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Merge pull request #9 from MachineLearningLifeScience/update-index-with-table-of-citations
Adds a table to the welcome page with references to the black boxes
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@@ -161,6 +161,38 @@ A version of Bayesian Optimization where the acquisition is optimized over a lin
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::::
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## Cite us and other relevant work
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If you use `poli`, we encourage you to cite us
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```
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@software{GonzalezDuqueBartelsMichael:poli:2024,
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author = {González-Duque, Miguel and Bartels, Simon and Michael, Richard},
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month = jan,
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title = {{poli: a libary of discrete sequence objectives}},
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url = {https://github.com/MachineLearningLifeScience/poli},
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version = {0.0.1},
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year = {2024}
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}
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```
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If you use certain black boxes, we also recommend citing the original work:
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|Black box|Reference(s)|
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|---------|---------|
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|`dockstring`|[(García-Ortegón et al. 2022)](https://pubs.acs.org/doi/10.1021/acs.jcim.1c01334)|
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|`drd3_docking`|[(Graff, Shakhnovich and Coley 2020)](https://pubs.acs.org/doi/10.1021/acs.jcim.1c01334), [(Graff and Coley 2022)](https://joss.theoj.org/papers/10.21105/joss.03950), [(Huang et al. 2022)](https://www.nature.com/articles/s41589-022-01131-2)|
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|`foldx_*`|[(Schymkowitz et al. 2005)](https://academic.oup.com/nar/article/33/suppl_2/W382/2505499)|
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|`gfp_cbas`|[(Brookes, Park and Listgarten 2019)](https://proceedings.mlr.press/v97/brookes19a.html)|
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|`gfp_select`|[(Brookes, Park and Listgarten 2019)](https://proceedings.mlr.press/v97/brookes19a.html)|
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|`penalized_logp_lambo`|[(Stanton et al. 2022)](https://github.com/samuelstanton/lambo)|
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|`rasp`|[(Blaabjerg et al. 2022)](https://github.com/KULL-Centre/_2022_ML-ddG-Blaabjerg)|
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|`rdkit_*`|[(rdkit)](https://github.com/rdkit/rdkit)|
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|`rfp_foldx_*`|[(Schymkowitz et al. 2005)](https://academic.oup.com/nar/article/33/suppl_2/W382/2505499), [(Stanton et al. 2022)](https://github.com/samuelstanton/lambo)|
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|`sa_tdc`|[(Huang et al. 2022)](https://www.nature.com/articles/s41589-022-01131-2), [(rdkit)](https://github.com/rdkit/rdkit), [(Ertl and Schuffenhauer 2009)](https://link.springer.com/article/10.1186/1758-2946-1-8)|
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|`super_mario_bros`|[(Volz et al. 2018)](https://github.com/CIGbalance/DagstuhlGAN), [(González-Duque 2023)](https://github.com/miguelgondu/minimal_VAE_on_Mario) |
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|`toy_continuous_problem`|[(Al-Roomi 2015)](https://www.al-roomi.org/benchmarks/unconstrained), [(Surjanovic and Bingham 2013)](https://www.sfu.ca/~ssurjano/optimization.html) |
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## Contribute problems or solvers
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‎docs/poli-docs/_build/html/index.html

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@@ -548,6 +548,7 @@ <h2> Contents </h2>
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</ul>
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</li>
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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="#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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</nav>
@@ -766,6 +767,66 @@ <h2>Black-box optimization algorithms<a class="headerlink" href="#black-box-opti
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</div>
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</div>
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</section>
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<section id="cite-us-and-other-relevant-work">
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<h2>Cite us and other relevant work<a class="headerlink" href="#cite-us-and-other-relevant-work" title="Permalink to this heading">#</a></h2>
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<p>If you use <code class="docutils literal notranslate"><span class="pre">poli</span></code>, we encourage you to cite us</p>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="nd">@software</span><span class="p">{</span><span class="n">GonzalezDuqueBartelsMichael</span><span class="p">:</span><span class="n">poli</span><span class="p">:</span><span class="mi">2024</span><span class="p">,</span>
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<span class="n">author</span> <span class="o">=</span> <span class="p">{</span><span class="n">González</span><span class="o">-</span><span class="n">Duque</span><span class="p">,</span> <span class="n">Miguel</span> <span class="ow">and</span> <span class="n">Bartels</span><span class="p">,</span> <span class="n">Simon</span> <span class="ow">and</span> <span class="n">Michael</span><span class="p">,</span> <span class="n">Richard</span><span class="p">},</span>
