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Add and reorganize regression problem files

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This commit is contained in:
Lee Spector 2024-01-17 15:32:12 -05:00
parent 6812f5e28c
commit 847341e4d8
6 changed files with 194 additions and 86 deletions
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2
src/propeller/gp.cljc
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@ -61,7 +61,7 @@
:bmx-complementary? false ; for bmx, whether mates selected using reverse case sequence of first parent :bmx-complementary? false ; for bmx, whether mates selected using reverse case sequence of first parent
:bmx-maximum-distance 1000000 ; for bmx, don't exchange if distance is greater than this :bmx-maximum-distance 1000000 ; for bmx, don't exchange if distance is greater than this
:bmx-same-gene-count false ; for bmx, only allow exchanges between individuals with same number of genes :bmx-same-gene-count false ; for bmx, only allow exchanges between individuals with same number of genes
:closes :specified ; :pecified, :balanced, :none :closes :specified ; :specified, :balanced, :none
:custom-report false ; if provided, should be a function that takes an argmap :custom-report false ; if provided, should be a function that takes an argmap
:dont-end false ; if true, keep running until limit regardless of success :dont-end false ; if true, keep running until limit regardless of success
:downsample? true ; wether to use downsampling :downsample? true ; wether to use downsampling

83
src/propeller/problems/float_regression.cljc
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@ -1,83 +0,0 @@
(ns propeller.problems.float-regression
(:require [propeller.genome :as genome]
[propeller.push.interpreter :as interpreter]
[propeller.push.state :as state]
[propeller.tools.math :as math]
[propeller.gp :as gp]
#?(:cljs [cljs.reader :refer [read-string]])))
(defn- target-function
"Target function: f(x) = (1+ x^3)^3 + 1"
[x]
(inc (* (inc (* x x x)) (inc (* x x x)) (inc (* x x x)))))
(def train-and-test-data
(let [train-inputs (range -1.5 1.5 0.1)
test-inputs (range -1.75 1.75 0.05)]
{:train (map (fn [x] {:input1 (vector x) :output1 (vector (target-function x))}) train-inputs)
:test (map (fn [x] {:input1 (vector x) :output1 (vector (target-function x))}) test-inputs)}))
(def instructions
(list :in1
:float_add
:float_subtract
:float_mult
:float_quot
:float_eq
:exec_dup
:exec_if
'close
0.0
1.0))
(defn error-function
"Finds the behaviors and errors of an individual. The error is the absolute
deviation between the target output value and the program's selected behavior,
or 1000000 if no behavior is produced. The behavior is here defined as the
final top item on the FLOAT stack."
([argmap data individual]
(let [program (genome/plushy->push (:plushy individual) argmap)
inputs (map (fn [x] (first (:input1 x))) data)
correct-outputs (map (fn [x] (first (:output1 x))) data)
outputs (map (fn [input]
(state/peek-stack
(interpreter/interpret-program
program
(assoc state/empty-state :input {:in1 input})
(:step-limit argmap))
:float))
inputs)
errors (map (fn [correct-output output]
(if (= output :no-stack-item)
1000000
(math/abs (- correct-output output))))
correct-outputs
outputs)]
(assoc individual
:behaviors outputs
:errors errors
:total-error #?(:clj (apply +' errors)
:cljs (apply + errors))))))
(defn -main
"Runs the top-level genetic programming function, giving it a map of
arguments with defaults that can be overridden from the command line
or through a passed map."
[& args]
(gp/gp
(merge
{:instructions instructions
:error-function error-function
:training-data (:train train-and-test-data)
:testing-data (:test train-and-test-data)
:max-generations 300
:population-size 1000
:max-initial-plushy-size 100
:step-limit 200
:parent-selection :epsilon-lexicase
:tournament-size 5
:umad-rate 0.1
:solution-error-threshold 0.5
:variation {:umad 1.0 :crossover 0.0}
:elitism false}
(apply hash-map (map #(if (string? %) (read-string %) %) args)))))

2
src/propeller/problems/UBall5D.cljc → src/propeller/problems/regression/UBall5D.cljc
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@ -1,4 +1,4 @@
(ns propeller.problems.UBall5D (ns propeller.problems.regression.UBall5D
(:require [propeller.genome :as genome] (:require [propeller.genome :as genome]
[propeller.push.interpreter :as interpreter] [propeller.push.interpreter :as interpreter]
[propeller.push.state :as state] [propeller.push.state :as state]

2
src/propeller/problems/integer_regression.cljc → src/propeller/problems/regression/integer_regression.cljc
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@ -1,4 +1,4 @@
(ns propeller.problems.integer-regression (ns propeller.problems.regression.integer-regression
(:require [propeller.genome :as genome] (:require [propeller.genome :as genome]
[propeller.push.interpreter :as interpreter] [propeller.push.interpreter :as interpreter]
[propeller.push.state :as state] [propeller.push.state :as state]

