to vectors.
Problem
I have written the following function makeKatexVector(x), which takes a string, list or list-of-lists and returns the same type of object, with each string wrapped in \vec{} (i.e. makeKatexVector(string) returns \vec{string} and makeKatexVector(["a","b"]) returns ["\vec{a}", "\vec{b}"] etc).
/* Flexible Make KaTeX Vector Version of List Items */
makeKatexVector(x):= block([ placeHolderList : x ],
if stringp(x) /* Special Handling if x is Just a String */
then placeHolderList : concat("\vec{", x, "}")
else if listp(x[1]) /* check to see if it is a list of lists */
then for j:1 thru length(x)
do placeHolderList[j] : makelist(concat("\vec{", k ,"}"), k, x[j] )
else if listp(x) /* check to see if it is just a list */
then placeHolderList : makelist(concat("\vec{", k, "}"), k, x)
else placeHolderList : "makeKatexVector error: not a list-of-lists, a list or a string",
return(placeHolderList));
Although I have my doubts about the efficiency or elegance of the above code, it seems to return the desired expressions; however, I would like to modify this function so that it can distinguish between single- and multi-character strings.
In particular, I'd like multi-character strings like x_1 to be returned as \vec{x}_1 and not \vec{x_1}.
In fact, I'd simply like to modify the above code so that \vec{} is wrapped around the first character of the string, regardless of how many characters there may be.
My Attempt
I was ready to tackle this with brute force (e.g. transcribing each character of a string into a list and then reassembling); however, the real programmer on the project suggested I look into "Regular Expressions". After exploring that endless rabbit hole, I found the command regex_subst; however, I can't find any Maxima documentation for it, and am struggling to reproduce the examples in the related documentation here.
Once I can work out the appropriate regex to use, I intend to implement this in the above code using an if statement, such as:
if slength(x) >1
then {regex command}
else {regular treatment}
If anyone knows of helpful resources on any of these fronts, I'd greatly appreciate any pointers at all.
Looks like you got the regex approach working, that's great. My advice about handling subscripted expressions in TeX, however, is to avoid working with names which contain underscores in Maxima, and instead work with Maxima expressions with indices, e.g. foo[k] instead of foo_k. While writing foo_k is a minor convenience in Maxima, you'll run into problems pretty quickly, and in order to straighten it out you might end up piling one complication on another.
E.g. Maxima doesn't know there's any relation between foo, foo_1, and foo_k -- those have no more in common than foo, abc, and xyz. What if there are 2 indices? foo_j_k will become something like foo_{j_k} by the preceding approach -- what if you want foo_{j, k} instead? (Incidentally the two are foo[j[k]] and foo[j, k] when represented by subscripts.) Another problematic expression is something like foo_bar_baz. Does that mean foo_bar[baz], foo[bar_baz] or foo_bar_baz?
The code for tex(x_y) yielding x_y in TeX is pretty old, so it's unlikely to go away, but over the years I've come to increasing feel like it should be avoided. However, the last time it came up and I proposed disabling that, there were enough people who supported it that we ended up keeping it.
Something that might be helpful, there is a function texput which allows you to specify how a symbol should appear in TeX output. For example:
(%i1) texput (v, "\\vec{v}");
(%o1) "\vec{v}"
(%i2) tex ([v, v[1], v[k], v[j[k]], v[j, k]]);
$$\left[ \vec{v} , \vec{v}_{1} , \vec{v}_{k} , \vec{v}_{j_{k}} ,
\vec{v}_{j,k} \right] $$
(%o2) false
texput can modify various aspects of TeX output; you can take a look at the documentation (see ? texput).
While I didn't expect that I'd work this out on my own, after several hours, I made some progress, so figured I'd share here, in case anyone else may benefit from the time I put in.
to load the regex in wxMaxima, at least on the MacOS version, simply type load("sregex");. I didn't have this loaded, and was trying to work through our custom platform, which cost me several hours.
take note that many of the arguments in the linked documentation by Dorai Sitaram occur in the reverse, or a different order than they do in their corresponding Maxima versions.
not all the "pregexp" functions exist in Maxima;
In addition to this, escaping special characters varied in important ways between wxMaxima, the inline Maxima compiler (running within Ace editor) and the actual rendered version on our platform; in particular, the inline compiler often returned false for expressions that compiled properly in wxMaxima and on the platform. Because I didn't have sregex loaded on wxMaxima from the beginning, I lost a lot of time to this.
Finally, the regex expression that achieved the desired substitution, in my case, was:
regex_subst("\vec{\\1}", "([[:alpha:]])", "v_1");
which returns vec{v}_1 in wxMaxima (N.B. none of my attempts to get wxMaxima to return \vec{v}_1 were successful; escaping the backslash just does not seem to work; fortunately, the usual escaped version \\vec{\\1} does return the desired form).
I have yet to adjust the code for the rest of the function, but I doubt that will be of use to anyone else, and wanted to be sure to post an update here, before anyone else took time to assist me.
Always interested in better methods / practices or any other pointers / feedback.

