Cleans the titles for the sections, adds cards to make the available objective functions more eye-catching

Author: miguelgondu

docs/protein-optimization/_toc.yml

@@ -7,17 +7,23 @@ parts:
   - caption: Getting started
     chapters:
       - file: getting_started/getting_started.md
-  - caption: Using poli - the basics
+  - caption: The basics
     chapters:
       - file: using_poli/the_basics/intro_to_poli.ipynb
       - file: using_poli/the_basics/registering_an_objective_function.md
       - file: using_poli/the_basics/defining_a_problem_solver.md
       - file: using_poli/the_basics/optimizing_an_objective_function.md
       - file: using_poli/the_basics/diving_deeper.md
-  - caption: Using poli - examples
+  - caption: Examples
     chapters:
       - file: using_poli/optimization_examples/protein-stability-foldx/optimizing_protein_stability.ipynb
-  - caption: Understanding FoldX
+  - caption: Some objective functions available
+    chapters:
+      - file: using_poli/objective_repository/white_noise.md
+      - file: using_poli/objective_repository/foldx_stability.md
+      - file: using_poli/objective_repository/super_mario_bros.md
+      - file: using_poli/objective_repository/small_molecule.md
+  - caption: "Appendix: Understanding FoldX"
     chapters:
     - file: understanding_foldx/00-installing-foldx.md
     - file: understanding_foldx/01-single-mutation-using-foldx/index.ipynb

docs/protein-optimization/getting_started/getting_started.md

@@ -87,12 +87,13 @@ $ python -c "from poli.objective_repository import AVAILABLE_OBJECTIVES ; print(
 Let's write a small script that installs `white_noise` from the repository:
 
 ```python
-# see examples/minimal_working_example.py
+# see poli/examples/minimal_working_example.py
+import numpy as np
 from poli import objective_factory
 
 problem_info, f, x0, y0, run_info = objective_factory.create(name="white_noise")
 
-x = np.array([[1]])  # must be of shape [b, d], in this case [1, 1].
+x = np.array([["1", "2", "3"]])  # must be of shape [b, L], in this case [1, 3].
 for _ in range(5):
     print(f"f(x) = {f(x)}")
 ```

docs/protein-optimization/index.md

@@ -1,24 +1,106 @@
-# Tutorials on protein optimization using poli
+# Protein optimization using `poli`
 
 This book contains documentation on how to use `poli` and `poli-baselines`, our tools for creating and optimizing black box objective functions.
 
 At its core, `poli` allows you to isolate calls to complicated objective functions which might, for example, depend on simulators, binaries, or a weird version of the Java runtime.
 Our promise is: if you can run your objective function reliably in a `conda` environment, then you can register it and call it from other projects without having to worry about re-installing all the dependencies.
 
-`poli` comes batteries-included. By this, we mean that there are already a collection of black box objective functions you could register and use out-of-the-box. Examples include:
-- standard white noise,
-- computing the stability of proteins and their mutations from a wildtype `pdb`,
-- optimizing the number of jumps Mario performs in a Super Mario Bros level sampled from the latent space of a Variational Autoencoder.
-- optimizing the QED and penalized logP of small molecules, presented as either SELFIES or SMILES. [WIP]
+`poli` comes batteries-included. By this, we mean that there are already a collection of black box objective functions you could register and use out-of-the-box.
 
