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Sphinx documentation for 813ab62
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20 changes: 10 additions & 10 deletions latest/_sources/examples/Backtesting/multi_target.md.txt
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Expand Up @@ -165,20 +165,20 @@ print(results)
```

Scenario Monte_Carlo_Run Iteration Num_Experiments Target_1_Measurements \
0 BayBE 0 0 1 [16.0]
1 BayBE 0 1 2 [12.0]
2 BayBE 1 0 1 [12.0]
0 BayBE 0 0 1 [12.0]
1 BayBE 0 1 2 [16.0]
2 BayBE 1 0 1 [16.0]
3 BayBE 1 1 2 [16.0]

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

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

22 changes: 9 additions & 13 deletions latest/_sources/examples/Basics/campaign.md.txt
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Expand Up @@ -119,13 +119,9 @@ print(recommendation)


Recommended measurements with batch_size = 2:
Solvent Base Ligand \
191 Butyornitrile Potassium pivalate (t-Bu)PhCPhos
401 p-Xylene Potassium acetate Di-tert-butylphenylphosphine

Temperature Concentration
191 90.0 0.153
401 105.0 0.153
Solvent Base Ligand Temperature Concentration
368 p-Xylene Cesium pivalate BrettPhos 120.0 0.153
406 p-Xylene Potassium pivalate (t-Bu)PhCPhos 90.0 0.100


Adding target values is done by creating a new column in the `recommendation`
Expand All @@ -143,13 +139,13 @@ print(recommendation)


Recommended experiments with fake measured values:
Solvent Base Ligand \
191 Butyornitrile Potassium pivalate (t-Bu)PhCPhos
401 p-Xylene Potassium acetate Di-tert-butylphenylphosphine
Solvent Base Ligand Temperature Concentration \
368 p-Xylene Cesium pivalate BrettPhos 120.0 0.153
406 p-Xylene Potassium pivalate (t-Bu)PhCPhos 90.0 0.100

Temperature Concentration yield
191 90.0 0.153 15.952156
401 105.0 0.153 5.471604
yield
368 5.951013
406 0.730310



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35 changes: 20 additions & 15 deletions latest/_sources/examples/Basics/recommenders.md.txt
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Expand Up @@ -113,11 +113,11 @@ Note that the availability of the acquisition functions might depend on the
- If a larger value is chosen, only those that allow batching.
That is, 'q'-variants of the acquisition functions must be chosen.

The default he acquisition function is q-Expected Improvement.
The default acquisition function is q-Log Expected Improvement.


```python
ACQ_FUNCTION = "qEI"
ACQ_FUNCTION = "qLogEI"
```

## Other parameters
Expand Down Expand Up @@ -169,7 +169,7 @@ print(recommender)
GaussianProcessSurrogate
Supports Transfer Learning: True
Kernel factory: DefaultKernelFactory()
Acquisition function: qExpectedImprovement()
Acquisition function: qLogExpectedImprovement()
Compatibility: SearchSpaceType.HYBRID
Sequential continuous: False
Hybrid sampler: None
Expand Down Expand Up @@ -266,10 +266,15 @@ print(recommendation)


Recommended experiments:
Solvent Base Ligand Temperature Concentration
12 Butyl Ester Cesium acetate BrettPhos 105.0 0.057
248 DMAc Cesium pivalate (t-Bu)PhCPhos 105.0 0.153
44 Butyl Ester Cesium pivalate BrettPhos 120.0 0.153
Solvent Base Ligand Temperature \
55 Butyl Ester Potassium acetate (t-Bu)PhCPhos 90.0
