Merge branch 'dev' into simplicial-complexes

.gitignore

@@ -27,4 +27,4 @@
 /doc/tutorials/icfca-2013/icfca2013-tutorial-live.html
 /.lsp/
 /.direnv/
-/.clj-kondo/
+/.clj-kondo/

AUTHORS.md

@@ -16,6 +16,8 @@ Additional Contributors are
 * Johannes Hirth        (pq-cores, scale-measures)
 * Gleb Kanterov         (interval-scale)
 * Maximilian Marx       (Wikidata)
+* Jannik Nordmeyer	(Metric Contexts, Causal Implications)
 * Maximilian Stubbemann (concept-robustness)
 * Anselm von Wangenheim (DimDraw)
 * Johannes Wollbold     (bug reports, feature requests)
+

README.md

@@ -32,6 +32,7 @@ much more.
    8. [Computing Traces in Contexts](doc/code/trace-context.clj)
    9. [Counting Quasiorders](doc/code/quasiorders.clj)
    10. [Rudolph's Algorithm for Computing Bases](doc/code/rudolph_computation.clj)
+   11. [Discovering Causal Implications](doc/Causal-Implications.org)
 5. Advanced Topics
    1. [pq-cores](doc/pq-cores-in-Formal-Contexts.md)
    2. [REST-API Usage](doc/REST-API-usage.md)