Can I query LTTNG if a given tracepoint with given args is going to be traced, before tracing it?

We need to adapt a huge number of existing traces, printf-like, to LTTNG. One of the issues we are foreseeing is that we will need a catch-all tracepoint with the format of args plus a char* string. We are trying to find a way to avoid having to compose the string before calling the LTTNG tracepoint. Is there any way to know beforehand if the tracepoint "will be traced" before passing it to the LTTNG library? Any method we can call to know if the trace is a match?
Thanks a lot!
P.S. We know that having this kind of tracepoint is a bad practice, but zillions of trace lines are flying above us.
Use tracepoint_enabled() and do_tracepoint() macros as following, code copied from man page:
if (tracepoint_enabled(ust_tests_hello, tptest)) {
/* prepare arguments */
do_tracepoint(ust_tests_hello, tptest, i, netint, values,
text, strlen(text), dbl, flt);
}
Note: For this to work you need to have atleast LTTng-UST 2.7.0-rc1
You could technically query the status of the tracing session through liblttng-ctl. However if your goal is to improve performance, I am not sure doing a lookup through this library every time you hit a tracepoint will be more efficient than a string formatting. You would have to benchmark it.
As a side note, if you are moving existing printf() calls to LTTng tracepoints, you may want to look at tracef(), which is basically a single-format-string tracepoint already defined by the tracer. There is also a slightly more advanced tracelog() function which will be introduced in LTTng 2.7.

Looping Filenames in Stata error

I am aware that there already exist related threads like how do I loop through file names in stata
I follow those instructions but however receive the invalid syntax r(198) error in Stata.
My code looks as follows:
foreach var of "*/ABC.dta" ABC{
infix observation 1-2 date 3 using "*/CC_ABC`var'.txt"
save "*/CC_ABC`var'.dta" ,replace
}
Where ABC.dta is a list of pretty random numbers which all occur in file names. Do you have an idea why I get errors here?
Thanks a lot!
Is this real code?
Stata wouldn't get past the lack of a listtype following of. This is the very first thing explained in the help for foreach.
If this isn't real code, please show us a real example of something that doesn't work, ideally one that we can reproduce.
(If you don't understand something, imposing your own abstraction or generalization is just likely to muddy your question for those who do.)

OCaml - issues connected with using fold__

I have a several questions connected with fold_left/right.
How to accumulate two or more values? If using a tuple is good solution ?
How to abort work of fold ? For example we must find firstly occurrence of any number, and return position. I mean a break (C++).
zurgl's comment is a great answer (maybe move it down to the answer region).
You can use an exception to terminate a fold early. It's good to try to structure your code so you don't have to do this (in my opinion). Code without exceptions is easier to understand, more composable, parallelizable, etc.
we must find firstly occurrence of any number then you must traverse all your list [1;1;1;1;5], no need to abort here. To deal with partial recursion there are other function like dropwhile, takewhile ... Or you can define the one you need. See folding as projection between type, you have a source type and a target type with a seed value (the accumulator), then folding is a procedure which realize this transformation. Yes using tuple is good solution, IMO.