48 Butyl Ester Cesium pivalate Di-tert-butylphenylphosphine 105.0
4 Butyl Ester Cesium acetate (t-Bu)PhCPhos 105.0

Concentration
55 0.100
48 0.057
4 0.100



Expand All @@ -282,15 +287,15 @@ print(recommendation)


Recommended experiments with fake measured values:
Solvent Base Ligand Temperature Concentration \
12 Butyl Ester Cesium acetate BrettPhos 105.0 0.057
248 DMAc Cesium pivalate (t-Bu)PhCPhos 105.0 0.153
44 Butyl Ester Cesium pivalate BrettPhos 120.0 0.153
Solvent Base Ligand Temperature \
55 Butyl Ester Potassium acetate (t-Bu)PhCPhos 90.0
48 Butyl Ester Cesium pivalate Di-tert-butylphenylphosphine 105.0
4 Butyl Ester Cesium acetate (t-Bu)PhCPhos 105.0

yield
12 4.081841
248 27.981630
44 29.246986
Concentration yield
55 0.100 26.268857
48 0.057 24.724293
4 0.100 4.104348



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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: 0.0014761649999854853
Consumed time of RandomRecommender: 0.0013269639999862193

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
29 10.0 200.0
1 1.0 111.111111


## 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 3.353523 19.654822 3.075198 0.308224 70.384363 3.223869
1 19.206794 2.495087 0.482521 0.827357 48.007319 28.980922
2 4.651592 14.592150 1.003440 3.440816 21.447111 54.864891
3 16.840047 1.169069 1.786092 2.132389 38.980910 39.091494
4 1.158361 17.238409 1.814759 1.733210 64.007646 14.047616
5 7.169952 12.852353 1.432934 1.196504 51.845792 25.502465
6 9.625065 8.116284 0.465268 3.935533 29.916537 47.941313
7 18.263297 10.945888 1.893444 2.706125 21.220186 44.971059
8 18.409266 0.573198 2.593532 0.184949 7.360000 70.879055
9 10.165157 10.349447 0.472423 1.006329 60.845011 17.161633
0 15.424088 15.483034 1.774463 2.564607 1.349968 63.403840
1 9.867693 9.161113 1.225527 1.575317 23.809962 54.360388
2 16.482221 0.922183 0.326441 4.384775 25.064485 52.819894
3 15.196090 17.343875 2.031599 2.433644 35.685558 27.309234
4 5.760099 17.172176 3.143510 0.639543 63.155880 10.128793
5 0.288925 18.088352 1.196861 3.325168 65.415564 11.685130
6 11.550698 9.579842 2.939837 0.964550 55.966665 18.998407
7 17.989342 17.070881 1.537935 1.358417 27.655118 34.388307
8 6.481276 19.528859 3.575574 0.326208 67.406662 2.681421
9 12.008461 11.923639 3.728560 0.262943 56.609307 15.467091


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 23.008345 3.383422
1 100.0 21.701881 1.309878
2 100.0 19.243742 4.444256
3 100.0 18.009115 3.918481
4 100.0 18.396769 3.547969
5 100.0 20.022305 2.629438
6 100.0 17.741350 4.400800
7 100.0 29.209186 4.599569
8 100.0 18.982463 2.778481
9 100.0 20.514604 1.478752
0 100.0 30.907122 4.339070
1 100.0 19.028806 2.800844
2 100.0 17.404405 4.711216
3 100.0 32.539965 4.465243
4 100.0 22.932275 3.783052
5 100.0 18.377278 4.522029
6 100.0 21.130540 3.904388
7 100.0 35.060224 2.896352
8 100.0 26.010135 3.901782
9 100.0 23.932099 3.991503



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108 changes: 51 additions & 57 deletions latest/_sources/examples/Multi_Target/desirability.md.txt
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Expand Up @@ -250,22 +250,22 @@ 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
