The Great conversation in USA presidential speeches


This document shows a way to chart in Mathematica / WL the evolution of topics in collections of texts. The making of this document (and related code) is primarily motivated by the fascinating concept of the Great Conversation, [Wk1, MA1]. In brief, all western civilization books are based on 103 great ideas; if we find the great ideas each significant book is based on we can construct a time-line (spanning centuries) of the great conversation between the authors; see [MA1, MA2, MA3].

Instead of finding the great ideas in a text collection we extract topics statistically, using dimension reduction with Non-Negative Matrix Factorization (NNMF), [AAp3, AA1, AA2].

The presented computational results are based on the text collections of State of the Union speeches of USA presidents [D2]. The code in this document can be easily configured to use the much smaller text collection [D1] available online and in Mathematica/WL. (The collection [D1] is fairly small, 51 documents; the collection [D2] is much larger, 2453 documents.)

The procedures (and code) described in this document, of course, work on other types of text collections. For example: movie reviews, podcasts, editorial articles of a magazine, etc.

A secondary objective of this document is to illustrate the use of the monadic programming pipeline as a Software design pattern, [AA3]. In order to make the code concise in this document I wrote the package MonadicLatentSemanticAnalysis.m, [AAp5]. Compare with the code given in [AA1].

The very first version of this document was written for the 2017 summer course “Data Science for the Humanities” at the University of Oxford, UK.

Outline of the procedure applied

The procedure described in this document has the following steps.

  1. Get a collection of documents with known dates of publishing.
    • Or other types of tags associated with the documents.
  2. Do preliminary analysis of the document collection.
    • Number of documents; number of unique words.

    • Number of words per document; number of documents per word.

    • (Some of the statistics of this step are done easier after the Linear vector space representation step.)

  3. Optionally perform Natural Language Processing (NLP) tasks.

    1. Obtain or derive stop words.

    2. Remove stop words from the texts.

    3. Apply stemming to the words in the texts.

  4. Linear vector space representation.

    • This means that we represent the collection with a document-word matrix.

    • Each unique word is a basis vector in that space.

    • For each document the corresponding point in that space is derived from the number of appearances of document’s words.

  5. Extract topics.

    • In this document NNMF is used.

    • In order to obtain better results with NNMF some experimentation and refinements of the topics search have to be done.

  6. Map the documents over the extracted topics.

    • The original matrix of the vector space representation is replaced with a matrix with columns representing topics (instead of words.)
  7. Order the topics according to their presence across the years (or other related tags).
    • This can be done with hierarchical clustering.

    • Alternatively,

      1. for a given topic find the weighted mean of the years of the documents that have that topic, and

      2. order the topics according to those mean values.

  8. Visualize the evolution of the documents according to their topics.

    1. This can be done by simply finding the contingency matrix year vs topic.

    2. For the president speeches we can use the president names for time-line temporal axis instead of years.

      • Because the corresponding time intervals of president office occupation do not overlap.

Remark: Some of the functions used in this document combine several steps into one function call (with corresponding parameters.)


This loads the packages [AAp1-AAp8]:


(Note that some of the packages that are imported automatically by [AAp5].)

The functions of the central package in this document, [AAp5], have the prefix “LSAMon”. Here is a sample of those names:


(* {"LSAMon", "LSAMonAddToContext", "LSAMonApplyTermWeightFunctions", <>, "LSAMonUnit", "LSAMonUnitQ", "LSAMonWhen"} *)

Data load

In this section we load a text collection from a specified source.

The text collection from “Presidential Nomination Acceptance Speeches”, [D1], is small and can be used for multiple code verifications and re-runnings. The “State of Union addresses of USA presidents” text collection from [D2] was converted to a Mathematica/WL object by Christopher Wolfram (and sent to me in a private communication.) The text collection [D2] provides far more interesting results (and they are shown below.)

  speeches = ResourceData[ResourceObject["Presidential Nomination Acceptance Speeches"]];
  names = StringSplit[Normal[speeches[[All, "Person"]]][[All, 2]], "::"][[All, 1]],

  (*State of the union addresses provided by Christopher Wolfram. *)      
  Get["~/MathFiles/Digital humanities/Presidential speeches/"];
  names = Normal[speeches[[All, "Name"]]];

dates = Normal[speeches[[All, "Date"]]];
texts = Normal[speeches[[All, "Text"]]];


(* {2453, 4} *)

Basic statistics for the texts

Using different contingency matrices we can derive basic statistical information about the document collection. (The document-word matrix is a contingency matrix.)

First we convert the text data in long-form:

docWordRecords = 
  Join @@ MapThread[
    Thread[{##}] &, {Range@Length@texts, names, 
     DateString[#, {"Year"}] & /@ dates, 
     DeleteStopwords@*TextWords /@ ToLowerCase[texts]}, 1];

Here is a sample of the rows of the long-form:

GridTableForm[RandomSample[docWordRecords, 6], 
 TableHeadings -> {"document index", "name", "year", "word"}]

Here is a summary:

 RecordsSummary[docWordRecords, {"document index", "name", "year", "word"}, "MaxTallies" -> 8], 4, Dividers -> All, Alignment -> Top]

Using the long form we can compute the document-word matrix:

ctMat = CrossTabulate[docWordRecords[[All, {1, -1}]]];
MatrixPlot[Transpose@Sort@Map[# &, Transpose[ctMat@"XTABMatrix"]], 
 MaxPlotPoints -> 300, ImageSize -> 800, 
 AspectRatio -> 1/3]

Here is the president-word matrix:

ctMat = CrossTabulate[docWordRecords[[All, {2, -1}]]];
MatrixPlot[Transpose@Sort@Map[# &, Transpose[ctMat@"XTABMatrix"]], MaxPlotPoints -> 300, ImageSize -> 800, AspectRatio -> 1/3]

Here is an alternative way to compute text collection statistics through the document-word matrix computed within the monad LSAMon:


Procedure application

Stop words

Here is one way to obtain stop words:

stopWords = Complement[DictionaryLookup["*"], DeleteStopwords[DictionaryLookup["*"]]];
RandomSample[stopWords, 12]

(* 304 *)

(* {"has", "almost", "next", "WHO", "seeming", "together", "rather", "runners-up", "there's", "across", "cannot", "me"} *)

We can complete this list with additional stop words derived from the collection itself. (Not done here.)

Linear vector space representation and dimension reduction

Remark: In the rest of the document we use “term” to mean “word” or “stemmed word”.

The following code makes a document-term matrix from the document collection, exaggerates the representations of the terms using “TF-IDF”, and then does topic extraction through dimension reduction. The dimension reduction is done with NNMF; see [AAp3, AA1, AA2].


mObj =
   LSAMonMakeDocumentTermMatrix[{}, stopWords]⟹
   LSAMonTopicExtraction[Max[5, Ceiling[Length[texts]/100]], 60, 12, "MaxSteps" -> 6, "PrintProfilingInfo" -> True];

This table shows the pipeline commands above with comments:

Detailed description

The monad object mObj has a context of named values that is an Association with the following keys:


(* {"texts", "docTermMat", "terms", "wDocTermMat", "W", "H", "topicColumnPositions", "automaticTopicNames"} *)

Let us clarify the values by briefly describing the computational steps.

  1. From texts we derive the document-term matrix \text{docTermMat}\in \mathbb{R}^{m \times n}, where n is the number of documents and m is the number of terms.
    • The terms are words or stemmed words.

    • This is done with LSAMonMakeDocumentTermMatrix.

  2. From docTermMat is derived the (weighted) matrix wDocTermMat using “TF-IDF”.

    • This is done with LSAMonApplyTermWeightFunctions.
  3. Using docTermMat we find the terms that are present in sufficiently large number of documents and their column indices are assigned to topicColumnPositions.

  4. Matrix factorization.

    1. Assign to \text{wDocTermMat}[[\text{All},\text{topicsColumnPositions}]], \text{wDocTermMat}[[\text{All},\text{topicsColumnPositions}]]\in \mathbb{R}^{m_1 \times n}, where m_1 = |topicsColumnPositions|.

    2. Compute using NNMF the factorization \text{wDocTermMat}[[\text{All},\text{topicsColumnPositions}]]\approx H W, where W\in \mathbb{R}^{k \times n}, H\in \mathbb{R}^{k \times m_1}, and k is the number of topics.

    3. The values for the keys “W, “H”, and “topicColumnPositions” are computed and assigned by LSAMonTopicExtraction.

  5. From the top terms of each topic are derived automatic topic names and assigned to the key automaticTopicNames in the monad context.

    • Also done by LSAMonTopicExtraction.

Statistical thesaurus

At this point in the object mObj we have the factors of NNMF. Using those factors we can find a statistical thesaurus for a given set of words. The following code calculates such a thesaurus, and echoes it in a tabulated form.

queryWords = {"arms", "banking", "economy", "education", "freedom", 
   "tariff", "welfare", "disarmament", "health", "police"};

  LSAMonStatisticalThesaurus[queryWords, 12]⟹

By observing the thesaurus entries we can see that the words in each entry are semantically related.

Note, that the word “welfare” strongly associates with “[applause]”. The rest of the query words do not, which can be seen by examining larger thesaurus entries:

thRes =
   LSAMonStatisticalThesaurus[queryWords, 100]⟹
Cases[thRes, "[applause]", Infinity]

(* {"[applause]", "[applause]"} *)

The second “[applause]” associated word is “education”.

Detailed description

The statistical thesaurus is computed by using the NNMF’s right factor H.

For a given term, its corresponding column in H is found and the nearest neighbors of that column are found in the space \mathbb{R}^{m_1} using Euclidean norm.

Extracted topics

The topics are the rows of the right factor H of the factorization obtained with NNMF .

Let us tabulate the topics found above with LSAMonTopicExtraction :

mObj⟹ LSAMonEchoTopicsTable["NumberOfTerms" -> 6, "MagnificationFactor" -> 0.8, Appearance -> "Horizontal"];

Map documents over the topics

The function LSAMonTopicsRepresentation finds the top outliers for each row of NNMF’s left factor W. (The outliers are found using the package [AAp4].) The obtained list of indices gives the topic representation of the collection of texts.


{{53}, {47, 53}, {25}, {46}, {44}, {15, 42}, {18}, <>, {30}, {33}, {7, 60}, {22, 25}, {12, 13, 25, 30, 49, 59}, {48, 57}, {14, 41}}

Further we can see that if the documents have tags associated with them — like author names or dates — we can make a contingency matrix of tags vs topics. (See [AAp8, AA4].) This is also done by the function LSAMonTopicsRepresentation that takes tags as an argument. If the tags argument is Automatic, then the tags are simply the document indices.

Here is a an example:

rsmat = mObj⟹LSAMonTopicsRepresentation[Automatic]⟹LSAMonTakeValue;

Here is an example of calling the function LSAMonTopicsRepresentation with arbitrary tags.

rsmat = mObj⟹LSAMonTopicsRepresentation[DateString[#, "MonthName"] & /@ dates]⟹LSAMonTakeValue;

Note that the matrix plots above are very close to the charting of the Great conversation that we are looking for. This can be made more obvious by observing the row names and columns names in the tabulation of the transposed matrix rsmat:

Magnify[#, 0.6] &@MatrixForm[Transpose[rsmat]]

Charting the great conversation

In this section we show several ways to chart the Great Conversation in the collection of speeches.

There are several possible ways to make the chart: using a time-line plot, using heat-map plot, and using appropriate tabulation (with MatrixForm or Grid).

In order to make the code in this section more concise the package RSparseMatrix.m, [AAp7, AA5], is used.