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<span class="n">month</span> <span class="o">=</span> <span class="n">jan</span><span class="p">,</span>
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<span class="n">title</span> <span class="o">=</span> <span class="p">{{</span><span class="n">poli</span><span class="p">:</span> <span class="n">a</span> <span class="n">libary</span> <span class="n">of</span> <span class="n">discrete</span> <span class="n">sequence</span> <span class="n">objectives</span><span class="p">}},</span>
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<span class="n">url</span> <span class="o">=</span> <span class="p">{</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">MachineLearningLifeScience</span><span class="o">/</span><span class="n">poli</span><span class="p">},</span>
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<span class="n">version</span> <span class="o">=</span> <span class="p">{</span><span class="mf">0.0.1</span><span class="p">},</span>
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<span class="n">year</span> <span class="o">=</span> <span class="p">{</span><span class="mi">2024</span><span class="p">}</span>
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<span class="p">}</span>
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</pre></div>
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</div>
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<p>If you use certain black boxes, we also recommend citing the original work:</p>
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<table class="colwidths-auto table">
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<thead>
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<tr class="row-odd"><th class="head"><p>Black box</p></th>
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<th class="head"><p>Reference(s)</p></th>
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</tr>
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</thead>
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<tbody>
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<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">dockstring</span></code></p></td>
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<td><p><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.jcim.1c01334">(García-Ortegón et al. 2022)</a></p></td>
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</tr>
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<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">drd3_docking</span></code></p></td>
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<td><p><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.jcim.1c01334">(Graff, Shakhnovich and Coley 2020)</a>, <a class="reference external" href="https://joss.theoj.org/papers/10.21105/joss.03950">(Graff and Coley 2022)</a>, <a class="reference external" href="https://www.nature.com/articles/s41589-022-01131-2">(Huang et al. 2022)</a></p></td>
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</tr>
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<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">foldx_*</span></code></p></td>
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<td><p><a class="reference external" href="https://academic.oup.com/nar/article/33/suppl_2/W382/2505499">(Schymkowitz et al. 2005)</a></p></td>
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</tr>
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<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">gfp_cbas</span></code></p></td>
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<td><p><a class="reference external" href="https://proceedings.mlr.press/v97/brookes19a.html">(Brookes, Park and Listgarten 2019)</a></p></td>
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</tr>
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<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">gfp_select</span></code></p></td>
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<td><p><a class="reference external" href="https://proceedings.mlr.press/v97/brookes19a.html">(Brookes, Park and Listgarten 2019)</a></p></td>
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</tr>
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<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">penalized_logp_lambo</span></code></p></td>
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<td><p><a class="reference external" href="https://github.com/samuelstanton/lambo">(Stanton et al. 2022)</a></p></td>
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</tr>
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<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">rasp</span></code></p></td>
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<td><p><a class="reference external" href="https://github.com/KULL-Centre/_2022_ML-ddG-Blaabjerg">(Blaabjerg et al. 2022)</a></p></td>
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</tr>
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<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">rdkit_*</span></code></p></td>
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<td><p><a class="reference external" href="https://github.com/rdkit/rdkit">(rdkit)</a></p></td>
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</tr>
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<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">rfp_foldx_*</span></code></p></td>
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<td><p><a class="reference external" href="https://academic.oup.com/nar/article/33/suppl_2/W382/2505499">(Schymkowitz et al. 2005)</a>, <a class="reference external" href="https://github.com/samuelstanton/lambo">(Stanton et al. 2022)</a></p></td>
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</tr>
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<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">sa_tdc</span></code></p></td>
