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8 changes: 6 additions & 2 deletions latest/_modules/baybe/searchspace/continuous.html
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Expand Up @@ -1309,10 +1309,14 @@ <h1>Source code for baybe.searchspace.continuous</h1><div class="highlight"><pre
<span class="k">return</span> <span class="n">SubspaceContinuous</span><span class="p">(</span>
<span class="n">parameters</span><span class="o">=</span><span class="p">[</span><span class="n">p</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parameters</span> <span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">parameter_names</span><span class="p">],</span>
<span class="n">constraints_lin_eq</span><span class="o">=</span><span class="p">[</span>
<span class="n">c</span><span class="o">.</span><span class="n">_drop_parameters</span><span class="p">(</span><span class="n">parameter_names</span><span class="p">)</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">constraints_lin_eq</span>
<span class="n">c</span><span class="o">.</span><span class="n">_drop_parameters</span><span class="p">(</span><span class="n">parameter_names</span><span class="p">)</span>
<span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">constraints_lin_eq</span>
<span class="k">if</span> <span class="nb">set</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">parameters</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">(</span><span class="n">parameter_names</span><span class="p">)</span>
<span class="p">],</span>
<span class="n">constraints_lin_ineq</span><span class="o">=</span><span class="p">[</span>
<span class="n">c</span><span class="o">.</span><span class="n">_drop_parameters</span><span class="p">(</span><span class="n">parameter_names</span><span class="p">)</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">constraints_lin_ineq</span>
<span class="n">c</span><span class="o">.</span><span class="n">_drop_parameters</span><span class="p">(</span><span class="n">parameter_names</span><span class="p">)</span>
<span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">constraints_lin_ineq</span>
<span class="k">if</span> <span class="nb">set</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">parameters</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">(</span><span class="n">parameter_names</span><span class="p">)</span>
<span class="p">],</span>
<span class="p">)</span>

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8 changes: 4 additions & 4 deletions latest/_sources/examples/Backtesting/multi_target.md.txt
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Expand Up @@ -167,18 +167,18 @@ print(results)
Scenario Monte_Carlo_Run Iteration Num_Experiments Target_1_Measurements \
0 BayBE 0 0 1 [12.0]
1 BayBE 0 1 2 [16.0]
2 BayBE 1 0 1 [12.0]
2 BayBE 1 0 1 [16.0]
3 BayBE 1 1 2 [16.0]

Target_2_Measurements Target_1_IterBest Target_1_CumBest \
0 [287.0] 12.0 12.0
1 [511.0] 16.0 16.0
2 [287.0] 12.0 12.0
2 [511.0] 16.0 16.0
3 [511.0] 16.0 16.0

Target_2_IterBest Target_2_CumBest
0 287.0 287.0
1 511.0 287.0
2 287.0 287.0
3 511.0 287.0
2 511.0 511.0
3 511.0 511.0

20 changes: 10 additions & 10 deletions latest/_sources/examples/Basics/campaign.md.txt
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Expand Up @@ -119,13 +119,13 @@ print(recommendation)


Recommended measurements with batch_size = 2:
Solvent Base Ligand \
60 Butyl Ester Potassium acetate (t-Bu)PhCPhos
318 DMAc Potassium pivalate Di-tert-butylphenylphosphine
Solvent Base Ligand \
365 p-Xylene Cesium pivalate BrettPhos
156 Butyornitrile Cesium pivalate Di-tert-butylphenylphosphine

Temperature Concentration
60 120.0 0.057
318 105.0 0.057
365 105.0 0.153
156 105.0 0.057


Adding target values is done by creating a new column in the `recommendation`
Expand All @@ -143,13 +143,13 @@ print(recommendation)


Recommended experiments with fake measured values:
Solvent Base Ligand \
60 Butyl Ester Potassium acetate (t-Bu)PhCPhos
318 DMAc Potassium pivalate Di-tert-butylphenylphosphine
Solvent Base Ligand \
365 p-Xylene Cesium pivalate BrettPhos
156 Butyornitrile Cesium pivalate Di-tert-butylphenylphosphine

Temperature Concentration yield
60 120.0 0.057 5.458533
318 105.0 0.057 8.704748
365 105.0 0.153 2.463500
156 105.0 0.057 0.656694



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32 changes: 16 additions & 16 deletions latest/_sources/examples/Basics/recommenders.md.txt
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Expand Up @@ -266,15 +266,15 @@ print(recommendation)