Topic name to topic words

This command makes an Association between the topic names and the top topic words.

aTopicNameToTopicTable = 
   mObj⟹LSAMonTopicsTable["NumberOfTerms" -> 12]⟹LSAMonTakeValue];

Here is a sample:

Magnify[#, 0.7] &@ aTopicNameToTopicTable[[1 ;; 3]]

Time-line plot

This command makes a contingency matrix between the documents and the topics (as described above):

rsmat = ToRSparseMatrix[mObj⟹LSAMonTopicsRepresentation[Automatic]⟹LSAMonTakeValue]

This time-plot shows great conversation in the USA presidents state of union speeches:

   Tooltip[#2, aTopicNameToTopicTable[#2]] -> dates[[ToExpression@#1]] &, 
 PlotTheme -> "Detailed", ImageSize -> 1000, AspectRatio -> 1/2, PlotLayout -> "Stacked"]

The plot is too cluttered, so it is a good idea to investigate other visualizations.

Topic vs president heatmap

We can use the USA president names instead of years in the Great Conversation chart because the USA presidents terms do not overlap.

This makes a contingency matrix presidents vs topics:

rsmat2 = ToRSparseMatrix[

Here we compute the chronological order of the presidents based on the dates of their speeches:

nameToMeanYearRules = 
  Map[#[[1, 1]] -> Mean[N@#[[All, 2]]] &, 
   GatherBy[MapThread[List, {names, ToExpression[DateString[#, "Year"]] & /@ dates}], First]];
ordRowInds = Ordering[RowNames[rsmat2] /. nameToMeanYearRules];

This heat-map plot uses the (experimental) package HeatmapPlot.m, [AAp6]:

Block[{m = rsmat2[[ordRowInds, All]]},
 HeatmapPlot[SparseArray[m], RowNames[m], 
  Thread[Tooltip[ColumnNames[m], aTopicNameToTopicTable /@ ColumnNames[m]]],
  DistanceFunction -> {None, Sort}, ImageSize -> 1000, 
  AspectRatio -> 1/2]

Note the value of the option DistanceFunction: there is not re-ordering of the rows and columns are reordered by sorting. Also, the topics on the horizontal names have tool-tips.


Text data

[D1] Wolfram Data Repository, "Presidential Nomination Acceptance Speeches".

[D2] US Presidents, State of the Union Addresses, Trajectory, 2016. ‪ISBN‬1681240009, 9781681240008‬.

[D3] Gerhard Peters, "Presidential Nomination Acceptance Speeches and Letters, 1880-2016", The American Presidency Project.

[D4] Gerhard Peters, "State of the Union Addresses and Messages", The American Presidency Project.


[AAp1] Anton Antonov, MathematicaForPrediction utilities, (2014), MathematicaForPrediction at GitHub.

[AAp2] Anton Antonov, Implementation of document-term matrix construction and re-weighting functions in Mathematica(2013), MathematicaForPrediction at GitHub.

[AAp3] Anton Antonov, Implementation of the Non-Negative Matrix Factorization algorithm in Mathematica, (2013), MathematicaForPrediction at GitHub.

[AAp4] Anton Antonov, Implementation of one dimensional outlier identifying algorithms in Mathematica, (2013), MathematicaForPrediction at GitHub.

[AAp5] Anton Antonov, Monadic latent semantic analysis Mathematica package, (2017), MathematicaForPrediction at GitHub.

[AAp6] Anton Antonov, Heatmap plot Mathematica package, (2017), MathematicaForPrediction at GitHub.

[AAp7] Anton Antonov, RSparseMatrix Mathematica package, (2015), MathematicaForPrediction at GitHub.

[AAp8] Anton Antonov, Cross tabulation implementation in Mathematica, (2017), MathematicaForPrediction at GitHub.

Books and articles

[AA1] Anton Antonov, "Topic and thesaurus extraction from a document collection", (2013), MathematicaForPrediction at GitHub.

[AA2] Anton Antonov, "Statistical thesaurus from NPR podcasts", (2013), MathematicaForPrediction at WordPress blog.

[AA3] Anton Antonov, "Monad code generation and extension", (2017), MathematicaForPrediction at GitHub.

[AA4] Anton Antonov, "Contingency tables creation examples", (2016), MathematicaForPrediction at WordPress blog.

[AA5] Anton Antonov, "RSparseMatrix for sparse matrices with named rows and columns", (2015), MathematicaForPrediction at WordPress blog.

[Wk1] Wikipedia entry, Great Conversation.

[MA1] Mortimer Adler, "The Great Conversation Revisited," in The Great Conversation: A Peoples Guide to Great Books of the Western World, Encyclopædia Britannica, Inc., Chicago,1990, p. 28.

[MA2] Mortimer Adler, "Great Ideas".

[MA3] Mortimer Adler, "How to Think About the Great Ideas: From the Great Books of Western Civilization", 2000, Open Court.


Monad code generation and extension

… in Mathematica / Wolfram Language

Anton Antonov

MathematicaForPrediction at GitHub

MathematicaVsR at GitHub

June 2017


This document aims to introduce monadic programming in Mathematica / Wolfram Language (WL) in a concise and code-direct manner. The core of the monad codes discussed is simple, derived from the fundamental principles of Mathematica / WL.

The usefulness of the monadic programming approach manifests in multiple ways. Here are a few we are interested in:

  1. easy to construct, read, and modify sequences of commands (pipelines),
  2. easy to program polymorphic behaviour,
  3. easy to program context utilization.

Speaking informally,

  • Monad programming provides an interface that allows interactive, dynamic creation and change of sequentially structured computations with polymorphic and context-aware behavior.

The theoretical background provided in this document is given in the Wikipedia article on Monadic programming, [Wk1], and the article “The essence of functional programming” by Philip Wadler, [H3]. The code in this document is based on the primary monad definition given in [Wk1,H3]. (Based on the “Kleisli triple” and used in Haskell.)

The general monad structure can be seen as:

  1. a software design pattern;
  2. a fundamental programming construct (similar to class in object-oriented programming);
  3. an interface for software types to have implementations of.

In this document we treat the monad structure as a design pattern, [Wk3]. (After reading [H3] point 2 becomes more obvious. A similar in spirit, minimalistic approach to Object-oriented Design Patterns is given in [AA1].)

We do not deal with types for monads explicitly, we generate code for monads instead. One reason for this is the “monad design pattern” perspective; another one is that in Mathematica / WL the notion of algebraic data type is not needed — pattern matching comes from the core “book of replacement rules” principle.

The rest of the document is organized as follows.

1. Fundamental sections The section “What is a monad?” gives the necessary definitions. The section “The basic Maybe monad” shows how to program a monad from scratch in Mathematica / WL. The section “Extensions with polymorphic behavior” shows how extensions of the basic monad functions can be made. (These three sections form a complete read on monadic programming, the rest of the document can be skipped.)

2. Monadic programming in practice The section “Monad code generation” describes packages for generating monad code. The section “Flow control in monads” describes additional, control flow functionalities. The section “General work-flow of monad code generation utilization” gives a general perspective on the use of monad code generation. The section “Software design with monadic programming” discusses (small scale) software design with monadic programming.

3. Case study sections The case study sections “Contextual monad classification” and “Tracing monad pipelines” hopefully have interesting and engaging examples of monad code generation, extension, and utilization.

What is a monad?

The monad definition

In this document a monad is any set of a symbol m and two operators unit and bind that adhere to the monad laws. (See the next sub-section.) The definition is taken from [Wk1] and [H3] and phrased in Mathematica / WL terms in this section. In order to be brief, we deliberately do not consider the equivalent monad definition based on unit, join, and map (also given in [H3].)

Here are operators for a monad associated with a certain symbol M:

  1. monad unit function (“return” in Haskell notation) is Unit[x_] := M[x];
  2. monad bind function (“>>=” in Haskell notation) is a rule like Bind[M[x_], f_] := f[x] with MatchQ[f[x],M[_]] giving True.

Note that:

  • the function Bind unwraps the content of M[_] and gives it to the function f;
  • the functions fi are responsible to return results wrapped with the monad symbol M.

Here is an illustration formula showing a monad pipeline:



From the definition and formula it should be clear that if for the result of Bind[_M,f[x]] the test MatchQ[f[x],_M] is True then the result is ready to be fed to the next binding operation in monad’s pipeline. Also, it is clear that it is easy to program the pipeline functionality with Fold:

Fold[Bind, M[x], {f1, f2, f3}]

(* Bind[Bind[Bind[M[x], f1], f2], f3] *)

The monad laws

The monad laws definitions are taken from [H1] and [H3].In the monad laws given below the symbol “⟹” is for monad’s binding operation and ↦ is for a function in anonymous form.

Here is a table with the laws:

Remark: The monad laws are satisfied for every symbol in Mathematica / WL with List being the unit operation and Apply being the binding operation.

Expected monadic programming features

Looking at formula (1) — and having certain programming experiences — we can expect the following features when using monadic programming.

  • Computations that can be expressed with monad pipelines are easy to construct and read.
  • By programming the binding function we can tuck-in a variety of monad behaviours — this is the so called “programmable semicolon” feature of monads.
  • Monad pipelines can be constructed with Fold, but with suitable definitions of infix operators like DoubleLongRightArrow (⟹) we can produce code that resembles the pipeline in formula (1).
  • A monad pipeline can have polymorphic behaviour by overloading the signatures of fi (and if we have to, Bind.)

These points are clarified below. For more complete discussions see [Wk1] or [H3].

The basic Maybe monad

It is fairly easy to program the basic monad Maybe discussed in [Wk1].

The goal of the Maybe monad is to provide easy exception handling in a sequence of chained computational steps. If one of the computation steps fails then the whole pipeline returns a designated failure symbol, say None otherwise the result after the last step is wrapped in another designated symbol, say Maybe.

Here is the special version of the generic pipeline formula (1) for the Maybe monad:



Here is the minimal code to get a functional Maybe monad (for a more detailed exposition of code and explanations see [AA7]):

MaybeUnitQ[x_] := MatchQ[x, None] || MatchQ[x, Maybe[___]];

MaybeUnit[None] := None;
MaybeUnit[x_] := Maybe[x];

MaybeBind[None, f_] := None;
MaybeBind[Maybe[x_], f_] := 
  Block[{res = f[x]}, If[FreeQ[res, None], res, None]];

MaybeEcho[x_] := Maybe@Echo[x];
MaybeEchoFunction[f___][x_] := Maybe@EchoFunction[f][x];

MaybeOption[f_][xs_] := 
  Block[{res = f[xs]}, If[FreeQ[res, None], res, Maybe@xs]];

In order to make the pipeline form of the code we write let us give definitions to a suitable infix operator (like “⟹”) to use MaybeBind:

DoubleLongRightArrow[x_?MaybeUnitQ, f_] := MaybeBind[x, f];
DoubleLongRightArrow[x_, y_, z__] := 
  DoubleLongRightArrow[DoubleLongRightArrow[x, y], z];

Here is an example of a Maybe monad pipeline using the definitions so far:

data = {0.61, 0.48, 0.92, 0.90, 0.32, 0.11};

MaybeUnit[data]⟹(* lift data into the monad *)
 (Maybe@ Join[#, RandomInteger[8, 3]] &)⟹(* add more values *)
 MaybeEcho⟹(* display current value *)
 (Maybe @ Map[If[# < 0.4, None, #] &, #] &)(* map values that are too small to None *)

(* {0.61,0.48,0.92,0.9,0.32,0.11,4,4,0}
 None *)

The result is None because:

  1. the data has a number that is too small, and
  2. the definition of MaybeBind stops the pipeline aggressively using a FreeQ[_,None] test.

Monad laws verification

Let us convince ourselves that the current definition of MaybeBind gives a monad.

The verification is straightforward to program and shows that the implemented Maybe monad adheres to the monad laws.



Extensions with polymorphic behavior

We can see from formulas (1) and (2) that the monad codes can be easily extended through overloading the pipeline functions.

For example the extension of the Maybe monad to handle of Dataset objects is fairly easy and straightforward.

Here is the formula of the Maybe monad pipeline extended with Dataset objects:

Here is an example of a polymorphic function definition for the Maybe monad:

MaybeFilter[filterFunc_][xs_] := Maybe@Select[xs, filterFunc[#] &];

MaybeFilter[critFunc_][xs_Dataset] := Maybe@xs[Select[critFunc]];

See [AA7] for more detailed examples of polymorphism in monadic programming with Mathematica / WL.

