Code

(py)Brush v1.0: islands!#55

Code

Merged

lacava merged 211 commits intomastercavalab/brush:masterfrom island_GAcavalab/brush:island_GACopy head branch name to clipboardJun 11, 2024

+9,153-2,252

Commits

Commits on Aug 8, 2023

• Merge pull request #45 from cavalab/initializing_weights

  Show description for 6159a28
  gAldeia

  authored
  6159a28

Commits on Aug 11, 2023

• Regressor now uses MSE (instead of squashed version of the metric)

  gAldeia

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  ddc280c

• Fixed wrong use of validation partition and MDCM

  gAldeia

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  9939d07

Commits on Aug 15, 2023

• Merge pull request #48 from cavalab/toggle_weight_on_off

  Show description for 38c3c6a
  gAldeia

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  38c3c6a

• Added mutation trace back

  Show description for dc328bb
  gAldeia

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  dc328bb

• Uniform weight initialization between mutation options and cx

  gAldeia

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  c6ccde4

Commits on Aug 30, 2023

• If mutation/cx fails, then the parent is inserted in offspring

  gAldeia

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  f29d94d

• Marked get_model functions as const

  gAldeia

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  9d1d153

• Additional check before doing PTC2

  gAldeia

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  29ae79e

• Mutation classes. bug fix in subtree mutation

  Show description for fdf0469
  gAldeia

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  fdf0469

• Updated tests

  gAldeia

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  1e35e2d

Commits on Aug 31, 2023

• Switched append(value) to extend([value])

  gAldeia

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  2aac8b0

• Better way to make sure PTC2, make_program and subtree will work

  gAldeia

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  d6e9778

• Improved find_spot and removed template in base class

  gAldeia

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  9044d5a

• Printing more informations for debug

  gAldeia

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  1082720

Commits on Sep 11, 2023

• Bug fixes. Avoiding re-fit. cloning expressions

  gAldeia

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  cb8e3ec

• Simple interface to clone a program and return a copy

  gAldeia

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  732a579

• Testing clone method

  gAldeia

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  20ef18d

• Implementation of simple GA with tournament selection

  gAldeia

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  e9424a7

Commits on Sep 26, 2023

• Initial structure to implement an Island GA. taskflow added as depend.

  gAldeia

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  c1e4366

• Changed GA so it doesnt require a new file

  gAldeia

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  058579b

Commits on Sep 27, 2023

• Fixed include of non-existing file

  gAldeia

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  099d9bf

• Changed get_params to have same arguments as base class from sklearn

  gAldeia

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  f238ebd

Commits on Sep 28, 2023

• Fixed bug fit with a dataframe but predict with an np.array

  gAldeia

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  91ba367

• Predict now use types from training data

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  gAldeia

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  9b2d716

Commits on Sep 29, 2023

• predict_proba returns 2d array for binary classification

  Show description for d4324a0
  gAldeia

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  d4324a0

• Fixed wrong comparison when throwing an error while copying from a reference dataset

  gAldeia

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  52611bb

Commits on Oct 2, 2023

• Bug fix - binary clf programs being created without logistic as root

  gAldeia

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  f42590d

Commits on Oct 3, 2023

• New fix. Some classification programs still being modified

  gAldeia

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  9a6c7f1

• Improved counting nodes

  gAldeia

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  74f9d3a

• Changed max arity in test_variation

  gAldeia

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  8f2b332

Commits on Oct 4, 2023

• MeanLabel node

  gAldeia

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  f0fa367

Commits on Oct 5, 2023

• Fixed algorithm==ga not returning the best individual

  gAldeia

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  2170146

• Added multiclass dataset (currently brush can do only binary clf)

  gAldeia

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  547bfdc

• Changed MeanLabel to be a terminal (not an operator)

  gAldeia

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  c25fedd

Commits on Oct 8, 2023

• python implementation of island model. fixed api and tests

  gAldeia

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  2a579b9

Commits on Oct 9, 2023

• Adding necessary functions if the user don't specify them

  gAldeia

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  a634a3d

• Implemented base for And and Or operators

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  gAldeia

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  cf81e1b

• Using boolean operators in test (not working yet)

  gAldeia

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  45b8de3

• Merge branch 'mutation_trace' of https://github.com/cavalab/brush into island_GA

