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Updating RL notebooks.
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‎.idea/misc.xml

+3
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‎notebooks/Reinforcement_Learning_Demo.ipynb

+18-18
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@@ -5,16 +5,16 @@
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"metadata": {},
66
"source": [
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"> **How to run this notebook (command-line)?**\n",
8-
"1. Install the `reinvent_shared.v2.1` environment:\n",
8+
"1. Install the `ReinventCommunity` environment:\n",
99
"`conda env create -f reinvent_shared.yml`\n",
1010
"2. Activate the environment:\n",
11-
"`conda activate reinvent_shared.v2.1`\n",
11+
"`conda activate ReinventCommunity`\n",
1212
"3. Execute `jupyter`:\n",
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"`jupyter notebook`\n",
1414
"4. Copy the link to a browser\n",
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"\n",
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"\n",
17-
"# `REINVENT 2.0`: reinforcement learning demo\n",
17+
"# `REINVENT 3.0`: reinforcement learning demo\n",
1818
"The aim of this notebook is to illustrate how `REINVENT` can be used for the _de novo_ design of molecules in a *Reinforcement Learning* (RL) setup. The general idea is to start with a (somewhat) focussed prior and to define a (complex) scoring function from a set of building blocks (*components*) to decide which molecules are \"good\" or \"bad\". Each molecule generated by the _agent_ will thus receive a score from 0 to 1 and this feedback is used to train the agent over time, i.e. to focus it on chemical regions of interest for a given project.\n",
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"\n",
2020
"![](img/REINVENT_RL_mode.png)\n",
@@ -45,7 +45,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"execution_count": 10,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -56,8 +56,8 @@
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"import tempfile\n",
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"\n",
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"# --------- change these path variables as required\n",
59-
"reinvent_dir = os.path.expanduser(\"~/Desktop/Projects/Publications/2020/2020-04_REINVENT_2.0/Reinvent\")\n",
60-
"reinvent_env = os.path.expanduser(\"~/miniconda3/envs/reinvent_shared.v2.1\")\n",
59+
"reinvent_dir = os.path.expanduser(\"~/Desktop/Projects/Publications/2020/2020-04_REINVENT_3.0/Reinvent\")\n",
60+
"reinvent_env = os.path.expanduser(\"~/miniconda3/envs/reinvent_shared.v.3.0\")\n",
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"output_dir = os.path.expanduser(\"~/Desktop/REINVENT_RL_demo\")\n",
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"\n",
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"# --------- do not change\n",
@@ -82,7 +82,7 @@
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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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"execution_count": 3,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -104,14 +104,14 @@
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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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"execution_count": 4,
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"metadata": {},
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"outputs": [],
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"source": [
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"# add block to specify whether to run locally or not and\n",
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"# where to store the results and logging\n",
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"configuration[\"logging\"] = {\n",
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" \"sender\": \"http://127.0.0.1\", # only relevant if \"recipient\" is set to \"remote\"\n",
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" \"sender\": \"0.0.0.0\", # only relevant if \"recipient\" is set to \"remote\"\n",
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" \"recipient\": \"local\", # either to local logging or use a remote REST-interface\n",
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" \"logging_frequency\": 10, # log every x-th steps\n",
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" \"logging_path\": os.path.join(output_dir, \"progress.log\"), # load this folder in tensorboard\n",
@@ -134,7 +134,7 @@
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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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"execution_count": 5,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -146,7 +146,7 @@
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" \"name\": \"IdenticalMurckoScaffold\", # other options are: \"IdenticalTopologicalScaffold\", \n",
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" # \"NoFilter\" and \"ScaffoldSimilarity\"\n",
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" # -> use \"NoFilter\" to disable this feature\n",
149-
" \"nbmax\": 25, # the bin size; penalization will start once this is exceeded\n",
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" \"bucket_size\": 25, # the bin size; penalization will start once this is exceeded\n",
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" \"minscore\": 0.4, # the minimum total score to be considered for binning\n",
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" \"minsimilarity\": 0.4 # the minimum similarity to be placed into the same bin\n",
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"}\n",
@@ -186,7 +186,7 @@
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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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"execution_count": 6,
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"metadata": {},
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"outputs": [],
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"source": [
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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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"execution_count": 7,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -309,7 +309,7 @@
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"The command-line execution looks like this:\n",
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"```\n",
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"# activate envionment\n",
312-
"conda activate reinvent_shared.v2.1\n",
312+
"conda activate reinvent_shared.v.3.0\n",
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"\n",
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"# execute REINVENT\n",
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"python <your_path>/input.py <config>.json\n",
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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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"execution_count": 8,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"execution_count": 9,
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"metadata": {},
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"outputs": [],
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"source": [
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"cd <your_path>/REINVENT_RL_demo\n",
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"\n",
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"# make sure, you have activated the proper environment\n",
458-
"conda activate reinvent_shared.v2.1\n",
458+
"conda activate reinvent_shared.v.3.0\n",
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"\n",
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"# start tensorboard\n",
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"tensorboard --logdir progress.log\n",
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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": "3.7.6"
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"version": "3.7.3"
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}
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},
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"nbformat": 4,