A complete discussion can be found in [H3]. (The main message of [H3] is the poly-functional and polymorphic properties of monad implementations.)

Polymorphic monads in R’s dplyr

The R package dplyr, [R1], has implementations centered around monadic polymorphic behavior. The command pipelines based on dplyrcan work on R data frames, SQL tables, and Spark data frames without changes.

Here is a diagram of a typical work-flow with dplyr:


The diagram shows how a pipeline made with dplyr can be re-run (or reused) for data stored in different data structures.

Monad code generation

We can see monad code definitions like the ones for Maybe as some sort of initial templates for monads that can be extended in specific ways depending on their applications. Mathematica / WL can easily provide code generation for such templates; (see [WL1]). As it was mentioned in the introduction, we do not deal with types for monads explicitly, we generate code for monads instead.

In this section are given examples with packages that generate monad codes. The case study sections have examples of packages that utilize generated monad codes.

Maybe monads code generation

The package [AA2] provides a Maybe code generator that takes as an argument a prefix for the generated functions. (Monad code generation is discussed further in the section “General work-flow of monad code generation utilization”.)

Here is an example:



data = {0.61, 0.48, 0.92, 0.90, 0.32, 0.11};

AnotherMaybeUnit[data]⟹(* lift data into the monad *)
 (AnotherMaybe@Join[#, RandomInteger[8, 3]] &)⟹(* add more values *)
 AnotherMaybeEcho⟹(* display current value *)
 (AnotherMaybe @ Map[If[# < 0.4, None, #] &, #] &)(* map values that are too small to None *)

(* {0.61,0.48,0.92,0.9,0.32,0.11,8,7,6}
   AnotherMaybeBind: Failure when applying: Function[AnotherMaybe[Map[Function[If[Less[Slot[1], 0.4], None, Slot[1]]], Slot[1]]]]
   None *)

We see that we get the same result as above (None) and a message prompting failure.

State monads code generation

The State monad is also basic and its programming in Mathematica / WL is not that difficult. (See [AA3].)

Here is the special version of the generic pipeline formula (1) for the State monad:



Note that since the State monad pipeline caries both a value and a state, it is a good idea to have functions that manipulate them separately. For example, we can have functions for context modification and context retrieval. (These are done in [AA3].)

This loads the package [AA3]:


This generates the State monad for the prefix “StMon”:


The following StMon pipeline code starts with a random matrix and then replaces numbers in the current pipeline value according to a threshold parameter kept in the context. Several times are invoked functions for context deposit and retrieval.

StMonUnit[RandomReal[{0, 1}, {3, 2}], <|"mark" -> "TooSmall", "threshold" -> 0.5|>]⟹
  (StMon[#1 /. (x_ /; x < #2["threshold"] :> #2["mark"]), #2] &)⟹

(* value: {{0.789884,0.831468},{0.421298,0.50537},{0.0375957,0.289442}}
   context: <|mark->TooSmall,threshold->0.5|>
   context: <|mark->TooSmall,threshold->0.5,data->{{0.789884,0.831468},{0.421298,0.50537},{0.0375957,0.289442}}|>
   value: {{0.789884,0.831468},{TooSmall,0.50537},{TooSmall,TooSmall}}
   value: {{0.789884,0.831468},{0.421298,0.50537},{0.0375957,0.289442}}
   value: TooSmall *)

Flow control in monads

We can implement dedicated functions for governing the pipeline flow in a monad.

Let us look at a breakdown of these kind of functions using the State monad StMon generated above.

Optional acceptance of a function result

A basic and simple pipeline control function is for optional acceptance of result — if failure is obtained applying f then we ignore its result (and keep the current pipeline value.)

Here is an example with StMonOption :

StMonUnit[RandomReal[{0, 1}, 5]]⟹
 StMonOption[If[# < 0.3, None] & /@ # &]⟹

(* value: {0.789884,0.831468,0.421298,0.50537,0.0375957}
   value: {0.789884,0.831468,0.421298,0.50537,0.0375957}
   StMon[{0.789884, 0.831468, 0.421298, 0.50537, 0.0375957}, <||>] *)

Without StMonOption we get failure:

StMonUnit[RandomReal[{0, 1}, 5]]⟹
 (If[# < 0.3, None] & /@ # &)⟹

(* value: {0.789884,0.831468,0.421298,0.50537,0.0375957}
   StMonBind: Failure when applying: Function[Map[Function[If[Less[Slot[1], 0.3], None]], Slot[1]]]
   None *)

Conditional execution of functions

It is natural to want to have the ability to chose a pipeline function application based on a condition.

This can be done with the functions StMonIfElse and StMonWhen.

StMonUnit[RandomReal[{0, 1}, 5]]⟹
  Or @@ (# < 0.4 & /@ #) &,
  (Echo["A too small value is present.", "warning:"]; 
    StMon[Style[#1, Red], #2]) &,
  StMon[Style[#1, Blue], #2] &]⟹

 (* value: {0.789884,0.831468,0.421298,0.50537,0.0375957}
    warning: A too small value is present.
    value: {0.789884,0.831468,0.421298,0.50537,0.0375957}
    StMon[{0.789884,0.831468,0.421298,0.50537,0.0375957},<||>] *)

Remark: Using flow control functions like StMonIfElse and StMonWhen with appropriate messages is a better way of handling computations that might fail. The silent failures handling of the basic Maybe monad is convenient only in a small number of use cases.

Iterative functions

The last group of pipeline flow control functions we consider comprises iterative functions that provide the functionalities of Nest, NestWhile, FoldList, etc.

In [AA3] these functionalities are provided through the function StMonIterate.

Here is a basic example using Nest that corresponds to Nest[#+1&,1,3]:

StMonUnit[1]⟹StMonIterate[Nest, (StMon[#1 + 1, #2]) &, 3]

(* StMon[4, <||>] *)

Consider this command that uses the full signature of NestWhileList:

NestWhileList[# + 1 &, 1, # < 10 &, 1, 4]

(* {1, 2, 3, 4, 5} *)

Here is the corresponding StMon iteration code:

StMonUnit[1]⟹StMonIterate[NestWhileList, (StMon[#1 + 1, #2]) &, (#[[1]] < 10) &, 1, 4]

(* StMon[{1, 2, 3, 4, 5}, <||>] *)

Here is another results accumulation example with FixedPointList :

 StMonIterate[FixedPointList, (StMon[(#1 + 2/#1)/2, #2]) &]

(* StMon[{1., 1.5, 1.41667, 1.41422, 1.41421, 1.41421, 1.41421}, <||>] *)

When the functions NestList, NestWhileList, FixedPointList are used with StMonIterate their results can be stored in the context. Here is an example:

 StMonIterate[FixedPointList, (StMon[(#1 + 2/#1)/2, #2]) &, "fpData"]

(* StMon[{1., 1.5, 1.41667, 1.41422, 1.41421, 1.41421, 1.41421}, <|"fpData" -> {StMon[1., <||>], 
    StMon[1.5, <||>], StMon[1.41667, <||>], StMon[1.41422, <||>], StMon[1.41421, <||>], 
    StMon[1.41421, <||>], StMon[1.41421, <||>]} |>] *)

More elaborate tests can be found in [AA8].

Partial pipelines

Because of the associativity law we can design pipeline flows based on functions made of “sub-pipelines.”

fEcho = Function[{x, ct}, StMonUnit[x, ct]⟹StMonEchoValue⟹StMonEchoContext];

fDIter = Function[{x, ct}, 
   StMonUnit[y^x, ct]⟹StMonIterate[FixedPointList, StMonUnit@D[#, y] &, 20]];


  value: 7
  context: <||>
  value: {y^7,7 y^6,42 y^5,210 y^4,840 y^3,2520 y^2,5040 y,5040,0,0}
  context: <||> *)

General work-flow of monad code generation utilization

With the abilities to generate and utilize monad codes it is natural to consider the following work flow. (Also shown in the diagram below.)

  1. Come up with an idea that can be expressed with monadic programming.
  2. Look for suitable monad implementation.
  3. If there is no such implementation, make one (or two, or five.)
  4. Having a suitable monad implementation, generate the monad code.
  5. Implement additional pipeline functions addressing envisioned use cases.
  6. Start making pipelines for the problem domain of interest.
  7. Are the pipelines are satisfactory? If not go to 5. (Or 2.)


Monad templates

The template nature of the general monads can be exemplified with the group of functions in the package StateMonadCodeGenerator.m, [4].

They are in five groups:

  1. base monad functions (unit testing, binding),
  2. display of the value and context,
  3. context manipulation (deposit, retrieval, modification),
  4. flow governing (optional new value, conditional function application, iteration),
  5. other convenience functions.

We can say that all monad implementations will have their own versions of these groups of functions. The more specialized monads will have functions specific to their intended use. Such special monads are discussed in the case study sections.

Software design with monadic programming

The application of monadic programming to a particular problem domain is very similar to designing a software framework or designing and implementing a Domain Specific Language (DSL).

The answers of the question “When to use monadic programming?” can form a large list. This section provides only a couple of general, personal viewpoints on monadic programming in software design and architecture. The principles of monadic programming can be used to build systems from scratch (like Haskell and Scala.) Here we discuss making specialized software with or within already existing systems.

Framework design

Software framework design is about architectural solutions that capture the commonality and variability in a problem domain in such a way that: 1) significant speed-up can be achieved when making new applications, and 2) a set of policies can be imposed on the new applications.

The rigidness of the framework provides and supports its flexibility — the framework has a backbone of rigid parts and a set of “hot spots” where new functionalities are plugged-in.

Usually Object-Oriented Programming (OOP) frameworks provide inversion of control — the general work-flow is already established, only parts of it are changed. (This is characterized with “leave the driving to us” and “don’t call us we will call you.”)

The point of utilizing monadic programming is to be able to easily create different new work-flows that share certain features. (The end user is the driver, on certain rail paths.)

In my opinion making a software framework of small to moderate size with monadic programming principles would produce a library of functions each with polymorphic behaviour that can be easily sequenced in monadic pipelines. This can be contrasted with OOP framework design in which we are more likely to end up with backbone structures that (i) are static and tree-like, and (ii) are extended or specialized by plugging-in relevant objects. (Those plugged-in objects themselves can be trees, but hopefully short ones.)

DSL development

Given a problem domain the general monad structure can be used to shape and guide the development of DSLs for that problem domain.

Generally, in order to make a DSL we have to choose the language syntax and grammar. Using monadic programming the syntax and grammar commands are clear. (The monad pipelines are the commands.) What is left is “just” the choice of particular functions and their implementations.

Another way to develop such a DSL is through a grammar of natural language commands. Generally speaking, just designing the grammar — without developing the corresponding interpreters — would be very helpful in figuring out the components at play. Monadic programming meshes very well with this approach and applying the two approaches together can be very fruitful.

Contextual monad classification (case study)

In this section we show an extension of the State monad into a monad aimed at machine learning classification work-flows.


We want to provide a DSL for doing machine learning classification tasks that allows us:

  1. to do basic summarization and visualization of the data,
  2. to control splitting of the data into training and testing sets;
  3. to apply the built-in classifiers;
  4. to apply classifier ensembles (see [AA9] and [AA10]);
  5. to evaluate classifier performances with standard measures and
  6. ROC plots.

Also, we want the DSL design to provide clear directions how to add (hook-up or plug-in) new functionalities.

The package [AA4] discussed below provides such a DSL through monadic programming.

Package and data loading

This loads the package [AA4]:


This gets some test data (the Titanic dataset):

dataName = "Titanic";
ds = Dataset[Flatten@*List @@@ ExampleData[{"MachineLearning", dataName}, "Data"]];
varNames = Flatten[List @@ ExampleData[{"MachineLearning", dataName}, "VariableDescriptions"]];
varNames = StringReplace[varNames, "passenger" ~~ (WhitespaceCharacter ..) -> ""];
If[dataName == "FisherIris", varNames = Most[varNames]];
ds = ds[All, AssociationThread[varNames -> #] &];

Monad design

The package [AA4] provides functions for the monad ClCon — the functions implemented in [AA4] have the prefix “ClCon”.