  gAldeia

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  35513d2

Commits on Oct 11, 2023

• Implemented boolean operators. Improved print of meanLabel and SplitOn

  gAldeia

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  7f47454

• Included boolean operators in tests

  gAldeia

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  0b950e0

• Option to use nsga or ga with island divisions

  gAldeia

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  e1fd0ca

• Added comparison test of weights between cloned and original program

  gAldeia

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  f747d63

• Fixed error causing tests to fail when inserting Logistic in the searchspace

  gAldeia

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  5e6d3f9

• Merge pull request #49 from cavalab/meanLabel_operator

  Show description for b2f495a
  gAldeia

  authored
  b2f495a

• Merge branch 'mutation_trace' into island_GA

  gAldeia

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  5210708

• Merge pull request #50 from cavalab/island_GA

  Show description for eaa4c6c
  gAldeia

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  eaa4c6c

• Implemented complexity. User can specify objectives

  gAldeia

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  d70339a

• Merge pull request #51 from cavalab/complexity

  Show description for cdfa39b
  gAldeia

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  cdfa39b

Commits on Oct 12, 2023

• Fixed zero complexities

  gAldeia

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  7243f06

• Making constant features have zero weight

  gAldeia

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  d079365

• New tests

  gAldeia

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  672b9ca

• Merge pull request #52 from cavalab/complexity

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  gAldeia

  authored
  9000430

Commits on Oct 17, 2023

• Renamed initialization methods

  gAldeia

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  6586934

• Merge branch 'mutation_trace' of https://github.com/cavalab/brush into mutation_trace

  gAldeia

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  ce56086

• New complexity measures

  gAldeia

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  aa9655e

Commits on Oct 18, 2023

• Non-zero probability for terminals if they are not nan

  gAldeia

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  06c642c

• Bug fix in crossover attempts

  gAldeia

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  ae55ad9

• Added weights_init parameter into pybind wrapper

  gAldeia

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  87ce49e

• Updated missing bind

  gAldeia

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  06caed0

• Improved how get_dot_model prints MeanLabel

  gAldeia

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  94daa7e

• Fixed strategy to pick best solution when there's no validation split

  gAldeia

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  30718c3

Commits on Oct 19, 2023

• Using weights_init argument properly

  gAldeia

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  0218150

• Fixed complexity not taking into account the node weights

  gAldeia

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  050a38a

• Changed classification default metric

  Show description for ec627b1
  gAldeia

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  ec627b1

• Avoid creating clones of programs

  gAldeia

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  1b3bb75

• Increased minimal probability of changing

  gAldeia

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  981726c

Commits on Oct 23, 2023

• Improved log. Fixed warnings in pytest.

  gAldeia

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  825264a

• Dont show MeanLabel in MeanLabel nodes

  gAldeia

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  aee7b30

Commits on Oct 24, 2023

• Fixed meanlabel. Updated how we initialize weights

  gAldeia

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  8c0979d

Commits on Nov 1, 2023

• Stop reinserting the same expression if mutation fails

  gAldeia

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  7c1d83f

Commits on Nov 2, 2023

• Stop reinserting parents into offspring. Fixed island indexes for that

  gAldeia

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  f341896

• Updated

  gAldeia

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  1794950

• Fixed not inserting value into list of failed variations

  gAldeia

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  69cc07e

• Basic files to implement island model

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  5510c86

Commits on Nov 3, 2023

• Individuals. Now program compiles again

  gAldeia

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  6556d76

• Starting to implement Individual

  gAldeia

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  7383776

• Merge pull request #53 from cavalab/mutation_trace

  Show description for a984c20
  gAldeia

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  a984c20

• Population and Selection templated for ProgramType

  gAldeia

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  a9b469d

Commits on Nov 6, 2023

• Implementation of individual class

  gAldeia

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  bfa4d1c

• Population implemented with island indexes control

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  7de001a

• Files for implementing nsga2

  gAldeia

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  cd73a62

Commits on Nov 7, 2023

• Draft of nsga2 selection implementation

  gAldeia

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  b510472

• Added TODOs

  gAldeia

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  f7469ee

• Added TODOs

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  22b9fe9

• Select and Survive now takes the island range as argument

  gAldeia

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  877fa0f

• nsga2 with islands

  gAldeia

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  3c31499

• Parameters implemented (but not effectively used yet)

  gAldeia

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  8a2d920

• Starting to implement Variation class

  Show description for 392aa7c
  gAldeia

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  392aa7c

Commits on Nov 8, 2023

• Commented broken tests

  gAldeia

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  47820fe

• Removed previous mutation and crossover interfaces with python

  gAldeia

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  e6da3e3

• Individual uses search space to create programs

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  5beec86

• Migration methods

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  232ee98

• Updating python wrapper (almost finishing it!)