doc/Causal-Implications.org

@@ -0,0 +1,141 @@
+#+property: header-args :wrap src text
+#+property: header-args:text :eval never
+
+* Computing Causal Rules in ~conexp-clj~
+
+~conexp-clj~ provides methods to discover causal rules within a context as described in "Mining Causal Association Rules" (https://www.researchgate.net/publication/262240022_Mining_Causal_Association_Rules).
+We will consider the following data set:
+
+#+begin_src clojure
+(def smoking-ctx (make-context [0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
+                                21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40]
+                               ["smoking" "male" "female" "education-level-high" "education-level-low" "cancer"]
+                               #{[0 "smoking"] [0 "male"] [0 "education-level-high"] [0 "cancer"]
+                                 [1 "smoking"] [1 "male"] [1 "education-level-high"] [1 "cancer"]
+                                 [2 "smoking"] [2 "male"] [2 "education-level-high"] [2 "cancer"]
+                                 [3 "smoking"] [3 "male"] [3 "education-level-high"] [3 "cancer"]
+                                 [4 "smoking"] [4 "male"] [4 "education-level-high"] [4 "cancer"]
+                                 [5 "smoking"] [5 "male"] [5 "education-level-high"] [5 "cancer"]
+                                 [6 "smoking"] [6 "male"] [6 "education-level-high"]
+                                 [7 "smoking"] [7 "male"] [7 "education-level-high"]
+                                 [8 "smoking"] [8 "male"] [8 "education-level-low"] [8 "cancer"]
+                                 [9 "smoking"] [9 "male"] [9 "education-level-low"] [9 "cancer"]
+                                 [10 "smoking"] [10 "male"] [10 "education-level-low"] [10 "cancer"]
+                                 [11 "smoking"] [11 "male"] [11 "education-level-low"] [11 "cancer"]
+                                 [12 "smoking"] [12 "male"] [12 "education-level-low"] 
+                                 [13 "smoking"] [13 "female"] [13 "education-level-high"] [13 "cancer"]
+                                 [14 "smoking"] [14 "female"] [14 "education-level-high"] [14 "cancer"]
+                                 [15 "smoking"] [15 "female"] [15 "education-level-high"] [15 "cancer"]
+                                 [16 "smoking"] [16 "female"] [16 "education-level-high"] [16 "cancer"]
+                                 [17 "smoking"] [17 "female"] [17 "education-level-high"] [17 "cancer"]
+                                 [18 "smoking"] [18 "female"] [18 "education-level-high"] 
+                                 [19 "smoking"] [19 "female"] [19 "education-level-high"]
+                                 [20 "smoking"] [20 "female"] [20 "education-level-low"] [20 "cancer"]
+                                 [21 "smoking"] [21 "female"] [21 "education-level-low"] [21 "cancer"]
+                                 [22 "smoking"] [22 "female"] [22 "education-level-low"] [22 "cancer"]
+                                 [23 "smoking"] [23 "female"] [23 "education-level-low"] [23 "cancer"]
+                                 [24 "smoking"] [24 "female"] [24 "education-level-low"] 
+                                 [25 "male"] [25 "education-level-high"] [25 "cancer"]
+                                 [26 "male"] [26 "education-level-high"] [26 "cancer"]
+                                 [27 "male"] [27 "education-level-high"] 
+                                 [28 "male"] [28 "education-level-high"]
+                                 [29 "male"] [29 "education-level-high"]
+                                 [30 "male"] [30 "education-level-low"] [30 "cancer"]
+                                 [31 "male"] [31 "education-level-low"] 
+                                 [32 "male"] [32 "education-level-low"] 
+                                 [33 "male"] [33 "education-level-low"]
+                                 [34 "female"] [34 "education-level-high"] [34 "cancer"]
+                                 [35 "female"] [35 "education-level-high"] 
+                                 [36 "female"] [36 "education-level-high"]
+                                 [37 "female"] [37 "education-level-low"] [37 "cancer"]
+                                 [38 "female"] [38 "education-level-low"]
+                                 [39 "female"] [39 "education-level-low"]
+                                 [40 "female"] [40 "education-level-low"]})
+)
+#+end_src
+
+We would like to ascertain, if smoking is causally related to cancer:
+
+#+begin_src clojure :exports both
+(def smoking-rule (make-implication #{"smoking"} #{"cancer"}))
+#+end_src
+
+The algorith determines causality by emulating a controlled study, in which one group is exposed to the premise attribute, in this case "smoking" and the control group is not. Additionally, we choose a set of controlled variables.
+These are supposed to have the same values across pairs of objects in the exposure group and control group, to make sure neither of these is the true cause for the conclusion attribute, in this case "cancer".
+
+If two objects in the context satisfy these conditions, they are considerd a matched record pair. For example, if we control for variables "male" "female" "education-level-high" and "education-level-low" (0, 25), (9, 31) and (13 34)
+each form a matched record pair. This can be verified using the method ~matched-record-pair?~:
+
+#+begin_src clojure :exports both
+(matched-record-pair? smoking-ctx 
+                            smoking-rule 
+                            #{"male" "female" "education-level-high" "education-level-low"}
+                            0
+                            25)
+
+(matched-record-pair? smoking-ctx 
+                            smoking-rule 
+                            #{"male" "female" "education-level-high" "education-level-low"}
+                            9
+                            31)
+(matched-record-pair? smoking-ctx 
+                            smoking-rule 
+                            #{"male" "female" "education-level-high" "education-level-low"}
+                            13
+                            34)
+#+end_src
+
+The method ~fair-data-set~ computes a set of matched record pairs, by trying to match each object to exactly one different object.
+
+#+begin_src clojure :exports both
+(= (fair-data-set smoking-ctx 
+                        smoking-rule 
+                        #{"male" "female" "education-level-high" "education-level-low"})
+         smoking-fair-data-set)
+#+end_src
+
+#+RESULTS:
+#+begin_src clojure
+([#{7 29}
+  #{13 34}
+  #{15 36}
+  #{6 26}
+  #{1 28}
+  #{0 27}
+  #{17 35}
+  #{33 9}
+  #{31 12}
+  #{30 10}
+  #{22 37}
+  #{4 25}
+  #{21 38}
+  #{32 11}
+  #{24 40}
+  #{20 39}])
+#+end_src
+
+This set is used to verify whether an association rule is causal in nature.
+The method ~causal?~ tests causality for a specific implication:
+
+#+begin_src clojure :exports both
+(causal? smoking-ctx smoking-rule #{} 1.7 1)
+#+end_src
+
+The final three parameters are: 
+-the irrelevant variables, variables that will not be controlled for 
+-the confidence in the causality of the implication; a value of 1.7 corresponds to a 70% confidence
+-a threshold for computing exclusive variables. Two variables a and b are mutually exclusive, if the absolute support for (a and b) or (b and not a) is no larger than the threshold
+
+To discover all causes of a certain attribute in the context the method ~causal-association-rule-discovery~ can be used:
+
+#+begin_src clojure :exports both
+(causal-association-rule-discovery  smoking-ctx 0.7 3 "cancer" 1.7)
+#+end_src
+
+#+RESULTS:
+#+begin_src clojure
+(#{"smoking"})
+#+end_src
+
+0.7 represents the minimum local support that a generated variable must exceet to be considered. 1.7 again represents the confidence of the rule, and 3 represents the maximum number of attributes of the premise.
+

doc/Getting-Started.org

@@ -17,15 +17,15 @@ java -jar conexp-clj-2.1.1-SNAPSHOT-standalone.jar
 This will get you a prompt for ~conexp-clj~ much like
 