260 33 very good 3.0 -9.0 40.350076 82.947295 53.849382
266 33 very good 4.0 -3.0 76.706286 18.422049 53.322272
258 33 very good 2.0 -3.0 60.789399 17.429428 51.872360
Cat_1 Cat_2 Num_disc_1 Num_disc_2 Target_1 Target_2 Target_3
0 22 OK 1.0 -9.0 17.270952 2.703781 52.480793
5 22 OK 2.0 -6.0 16.620479 93.643522 52.173002
167 33 OK 10.0 -1.0 17.370195 48.778035 53.109152

Internal measurement database with desirability values:

Cat_1 Cat_2 Num_disc_1 Num_disc_2 Target_1 Target_2 Target_3 \
0 33 very good 3.0 -9.0 40.350076 82.947295 53.849382
1 33 very good 4.0 -3.0 76.706286 18.422049 53.322272
2 33 very good 2.0 -3.0 60.789399 17.429428 51.872360
Cat_1 Cat_2 Num_disc_1 Num_disc_2 Target_1 Target_2 Target_3 \
0 22 OK 1.0 -9.0 17.270952 2.703781 52.480793
1 22 OK 2.0 -6.0 16.620479 93.643522 52.173002
2 33 OK 10.0 -1.0 17.370195 48.778035 53.109152

BatchNr FitNr Desirability
0 1 NaN 0.560920
1 1 NaN 0.797719
2 1 NaN 0.846092
0 1 NaN 0.759647
1 1 NaN 0.591884
2 1 NaN 0.631707



Expand All @@ -274,35 +274,29 @@ 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 \
index
226 33 very bad 1.0 -3.0 31.650155 32.789952
255 33 very good 1.0 -1.0 36.104211 3.972519
114 22 very good 1.0 -3.0 69.949865 10.936628

Target_3
index
226 53.987045
255 51.615686
114 56.968097
Cat_1 Cat_2 Num_disc_1 Num_disc_2 Target_1 Target_2 Target_3
index
28 22 bad 1.0 -9.0 28.625872 0.258456 53.375854
8 22 OK 3.0 -9.0 20.756686 94.631213 54.952656
140 33 OK 1.0 -9.0 33.333648 15.662635 55.318242

Internal measurement database with desirability values:

Cat_1 Cat_2 Num_disc_1 Num_disc_2 Target_1 Target_2 Target_3 \
0 33 very good 3.0 -9.0 40.350076 82.947295 53.849382
1 33 very good 4.0 -3.0 76.706286 18.422049 53.322272
2 33 very good 2.0 -3.0 60.789399 17.429428 51.872360
3 33 very bad 1.0 -3.0 31.650155 32.789952 53.987045
4 33 very good 1.0 -1.0 36.104211 3.972519 51.615686
5 22 very good 1.0 -3.0 69.949865 10.936628 56.968097
Cat_1 Cat_2 Num_disc_1 Num_disc_2 Target_1 Target_2 Target_3 \
0 22 OK 1.0 -9.0 17.270952 2.703781 52.480793
1 22 OK 2.0 -6.0 16.620479 93.643522 52.173002
2 33 OK 10.0 -1.0 17.370195 48.778035 53.109152
3 22 bad 1.0 -9.0 28.625872 0.258456 53.375854
4 22 OK 3.0 -9.0 20.756686 94.631213 54.952656
5 33 OK 1.0 -9.0 33.333648 15.662635 55.318242

BatchNr FitNr Desirability
0 1 1.0 0.560920
1 1 1.0 0.797719
2 1 1.0 0.846092
3 2 NaN 0.634312
4 2 NaN 0.833742
5 2 NaN 0.545229
0 1 1.0 0.759647
1 1 1.0 0.591884
2 1 1.0 0.631707
3 2 NaN 0.734444
4 2 NaN 0.419615
5 2 NaN 0.576128


#### ITERATION 3 ####
Expand All @@ -311,33 +305,33 @@ for kIter in range(N_ITERATIONS):

Cat_1 Cat_2 Num_disc_1 Num_disc_2 Target_1 Target_2 Target_3
index
24 22 OK 10.0 -9.0 3.674533 10.309492 53.890179
167 33 OK 10.0 -1.0 20.526413 99.662726 52.893602
31 22 bad 1.0 -1.0 58.593021 59.762472 52.403895
1 22 OK 1.0 -6.0 61.173270 35.158627 56.680576
165 33 OK 10.0 -6.0 6.509212 93.919595 56.238915
163 33 OK 8.0 -1.0 30.876283 79.154161 52.108587

Internal measurement database with desirability values:

Cat_1 Cat_2 Num_disc_1 Num_disc_2 Target_1 Target_2 Target_3 \
0 33 very good 3.0 -9.0 40.350076 82.947295 53.849382
1 33 very good 4.0 -3.0 76.706286 18.422049 53.322272