The classifier contexts are Association objects. The pipeline values can have the form:

ClCon[ val, context:(_String|_Association) ]

The ClCon specific monad functions deposit or retrieve values from the context with the keys: “trainData”, “testData”, “classifier”. The general idea is that if the current value of the pipeline cannot provide all arguments for a ClCon function, then the needed arguments are taken from the context. If that fails, then an message is issued. This is illustrated with the following pipeline with comments example.


The pipeline and results above demonstrate polymorphic behaviour over the classifier variable in the context: different functions are used if that variable is a ClassifierFunction object or an association of named ClassifierFunction objects.

Note the demonstrated granularity and sequentiality of the operations coming from using a monad structure. With those kind of operations it would be easy to make interpreters for natural language DSLs.

Another usage example

This monadic pipeline in this example goes through several stages: data summary, classifier training, evaluation, acceptance test, and if the results are rejected a new classifier is made with a different algorithm using the same data splitting. The context keeps track of the data and its splitting. That allows the conditional classifier switch to be concisely specified.

First let us define a function that takes a Classify method as an argument and makes a classifier and calculates performance measures.

ClSubPipe[method_String] :=
  Function[{x, ct},
   ClConUnit[x, ct]⟹
     ClassifierInformation[#["classifier"], Method] &]⟹
    ClConEchoFunctionContext["training time:", ClassifierInformation[#["classifier"], "TrainingTime"] &]⟹
    ClConClassifierMeasurements[{"Accuracy", "Precision", "Recall"}]⟹
     ClConToNormalClassifierData[#["testData"]], "ROCCurve"] &]

Using the sub-pipeline function ClSubPipe we make the outlined pipeline.

res =
   ClConEchoFunctionValue["summaries:", ColumnForm[Normal[RecordsSummary /@ #]] &]⟹
    MatrixForm[CrossTensorate[Count == varNames[[1]] + varNames[[-1]], #]] & /@ # &]⟹
   (If[#1["Accuracy"] > 0.8,
      Echo["Good accuracy!", "Success:"]; ClConFail,
      Echo["Make a new classifier", "Inaccurate:"]; 
      ClConUnit[#1, #2]] &)⟹


Tracing monad pipelines (case study)

The monadic implementations in the package MonadicTracing.m, [AA5] allow tracking of the pipeline execution of functions within other monads.

The primary reason for developing the package was the desire to have the ability to print a tabulated trace of code and comments using the usual monad pipeline notation. (I.e. without conversion to strings etc.)

It turned out that by programming MonadicTracing.m I came up with a monad transformer; see [Wk2], [H2].

Package loading

This loads the package [AA5]:


Usage example

This generates a Maybe monad to be used in the example (for the prefix “Perhaps”):


In following example we can see that pipeline functions of the Perhaps monad are interleaved with comment strings. Producing the grid of functions and comments happens “naturally” with the monad function TraceMonadEchoGrid.

data = RandomInteger[10, 15];

TraceMonadUnit[PerhapsUnit[data]]⟹"lift to monad"⟹
  PerhapsFilter[# > 3 &]⟹"filter current value"⟹
  PerhapsEcho⟹"display current value"⟹
  PerhapsWhen[#[[3]] > 3 &, 
   PerhapsEchoFunction[Style[#, Red] &]]⟹
  (Perhaps[#/4] &)⟹
  PerhapsEcho⟹"display current value again"⟹
  TraceMonadEchoGrid[Grid[#, Alignment -> Left] &];

Note that :

  1. the tracing is initiated by just using TraceMonadUnit;
  2. pipeline functions (actual code) and comments are interleaved;
  3. putting a comment string after a pipeline function is optional.

Another example is the ClCon pipeline in the sub-section “Monad design” in the previous section.


This document presents a style of using monadic programming in Wolfram Language (Mathematica). The style has some shortcomings, but it definitely provides convenient features for day-to-day programming and in coming up with architectural designs.

The style is based on WL’s basic language features. As a consequence it is fairly concise and produces light overhead.

Ideally, the packages for the code generation of the basic Maybe and State monads would serve as starting points for other more general or more specialized monadic programs.


Monadic programming

[Wk1] Wikipedia entry: Monad (functional programming), URL: .

[Wk2] Wikipedia entry: Monad transformer, URL: .

[Wk3] Wikipedia entry: Software Design Pattern, URL: .

[H1] article: Monad laws, URL:

[H2] Sheng Liang, Paul Hudak, Mark Jones, “Monad transformers and modular interpreters”, (1995), Proceedings of the 22nd ACM SIGPLAN-SIGACT symposium on Principles of programming languages. New York, NY: ACM. pp. 333[Dash]343. doi:10.1145/199448.199528.

[H3] Philip Wadler, “The essence of functional programming”, (1992), 19’th Annual Symposium on Principles of Programming Languages, Albuquerque, New Mexico, January 1992.


[R1] Hadley Wickham et al., dplyr: A Grammar of Data Manipulation, (2014), tidyverse at GitHub, URL: . (See also, .)

Mathematica / Wolfram Language

[WL1] Leonid Shifrin, “Metaprogramming in Wolfram Language”, (2012), Mathematica StackExchange. (Also posted at Wolfram Community in 2017.) URL of the Mathematica StackExchange answer: . URL of the Wolfram Community post: .


[AA1] Anton Antonov, “Implementation of Object-Oriented Programming Design Patterns in Mathematica”, (2016) MathematicaForPrediction at GitHub,

[AA2] Anton Antonov, Maybe monad code generator Mathematica package, (2017), MathematicaForPrediction at GitHub. URL: .

[AA3] Anton Antonov, State monad code generator Mathematica package, (2017), MathematicaForPrediction at GitHub. URL: .

[AA4] Anton Antonov, Monadic contextual classification Mathematica package, (2017), MathematicaForPrediction at GitHub. URL: .

[AA5] Anton Antonov, Monadic tracing Mathematica package, (2017), MathematicaForPrediction at GitHub. URL: .

[AA6] Anton Antonov, MathematicaForPrediction utilities, (2014), MathematicaForPrediction at GitHub. URL: .

[AA7] Anton Antonov, Simple monadic programming, (2017), MathematicaForPrediction at GitHub. (Preliminary version, 40% done.) URL: .

[AA8] Anton Antonov, Generated State Monad Mathematica unit tests, (2017), MathematicaForPrediction at GitHub. URL: .

[AA9] Anton Antonov, Classifier ensembles functions Mathematica package, (2016), MathematicaForPrediction at GitHub. URL: .

[AA10] Anton Antonov, “ROC for classifier ensembles, bootstrapping, damaging, and interpolation”, (2016), MathematicaForPrediction at WordPress. URL: .

Comparison of dimension reduction algorithms over mandala images generation


This document discusses concrete algorithms for two different approaches of generation of mandala images, [1]: direct construction with graphics primitives, and use of machine learning algorithms.

In the experiments described in this document better results were obtained with the direct algorithms. The direct algorithms were made for the Mathematica StackExchange question "Code that generates a mandala", [3].

The main goals of this document are:

  1. to show some pretty images exploiting symmetry and multiplicity (see this album),

  2. to provide an illustrative example of comparing dimension reduction methods,

  3. to give a set-up for further discussions and investigations on mandala creation with machine learning algorithms.

Two direct construction algorithms are given: one uses "seed" segment rotations, the other superimposing of layers of different types. The following plots show the order in which different mandala parts are created with each of the algorithms.


In this document we use several algorithms for dimension reduction applied to collections of images following the procedure described in [4,5]. We are going to show that with Non-Negative Matrix Factorization (NNMF) we can use mandalas made with the seed segment rotation algorithm to extract layer types and superimpose them to make colored mandalas. Using the same approach with Singular Value Decomposition (SVD) or Independent Component Analysis (ICA) does not produce good layers and the superimposition produces more "watered-down", less diverse mandalas.

From a more general perspective this document compares the statistical approach of "trying to see without looking" with the "direct simulation" approach. Another perspective is the creation of "design spaces"; see [6].

The idea of using machine learning algorithms is appealing because there is no need to make the mental effort of understanding, discerning, approximating, and programming the principles of mandala creation. We can "just" use a large collection of mandala images and generate new ones using the "internal knowledge" data of machine learning algorithms. For example, a Neural network system like Deep Dream, [2], might be made to dream of mandalas.

Direct algorithms for mandala generation

In this section we present two different algorithms for generating mandalas. The first sees a mandala as being generated by rotation of a "seed" segment. The second sees a mandala as being generated by different component layers. For other approaches see [3].

The request of [3] is for generation of mandalas for coloring by hand. That is why the mandala generation algorithms are in the grayscale space. Coloring the generated mandala images is a secondary task.

By seed segment rotations

One way to come up with mandalas is to generate a segment and then by appropriate number of rotations to produce a mandala.

Here is a function and an example of random segment (seed) generation:

MakeSeedSegment[radius_, angle_, n_Integer: 10, 
   connectingFunc_: Polygon, keepGridPoints_: False] :=
   t = Table[
     Line[{radius*r*{Cos[angle], Sin[angle]}, {radius*r, 0}}], {r, 0, 1, 1/n}];
   Join[If[TrueQ[keepGridPoints], t, {}], {GrayLevel[0.25], 
     connectingFunc@RandomSample[Flatten[t /. Line[{x_, y_}] :> {x, y}, 1]]}]

seed = MakeSeedSegment[10, Pi/12, 10];
Graphics[seed, Frame -> True]

This function can make a seed segment symmetric:

MakeSymmetric[seed_] := {seed, 
   GeometricTransformation[seed, ReflectionTransform[{0, 1}]]};

seed = MakeSymmetric[seed];
Graphics[seed, Frame -> True]

Using a seed we can generate mandalas with different specification signatures:

MakeMandala[opts : OptionsPattern[]] :=      
    MakeSeedSegment[20, Pi/12, 12, 
     RandomChoice[{Line, Polygon, BezierCurve, 
       FilledCurve[BezierCurve[#]] &}], False]], Pi/6, opts];

MakeMandala[seed_, angle_?NumericQ, opts : OptionsPattern[]] :=      
    Table[RotationMatrix[a], {a, 0, 2 Pi - angle, angle}]], opts];

This code randomly selects symmetricity and seed generation parameters (number of concentric circles, angles):

n = 12;
     MakeMandala[MakeSeedSegment[10, #2, #3], #2],
      MakeSymmetric[MakeSeedSegment[10, #2, #3, #4, False]], 2 #2]
     ] &, {RandomChoice[{False, True}, n], 
   RandomChoice[{Pi/7, Pi/8, Pi/6}, n], 
   RandomInteger[{8, 14}, n], 
   RandomChoice[{Line, Polygon, BezierCurve, 
     FilledCurve[BezierCurve[#]] &}, n]}]

Here is a more concise way to generate symmetric segment mandalas:

Multicolumn[Table[Image@MakeMandala[], {12}], 5]

Note that with this approach the programming of the mandala coloring is not that trivial — weighted blending of colorized mandalas is the easiest thing to do. (Shown below.)

By layer types

This approach was given by Simon Woods in [3].

"For this one I’ve defined three types of layer, a flower, a simple circle and a ring of small circles. You could add more for greater variety."

The coloring approach with image blending given below did not work well for this algorithm, so I modified the original code in order to produce colored mandalas.