  gAldeia

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  e5a6d7a

• Generation basic operations almost done (evaluator is missing)

  gAldeia

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  9ea4bb4

• Starting to implement evaluation

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  5e862b3

Commits on Nov 9, 2023

• Evaluation implemented

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  9f7f11c

Commits on Nov 13, 2023

• Setting and using individual objective values

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  37952eb

• Evaluation now has the option to not re-fit the individual

  Show description for ecfc12d
  gAldeia

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  ecfc12d

• Generation and fit methods

  gAldeia

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  d76cfd0

• Moving the python implementation out of cpp src. Starting to rewrite it

  gAldeia

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  4216e90

• Renamed variable

  gAldeia

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  fdde3b2

Commits on Nov 14, 2023

• Bug fix in cx. improved spot selection in cx. cx and mut are now public

  gAldeia

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  dd8ae26

• Default values for mutation probs. New comments with TODOs

  gAldeia

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  cec5354

• Individual constructor

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  95efb07

• all previous cpp tests are pdated and working!

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  eafb245

Commits on Nov 15, 2023

• Templated selection. Bug fixes.

  gAldeia

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  5f7957a

• Tests for population (working! I just dont know if they are correct yet)

  gAldeia

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  c9d763a

Commits on Nov 16, 2023

• Rewriting to store island ind indexes --- instead of (start_idx, end_idx)

  gAldeia

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  446f22d

Commits on Nov 17, 2023

• Fixed printing individuals in population

  gAldeia

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  186895b

• Update to work with island indexes

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  6f2b13c

Commits on Nov 20, 2023

• Clean up. Moving to finish pending TODOs and fix python wrapper

  gAldeia

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  a68acfc

Commits on Dec 12, 2023

• Moving python files outside src directory

  gAldeia

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  344b93e

• Improved individuals, parameters, types and variation

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  bf81b8b

• Lots of new bindings. Rework to make previous keep working

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  3ecfb44

• Updated tests to run with all the rework

  Show description for 99ba4ce
  gAldeia

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  99ba4ce

Commits on Feb 7, 2024

• Updated DEAP to use brush's individuals

  gAldeia

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  37c73d0

• Updated python wrapper to use Brush's individual class

  gAldeia

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  63b0b5f

• Updated tests to work with Brush's individuals

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  618af55

• Updated variation operators to operate completely in C++

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  9429021

Commits on Feb 9, 2024

• Implemented interface to evaluate in c++

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  ce83807

Commits on Feb 10, 2024

• Fixed evaluator not working for classification

  gAldeia

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  5f392e2

• Fitness evaluation is now in c++

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  774c448

Commits on Feb 23, 2024

• Fixed ceres version (newer is crashing due google docs dep)

  gAldeia

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  3388f5a

• Implemented working selection and survival in cpp

  gAldeia

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  b6dcd9b

• Updated wrapper to use cpp instead of deap sel and surv

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  f1bcdce

• Updated test

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  95fec29

Commits on Feb 26, 2024

• Lexicase selection. Fix migration. Sel, surv, and migration bindings.

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  6d9369b

Commits on Feb 27, 2024

• Bug fix in lexicase selecting from the wrong island

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  02c5058

• pop variation entirely in cpp

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  baaf37c

Commits on Mar 2, 2024

• added annotation with todo

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  e5aed9c

• Replacing population in update is now better

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  de84b3c

• Island algorithm with taskflow implemented

  Show description for 9a0f36a
  gAldeia

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  9a0f36a

• Updated tests, bindings, and wrapper

  gAldeia

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  6d3c3cc

Commits on Mar 10, 2024

• Fixed core dump due to parallel calculations

  

  Guilherme Aldeia

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  d1f5d25

• Assert in eval (for debug reasons). Will be removed later

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  61f9e59

• added some comments

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  23fbd84

• Fixed core dumps. Forcing unused indexes in pop to be nullptr

  Show description for d768db9
  not-gAldeia

  committed
  d768db9

Commits on Mar 12, 2024

• Replaced creator.Individual with brush's individual

  gAldeia

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  4ede2fd

• Renamed cpp's estimator to engine

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  0b2ab96

• fixed population and selection implementations

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  b0b27fd

• trying to solve GIL problem

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  e7259c6

Commits on Mar 13, 2024

• Fixed variator not being initialize

  not-gAldeia

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  f0e3d43

• Cleaning up some TODOs

  not-gAldeia

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  2474025

• fixed typo

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  17cb266

• cleaning and refactoring

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  cde53e5

• fixed bind fitness not working

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  d7e47ab

Commits on Mar 15, 2024

• Starting to implement pure c++ BrushEstimator

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  84dd495

Commits on Mar 19, 2024

• n_jobs and random_state in engine. new tests.

