probmods/chapters

The online textbook Probabilistic Models of Cognition

chapters's Issues

Displaying multiple Histograms

Not sure if this is an issue really, but when multiple histograms are used, e.g.:

(hist (repeat 2000 (lambda () (chain 'a 2))) "a 2")
(hist (repeat 2000 (lambda () (chain 'c 2))) "c 2")
(hist (repeat 2000 (lambda () (chain 'a 10))) "a 10")
(hist (repeat 2000 (lambda () (chain 'c 10))) "c 10")

Only the last one is displayed. If "'done" is added to the end, no histogram at all is displayed. This makes for unclear comparisons and should perhaps be made into subplots all displayed at once.

Set index page to render in UTF-8.

Error message thrown by exact-query

exact-query returns error:

Running the following:
"(exact-query
(define A 1)
A
(equals 2 2)
)"

returns:

_A is not defined

Histogram way too big

In the joint lung-cancer / TB inference example on the conditioning page, the resulting histogram is humongous - each bar takes up way too much space. NB: this example takes a while to run.

Fix references

In content, some references are still in Mediawiki format

truehist not defined

Trying to use 'truehist' returns:

_truehist is not defined

Deleting things in the play space?

It would be useful to be able to delete things from the play-space to avoid clutter, and also to load multiple files into one another to again, avoid clutter.

Within chapters, fix links to other chapters

Lineplots

Update for most recent pandoc

Citations cause an error for most recent pandoc (1.12.1).

Tab should re-indent.

Pressing tab in codebox should re-indent the current line (or current region when selected), not be a tab character.

Error in chapter 6: "_drop_45right is not defined"

Running the example 'states with structure and Gibbs sampling' in chapter 6 (https://www.probmods.org/inference-process.html) returns the error:

_drop_45right is not defined

Chapter menu is buggy when hovering

two conditions in a row register as a query (on the condition) and then the other condition

Also this comes out completely crazy in the version of webchurch that chapters is using. The craziness is fixed in the most up-to-date webchurch.

Here's the code examples that's wrong (In "Patterns of Inference")

(define observed-luminance 3.0)

(define samples
   (mh-query
    1000 10

    (define reflectance (gaussian 1 1))
    (define illumination (gaussian 3 0.5))
    (define luminance (* reflectance illumination))

    reflectance

    (condition (= luminance (gaussian observed-luminance 0.1)))
    (condition (= illumination (gaussian 0.5  0.1)))))

(multiviz "Mean reflectance: " (mean samples)
          (hist samples "Reflectance"))

If you replace the two conditions with an and statement it takes a reallllly long time to run, but I think it would do the correct thing.

Density plot

sample_gamma is not defined

Running the third code block in the ninth chapter (https://www.probmods.org/hierarchical-models.html) returns the following error:

sample_gamma is not defined

Histogram bars: Bob's strength example in Conditioning

Bars are too big.

Live-update histograms for query results

Have a flag to or variant of mh-query and rejection-query that makes a histogram of samples and updates it on each sample. This can be done by extending probabilistic-js inference routines to take a listener function (which is called when a sample is taken), and then creating a listener that calls the _hist vizualization tool.

Add javascript-based site search

Scatterplots

Conditional probability formatting

conditional probabilities should be formatted as P(x \mid y), not P(x|y)

Refactor CSS

Also, think about using something like Less / Sass.

In Bibtex file, programatically copy citekey into "note" field

_drop not defined

In the "markov chains with lag" example, in chapter 6 here:

https://www.probmods.org/inference-process.html

The following use of "drop":

(hist (drop (chain 'a 100) 30) "burn-in 30, lag 0")

returns the error:

_drop is not defined

Refactor to separate content

Separate the content .md files from the scripts and resources.

The scripts repo should have a build script that takes a folder location as input, builds all .md files in that directory, optionally builds an index if there is a chapters.txt file, and puts the generated html and all runtime scripts into a new subdirectory. (Runtime scripts might be just one merged and minified js with all the scripts?)

Ultimately we should move the chapter md files to a separate repository, but for now can just move them to a subdirectory.

CodeMirror injection slow

Is it possible to batch DOM updates?

Preliminary attempts at this have a weird quirk where CodeMirror content isn't actually visible until mousedown on codebox.

Give unique ids to exercises (for recording in database)

take is not defined

trying to use "take" returns:

_take is not defined

(take is used in some examples on the website)

Integrate other Church engines

Add quizzes.

Add machinery for simple quizzes (with, e.g., multiple choice answers). Should play nice with accounts so that when students are logged in their quiz results will be logged (and retrievable by admin based on email address). These will be use to make "comprehension tests" for the chapters.

Add service hook: compile on server after push to Github

pass around objectLists instead of worlds in intuitive physics

no method "wrapped_beta"

trying to run the fourth code-block in the seventh chapter ( https://www.probmods.org/learning-as-conditional-inference.html) returns the error:

Object # has no method 'wrapped_beta'

Code folding

It would be useful to have code folding possible in the codemirror boxes, and have a way in the markdown to tell a region to start out folded. This way helper routines could be hidden from sight. Eg:

(define coolfun ...)

;;;folded helper code
(define boringfun ...)
;;;

..the real stuff..

Why? There are lots of examples that build progressively meaning we repeat the same code... It would look much better to hide this code from sight after the first time.

Collect app-level JS variables in one-place

Would be useful to have, inter alia:

• whether accounts server is reachable
• whether user is logged in

Disable run button when code is running

Multiple visualizations from one codebox

Enhance syntax coloring

In codemirror church style, it would be nice to:

-have a different syntax coloring for erps.

-color queries specially: special color for the query (and matching bracket?), special color for query expression and condition expression.

Rectangle visualizations (for rectangle game example)

make script

Switch to make for building project. (Fairly low priority, as everything works right now, but should be done at some point.)

Build html files into a subdirectory.

Add reset button to code editor

Viz elements have X on mouseover

Rather than a "delete" button, we should have a little X in upper right hand corner on mouseover to delete a viz plot.

Simple query returning error

For example, running this:

(query
(define x 3)
x
(> x 2))

returns this:

_x is not defined

JS loading inefficient

Could use Google Closure compiler to collect all/many JS dependencies in one file.

Viz boxes should get replaced when code is re-run.

Currently histograms and such pile up as we run a code box. Want to replace instead of adding.

Add login / register actions as iframes

_make_45beta_45binomial is not defined

Trying to run the second (and last) code block in chapter 8 (https://www.probmods.org/grammar-based-induction-LoT.html) returns the error:

_make_45beta_45binomial is not defined

Hist does not perform correctly for lists of continuous values.

To be more specific, I think the y-axis labels are flipped. Here is a little bit of code that exhibits the problem.

(define samps
  (mh-query
   500 2

   (define x (multinomial '(.1 .3 .5 .7) '(1 3 5 7)))

   (define y (+ x (gaussian 0 0.001)))

   y

   true
   )
  )

(hist samps)

Add analytics

Add analytics hooks so that we can track site usage.

(Use google analytics?)

_list_45ref is not defined

Trying to run the first code block in chapter 8 (https://www.probmods.org/grammar-based-induction-LoT.html) returns:

_list_45ref is not defined