Recommended experiments:
Solvent Base Ligand \
194 Butyornitrile Potassium pivalate (t-Bu)PhCPhos
339 p-Xylene Cesium acetate BrettPhos
267 DMAc Cesium pivalate Di-tert-butylphenylphosphine
Solvent Base Ligand Temperature \
276 DMAc Potassium acetate (t-Bu)PhCPhos 120.0
293 DMAc Potassium acetate Di-tert-butylphenylphosphine 105.0
235 DMAc Cesium acetate Di-tert-butylphenylphosphine 90.0

Temperature Concentration
194 105.0 0.153
339 120.0 0.057
267 120.0 0.057
Concentration
276 0.057
293 0.153
235 0.100



Expand All @@ -287,15 +287,15 @@ print(recommendation)


Recommended experiments with fake measured values:
Solvent Base Ligand \
194 Butyornitrile Potassium pivalate (t-Bu)PhCPhos
339 p-Xylene Cesium acetate BrettPhos
267 DMAc Cesium pivalate Di-tert-butylphenylphosphine
Solvent Base Ligand Temperature \
276 DMAc Potassium acetate (t-Bu)PhCPhos 120.0
293 DMAc Potassium acetate Di-tert-butylphenylphosphine 105.0
235 DMAc Cesium acetate Di-tert-butylphenylphosphine 90.0

Temperature Concentration yield
194 105.0 0.153 11.207594
339 120.0 0.057 24.177565
267 120.0 0.057 28.137615
Concentration yield
276 0.057 31.283463
293 0.153 1.452494
235 0.100 10.588720



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2 changes: 1 addition & 1 deletion latest/_sources/examples/Custom_Hooks/basics.md.txt
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Expand Up @@ -134,5 +134,5 @@ recommendation = recommender.recommend(batch_size=3, searchspace=searchspace)

Recommender type: RandomRecommender
Search space parameters: ['Concentration', 'Temperature']
Consumed time of RandomRecommender: 0.0013340110000399363
Consumed time of RandomRecommender: 0.001209985000002689

2 changes: 1 addition & 1 deletion latest/_sources/examples/Custom_Surrogates/custom_pretrained.md.txt
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Expand Up @@ -619,7 +619,7 @@ print(recommendation)
Recommendation from campaign:
Pressure[bar] Temperature[degree_C]
index
20 10.0 100.0
9 1.0 200.0


## Using configuration instead
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40 changes: 20 additions & 20 deletions latest/_sources/examples/Mixtures/traditional.md.txt
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Expand Up @@ -128,16 +128,16 @@ print(recommendations)
```

Base1 Base2 PhaseAgent1 PhaseAgent2 Solvent1 Solvent2
0 19.265682 0.811571 0.117880 1.991022 62.861540 14.952305
1 19.453215 16.010399 1.625516 1.911250 60.622220 0.377401
2 19.360706 5.384286 0.281719 4.192845 11.451554 59.328890
3 11.804689 16.275282 0.507592 0.755422 40.708202 29.948814
4 17.338869 9.695451 0.387009 2.027296 49.572981 20.978394
5 17.942072 18.407323 2.134392 0.702276 30.976302 29.837635
6 15.286349 16.877133 4.067668 0.004934 15.918797 47.845120
7 1.827779 12.745687 4.043107 0.955448 21.001203 59.426776
8 4.197495 11.405601 3.356073 1.638358 33.659543 45.742930
9 16.671789 7.780304 0.651715 1.601898 25.317099 47.977195
0 6.461321 14.445282 2.961481 1.501310 27.836867 46.793737
1 4.642657 5.623648 0.745832 2.626456 33.184273 53.177133
2 5.967978 19.516491 4.062285 0.929325 15.790921 53.732999
3 17.919650 0.547912 0.386836 3.170953 47.861868 30.112781
4 8.780356 19.259513 4.233344 0.748593 43.606132 23.372062
5 1.862073 12.777083 1.149829 3.118557 65.791170 15.301288
6 11.402974 1.499452 0.389961 4.335186 14.780170 67.592258
7 4.641703 8.133835 0.892765 1.239568 74.330755 10.761373
8 2.342823 15.133408 2.178940 1.466343 10.550083 68.328405
9 0.548667 19.323581 3.895240 0.194994 70.669440 5.368079


Computing the respective row sums reveals the expected result:
Expand All @@ -155,16 +155,16 @@ print(stats)
```