 #+begin_src text
-conexp.main=>
+conexp.analysis=>
 #+end_src
 
 You can now use all the power of formal concept analysis from ~conexp-clj~, and
 also everything Clojure provides.  For example, you can compute the value of the
 expression ~1 + 1~ as
 
 #+begin_src text
-conexp.main=> (+ 1 1)
+conexp.analysis=> (+ 1 1)
 2
 #+end_src
 

flake.nix

@@ -116,3 +116,4 @@
 # Local Variables:
 # apheleia-formatter: alejandra
 # End:
+

project.clj

@@ -7,24 +7,24 @@
 ;; You must not remove this notice, or any other, from this software.
 
 
-(defproject conexp-clj "2.4.1-SNAPSHOT"
+(defproject conexp-clj "2.5.0-SNAPSHOT"
 
   :min-lein-version "2.0.0"
   :description "A ConExp rewrite in clojure -- and so much more ..."
   :url "http://github.com/tomhanika/conexp-clj/"
   :scm {:url "[email protected]:tomhanika/conexp-clj.git"}
   :license {:name "Eclipse Public License"
             :url "http://www.eclipse.org/legal/epl-v10.html"}
-  :dependencies [[org.clojure/clojure             "1.10.1"]
-                 [org.clojure/core.async          "1.6.673"]
-                 [org.clojure/data.int-map        "1.2.1"]
-                 [org.clojure/data.json           "2.4.0"]
+  :dependencies [[org.clojure/clojure             "1.11.3"]
+                 [org.clojure/core.async          "1.6.681"]
+                 [org.clojure/data.int-map        "1.3.0"]
+                 [org.clojure/data.json           "2.5.0"]
                  [org.clojure/data.xml            "0.0.8"]
-                 [org.clojure/math.combinatorics  "0.2.0"]
-                 [org.clojure/math.numeric-tower  "0.0.5"]
-                 [org.clojure/tools.cli           "1.0.219"]
+                 [org.clojure/math.combinatorics  "0.3.0"]
+                 [org.clojure/math.numeric-tower  "0.1.0"]
+                 [org.clojure/tools.cli           "1.1.230"]
                  [org.apache.commons/commons-math "2.2"]
-                 [org.clojure/algo.generic        "0.1.3"]
+                 [org.clojure/algo.generic        "1.0.1"]
                  [seesaw                          "1.5.0"]
                  [reply                           "0.5.1"
                   :exclusions [org.clojure/clojure
@@ -33,35 +33,37 @@
                  [aysylu/loom "1.0.2"]
                  [rolling-stones "1.0.3"
                   :exclusions [org.clojure/clojure]]
-                 [clj-http "3.12.3"]
+                 [clj-http "3.13.0"]
                  [clojure-complete "0.2.5"]
-                 [ring/ring-devel "1.10.0"]
-                 [ring/ring-core "1.10.0"]
+                 [ring/ring-devel "1.12.1"]
+                 [ring/ring-core "1.12.1"]
                  [ring/ring-json "0.5.1"]
                  [ring-cors "0.1.13"]
-                 [http-kit "2.6.0"]
+                 [http-kit "2.8.0"]
                  [org.apache.commons/commons-math3 "3.6.1"]
-                 [luposlip/json-schema             "0.4.1"]
-                 [org.clojure/data.csv "1.0.1"]]
+                 [luposlip/json-schema             "0.4.5"]
+                 [org.clojure/data.csv "1.1.0"]]
   :profiles {:uberjar {:main conexp.main
                        :dependencies [[javax.servlet/servlet-api "2.5"]
                                       [ring/ring-mock "0.4.0"]
-                                      [nrepl/nrepl "1.0.0"]]
+                                      [nrepl/nrepl "1.1.2"]]
                        :plugins [[lein-aot-order "0.1.0"]]
                        :aot :order}
              :dev {:main conexp.main
                    :dependencies [[javax.servlet/servlet-api "2.5"]
                                   [ring/ring-mock "0.4.0"]
-                                  [nrepl/nrepl "1.0.0"]]
+                                  [nrepl/nrepl "1.1.2"]
+                                  [com.clojure-goes-fast/clj-async-profiler "1.2.2"]]
                    :plugins [[lein-aot-order "0.1.0"]]
-                   :javac-options ["-Xlint:deprecation" "-Xlint:unchecked"]}
-             :gorilla {:main conexp.main
-                       :plugins [[org.clojars.benfb/lein-gorilla "0.7.0"]]}}
+                   :javac-options ["-Xlint:deprecation" "-Xlint:unchecked"]
+                   :jvm-opts ["-Djdk.attach.allowAttachSelf"]}}
   :keep-non-project-classes true
   :source-paths ["src/main/clojure" "src/test/clojure"]
   :java-source-paths ["src/main/java"]
   :test-paths ["src/test/clojure"]
   :resource-paths ["src/main/resources"]
   :target-path "builds/%s"
   :compile-path "%s/classes/"
-  :java-opts ["-Dawt.useSystemAAFontSettings=lcd_hbgr" "-Xmx4G"])
+  :java-opts ["-Dawt.useSystemAAFontSettings=on" "-Xmx4G"]
+  :repl-options {:init-ns conexp.analysis
+               :init (use 'conexp.analysis :reload)})