ClearAll[LayerFlower, LayerDisk, LayerSpots, MandalaByLayers]

LayerFlower[n_, a_, r_, colorSchemeInd_Integer] := 
  Module[{b = RandomChoice[{-1/(2 n), 0}]}, {If[
     colorSchemeInd == 0, White, 
     RandomChoice[ColorData[colorSchemeInd, "ColorList"]]], 
      r (a + Cos[n t])/(a + 1) {Cos[t + b Sin[2 n t]], Sin[t + b Sin[2 n t]]}, {t, 0, 2 Pi}], 
     l_Line :> FilledCurve[l], -1]}];

LayerDisk[_, _, r_, colorSchemeInd_Integer] := {If[colorSchemeInd == 0, White, 
    RandomChoice[ColorData[colorSchemeInd, "ColorList"]]], 
   Disk[{0, 0}, r]};

LayerSpots[n_, a_, r_, colorSchemeInd_Integer] := {If[colorSchemeInd == 0, White, 
    RandomChoice[ColorData[colorSchemeInd, "ColorList"]]], 
   Translate[Disk[{0, 0}, r a/(4 n)], r CirclePoints[n]]};

MandalaByLayers[n_, m_, coloring : (False | True) : False, opts : OptionsPattern[]] := 
  Graphics[{EdgeForm[Black], White, 
    Table[RandomChoice[{3, 2, 1} -> {LayerFlower, LayerDisk, LayerSpots}][n, RandomReal[{3, 5}], i, 
       If[coloring, RandomInteger[{1, 17}], 0]]~Rotate~(Pi i/n), {i, m, 1, -1}]}, opts];

Here are generated black-and-white mandalas.

ImageCollage[Table[Image@MandalaByLayers[16, 20], {12}], Background -> White, ImagePadding -> 3, ImageSize -> 1200]

Here are some colored mandalas. (Which make me think more of Viking and Native American art than mandalas.)

ImageCollage[Table[Image@MandalaByLayers[16, 20, True], {12}], Background -> White, ImagePadding -> 3, ImageSize -> 1200]

Training data

Images by direct generation

iSize = 400;

 mandalaImages = 
       MakeSeedSegment[10, Pi/12, 12, RandomChoice[{Polygon, FilledCurve[BezierCurve[#]] &}]], Pi/6], 
     ImageSize -> {iSize, iSize}, ColorSpace -> "Grayscale"], {300}];

(* {39.31, Null} *)

ImageCollage[ColorNegate /@ RandomSample[mandalaImages, 12], Background -> White, ImagePadding -> 3, ImageSize -> 400]

External image data

See the section "Using World Wide Web images".

Direct blending

The most interesting results are obtained with the image blending procedure coded below over mandala images generated with the seed segment rotation algorithm.

directBlendingImages = Table[
         ColorFunction -> 
          RandomChoice[{"IslandColors", "FruitPunchColors", 
            "AvocadoColors", "Rainbow"}]] & /@ 
       RandomChoice[mandalaImages, 4], RandomReal[1, 4]]], {36}];

ImageCollage[directBlendingImages, Background -> White, ImagePadding -> 3, ImageSize -> 1200]


Dimension reduction algorithms application

In this section we are going to apply the dimension reduction algorithms Singular Value Decomposition (SVD), Independent Component Analysis (ICA), and Non-Negative Matrix Factorization (NNMF) to a linear vector space representation (a matrix) of an image dataset. In the next section we use the bases generated by those algorithms to make mandala images.
We are going to use the packages [7,8] for ICA and NNMF respectively.


Linear vector space representation

The linear vector space representation of the images is simple — each image is flattened to a vector (row-wise), and the image vectors are put into a matrix.

mandalaMat = Flatten@*ImageData@*ColorNegate /@ mandalaImages;

(* {300, 160000} *)

Re-factoring and basis images

The following code re-factors the images matrix with SVD, ICA, and NNMF and extracts the basis images.

 svdRes = SingularValueDecomposition[mandalaMat, 20];
(* {5.1123, Null} *)

svdBasisImages = Map[ImageAdjust@Image@Partition[#, iSize] &, Transpose@svdRes[[3]]];

 icaRes = 
   IndependentComponentAnalysis[Transpose[mandalaMat], 20, 
    PrecisionGoal -> 4, "MaxSteps" -> 100];
(* {23.41, Null} *)

icaBasisImages = Map[ImageAdjust@Image@Partition[#, iSize] &, Transpose[icaRes[[1]]]];

 nnmfRes = 
   GDCLS[mandalaMat, 20, PrecisionGoal -> 4, 
    "MaxSteps" -> 20, "RegularizationParameter" -> 0.1];
(* {233.209, Null} *)

nnmfBasisImages = Map[ImageAdjust@Image@Partition[#, iSize] &, nnmfRes[[2]]];


Let us visualize the bases derived with the matrix factorization methods.

Grid[{{"SVD", "ICA", "NNMF"},
      Map[ImageCollage[#, Automatic, {400, 500}, 
        Background -> LightBlue, ImagePadding -> 5, ImageSize -> 350] &, 
      {svdBasisImages, icaBasisImages, nnmfBasisImages}]
     }, Dividers -> All]


Here are some observations for the bases.

  1. The SVD basis has an average mandala image as its first vector and the other vectors are "differences" to be added to that first vector.

  2. The SVD and ICA bases are structured similarly. That is because ICA and SVD are both based on orthogonality — ICA factorization uses an orthogonality criteria based on Gaussian noise properties (which is more relaxed than SVD’s standard orthogonality criteria.)

  3. As expected, the NNMF basis images have black background because of the enforced non-negativity. (Black corresponds to 0, white to 1.)

  4. Compared to the SVD and ICA bases the images of the NNMF basis are structured in a radial manner. This can be demonstrated using image binarization.

Grid[{{"SVD", "ICA", "NNMF"}, Map[ImageCollage[Binarize[#, 0.5] & /@ #, Automatic, {400, 500}, Background -> LightBlue, ImagePadding -> 5, ImageSize -> 350] &, {svdBasisImages, icaBasisImages, nnmfBasisImages}] }, Dividers -> All]

We can see that binarizing of the NNMF basis images shows them as mandala layers. In other words, using NNMF we can convert the mandalas of the seed segment rotation algorithm into mandalas generated by an algorithm that superimposes layers of different types.

Blending with image bases samples

In this section we just show different blending images using the SVD, ICA, and NNMF bases.

Blending function definition

Options[MandalaImageBlending] = {"BaseImage" -> {}, "BaseImageWeight" -> Automatic, "PostBlendingFunction" -> (RemoveBackground@*ImageAdjust)};
MandalaImageBlending[basisImages_, nSample_Integer: 4, n_Integer: 12, opts : OptionsPattern[]] :=      
  Block[{baseImage, baseImageWeight, postBlendingFunc, sImgs, sImgWeights},
   baseImage = OptionValue["BaseImage"];
   baseImageWeight = OptionValue["BaseImageWeight"];
   postBlendingFunc = OptionValue["PostBlendingFunction"];
     sImgs = 
      Flatten@Join[{baseImage}, RandomSample[basisImages, nSample]];
     If[NumericQ[baseImageWeight] && ImageQ[baseImage],
      sImgWeights = 
       Join[{baseImageWeight}, RandomReal[1, Length[sImgs] - 1]],
      sImgWeights = RandomReal[1, Length[sImgs]]
          DeleteCases[{opts}, ("BaseImage" -> _) | ("BaseImageWeight" -> _) | ("PostBlendingFunction" -> _)],               
          ColorFunction -> 
           RandomChoice[{"IslandColors", "FruitPunchColors", 
             "AvocadoColors", "Rainbow"}]] & /@ sImgs, 
       sImgWeights]), {n}]

SVD image basis blending

svdBlendedImages = MandalaImageBlending[Rest@svdBasisImages, 4, 24];
ImageCollage[svdBlendedImages, Background -> White, ImagePadding -> 3, ImageSize -> 1200]


svdBlendedImages = MandalaImageBlending[Rest@svdBasisImages, 4, 24, "BaseImage" -> First[svdBasisImages], "BaseImageWeight" -> 0.5];
ImageCollage[svdBlendedImages, Background -> White, ImagePadding -> 3, ImageSize -> 1200]


ICA image basis blending

icaBlendedImages = MandalaImageBlending[Rest[icaBasisImages], 4, 36, "BaseImage" -> First[icaBasisImages], "BaseImageWeight" -> Automatic];
ImageCollage[icaBlendedImages, Background -> White, ImagePadding -> 3, ImageSize -> 1200]


NNMF image basis blending

nnmfBlendedImages = MandalaImageBlending[nnmfBasisImages, 4, 36];
ImageCollage[nnmfBlendedImages, Background -> White, ImagePadding -> 3, ImageSize -> 1200]


Using World Wide Web images

A natural question to ask is:

What would be the outcomes of the above procedures to mandala images found in the World Wide Web (WWW) ?

Those WWW images are most likely man made or curated.

The short answer is that the results are not that good. Better results might be obtained using a larger set of WWW images (than just 100 in the experiment results shown below.)

Here is a sample from the WWW mandala images:


Here are the results obtained with NNMF basis:


Future plans

My other motivation for writing this document is to set up a basis for further investigations and discussions on the following topics.

  1. Having a large image database of "real world", human made mandalas.

  2. Utilization of Neural Network algorithms to mandala creation.

  3. Utilization of Cellular Automata to mandala generation.

  4. Investigate mandala morphing and animations.

  5. Making a domain specific language of specifications for mandala creation and modification.

The idea of using machine learning algorithms for mandala image generation was further supported by an image classifier that recognizes fairly well (suitably normalized) mandala images obtained in different ways:



[1] Wikipedia entry: Mandala, .

[2] Wikipedia entry: DeepDream, .

[3] "Code that generates a mandala", Mathematica StackExchange, .

[4] Anton Antonov, "Comparison of PCA and NNMF over image de-noising", (2016), MathematicaForPrediction at WordPress blog. URL: .

[5] Anton Antonov, "Handwritten digits recognition by matrix factorization", (2016), MathematicaForPrediction at WordPress blog. URL: .

[6] Chris Carlson, "Social Exploration of Design Spaces: A Proposal", (2016), Wolfram Technology Conference 2016. URL: http://wac , YouTube: .

[7] Anton Antonov, Independent Component Analysis Mathematica package, (2016), source code at MathematicaForPrediction at GitHub, package IndependentComponentAnalysis.m .

[8] Anton Antonov, Implementation of the Non-Negative Matrix Factorization algorithm in Mathematica, (2013), source code at MathematicaForPrediction at GitHub, package NonNegativeMatrixFactorization.m.

Tries with frequencies in Java


This blog post describes the installation and use in Mathematica of Tries with frequencies [1] implemented in Java [2] through a corresponding Mathematica package [3].

Prefix tree or Trie, [6], is a tree data structure that stores a set of "words" that consist of "characters" — each element can be seen as a key to itself. The article [1] and packages [2,3,4] extend that data structure to have additional data (frequencies) associated with each key.

The packages [2,3] work with lists of strings only. The package [4] can work with more general data but it is much slower.

The main motivation to create the package [3] was to bring the fast Trie functions implementations of [2] into Mathematica in order to prototype, implement, and experiment with different text processing algorithms. (Like, inductive grammar parsers generation and entity name recognition.) The speed of combining [2] and [3] is evaluated in the section "Performance tests" below.


This following directory path has to have the jar file "TriesWithFrequencies.jar".

$JavaTriesWithFrequenciesPath = 
 FileNameJoin[{$JavaTriesWithFrequenciesPath, "TriesWithFrequencies.jar"}]]

(* True *)

For more details see the explanations in the README file in the GitHub directory of [2].

The following directory is expected to have the Mathematica package [3].

dirName = "/Users/antonov/MathFiles/MathematicaForPrediction";
FileExistsQ[FileNameJoin[{dirName, "JavaTriesWithFrequencies.m"}]]

(* True *)

AppendTo[$Path, dirName];

This commands installs Java (via JLink`) and loads the necessary Java libraries.


Basic examples

For brevity the basic examples are not included in this blog post. Here is album of images that shows the "JavaTrie.*" commands with their effects:

"JavaTrieExample" .

More detailed explanations can be found in the Markdown document, [7]:

Next, we are going to look into performance evaluation examples (also given in [7].)

Membership of words

Assume we want find the words of "Hamlet" that are not in the book "Origin of Species". This section shows that the Java trie creation and query times for this task are quite small.