Total Total_Bases Total_Phase_Agents
0 100.0 20.077253 2.108902
1 100.0 35.463613 3.536766
2 100.0 24.744992 4.474564
3 100.0 28.079971 1.263013
4 100.0 27.034320 2.414305
5 100.0 36.349395 2.836668
6 100.0 32.163482 4.072602
7 100.0 14.573466 4.998555
8 100.0 15.603095 4.994431
9 100.0 24.452093 2.253613
0 100.0 20.906604 4.462791
1 100.0 10.266306 3.372288
2 100.0 25.484470 4.991610
3 100.0 18.467562 3.557789
4 100.0 28.039869 4.981937
5 100.0 14.639156 4.268386
6 100.0 12.902425 4.725147
7 100.0 12.775538 2.132333
8 100.0 17.476230 3.645282
9 100.0 19.872248 4.090233



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102 changes: 51 additions & 51 deletions latest/_sources/examples/Multi_Target/desirability.md.txt
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Expand Up @@ -251,21 +251,21 @@ for kIter in range(N_ITERATIONS):
Recommended measurements with fake measured results:

Cat_1 Cat_2 Num_disc_1 Num_disc_2 Target_1 Target_2 Target_3
24 22 OK 10.0 -9.0 9.355922 91.587269 51.163894
238 33 very bad 4.0 -3.0 23.051089 64.964941 51.503606
125 22 very good 4.0 -6.0 79.073890 13.300612 54.220656
199 33 good 1.0 -1.0 84.920950 45.495528 53.819254
123 22 very good 3.0 -1.0 10.926985 75.046472 55.888679
270 33 very good 6.0 -3.0 82.696388 48.073559 51.106742

Internal measurement database with desirability values:

Cat_1 Cat_2 Num_disc_1 Num_disc_2 Target_1 Target_2 Target_3 \
0 22 OK 10.0 -9.0 9.355922 91.587269 51.163894
1 33 very bad 4.0 -3.0 23.051089 64.964941 51.503606
2 22 very good 4.0 -6.0 79.073890 13.300612 54.220656
0 33 good 1.0 -1.0 84.920950 45.495528 53.819254
1 22 very good 3.0 -1.0 10.926985 75.046472 55.888679
2 33 very good 6.0 -3.0 82.696388 48.073559 51.106742

BatchNr FitNr Desirability
0 1 NaN 0.619500
1 1 NaN 0.689647
2 1 NaN 0.751713
0 1 NaN 0.727031
1 1 NaN 0.371646
2 1 NaN 0.854726



Expand All @@ -276,33 +276,33 @@ for kIter in range(N_ITERATIONS):

Cat_1 Cat_2 Num_disc_1 Num_disc_2 Target_1 Target_2 \
index
117 22 very good 2.0 -6.0 1.035971 68.109381
129 22 very good 6.0 -6.0 27.040849 48.503767
97 22 very bad 4.0 -6.0 20.034131 2.057792
242 33 very bad 6.0 -3.0 61.919889 75.801160
271 33 very good 6.0 -1.0 56.036412 54.891053
269 33 very good 6.0 -6.0 23.761042 7.326857

Target_3
index
117 53.706472
129 51.473553
97 52.264858
242 53.529570
271 55.321837
269 54.580200

Internal measurement database with desirability values:

Cat_1 Cat_2 Num_disc_1 Num_disc_2 Target_1 Target_2 Target_3 \
0 22 OK 10.0 -9.0 9.355922 91.587269 51.163894
1 33 very bad 4.0 -3.0 23.051089 64.964941 51.503606
2 22 very good 4.0 -6.0 79.073890 13.300612 54.220656
3 22 very good 2.0 -6.0 1.035971 68.109381 53.706472
4 22 very good 6.0 -6.0 27.040849 48.503767 51.473553
5 22 very bad 4.0 -6.0 20.034131 2.057792 52.264858
0 33 good 1.0 -1.0 84.920950 45.495528 53.819254
1 22 very good 3.0 -1.0 10.926985 75.046472 55.888679
2 33 very good 6.0 -3.0 82.696388 48.073559 51.106742
3 33 very bad 6.0 -3.0 61.919889 75.801160 53.529570
4 33 very good 6.0 -1.0 56.036412 54.891053 55.321837
5 33 very good 6.0 -6.0 23.761042 7.326857 54.580200

BatchNr FitNr Desirability
0 1 1.0 0.619500
1 1 1.0 0.689647
2 1 1.0 0.751713
3 2 NaN 0.521706
4 2 NaN 0.731576
5 2 NaN 0.777450
0 1 1.0 0.727031
1 1 1.0 0.371646
2 1 1.0 0.854726
3 2 NaN 0.639912
4 2 NaN 0.542816
5 2 NaN 0.627268