‎notebooks/Reinforcement_Learning_Demo_Selectivity.ipynb

+10-10
Original file line numberDiff line numberDiff line change
@@ -5,16 +5,16 @@
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"metadata": {},
66
"source": [
77
"> **How to run this notebook (command-line)?**\n",
8-
"1. Install the `reinvent_shared.v2.1` environment:\n",
8+
"1. Install the `ReinventCommunity` environment:\n",
99
"`conda env create -f reinvent_shared.yml`\n",
1010
"2. Activate the environment:\n",
11-
"`conda activate reinvent_shared.v2.1`\n",
11+
"`conda activate ReinventCommunity`\n",
1212
"3. Execute `jupyter`:\n",
1313
"`jupyter notebook`\n",
1414
"4. Copy the link to a browser\n",
1515
"\n",
1616
"\n",
17-
"# `REINVENT 2.0`: reinforcement learning selectivity demo\n",
17+
"# `REINVENT 3.0`: reinforcement learning selectivity demo\n",
1818
"This illustrates the use of a selectivity score component. This component is normally used in a scenario where ligands are designed to bind to a concrete target and at the same time should not be binding to one or more off-targets. The example here looks at a single off-target case.\n",
1919
"\n",
2020
"We will demonstrate how to set up a `REINVENT` run that optimizes molecules to be selective against _Aurora_ kinase by minimizing at the same time their affinity to _B RAF_ kinase.\n",
@@ -32,7 +32,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"execution_count": 2,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -43,8 +43,8 @@
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"import tempfile\n",
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"\n",
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"# --------- change these path variables as required\n",
46-
"reinvent_dir = os.path.expanduser(\"~/Desktop/Projects/Publications/2020/2020-04_REINVENT_2.0/Reinvent\")\n",
47-
"reinvent_env = os.path.expanduser(\"~/miniconda3/envs/reinvent_shared.v2.1\")\n",
46+
"reinvent_dir = os.path.expanduser(\"~/Desktop/Projects/Publications/2020/2020-04_REINVENT_3.0/Reinvent\")\n",
47+
"reinvent_env = os.path.expanduser(\"~/miniconda3/envs/reinvent_shared.v.3.0\")\n",
4848
"output_dir = os.path.expanduser(\"~/Desktop/REINVENT_RL_demo\")\n",
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"\n",
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"# --------- do not change\n",
@@ -155,7 +155,7 @@
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" \"name\": \"IdenticalMurckoScaffold\", # other options are: \"IdenticalTopologicalScaffold\", \n",
156156
" # \"NoFilter\" and \"ScaffoldSimilarity\"\n",
157157
" # -> use \"NoFilter\" to disable this feature\n",
158-
" \"nbmax\": 25, # the bin size; penalization will start once this is exceeded\n",
158+
" \"bucket_size\": 25, # the bin size; penalization will start once this is exceeded\n",
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" \"minscore\": 0.4, # the minimum total score to be considered for binning\n",
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" \"minsimilarity\": 0.4 # the minimum similarity to be placed into the same bin\n",
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"}"
@@ -398,7 +398,7 @@
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"The command-line execution looks like this:\n",
399399
"```\n",
400400
"# activate envionment\n",
401-
"conda activate reinvent_shared.v2.1\n",
401+
"conda activate reinvent_shared.v.3.0\n",
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"\n",
403403
"# execute REINVENT\n",
404404
"python <your_path>/input.py <config>.json\n",
@@ -544,7 +544,7 @@
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"cd <your_path>/REINVENT_RL_demo\n",
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"\n",
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"# make sure, you have activated the proper environment\n",
547-
"conda activate reinvent_shared.v2.1\n",
547+
"conda activate reinvent_shared.v.3.0\n",
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"\n",
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"# start tensorboard\n",
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"tensorboard --logdir progress.log\n",
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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": "3.7.6"
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"version": "3.7.3"
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}
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},
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"nbformat": 4,