Read words

The following code reads the words in the texts. We get 33000 words from "Hamlet" and 151000 words from "Origin of Species".

hWords =
   words = 
     ExampleData[{"Text", "Hamlet"}], {Whitespace, 
   words = Select[ToLowerCase[words], StringLength[#] > 0 &]

(* 32832 *)

osWords =
   words = 
     ExampleData[{"Text", "OriginOfSpecies"}], {Whitespace, 
   words = Select[ToLowerCase[words], StringLength[#] > 0 &]

(* 151205 *)


First we create trie with "Origin of species" words:

 jOStr = JavaTrieCreateBySplit[osWords];

(* {0.682531, Null} *)

Sanity check — the "Origin of species" words are in the trie:

 And @@ JavaObjectToExpression[
   JavaTrieContains[jOStr, Characters /@ osWords]]

(* {1.32224, True} *)

Membership of "Hamlet" words into "Origin of Species":

 res = JavaObjectToExpression[
    JavaTrieContains[jOStr, Characters /@ hWords]];

(* {0.265307, Null} *)

Tallies of belonging:


(* {{True, 24924}, {False, 7908}} *)

Sample of words from "Hamlet" that do not belong to "Origin of Species":

RandomSample[Pick[hWords, Not /@ res], 30]

(* {"rosencrantz", "your", "mar", "airy", "rub", "honesty", \
"ambassadors", "oph", "returns", "pale", "virtue", "laertes", \
"villain", "ham", "earnest", "trail", "unhand", "quit", "your", \
"your", "fishmonger", "groaning", "your", "wake", "thou", "liest", \
"polonius", "upshot", "drowned", "grosser"} *)

Common words sample:

RandomSample[Pick[hWords, res], 30]

(* {"as", "indeed", "it", "with", "wild", "will", "to", "good", "so", \
"dirt", "the", "come", "not", "or", "but", "the", "why", "my", "to", \
"he", "and", "you", "it", "to", "potent", "said", "the", "are", \
"question", "soft"} *)


The node counts statistics calculation is fast:


(* {0.002344, <|"total" -> 20723, "internal" -> 15484, "leaves" -> 5239|>} *)

The node counts statistics computation after shrinking is comparably fast :


(* {0.00539, <|"total" -> 8918,  "internal" -> 3679, "leaves" -> 5239|>} *)

The conversion of a large trie to JSON and computing statistics over the obtained tree is reasonably fast:

 res = JavaTrieToJSON[jOStr];

(* {0.557221, Null} *)

  Cases[res, ("value" -> v_) :> v, \[Infinity]], 
  Range[0, 1, 0.1]]

(* {0.019644, {1., 1., 1., 1., 2., 3., 5., 9., 17., 42., 151205.}} *)

Dictionary infixes

Get all words from a dictionary:

allWords =  DictionaryLookup["*"];
allWords // Length

(* 92518 *)

Trie creation and shrinking:

 jDTrie = JavaTrieCreateBySplit[allWords];
 jDShTrie = JavaTrieShrink[jDTrie];

(* {0.30508, Null} *)

JSON form extraction:

 jsonRes = JavaTrieToJSON[jDShTrie];

(* {3.85955, Null} *)

Here are the node statistics of the original and shrunk tries:


Find the infixes that have more than three characters and appear more than 10 times:

Multicolumn[#, 4] &@
     jsonRes, ("key" -> v_) :> v, Infinity]], -#[[-1]] &], StringLength[#[[1]]] > 3 && #[[2]] > 10 &]

Unit tests

Many of example shown in this document have corresponding tests in the file JavaTriesWithFrequencies-Unit-Tests.wlt hosted at GitHub.

tr = TestReport[
  dirName <> "/UnitTests/JavaTriesWithFrequencies-Unit-Tests.wlt"]


[1] Anton Antonov, "Tries with frequencies for data mining", (2013), MathematicaForPrediction at WordPress blog. URL: .

[2] Anton Antonov, Tries with frequencies in Java, (2017), source code at MathematicaForPrediction at GitHub, project Java/TriesWithFrequencies.

[3] Anton Antonov, Java tries with frequencies Mathematica package, (2017), source code at MathematicaForPrediction at GitHub, package JavaTriesWithFrequencies.m .

[4] Anton Antonov, Tries with frequencies Mathematica package, (2013), source code at MathematicaForPrediction at GitHub, package TriesWithFrequencies.m .

[5] Anton Antonov, Java tries with frequencies Mathematica unit tests, (2017), source code at MathematicaForPrediction at GitHub, unit tests file JavaTriesWithFrequencies-Unit-Tests.wlt .

[6] Wikipedia, Trie, .

[7] Anton Antonov, "Tries with frequencies in Java", (2017), MathematicaForPrediction at GitHub.

Pareto principle adherence examples

This post (document) is made to provide examples of the Pareto principle manifestation in different datasets.

The Pareto principle is an interesting law that manifests in many contexts. It is also known as "Pareto law", "the law of significant few", "the 80-20 rule".

For example:

  • "80% of the land is owned by 20% of the population",

  • "10% of all lakes contain 90% of all lake water."

For extensive discussion and studied examples see the Wikipedia entry "Pareto principle", [4].

It is a good idea to see for which parts of the analyzed data the Pareto principle manifests. Testing for the Pareto principle is usually simple. For example, assume that we have the GDP of all countries:

countries = CountryData["Countries"];
gdps = {CountryData[#, "Name"], CountryData[#, "GDP"]} & /@ countries;
gdps = DeleteCases[gdps, {_, _Missing}] /. Quantity[x_, _] :> x;

Grid[{RecordsSummary[gdps, {"country", "GDP"}]}, Alignment -> Top, Dividers -> All]


In order to test for the manifestation of the Pareto principle we have to (i) sort the GDP values in descending order, (ii) find the cumulative sums, (iii) normalize the obtained vector by the sum of all values, and (iv) plot the result. These steps are done with the following two commands:

t = Reverse@Sort@gdps[[All, 2]];
ListPlot[Accumulate[t]/Total[t], PlotRange -> All, GridLines -> {{0.2} Length[t], {0.8}}, Frame -> True]


In this document we are going to use the special function ParetoLawPlot defined in the next section and the package [1]. Most of the examples use data that is internally accessible within Mathematica. Several external data examples are considered.

See the package [1] for the function RecordsSummary. See the source file [2] for R functions that facilitate the plotting of Pareto principle graphs. See the package [3] for the outlier detection functions used below.


This simple function makes a list plot that would help assessing the manifestation of the Pareto principle. It takes the same options as ListPlot.

Options[ParetoLawPlot] = Options[ListPlot];
ParetoLawPlot[dataVec : {_?NumberQ ..}, opts : OptionsPattern[]] := ParetoLawPlot[{Tooltip[dataVec, 1]}, opts];
ParetoLawPlot[dataVecs : {{_?NumberQ ..} ..}, opts : OptionsPattern[]] := ParetoLawPlot[MapThread[Tooltip, {dataVecs, Range[Length[dataVecs]]}], opts];
ParetoLawPlot[dataVecs : {Tooltip[{_?NumberQ ..}, _] ..}, opts : OptionsPattern[]] :=
  Block[{t, mc = 0.5},
   t = Map[Tooltip[(Accumulate[#]/Total[#] &)[SortBy[#[[1]], -# &]], #[[2]]] &, dataVecs];
   ListPlot[t, opts, PlotRange -> All, GridLines -> {Length[t[[1, 1]]] Range[0.1, mc, 0.1], {0.8}}, Frame -> True, FrameTicks -> {{Automatic, Automatic}, {Automatic, Table[{Length[t[[1, 1]]] c, ToString[Round[100 c]] <> "%"}, {c, Range[0.1, mc, 0.1]}]}}]

This function is useful for coloring the outliers in the list plots.

ColorPlotOutliers[] := # /. {Point[ps_] :> {Point[ps], Red, Point[ps[[OutlierPosition[ps[[All, 2]]]]]]}} &;
ColorPlotOutliers[oid_] := # /. {Point[ps_] :> {Point[ps], Red, Point[ps[[OutlierPosition[ps[[All, 2]], oid]]]]}} &;

These definitions can be also obtained by loading the packages MathematicaForPredictionUtilities.m and OutlierIdentifiers.m; see [1,3].



Below we are going to use the metric system of units. (If preferred we can easily switch to the imperial system.)

$UnitSystem = "Metric";(*"Imperial"*)


We are going to consider a typical Pareto principle example — weatlh of income distribution.


This code find the Gross Domestic Product (GDP) of different countries:

gdps = {CountryData[#, "Name"], CountryData[#, "GDP"]} & /@CountryData["Countries"];
gdps = DeleteCases[gdps, {_, _Missing}] /. Quantity[x_, _] :> x;

The corresponding Pareto plot (note the default grid lines) shows that 10% of countries have 90% of the wealth:

ParetoLawPlot[gdps[[All, 2]], ImageSize -> 400]


Here is the log histogram of the GDP values.

Histogram[Log10@gdps[[All, 2]], 20, PlotRange -> All]


The following code shows the log plot of countries GDP values and the found outliers.

 DynamicModule[{data = Transpose[{Range[Length[gdps]], Sort[gdps[[All, 2]]]}], pos},
  pos = OutlierPosition[modFunc@data[[All, 2]], tb@*opar];
  If[Length[pos] > 0,
   ListLogPlot[{data, data[[pos]]}, PlotRange -> All, PlotTheme -> "Detailed", FrameLabel -> {"Index", "GDP"}, PlotLegends -> SwatchLegend[{"All", "Outliers"}]],
   ListLogPlot[{data}, PlotRange -> All, PlotTheme -> "Detailed", FrameLabel -> {"Index", "GDP"}, PlotLegends -> SwatchLegend[{"All", "Outliers"}]]
 {{opar, SPLUSQuartileIdentifierParameters, "outliers detector"}, {HampelIdentifierParameters, SPLUSQuartileIdentifierParameters}},
 {{tb, TopOutliers, "bottom|top"}, {BottomOutliers, TopOutliers}},
 {{modFunc, Identity, "data modifier function"}, {Identity, Log}}


This table gives the values for countries with highest GDP.

Block[{data = gdps[[OutlierPosition[gdps[[All, 2]], TopOutliers@*SPLUSQuartileIdentifierParameters]]]},
 Row[Riffle[#, " "]] &@Map[Grid[#, Dividers -> All, Alignment -> {Left, "."}] &, Partition[SortBy[data, -#[[-1]] &], Floor[Length[data]/3]]]



Similar data retrieval and plots can be made for countries populations.

pops = {CountryData[#, "Name"], CountryData[#, "Population"]} & /@CountryData["Countries"];
unit = QuantityUnit[pops[[All, 2]]][[1]];
pops = DeleteCases[pops, {_, _Missing}] /. Quantity[x_, _] :> x;

In the following Pareto plot we can see that 15% of countries have 80% of the total population:

ParetoLawPlot[pops[[All, 2]], PlotLabel -> Row[{"Population", ", ", unit}]]


Here are the countries with most people:

Block[{data = pops[[OutlierPosition[pops[[All, 2]], TopOutliers@*SPLUSQuartileIdentifierParameters]]]},
 Row[Riffle[#, " "]] &@Map[Grid[#, Dividers -> All, Alignment -> {Left, "."}] &, Partition[SortBy[data, -#[[-1]] &], Floor[Length[data]/3]]]



We can also see that the Pareto principle holds for the countries areas:

areas = {CountryData[#, "Name"], CountryData[#, "Area"]} & /@CountryData["Countries"];
areas = DeleteCases[areas, {_, _Missing}] /. Quantity[x_, _] :> x;
ParetoLawPlot[areas[[All, 2]]]


Block[{data = areas[[OutlierPosition[areas[[All, 2]], TopOutliers@*SPLUSQuartileIdentifierParameters]]]},
 Row[Riffle[#, " "]] &@Map[Grid[#, Dividers -> All, Alignment -> {Left, "."}] &, Partition[SortBy[data, -#[[-1]] &], Floor[Length[data]/3]]]


Time series-wise

An interesting diagram is to plot together the curves of GDP changes for different countries. We can see China and Poland have had rapid growth.

res = Table[
    (t = CountryData[countryName, {{"GDP"}, {1970, 2015}}];
     t = Reverse@Sort[t["Path"][[All, 2]] /. Quantity[x_, _] :> x];
     Tooltip[t, countryName])
    , {countryName, {"USA", "China", "Poland", "Germany", "France", "Denmark"}}];

ParetoLawPlot[res, PlotRange -> All, Joined -> True, PlotLegends -> res[[All, 2]]]



This dynamic interface can be used for a given country to compare (i) the GDP evolution in time and (ii) the corresponding Pareto plot.