src/main/clojure/conexp/analysis.clj

@@ -0,0 +1,64 @@
+(ns conexp.analysis
+  "Dafault Namespace."
+  (:require
+   [conexp.main :refer :all]
+   [conexp.base :refer :all]
+   [conexp.layouts :refer :all]
+   [conexp.gui :refer :all]
+   [conexp.api :refer :all]
+   [conexp.fca 
+    [causal-implications :refer :all]
+    [contexts :refer :all]
+    [cover :refer :all]
+    [dependencies :refer :all]
+    [exploration :refer :all]
+    [graph :refer :all]
+    [implications :refer :all]
+    [incremental-ganter :refer :all]
+    [lattices :refer :all]
+    [many-valued-contexts :refer :all]
+    [metrics :refer :all]
+    [more :refer :all]
+    [posets :refer :all]
+    [pqcores :refer :all]
+    [protoconcepts :refer :all]
+    [random-contexts :refer :all]
+    [triadic-exploration :refer :all]]
+   [conexp.math
+    [algebra :refer :all]
+    [markov :refer :all]
+    [numbers :refer :all]
+    [optimize :refer :all]
+    [sampling :refer :all]
+    [statistics :refer :all]
+    [util :refer :all]]
+   [conexp.layouts
+    [base :refer :all]
+    [common :refer :all]
+    [dim-draw :refer :all]
+    ;[force :refer :all]
+    [freese :refer :all]
+    [layered :refer :all]
+    [util :refer :all]]
+   [conexp.io
+	[base :refer :all]
+	[contexts :refer :all]
+	[fcas :refer :all]
+	[implications :refer :all]
+	[incomplete-contexts :refer :all]
+	[json :refer :all]
+	[latex :refer :all]
+	[lattices :refer :all]
+	[layouts :refer :all]
+	[many-valued-contexts :refer :all]
+	[util :refer :all]]
+   [conexp.gui 
+    [base :refer :all]
+    [draw :refer :all]
+    [plugins :refer :all]
+    [repl :refer :all]
+    [repl-utils :refer :all]]
+   [clojure.set :as set]
+   [clojure.edn :as edn]
+   [clojure.java.io :as io]))
+

src/main/clojure/conexp/api/namespace.clj

@@ -12,7 +12,8 @@
         conexp.layouts.freese
         conexp.layouts.layered
         conexp.layouts.dim-draw
-        conexp.api.shorthands))
+        conexp.api.shorthands
+        clojure.set))
 
 ;;;
 
@@ -24,7 +25,8 @@
                  conexp.layouts.freese
                  conexp.layouts.layered
                  conexp.layouts.dim-draw
-                 conexp.api.shorthands]))
+                 conexp.api.shorthands
+                 clojure.set])) ;; basic set operations
 
 (def functions
   (concat