-On top of `poli`, we provide `poli-baselines`, a collection of black-box optimization algorithms (focusing especially on *discrete* sequences). Examples include
-- Random mutations,
-- Evolutionary and genetic algorithms like CMA-ES, or NSGA-2 [WIP],
-- Bayesian Optimization in latent space [WIP].
+## Black-box objective functions
+
+These are some objective functions available on `poli`. **For a full list**, check [getting started](./getting_started/getting_started.md).
+
+::::{grid}
+:gutter: 3
+
+:::{grid-item-card} White noise
+:link: ./using_poli/objective_repository/white_noise.html
+:columns: 4
+White noise drawn from a unit Gaussian
+:::
+
+:::{grid-item-card} Aloha
+:link: ./using_poli/objective_repository/aloha.html
+:columns: 4
+A toy example about optimizing 5-letter words to spell "ALOHA"
+:::
+
+:::{grid-item-card} Protein Stability
+:link: ./using_poli/objective_repository/foldx_stability.html
+:columns: 4
+Stability of mutations of a wildtype using `foldx`
+:::
+
+:::{grid-item-card} Mario jumps
+:link: ./using_poli/objective_repository/super_mario_bros.html
+:columns: 4
+Optimizing the number of jumps on a Super Mario Bros level
+:::
+
+:::{grid-item-card} Small molecule properties
+:link: ./using_poli/objective_repository/small_molecule.html
+:columns: 4
+Small molecule's synthesizability, druglikeness, and more. [WIP]
+:::
+
+:::{grid-item-card} RaSP
+:link: ./using_poli/objective_repository/RaSP.html
+:columns: 4
+Rapid Stability Predictions of single mutations from a wildtype. [WIP]
+:::
+
+:::{grid-item-card} TDC oracles
+:link: ./using_poli/objective_repository/tdc_oracles.html
+:columns: 4
+Some of the oracles provided by the Therapeutics Data Commons. [WIP]
+:::
+
+::::
+## Black-box optimization algorithms
+
+On top of `poli`, we provide `poli-baselines`, a collection of **black-box optimization algorithms** (focusing especially on *discrete* sequences). Examples include
+
+::::{grid}
+:gutter: 3
+
+:::{grid-item-card} Random Mutations
+:link: ./using_poli_baselines/random_mutations.html
+:columns: 4
+Optimizing a discrete sequence by performing random mutations
+:::
+
+:::{grid-item-card} NSGA-2
+:link: ./using_poli_baselines/nsga_2.html
+:columns: 4
+A Genetic algorithm for optimizing more than one metric [WIP]
+:::
+
+:::{grid-item-card} CMA-ES
+:link: ./using_poli_baselines/cma_es.html
+:columns: 4
+An evolutionary strategy for continuous problems [WIP]
+:::
+
+:::{grid-item-card} Latent Space Bayesian Optimization
+:link: ./using_poli_baselines/latent_space_bo.html
+:columns: 4
+Learning continuous representations and optimizing in latent space. [WIP]
+:::
+
+:::{grid-item-card} Graph GA
+:link: ./using_poli_baselines/graph_ga.html
+:columns: 4
+Graph Genetic Algorithms for small molecules. [WIP]
+:::
+
+::::
+
+## Get started!
 
 A good place to start is the next chapter! [Go to Getting Started](./getting_started/getting_started.md).
 
-## Contents
+<!-- ## Contents of the book
 
 ```{tableofcontents}
-```
+``` -->

docs/protein-optimization/using_poli/objective_repository/RaSP.md

@@ -0,0 +1,3 @@
+# Rapid Stability Predictions
+
+[TODO: write]

docs/protein-optimization/using_poli/objective_repository/aloha.md

@@ -0,0 +1,3 @@
+# Aloha objective function
+
+[TODO: write]

docs/protein-optimization/using_poli/objective_repository/foldx_stability.md

@@ -0,0 +1,3 @@
+# Protein stability using `foldx`
+
+[TODO: write]

docs/protein-optimization/using_poli/objective_repository/small_molecule.md

@@ -0,0 +1,3 @@
+# Small molecule properties
+
+[TODO: write]

docs/protein-optimization/using_poli/objective_repository/super_mario_bros.md

@@ -0,0 +1,3 @@
+# Optimizing jumps in Super Mario Bros
+
+[TODO: write]

docs/protein-optimization/using_poli/objective_repository/tdc_oracles.md

@@ -0,0 +1,3 @@
+# Therapeutics Data Commons' oracles
+
+[TODO: write]

docs/protein-optimization/using_poli/objective_repository/white_noise.md

@@ -0,0 +1,3 @@
+# White Noise objective function
+
+[TODO: write]