#### ITERATION 3 ####
Expand All @@ -311,39 +311,39 @@ for kIter in range(N_ITERATIONS):

Cat_1 Cat_2 Num_disc_1 Num_disc_2 Target_1 Target_2 \
index
17 22 OK 6.0 -6.0 83.172994 43.694599
130 22 very good 6.0 -3.0 37.107250 67.848956
68 22 good 4.0 -9.0 70.603404 19.884419
266 33 very good 4.0 -3.0 62.284034 44.322718
274 33 very good 8.0 -3.0 56.978779 68.706933
143 33 OK 1.0 -1.0 49.118042 39.920523

Target_3
index
17 51.771360
130 54.478676
68 52.389191
266 53.583516
274 53.877006
143 53.290144

Internal measurement database with desirability values:

Cat_1 Cat_2 Num_disc_1 Num_disc_2 Target_1 Target_2 Target_3 \
0 22 OK 10.0 -9.0 9.355922 91.587269 51.163894
1 33 very bad 4.0 -3.0 23.051089 64.964941 51.503606
2 22 very good 4.0 -6.0 79.073890 13.300612 54.220656
3 22 very good 2.0 -6.0 1.035971 68.109381 53.706472
4 22 very good 6.0 -6.0 27.040849 48.503767 51.473553
5 22 very bad 4.0 -6.0 20.034131 2.057792 52.264858
6 22 OK 6.0 -6.0 83.172994 43.694599 51.771360
7 22 very good 6.0 -3.0 37.107250 67.848956 54.478676
8 22 good 4.0 -9.0 70.603404 19.884419 52.389191
0 33 good 1.0 -1.0 84.920950 45.495528 53.819254
1 22 very good 3.0 -1.0 10.926985 75.046472 55.888679
2 33 very good 6.0 -3.0 82.696388 48.073559 51.106742
3 33 very bad 6.0 -3.0 61.919889 75.801160 53.529570
4 33 very good 6.0 -1.0 56.036412 54.891053 55.321837
5 33 very good 6.0 -6.0 23.761042 7.326857 54.580200
6 33 very good 4.0 -3.0 62.284034 44.322718 53.583516
7 33 very good 8.0 -3.0 56.978779 68.706933 53.877006
8 33 OK 1.0 -1.0 49.118042 39.920523 53.290144

BatchNr FitNr Desirability
0 1 1.0 0.619500
1 1 1.0 0.689647
2 1 1.0 0.751713
3 2 2.0 0.521706
4 2 2.0 0.731576
5 2 2.0 0.777450
6 3 NaN 0.842461
7 3 NaN 0.540238
8 3 NaN 0.836705
0 1 1.0 0.727031
1 1 1.0 0.371646
2 1 1.0 0.854726
3 2 2.0 0.639912
4 2 2.0 0.542816
5 2 2.0 0.627268
6 3 NaN 0.700022
7 3 NaN 0.620758
8 3 NaN 0.701594


## Addendum: Description of `transformation` functions
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6 changes: 3 additions & 3 deletions latest/_sources/examples/Searchspaces/continuous_space_botorch_function.md.txt
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Expand Up @@ -133,7 +133,7 @@ print(recommendation)

Recommended experiments with measured values:
x_1 x_2 x_3 x_4 Target
0 -3.633507 1.987442 -2.092419 2.271490 56.389738
1 -1.137338 -0.553995 2.572502 -3.155337 64.479077
2 3.045789 3.060791 -2.602792 4.265354 73.693725
0 4.028299 -3.372229 -0.333822 -1.093484 62.713355
1 -2.859714 0.712345 -4.488788 2.414860 89.227821
2 -0.894644 2.641240 4.339568 3.931880 76.731644

6 changes: 3 additions & 3 deletions latest/_sources/examples/Searchspaces/continuous_space_custom_function.md.txt
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Expand Up @@ -123,7 +123,7 @@ print(recommendation)

Recommended experiments with measured values:
x_1 x_2 x_3 x_4 Target
0 1.420138 0.798285 1.065526 1.344263 5.596436
1 -1.138527 -1.094842 -0.979810 1.557869 5.881909
2 -0.236226 1.790565 1.843527 0.759828 7.237855
0 0.556265 -1.407192 -1.907498 -0.158976 5.953441
1 1.147475 -1.329386 -1.714284 0.489744 6.262585
2 -0.605588 -0.952543 -0.364810 0.578576 1.741910

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