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Adds a small tag for continuous and discrete optimizers
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13 files changed

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‎docs/poli-docs/_build/.doctrees/environment.pickle

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‎docs/poli-docs/_build/.doctrees/index.doctree

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‎docs/poli-docs/_build/.doctrees/using_poli/optimization_examples/protein-stability-foldx/optimizing_protein_stability.doctree

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‎docs/poli-docs/_build/.doctrees/using_poli/the_basics/isolation.doctree

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‎docs/poli-docs/_build/.jupyter_cache/executed/446bf9e357d4c8f4d26df02b81ac5e1a/base.ipynb

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"outputs": [],
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"source": [
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"# No output: we don't have it installed.\n",
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"!pip freeze | grep dockstring"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"poli 🧪: creating environment poli__dockstring from dockstring/environment.yml\n"
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]
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},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"poli 🧪: creating environment poli__dockstring from dockstring/environment.yml\n",
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"poli 🧪: running registration of dockstring from environment poli__dockstring\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/Users/sjt972/Projects/poli/src/poli/core/registry.py:258: UserWarning: Environment poli__dockstring already exists. Will not create it.\n",
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" warnings.warn(f\"Environment {env_name} already exists. Will not create it.\")\n",
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"/Users/sjt972/Projects/poli/src/poli/core/registry.py:269: UserWarning: Running the following command: conda run -n poli__dockstring python /Users/sjt972/Projects/poli/src/poli/objective_repository/dockstring/register.py. \n",
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" warnings.warn(\"Running the following command: %s. \" % command)\n"
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]
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},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"poli 🧪: creating an isolated black box function.\n",
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"poli 🧪: starting the isolated objective process.\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/Users/sjt972/anaconda3/envs/poli__dockstring/lib/python3.9/site-packages/dockstring/utils.py:77: DockstringWarning: Although Mac use is supported, docking scores on Mac do not always perfectly match scores from Linux. Therefore, extra care should be taken when comparing results to other platforms. In particular, the baselines in the DOCKSTRING paper were computed on Linux, so please do not directly compare your docking scores to the scores reported on the paper.\n",
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" warnings.warn(\n"
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]
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}
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],
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"source": [
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"from poli import create\n",
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"\n",
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"f, x0, y0 = create(\n",
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" name=\"dockstring\",\n",
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" target_name=\"drd2\" # The target protein.\n",
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")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"ExternalBlackBox(L=inf, num_evaluations=0)\n"
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]
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}
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],
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"source": [
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"print(f)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/Users/sjt972/anaconda3/envs/poli__dockstring/lib/python3.9/site-packages/dockstring/utils.py:77: DockstringWarning: Although Mac use is supported, docking scores on Mac do not always perfectly match scores from Linux. Therefore, extra care should be taken when comparing results to other platforms. In particular, the baselines in the DOCKSTRING paper were computed on Linux, so please do not directly compare your docking scores to the scores reported on the paper.\n",
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" warnings.warn(\n"
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]
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},
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{
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"data": {
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"text/plain": [
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"array([[11.9]])"
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]
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},
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"execution_count": 4,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"f(x0)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"ExternalBlackBox(L=inf, num_evaluations=1)\n"
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]
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}
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],
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"source": [
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"print(f)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"poli 🧪: Creating the objective from the repository.\n"
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]
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}
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],
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"source": [
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"f_logp, x0_logp, y0_logp = create(\n",
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" name=\"rdkit_logp\"\n",
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")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"LogPBlackBox(L=inf, num_evaluations=1)\n"
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]
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}
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],
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"source": [
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"print(f_logp)"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "poli-docs",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.18"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}

‎docs/poli-docs/_build/.jupyter_cache/global.db

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‎docs/poli-docs/_build/html/_sources/index.md

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On top of `poli`, we provide `poli-baselines`, a collection of **black-box optimization algorithms** (focusing especially on *discrete* sequences). Examples include
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## Discrete
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::::{grid}
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Optimizing a discrete sequence by performing random mutations
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:::
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::::
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## Continuous
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::::{grid}
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:gutter: 3
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:::{grid-item-card} CMA-ES
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:link: ./using_poli_baselines/cma_es.html
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:columns: 6

‎docs/poli-docs/_build/html/index.html

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<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#black-box-optimization-algorithms">Black-box optimization algorithms</a></li>
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<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#discrete">Discrete</a></li>
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<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#continuous">Continuous</a></li>
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<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#cite-us-and-other-relevant-work">Cite us and other relevant work</a></li>
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<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#contribute-problems-or-solvers">Contribute problems or solvers</a></li>
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</ul>
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<section id="black-box-optimization-algorithms">
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<h2>Black-box optimization algorithms<a class="headerlink" href="#black-box-optimization-algorithms" title="Permalink to this heading">#</a></h2>
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<p>On top of <code class="docutils literal notranslate"><span class="pre">poli</span></code>, we provide <code class="docutils literal notranslate"><span class="pre">poli-baselines</span></code>, a collection of <strong>black-box optimization algorithms</strong> (focusing especially on <em>discrete</em> sequences). Examples include</p>
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</section>
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<section id="discrete">
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<h2>Discrete<a class="headerlink" href="#discrete" title="Permalink to this heading">#</a></h2>
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</div>
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</div>
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</section>
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<section id="continuous">
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<h2>Continuous<a class="headerlink" href="#continuous" title="Permalink to this heading">#</a></h2>
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<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#black-box-optimization-algorithms">Black-box optimization algorithms</a></li>
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<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#discrete">Discrete</a></li>
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<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#continuous">Continuous</a></li>
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<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#cite-us-and-other-relevant-work">Cite us and other relevant work</a></li>
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<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#contribute-problems-or-solvers">Contribute problems or solvers</a></li>
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</ul>

‎docs/poli-docs/_build/html/searchindex.js

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