 DynamicModule[{ts, t},
  ts = CountryData[countryName, {{"GDP"}, {1970, 2015}}];
  t = Reverse@Sort[ts["Path"][[All, 2]] /. Quantity[x_, _] :> x];
  Grid[{{"Date list plot of GDP values", "GDP Pareto plot"}, {DateListPlot[ts, ImageSize -> Medium],
     ParetoLawPlot[t, ImageSize -> Medium]}}]
 ], {countryName, {"USA", "China", "Poland", "Germany", "France", "Denmark"}}]


Country flag colors

The following code demonstrates that the colors of the pixels in country flags also adhere to the Pareto principle.

flags = CountryData[#, "Flag"] & /@ CountryData["Countries"];

flags[[1 ;; 12]]


ids = ImageData /@ flags;

pixels = Apply[Join, Flatten[ids, 1]];

ToBinFunc[x_] := Evaluate[Piecewise[MapIndexed[{#2[[1]], #1[[1]] < x <= #1[[2]]} &, Partition[Range[0, 1, 0.1], 2, 1]]]];

pixelsInt = Transpose@Table[Map[ToBinFunc, pixels[[All, i]]], {i, 1, 3}];

pixelsIntTally = SortBy[Tally[pixelsInt], -#[[-1]] &];

ParetoLawPlot[pixelsIntTally[[All, 2]]]



Loking at lengths in the tunnel data we can see the manifestation of an exaggerated Pareto principle.

tunnelLengths = TunnelData[All, {"Name", "Length"}];
tunnelLengths // Length

(* 1552 *)

t = Reverse[Sort[DeleteMissing[tunnelLengths[[All, -1]]] /. Quantity[x_, _] :> x]];



Here is the logarithmic histogram of the lengths:

Histogram[Log10@t, PlotRange -> All, PlotTheme -> "Detailed"]



The following code gathers the data and make the Pareto plots surface areas, volumes, and fish catch values for lakes. We can that the lakes volumes show exaggerated Pareto principle.

lakeAreas = LakeData[All, "SurfaceArea"];
lakeVolumes = LakeData[All, "Volume"];
lakeFishCatch = LakeData[All, "CommercialFishCatch"];

data = {lakeAreas, lakeVolumes, lakeFishCatch};
t = N@Map[DeleteMissing, data] /. Quantity[x_, _] :> x;

opts = {PlotRange -> All, ImageSize -> Medium}; MapThread[ParetoLawPlot[#1, PlotLabel -> Row[{#2, ", ", #3}], opts] &, {t, {"Lake area", "Lake volume", "Commercial fish catch"}, DeleteMissing[#][[1, 2]] & /@ data}]


City data

One of the examples given in [5] is that the city areas obey the Power Law. Since the Pareto principle is a kind of Power Law we can confirm that observation using Pareto principle plots.

The following grid of Pareto principle plots is for areas and population sizes of cities in selected states of USA.

res = Table[
    (cities = CityData[{All, stateName, "USA"}];
     t = Transpose@Outer[CityData, cities, {"Area", "Population"}];
     t = Map[DeleteMissing[#] /. Quantity[x_, _] :> x &, t, {1}];
     ParetoLawPlot[MapThread[Tooltip, {t, {"Area", "Population"}}], PlotLabel -> stateName, ImageSize -> 250])
    , {stateName, {"Alabama", "California", "Florida", "Georgia", "Illinois", "Iowa", "Kentucky", "Ohio", "Tennessee"}}];

Legended[Grid[ArrayReshape[res, {3, 3}]], SwatchLegend[Cases[res[[1]], _RGBColor, Infinity], {"Area", "Population"}]]


Movie ratings in MovieLens datasets

Looking into the MovieLens 20M dataset, [6], we can see that the Pareto princple holds for (1) most rated movies and (2) most active users. We can also see the manifestation of an exaggerated Pareto law — 90% of all ratings are for 10% of the movies.



The following plot taken from the blog post "PIN analysis", [7], shows that the four digit passwords people use adhere to the Pareto principle: the first 20% of (the unique) most frequently used passwords correspond to the 70% of all passwords use.




[1] Anton Antonov, "MathematicaForPrediction utilities", (2014), source code MathematicaForPrediction at GitHub,, package MathematicaForPredictionUtilities.m.

[2] Anton Antonov, Pareto principle functions in R, source code MathematicaForPrediction at GitHub,, source code file ParetoLawFunctions.R .

[3] Anton Antonov, Implementation of one dimensional outlier identifying algorithms in Mathematica, (2013), MathematicaForPrediction at GitHub, URL: .

[4] Wikipedia entry, "Pareto principle", URL: .

[5] Wikipedia entry, "Power law", URL: .

[6] GroupLens Research, MovieLens 20M Dataset, (2015).

[7] "PIN analysis", (2012), DataGenetics.

Basic example of using ROC with Linear regression


This post is for using the package [2] that provides Mathematica implementations of Receiver Operating Characteristic (ROC) functions calculation and plotting. The ROC framework is used for analysis and tuning of binary classifiers, [3]. (The classifiers are assumed to classify into a positive/true label or a negative/false label. )

The function ROCFuntions gives access to the individual ROC functions through string arguments. Those ROC functions are applied to special objects, called ROC Association objects.

Each ROC Association object is an Association that has the following four keys: "TruePositive", "FalsePositive", "TrueNegative", and "FalseNegative" .

Given two lists of actual and predicted labels a ROC Association object can be made with the function ToROCAssociation .

For more definitions and example of ROC terminology and functions see [3].

Why Linear regression

I was asked in this discussion why Linear regression and not, say, Logistic regression.

Here is my answer:

1. I am trying to do a minimal and quick to execute example — the code of the post is included in the package ROCFunctions.m.

2. I am aware that there are better alternatives of LinearModelFit, but I plan to discuss those in the MathematicaVsR project: “Regression with ROC”. (As the name hints, it is not just about Linear regression.)

3. Another point is that although the Linear regression is not a good method for this classification, nevertheless using ROC it can be made to give better results than, say, the built-in “NeuralNetwork” method. See the last section of “Linear regression with”.

Minimal example

Note that here although we use both of the provided Titanic training and test data, the code is doing only training. The test data is used to find the best tuning parameter (threshold) through ROC analysis.

Get packages

These commands load the packages [1,2]:


Using Titanic data

Here is the summary of the Titanic data used below:

titanicData = (Flatten@*List) @@@ExampleData[{"MachineLearning", "Titanic"}, "Data"];
columnNames = (Flatten@*List) @@ExampleData[{"MachineLearning", "Titanic"}, "VariableDescriptions"];
RecordsSummary[titanicData, columnNames]


This variable dependence grid shows the relationships between the variables.

Magnify[#, 0.7] &@VariableDependenceGrid[titanicData, columnNames]


Get training and testing data

data = ExampleData[{"MachineLearning", "Titanic"}, "TrainingData"];
data = ((Flatten@*List) @@@ data)[[All, {1, 2, 3, -1}]];
trainingData = DeleteCases[data, {___, _Missing, ___}];

(* {732, 4} *)

data = ExampleData[{"MachineLearning", "Titanic"}, "TestData"];
data = ((Flatten@*List) @@@ data)[[All, {1, 2, 3, -1}]];
testData = DeleteCases[data, {___, _Missing, ___}];

(* {314, 4} *)

Replace categorical with numerical values

trainingData = trainingData /. {"survived" -> 1, "died" -> 0, "1st" -> 0, "2nd" -> 1, "3rd" -> 2, "male" -> 0, "female" -> 1};

testData = testData /. {"survived" -> 1, "died" -> 0, "1st" -> 1, "2nd" -> 2, "3rd" -> 3, "male" -> 0, "female" -> 1};

Do linear regression

lfm = LinearModelFit[{trainingData[[All, 1 ;; -2]], trainingData[[All, -1]]}]


Get the predicted values

modelValues = lfm @@@ testData[[All, 1 ;; -2]];

Histogram[modelValues, 20]




Obtain ROC associations over a set of parameter values

testLabels = testData[[All, -1]];

thRange = Range[0.1, 0.9, 0.025];
aROCs = Table[ToROCAssociation[{0, 1}, testLabels, Map[If[# > \[Theta], 1, 0] &, modelValues]], {\[Theta], thRange}];

Evaluate ROC functions for given ROC association

Through[ROCFunctions[{"PPV", "NPV", "TPR", "ACC", "SPC"}][aROCs[[3]]]]

(* {34/43, 19/37, 17/32, 197/314, 95/122} *)

Standard ROC plot

ROCPlot[thRange, aROCs, "PlotJoined" -> Automatic, "ROCPointCallouts" -> True, "ROCPointTooltips" -> True, GridLines -> Automatic]


Plot ROC functions wrt to parameter values

ListLinePlot[Map[Transpose[{thRange, #}] &, Transpose[Map[Through[ROCFunctions[{"PPV", "NPV", "TPR", "ACC", "SPC"}][#]] &, aROCs]]],
 Frame -> True, FrameLabel -> Map[Style[#, Larger] &, {"threshold, \[Theta]", "rate"}], PlotLegends -> Map[# <> ", " <> (ROCFunctions["FunctionInterpretations"][#]) &, {"PPV", "NPV", "TPR", "ACC", "SPC"}], GridLines -> Automatic]


Finding the intersection point of PPV and TPR

We want to find a point that provides balanced positive and negative labels success rates. One way to do this is to find the intersection point of the ROC functions PPV (positive predictive value) and TPR (true positive rate).

Examining the plot above we can come up with the initial condition for \(x\).

ppvFunc = Interpolation[Transpose@{thRange, ROCFunctions["PPV"] /@ aROCs}];
tprFunc = Interpolation[Transpose@{thRange, ROCFunctions["TPR"] /@ aROCs}];
FindRoot[ppvFunc[x] - tprFunc[x] == 0, {x, 0.2}]

(* {x -> 0.3} *)

Area under the ROC curve

The Area Under the ROC curve (AUROC) tells for a given range of the controlling parameter "what is the probability of the classifier to rank a randomly chosen positive instance higher than a randomly chosen negative instance, (assuming ‘positive’ ranks higher than ‘negative’)", [3,4]

Calculating AUROC is easy using the Trapezoidal quadrature formula:

 N@Total[Partition[Sort@Transpose[{ROCFunctions["FPR"] /@ aROCs, ROCFunctions["TPR"] /@ aROCs}], 2, 1] 
   /. {{x1_, y1_}, {x2_, y2_}} :> (x2 - x1) (y1 + (y2 - y1)/2)]

 (* 0.698685 *)

It is also implemented in [2]:


(* 0.698685 *)


[1] Anton Antonov, MathematicaForPrediction utilities, (2014), source code MathematicaForPrediction at GitHub, package MathematicaForPredictionUtilities.m.

[2] Anton Antonov, Receiver operating characteristic functions Mathematica package, (2016), source code MathematicaForPrediction at GitHub, package ROCFunctions.m .

[3] Wikipedia entry, Receiver operating characteristic. URL: .

[4] Tom Fawcett, An introduction to ROC analysis, (2006), Pattern Recognition Letters, 27, 861-874.