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<td><p><a class="reference external" href="https://www.nature.com/articles/s41589-022-01131-2">(Huang et al. 2022)</a>, <a class="reference external" href="https://github.com/rdkit/rdkit">(rdkit)</a>, <a class="reference external" href="https://link.springer.com/article/10.1186/1758-2946-1-8">(Ertl and Schuffenhauer 2009)</a></p></td>
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</tr>
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<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">super_mario_bros</span></code></p></td>
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<td><p><a class="reference external" href="https://github.com/CIGbalance/DagstuhlGAN">(Volz et al. 2018)</a>, <a class="reference external" href="https://github.com/miguelgondu/minimal_VAE_on_Mario">(González-Duque 2023)</a></p></td>
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</tr>
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<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">toy_continuous_problem</span></code></p></td>
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<td><p><a class="reference external" href="https://www.al-roomi.org/benchmarks/unconstrained">(Al-Roomi 2015)</a>, <a class="reference external" href="https://www.sfu.ca/~ssurjano/optimization.html">(Surjanovic and Bingham 2013)</a></p></td>
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</tr>
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</tbody>
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</table>
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</section>
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<section id="contribute-problems-or-solvers">
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<h2>Contribute problems or solvers<a class="headerlink" href="#contribute-problems-or-solvers" title="Permalink to this heading">#</a></h2>
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<p>These are a couple of guides about how to contribute a new problem factory (i.e. black-box objective function), or a new optimization algorithm.</p>
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</ul>
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</li>
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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="#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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</nav></div>

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

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‎docs/poli-docs/index.md

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::::
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## Cite us and other relevant work
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If you use `poli`, we encourage you to cite us
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```
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@software{GonzalezDuqueBartelsMichael:poli:2024,
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author = {González-Duque, Miguel and Bartels, Simon and Michael, Richard},
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month = jan,
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title = {{poli: a libary of discrete sequence objectives}},
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url = {https://github.com/MachineLearningLifeScience/poli},
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version = {0.0.1},
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year = {2024}
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}
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```
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If you use certain black boxes, we also recommend citing the original work:
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|Black box|Reference(s)|
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|---------|---------|
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|`dockstring`|[(García-Ortegón et al. 2022)](https://pubs.acs.org/doi/10.1021/acs.jcim.1c01334)|
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|`drd3_docking`|[(Graff, Shakhnovich and Coley 2020)](https://pubs.acs.org/doi/10.1021/acs.jcim.1c01334), [(Graff and Coley 2022)](https://joss.theoj.org/papers/10.21105/joss.03950), [(Huang et al. 2022)](https://www.nature.com/articles/s41589-022-01131-2)|
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|`foldx_*`|[(Schymkowitz et al. 2005)](https://academic.oup.com/nar/article/33/suppl_2/W382/2505499)|
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|`gfp_cbas`|[(Brookes, Park and Listgarten 2019)](https://proceedings.mlr.press/v97/brookes19a.html)|
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|`gfp_select`|[(Brookes, Park and Listgarten 2019)](https://proceedings.mlr.press/v97/brookes19a.html)|
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|`penalized_logp_lambo`|[(Stanton et al. 2022)](https://github.com/samuelstanton/lambo)|
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|`rasp`|[(Blaabjerg et al. 2022)](https://github.com/KULL-Centre/_2022_ML-ddG-Blaabjerg)|
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|`rdkit_*`|[(rdkit)](https://github.com/rdkit/rdkit)|
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|`rfp_foldx_*`|[(Schymkowitz et al. 2005)](https://academic.oup.com/nar/article/33/suppl_2/W382/2505499), [(Stanton et al. 2022)](https://github.com/samuelstanton/lambo)|
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|`sa_tdc`|[(Huang et al. 2022)](https://www.nature.com/articles/s41589-022-01131-2), [(rdkit)](https://github.com/rdkit/rdkit), [(Ertl and Schuffenhauer 2009)](https://link.springer.com/article/10.1186/1758-2946-1-8)|
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|`super_mario_bros`|[(Volz et al. 2018)](https://github.com/CIGbalance/DagstuhlGAN), [(González-Duque 2023)](https://github.com/miguelgondu/minimal_VAE_on_Mario) |
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|`toy_continuous_problem`|[(Al-Roomi 2015)](https://www.al-roomi.org/benchmarks/unconstrained), [(Surjanovic and Bingham 2013)](https://www.sfu.ca/~ssurjano/optimization.html) |
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## Contribute problems or solvers
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