94
src/propeller/problems/regression/nguyen_f1.cljc Normal file
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@ -0,0 +1,94 @@
;; This file implements a version of the Nguyen-F1 symbolic regression problem, as described in various
;; publications in the genetic programming literature including:
;;
;; Makke, N., Chawla, S. Interpretable scientific discovery with symbolic regression: a review.
;; Artif Intell Rev 57, 2 (2024). https://doi.org/10.1007/s10462-023-10622-0
;;
;; Note however that it may differ in some respects from the problem used elsewhere, for example
;; in the data ranges and gentic programming function sets which are not always fully documented
;; in the literature. For this reason, while this code can be used as an example and for comparing
;; different configurations of the present system, results obtained with this code may not be directly
;; comparable to those published in the literature.
(ns propeller.problems.regression.nguyen-f1
(:require [propeller.genome :as genome]
[propeller.push.interpreter :as interpreter]
[propeller.push.state :as state]
[propeller.tools.math :as math]
[propeller.gp :as gp]
#?(:cljs [cljs.reader :refer [read-string]])))
(defn- target-function
"Nguyen F1 = x^3 + x^2 + x"
[x]
(+ (* x x x) (* x x) x))
(def train-and-test-data
(let [train-inputs (range -4.0 4.0 0.1)
test-inputs (range -4.0 4.0 0.05)]
{:train (map (fn [x] {:input1 (vector x) :output1 (vector (target-function x))}) train-inputs)
:test (map (fn [x] {:input1 (vector x) :output1 (vector (target-function x))}) test-inputs)}))
(def instructions
(list :in1
:float_add
:float_subtract
:float_mult
:float_div
:float_sin
:float_cos
:float_tan
0.0
1.0))
(defn error-function
"Finds the behaviors and errors of an individual. The error is the absolute
deviation between the target output value and the program's selected behavior,
or 1000000 if no behavior is produced. The behavior is here defined as the
final top item on the FLOAT stack."
([argmap data individual]
(let [program (genome/plushy->push (:plushy individual) argmap)
inputs (map (fn [x] (first (:input1 x))) data)
correct-outputs (map (fn [x] (first (:output1 x))) data)
outputs (map (fn [input]
(state/peek-stack
(interpreter/interpret-program
program
(assoc state/empty-state :input {:in1 input})
(:step-limit argmap))
:float))
inputs)
errors (map (fn [correct-output output]
(if (= output :no-stack-item)
1000000
(math/abs (- correct-output output))))
correct-outputs
outputs)]
(assoc individual
:behaviors outputs
:errors errors
:total-error #?(:clj (apply +' errors)
:cljs (apply + errors))))))
(defn -main
"Runs the top-level genetic programming function, giving it a map of
arguments with defaults that can be overridden from the command line
or through a passed map."
[& args]
(gp/gp
(merge
{:instructions instructions
:error-function error-function
:training-data (:train train-and-test-data)
:testing-data (:test train-and-test-data)
:downsample? false
:solution-error-threshold 0.1
:max-generations 300
:population-size 1000
:max-initial-plushy-size 50
:step-limit 100
:parent-selection :epsilon-lexicase
:umad-rate 0.05
:variation {:umad 1.0}
:simplification? true}
(apply hash-map (map #(if (string? %) (read-string %) %) args)))))

97
src/propeller/problems/regression/nguyen_f5.cljc Normal file
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@ -0,0 +1,97 @@
;; This file implements a version of the Nguyen-F5 symbolic regression problem, as described in various
;; publications in the genetic programming literature including:
;;
;; Makke, N., Chawla, S. Interpretable scientific discovery with symbolic regression: a review.
;; Artif Intell Rev 57, 2 (2024). https://doi.org/10.1007/s10462-023-10622-0
;;
;; Note however that it may differ in some respects from the problem used elsewhere, for example
;; in the data ranges and gentic programming function sets which are not always fully documented
;; in the literature. For this reason, while this code can be used as an example and for comparing
;; different configurations of the present system, results obtained with this code may not be directly
;; comparable to those published in the literature.
(ns propeller.problems.regression.nguyen-f5
(:require [propeller.genome :as genome]
[propeller.push.interpreter :as interpreter]
[propeller.push.state :as state]
[propeller.tools.math :as math]
[propeller.gp :as gp]
#?(:cljs [cljs.reader :refer [read-string]])))
(defn- target-function
"Nguyen F5 = sin(x^2)cos(x) - 1"
[x]
(- (* (Math/sin (* x x))
(Math/cos x))
1))
(def train-and-test-data
(let [train-inputs (range -4.0 4.0 0.1)
test-inputs (range -4.0 4.0 0.05)]
{:train (map (fn [x] {:input1 (vector x) :output1 (vector (target-function x))}) train-inputs)
:test (map (fn [x] {:input1 (vector x) :output1 (vector (target-function x))}) test-inputs)}))
(def instructions
(list :in1
:float_add
:float_subtract
:float_mult
:float_div
:float_sin
:float_cos
:float_tan
0.0
1.0))
(defn error-function
"Finds the behaviors and errors of an individual. The error is the absolute
deviation between the target output value and the program's selected behavior,
or 1000000 if no behavior is produced. The behavior is here defined as the
final top item on the FLOAT stack."
([argmap data individual]
(let [program (genome/plushy->push (:plushy individual) argmap)
inputs (map (fn [x] (first (:input1 x))) data)
correct-outputs (map (fn [x] (first (:output1 x))) data)
outputs (map (fn [input]
(state/peek-stack
(interpreter/interpret-program
program
(assoc state/empty-state :input {:in1 input})
(:step-limit argmap))
:float))
inputs)
errors (map (fn [correct-output output]
(if (= output :no-stack-item)
1000000
(math/abs (- correct-output output))))
correct-outputs
outputs)]
(assoc individual
:behaviors outputs
:errors errors
:total-error #?(:clj (apply +' errors)
:cljs (apply + errors))))))
(defn -main
"Runs the top-level genetic programming function, giving it a map of
arguments with defaults that can be overridden from the command line
or through a passed map."
[& args]
(gp/gp
(merge
{:instructions instructions
:error-function error-function
:training-data (:train train-and-test-data)
:testing-data (:test train-and-test-data)
:downsample? false
:solution-error-threshold 0.1
:max-generations 300
:population-size 1000
:max-initial-plushy-size 50
:step-limit 100
:parent-selection :epsilon-lexicase
:umad-rate 0.05
:variation {:umad 1.0}
:simplification? true}
(apply hash-map (map #(if (string? %) (read-string %) %) args)))))