‎notebooks/Reinforcement_Learning_Demo_Simple_Tanimoto.ipynb

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@@ -5,16 +5,16 @@
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"metadata": {},
66
"source": [
77
"> **How to run this notebook (command-line)?**\n",
8-
"1. Install the `reinvent_shared.v2.1` environment:\n",
8+
"1. Install the `ReinventCommunity` environment:\n",
99
"`conda env create -f reinvent_shared.yml`\n",
1010
"2. Activate the environment:\n",
11-
"`conda activate reinvent_shared.v2.1`\n",
11+
"`conda activate ReinventCommunity`\n",
1212
"3. Execute `jupyter`:\n",
1313
"`jupyter notebook`\n",
1414
"4. Copy the link to a browser\n",
1515
"\n",
1616
"\n",
17-
"# `REINVENT 2.0`: reinforcement learning with tanimoto similarity\n",
17+
"# `REINVENT 3.0`: reinforcement learning with tanimoto similarity\n",
1818
"\n",
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"\n",
2020
"This is a simple example of running `Reinvent` with only 1 score component.\n",
@@ -32,7 +32,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 13,
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"execution_count": 2,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -43,8 +43,8 @@
4343
"import tempfile\n",
4444
"\n",
4545
"# --------- change these path variables as required\n",
46-
"reinvent_dir = os.path.expanduser(\"~/Desktop/Projects/Publications/2020/2020-04_REINVENT_2.0/Reinvent\")\n",
47-
"reinvent_env = os.path.expanduser(\"~/miniconda3/envs/reinvent_shared.v2.1\")\n",
46+
"reinvent_dir = os.path.expanduser(\"~/Desktop/Projects/Publications/2020/2020-04_REINVENT_3.0/Reinvent\")\n",
47+
"reinvent_env = os.path.expanduser(\"~/miniconda3/envs/reinvent_shared.v.3.0\")\n",
4848
"output_dir = os.path.expanduser(\"~/Desktop/REINVENT_RL_demo\")\n",
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"\n",
5050
"# --------- do not change\n",
@@ -155,7 +155,7 @@
155155
" \"name\": \"IdenticalMurckoScaffold\", # other options are: \"IdenticalTopologicalScaffold\", \n",
156156
" # \"NoFilter\" and \"ScaffoldSimilarity\"\n",
157157
" # -> use \"NoFilter\" to disable this feature\n",
158-
" \"nbmax\": 25, # the bin size; penalization will start once this is exceeded\n",
158+
" \"bucket_size\": 25, # the bin size; penalization will start once this is exceeded\n",
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" \"minscore\": 0.4, # the minimum total score to be considered for binning\n",
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" \"minsimilarity\": 0.4 # the minimum similarity to be placed into the same bin\n",
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"}"
@@ -294,7 +294,7 @@
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"The command-line execution looks like this:\n",
295295
"```\n",
296296
"# activate envionment\n",
297-
"conda activate reinvent_shared.v2.1\n",
297+
"conda activate reinvent_shared.v.3.0\n",
298298
"\n",
299299
"# execute REINVENT\n",
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"python <your_path>/input.py <config>.json\n",
@@ -440,7 +440,7 @@
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"cd <your_path>/REINVENT_RL_demo\n",
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"\n",
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"# make sure, you have activated the proper environment\n",
443-
"conda activate reinvent_shared.v2.1\n",
443+
"conda activate reinvent_shared.v.3.0\n",
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"\n",
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"# start tensorboard\n",
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"tensorboard --logdir progress.log\n",
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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": "3.7.6"
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"version": "3.7.3"
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}
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},
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"nbformat": 4,