2 33 very good 2.0 -3.0 60.789399 17.429428 51.872360
3 33 very bad 1.0 -3.0 31.650155 32.789952 53.987045
4 33 very good 1.0 -1.0 36.104211 3.972519 51.615686
5 22 very good 1.0 -3.0 69.949865 10.936628 56.968097
6 22 OK 10.0 -9.0 3.674533 10.309492 53.890179
7 33 OK 10.0 -1.0 20.526413 99.662726 52.893602
8 22 bad 1.0 -1.0 58.593021 59.762472 52.403895
Cat_1 Cat_2 Num_disc_1 Num_disc_2 Target_1 Target_2 Target_3 \
0 22 OK 1.0 -9.0 17.270952 2.703781 52.480793
1 22 OK 2.0 -6.0 16.620479 93.643522 52.173002
2 33 OK 10.0 -1.0 17.370195 48.778035 53.109152
3 22 bad 1.0 -9.0 28.625872 0.258456 53.375854
4 22 OK 3.0 -9.0 20.756686 94.631213 54.952656
5 33 OK 1.0 -9.0 33.333648 15.662635 55.318242
6 22 OK 1.0 -6.0 61.173270 35.158627 56.680576
7 33 OK 10.0 -6.0 6.509212 93.919595 56.238915
8 33 OK 8.0 -1.0 30.876283 79.154161 52.108587

BatchNr FitNr Desirability
0 1 1.0 0.560920
1 1 1.0 0.797719
2 1 1.0 0.846092
3 2 2.0 0.634312
4 2 2.0 0.833742
5 2 2.0 0.545229
6 3 NaN 0.630036
7 3 NaN 0.549214
8 3 NaN 0.732174
0 1 1.0 0.759647
1 1 1.0 0.591884
2 1 1.0 0.631707
3 2 2.0 0.734444
4 2 2.0 0.419615
5 2 2.0 0.576128
6 3 NaN 0.497782
7 3 NaN 0.300641
8 3 NaN 0.652394


## Addendum: Description of `transformation` functions
Expand Down
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 -1.262618 3.514526 -0.866085 2.977682 57.747226
1 3.616407 -1.571995 -2.997078 -0.655423 76.998696
2 4.080725 -1.874735 0.558634 1.955366 48.221856
0 5.019620 -2.353346 2.288716 -2.004918 68.528705
1 0.026129 -2.967297 0.706187 1.865806 29.197501
2 -3.571491 0.780301 1.161809 -3.464889 78.330964

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 0.504134 0.399150 1.882305 -1.693912 6.825879
1 1.106643 -1.323515 -0.472720 1.765690 6.317474
2 1.327344 0.765187 -0.903415 -1.647991 5.879385
0 1.090092 1.690475 0.446202 -1.001200 5.247506
1 -0.319849 -0.155378 0.939458 1.088984 2.194914
2 1.360450 1.358037 -1.004247 1.310631 6.421354

8 changes: 4 additions & 4 deletions latest/_sources/examples/Searchspaces/discrete_space.md.txt
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Expand Up @@ -158,8 +158,8 @@ print(recommendation)


Recommended experiments with measured values:
x_1 x_2 x_3 x_4 Target
48 -5.120000 5.12 -5.120000 -5.120000 115.698855
187 1.706667 5.12 1.706667 5.120000 89.053246
10 -5.120000 -5.12 1.706667 1.706667 89.053246
x_1 x_2 x_3 x_4 Target
22 -5.120000 -1.706667 -1.706667 1.706667 75.730442
5 -5.120000 -5.120000 -1.706667 -1.706667 89.053246
187 1.706667 5.120000 1.706667 5.120000 89.053246

6 changes: 3 additions & 3 deletions latest/_sources/examples/Searchspaces/hybrid_space.md.txt
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Expand Up @@ -205,7 +205,7 @@ print(recommendation)

Recommended experiments with measured values:
x_1 x_2 x_3 x_4 x_5 x_6 Target
16 0.00 5.12 0.00 -1.981100 2.844840 -4.142730 66.321525
5 -5.12 0.00 5.12 2.346828 -1.908385 1.429338 105.399437
6 -5.12 5.12 -5.12 -2.749081 -4.599875 1.416140 164.292091
10 0.00 -5.12 0.00 -0.203904 1.311253 -2.181600 62.176734
20 5.12 -5.12 5.12 -2.147161 -0.229926 2.585545 129.433097
14 0.00 0.00 5.12 -0.551382 4.728800 1.155669 88.151313

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