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  f9a7070

• TODO: check selection implementation

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  a3c9650

• Saving and load population

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  8759c09

• Merge branch 'island_GA' of https://github.com/cavalab/brush into island_GA

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  92e152e

Commits on Mar 20, 2024

• Resolve offspring bottleneck

  gAldeia

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  f1ab6b1

Commits on Apr 2, 2024

• Fixed PTC2 creating huge trees when max_depth is a high number

  gAldeia

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  28067b0

• Missing if statement in search space ptc2

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  9f6be61

Commits on Apr 10, 2024

• Fixed tree creation with logistic/softmax when not specified in function set

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  1efedd3

• OffsetSum (sum with W as argument, not as weight)

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  4af5d4d

Commits on Apr 12, 2024

• Fixed bad logic when adding Logistic to search space

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  a9b4cab

Commits on Apr 14, 2024

• Better dot models for OffsetSum

  gAldeia

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  3908eb2

• Minor changes

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  f96c594

• Implemented max_stall

  gAldeia

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  39a1e16

• Improving PTC2 to work with strong typed programs. Fixed infinite loop in PTC2

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  2c438e0

Commits on Apr 15, 2024

• Implemented max_time

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  7c364ea

Commits on Apr 16, 2024

• OffsetSum as an unary operator

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  c2d3648

• Logistic(Add(Const, <>))

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  4f077a7

• is_fitted_ flag to avoid re-fitting individuals

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  dad0ba8

• Fixed constants having higher complexity than they should

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  69d569e

• Improved dot model for OffsetSum nodes

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  7976fe2

• Fixed scorer_ not visible to python

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  658b68d

Commits on Apr 21, 2024

• Fixed bad logic when calculating complexity of constant terminals

  gAldeia

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  abd7841

• Logfile and verbosity. Lots of new TODOs to fix!

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  d3f20dd

Commits on Apr 22, 2024

• Starting to implement archive

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Commits on Apr 23, 2024

• Notebook to test the island implementation

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  b6476de

• comments print statements

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  e06cd7c

Commits on Apr 24, 2024

• Cleaning some TODOs. Organizing files

  gAldeia

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  be98ce5

• Fixed bad minimization of fitness. Classification working

  gAldeia

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  1341183

• get_rank instead of just rank (was failing to install in older python versions)

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  5ee9393

• Cleaning more TODOs

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  c64fad7

Commits on Apr 25, 2024

• Fit, predict and predict_proba for individual classes

  gAldeia

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  ddeb6fd

• Engine bindings for fit and predict. Engine serialization

  gAldeia

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  ee5379d

• Merge branch 'master' of https://github.com/cavalab/brush into island_GA

  gAldeia

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  160b39a

• Deleted test notebook

  gAldeia

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  bd6a5d4

• Fixed missing taskflow. simple test to see if validation is being used

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  d3538e3

Commits on May 2, 2024

• Working (but slightly incorrect) implementation of archive

  gAldeia

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  fe84d8d

Commits on May 3, 2024

• Archive implementation. Individual ids. New TODOs to solve

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  12a8772

Commits on May 4, 2024

• fixed missing val_from_arch parameter and pybrush breaking

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  78314fc

Commits on Jun 5, 2024

• Updated examples in readme

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  7ea90c2

• removing unused file

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  4381134

• cleaning a lot of comments and TODOs

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  cd9436c

• adding some new TODOs

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  30e7bad

• Instructions to build docs locally

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  29afbe7

• Updated example notebooks and started writing new ones

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  62aff7a

• Fixed bug when passing a list of functions

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  f036a2d

• more cleaning. Implemented string representation for fitness

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  9375c88

Commits on Jun 6, 2024

• Final adjustments to save/load pop and use archive

  gAldeia

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  cbcfcbe

• Fix print statement when using archive

  gAldeia

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  e021f13

• Removed useless lambda function

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  17de2b0

• Spacing

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  6fd411d

• new example notebooks!!

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  3112a18

• Added new files. Now it is time to write documentation

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  6be28de

• Todo: version for docs should be set automatically

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  452ad67

Commits on Jun 7, 2024

• Implemented average_precision_score metric in cpp

  gAldeia

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  3506898

• Fixed python docs not being found

  gAldeia

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  6af5ce0

Commits on Jun 11, 2024

• Documentation. setting n_classes in cpp side

  gAldeia

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  d675707

• Documentation

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  ae0a886

• Improved variation. Fixed lots of TODOs. implemented get_size in trees, so we dont have several reimplementations of same function

  gAldeia

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  e1b2f19

• Updated tedts to work with new variation

  gAldeia

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  dd1eb30

• Fixed bad doxygen instructions

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  f5d26eb

• lots of docs

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  5210dd7

• Documentation for Engine class (just the class definition, not its methods)

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