Contingency tables creation examples


In statistics contingency tables are matrices used to show the co-occurrence of variable values of multi-dimensional data. They are fundamental in many types of research. This document shows how to use several functions implemented in Mathematica for the construction of contingency tables.


In this document we are going to use the implementations in the package MathematicaForPredictionUtilities.m from MathematicaForPrediction at GitHub, [1].


The implementation of CrossTabulate in [1] is based on Tally, GatherBy, and SparseArray. The implementation of xtabsViaRLink in [1] is based on R‘s function xtabs called via RLink.

Other package used in this document are [2] and [4] imported with these commands:


For a different approach to implementing cross-tabulation than those taken in [1] see the Stack Overflow answer by Mr.Wizard.

Using Titanic data

Getting data

titanicData = 
  Flatten@*List @@@ ExampleData[{"MachineLearning", "Titanic"}, "Data"];
titanicData = DeleteCases[titanicData, {___, _Missing, ___}];

titanicColumnNames = 
  Flatten@*List @@ ExampleData[{"MachineLearning", "Titanic"}, "VariableDescriptions"];
aTitanicColumnNames = 
  AssociationThread[titanicColumnNames -> Range[Length[titanicColumnNames]]];

Note that we have removed the records with missing data (for simpler exposition).

Data summary

(* {1046, 4} *)

RecordsSummary[titanicData, titanicColumnNames]


Using CrossTabulate

Assume that we want to group the people according to their passenger class and survival and we want to find the average age for each group.

We can do that by

1. finding the counts contingency table C for the variables "passenger class" and "passenger survival",

2. finding the age contingency table A for the same variables, and

3. do the element-wise division \frac{A}{C}.

ctCounts = 
   titanicData[[All, aTitanicColumnNames /@ {"passenger class", "passenger survival"}]]];
MatrixForm[#1, TableHeadings -> {#2, #3}] & @@ ctCounts


ctTotalAge = 
    aTitanicColumnNames /@ {"passenger class", "passenger survival", 
      "passenger age"}]]];
MatrixForm[#1, TableHeadings -> {#2, #3}] & @@ ctTotalAge


 TableHeadings -> Values[Rest[ctTotalAge]]]


(We have to make the sparse array ctCounts a regular array because otherwise we get warnings for division by zero because of the sparse array’s default value.)

Let us repeat the steps above by dividing the passengers before-hand according to their sex.

  (mCount = 
     CrossTabulate[#[[All, aTitanicColumnNames /@ {"passenger class", "passenger survival"}]]]; 
   mAge = CrossTabulate[#[[All, aTitanicColumnNames /@ {"passenger class", "passenger survival", "passenger age"}]]];
   #[[1,  aTitanicColumnNames["passenger sex"]]] -> 
     MatrixForm[mAge[[1]]/Normal[mCount[[1]]], TableHeadings -> Values[Rest[mAge]]]) &, 
  GatherBy[titanicData, #[[aTitanicColumnNames["passenger sex"]]] &]]


The alternative of CrossTabulate is xtabsViaRLink that is uses R’s function xtabs via RLink.


(* {Paclet[RLinkRuntime,, <>]} *)

ctCounts = 
    titanicData[[All, aTitanicColumnNames /@ {"passenger class", "passenger survival"}]],
    {"", "passenger.survival"},
    " ~ + passenger.survival"];
MatrixForm[#1, TableHeadings -> {#2, #3}] & @@ ctCounts


Relation to mosaic plots

The graphical visualization of a dataset with mosaic plots, [2,3], is similar in spirit to contingency tables. Compare the following mosaic plot with the contingency table in the last section.

 titanicData[[All, aTitanicColumnNames /@ {"passenger class", "passenger survival"}]] ]


Straightforward calling of MatrixForm

At this point we might want to be able to call MatrixForm more directly for the output of CrossTabulate and FromRXTabsForm. One way to do this is to define an up-value for Association .

MatrixForm[x_Association /; (KeyExistsQ[x, "XTABMatrix"] || KeyExistsQ[x, "XTABTensor"])] ^:= (MatrixForm[#1, TableHeadings -> Rest[{##}]] & @@ x);

Now we can do this:

MatrixForm @
 CrossTabulate[titanicData[[All, aTitanicColumnNames /@ {"passenger class", "passenger survival"}]]]


Remark: Because of this up-value definition for Association with MatrixForm we have the associations returned by CrossTabulate and FromRXTabsForm to have the key "XTABMatrix" instead of "Matrix", the former assumed to be much more rarely to be used than the latter.

Using larger data

Let us consider an example with larger data that has larger number of unique values in its columns.

Getting online retail invoices data

The following dataset is taken from [6].

data = Import[ "/Volumes/WhiteSlimSeagate/Datasets/UCI Online Retail Data Set/Online Retail.csv"];
columnNames = First[data];
data = Rest[data];

aColumnNames = AssociationThread[columnNames -> Range[Length[columnNames]]];

Data summary

We have \approx 66000 rows and 8 columns:

(* {65499, 8} *)

Here is a summary of the columns:

Magnify[#, 0.75] &@RecordsSummary[data, columnNames]


Contingency tables

Country vs. StockCode

There is no one-to-one correspondence between the values of the column "Description" and the column "StockCode" which can be seen with this command:

  GatherBy[data[[All, aColumnNames /@ {"Description", "StockCode"}]], First]]
(* {1,144} *)

The way in which the column "StockCode" was ingested made it have multiple types for its values:

Tally[NumberQ /@ data[[All, aColumnNames["StockCode"]]]]
(* {{False,9009},{True,56490}} *)

So let us convert it to all strings:

data[[All, aColumnNames["StockCode"]]] = 
  ToString /@ data[[All, aColumnNames["StockCode"]]];

Here we find the contingency table for "Country" and "StockCode" over "Quantity" using CrossTabulate:

 ctRes = CrossTabulate[
    data[[All, aColumnNames /@ {"Country", "StockCode", "Quantity"}]]];
(* {0.256339,Null} *)

Here we find the contingency table for "Country" and "StockCode" over "Quantity" using xtabsViaRLink:

 rres = xtabsViaRLink[
   data[[All, aColumnNames /@ {"Country", "StockCode", "Quantity"}]],
   {"Country", "StockCode", "Quantity"},
   "Quantity ~ Country + StockCode"]; 
 ctRRes = FromRXTabsForm[rres];
(* {0.843621,Null} *)

Both functions produce the same result:

ctRRes["matrix"] == N@ctRRes[[1]]
(* True *)

Note that xtabsViaRLink is slower but still fairly quick.

Here we plot the contingency table using MatrixPlot :

MatrixPlot[ctRRes["matrix"], AspectRatio -> 1/1.5, 
  FrameTicks -> {{#, #} &@ Table[{i, ctRRes["rownames"][[i]]}, {i, Length[ctRRes["rownames"]]}], 
  {Automatic, Automatic}}, ImageSize -> 550]


Country vs. Quarter

Let us extend the data with columns that have months and quarters corresponding to the invoice dates.

The following commands computing date objects and extracting month and quarter values from them are too slow.

(*AbsoluteTiming[dobjs=DateObject[{#,{"Month","/","Day","/","Year"," \
(* {30.2595,Null} *)

(* {91.1732,Null} *)

We can use the following ad hoc computation instead.

dvals = StringSplit[#, {"/", " ", ":"}] & /@ 

This summary shows that the second value in the dates is day of month, and the first value is most likely month.

Magnify[#, 0.75] &@ RecordsSummary[dvals[[All, 1 ;; 3]], "MaxTallies" -> 16]


These commands extend the data and the corresponding column-name-to-index association.

ms = DateValue[Table[DateObject[{2016, i, 1}], {i, 12}], "MonthName"];
dvals = Map[{ms[[#]], "Q" <> ToString[Quotient[#, 4] + 1]} &, ToExpression @ dvals[[All, 1]]];
dataM = MapThread[Join[#1, #2] &, {data, dvals}];
aColumnNamesM = 
  Join[aColumnNames, <|"MonthName" -> (Length[aColumnNames] + 1), "QuarterNameShort" -> (Length[aColumnNames] + 2)|>];
(* {0.054877,Null} *)

Here is the contingency table for "Country" vs "QuarterNameShort" over "Quantity".

ctRes = CrossTabulate[ dataM[[All, aColumnNamesM /@ {"Country", "QuarterNameShort", "Quantity"}]]];
Magnify[#, 0.75] &@ MatrixForm[#1, TableHeadings -> {#2, #3}] & @@ ctRes


Uniform tables

Often when making contingency tables over subsets of the data we obtain contingency tables with different rows and columns. For various reasons (programming, esthetics, comprehension) it is better to have the tables with the same rows and columns.

Here is an example of non-uniform contingency tables derived from the online retail data of the previous section. We split the data over the countries and find contingency tables of "MonthName" vs "QuarterNameShort" over "Quantity".

tbs = Association @
    (xtab = CrossTabulate[#[[All, aColumnNamesM /@ {"MonthName", "QuarterNameShort", "Quantity"}]]];
     #[[1, aColumnNamesM["Country"]]] -> xtab) &,
    GatherBy[ dataM, #[[aColumnNamesM[ "Country"]]] &]];

Magnify[#, 0.75] &@
 Map[MatrixForm[#["Matrix"], TableHeadings -> (# /@ {"RowNames", "ColumnNames"})] &, tbs](*[[{1,12,-1}]]*)


Using the object RSparseMatrix, see [4,5], we can impose row and column names on each table.

First we convert the contingency tables into RSparseMatrix objects:

tbs2 = Map[ ToRSparseMatrix[#["Matrix"], "RowNames" -> #["RowNames"], "ColumnNames" -> #["ColumnNames"]] &, tbs];

And then we impose the desired row and column names:

tbs2 = Map[ ImposeColumnNames[ ImposeRowNames[#, {"January", "December"}], {"Q1", "Q2", "Q3", "Q4"}] &, tbs2];
Magnify[#, 0.75] &@(MatrixForm /@ tbs2)


Generalization : CrossTensorate

A generalization of CrossTabulate is the function CrossTensorate implemented in [1] that takes a "formula" argument similar to R’s xtabs.

This finds number of people of different sub-groups of Titanic data:

ctRes = CrossTensorate[Count == "passenger survival" + "passenger sex" + "passenger class", titanicData, aTitanicColumnNames];


We can verify the result using Count:

Count[titanicData, {"1st", _, "female", "died"}]
(* 5 *)

Count[titanicData, {"2nd", _, "male", "survived"}]
(* 23 *)

To split the cross-tensor across its first variable we can use this command:

sctRes = Association@
  MapThread[Rule[#1, Join[<|"XTABTensor" -> #2|>, Rest@Rest@ctRes]] &, {ctRes[[2]], # & /@ ctRes["XTABTensor"]}];
MatrixForm /@ sctRes


Or we can call the more general function CrossTensorateSplit implemented in [1]:

Map[MatrixForm /@ CrossTensorateSplit[ctRes, #] &, Rest@Keys[ctRes]]


CrossTensorateSplit can also be called with one argument that is a variable name.This will produce a splitting function. For example, the above command can be re-written as :

Map[MatrixForm /@ CrossTensorateSplit[#] @ ctRes &, Rest@Keys[ctRes]]


[1] Anton Antonov, MathematicaForPrediction utilities, (2014), source code MathematicaForPrediction at GitHub, package MathematicaForPredictionUtilities.m.

[2] Anton Antonov, Mosaic plot for data visualization implementation in Mathematica, (2014), MathematicaForPrediction at GitHub, package MosaicPlot.m.

[3] Anton Antonov, "Mosaic plots for data visualization", (2014), MathematicaForPrediction at WordPress blog. URL: .

[4] Anton Antonov, RSparseMatrix Mathematica package, (2015) MathematicaForPrediction at GitHub. URL: .

[5] Anton Antonov, "RSparseMatrix for sparse matrices with named rows and columns", (2015), MathematicaForPrediction at WordPress blog. URL: .

[6] Daqing Chen, Online Retail Data Set, (2015), UCI Machine Learning Repository. URL: .