‎notebooks/Reinforcement_Learning_Exploitation_Demo.ipynb

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@@ -5,16 +5,16 @@
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"metadata": {},
66
"source": [
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"> **How to run this notebook (command-line)?**\n",
8-
"1. Install the `reinvent_shared.v2.1` environment:\n",
8+
"1. Install the `ReinventCommunity` environment:\n",
99
"`conda env create -f reinvent_shared.yml`\n",
1010
"2. Activate the environment:\n",
11-
"`conda activate reinvent_shared.v2.1`\n",
11+
"`conda activate ReinventCommunity`\n",
1212
"3. Execute `jupyter`:\n",
1313
"`jupyter notebook`\n",
1414
"4. Copy the link to a browser\n",
1515
"\n",
1616
"\n",
17-
"# `REINVENT 2.0`: reinforcement learning exploitation demo\n",
17+
"# `REINVENT 3.0`: reinforcement learning exploitation demo\n",
1818
"This demo illustrates how to set up a `REINVENT` run to optimize molecules that are active against _Aurora_ kinase. We use here predictive model as the main component to guide the generation of the molecules. we also include a `qed_score` component to stimulate the generation of more \"drug-like\" molecules.\n",
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"\n",
2020
"\n"
@@ -41,8 +41,8 @@
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"import tempfile\n",
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"\n",
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"# --------- change these path variables as required\n",
44-
"reinvent_dir = os.path.expanduser(\"~/Desktop/Projects/Publications/2020/2020-04_REINVENT_2.0/Reinvent\")\n",
45-
"reinvent_env = os.path.expanduser(\"~/miniconda3/envs/reinvent_shared.v2.1\")\n",
44+
"reinvent_dir = os.path.expanduser(\"~/Desktop/Projects/Publications/2020/2020-04_REINVENT_3.0/Reinvent\")\n",
45+
"reinvent_env = os.path.expanduser(\"~/miniconda3/envs/reinvent_shared.v.3.0\")\n",
4646
"output_dir = os.path.expanduser(\"~/Desktop/REINVENT_RL_demo\")\n",
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"\n",
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"# --------- do not change\n",
@@ -155,7 +155,7 @@
155155
" \"name\": \"NoFilter\", # other options are: \"IdenticalTopologicalScaffold\", \n",
156156
" # \"IdenticalMurckoScaffold\" and \"ScaffoldSimilarity\"\n",
157157
" # -> use \"NoFilter\" to disable this feature\n",
158-
" \"nbmax\": 25, # the bin size; penalization will start once this is exceeded\n",
158+
" \"bucket_size\": 25, # the bin size; penalization will start once this is exceeded\n",
159159
" \"minscore\": 0.4, # the minimum total score to be considered for binning\n",
160160
" \"minsimilarity\": 0.4 # the minimum similarity to be placed into the same bin\n",
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"}"
@@ -358,7 +358,7 @@
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"The command-line execution looks like this:\n",
359359
"```\n",
360360
"# activate envionment\n",
361-
"conda activate reinvent_shared.v2.1\n",
361+
"conda activate reinvent_shared.v.3.0\n",
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"\n",
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"# execute REINVENT\n",
364364
"python <your_path>/input.py <config>.json\n",
@@ -504,7 +504,7 @@
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"cd <your_path>/REINVENT_RL_demo\n",
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"\n",
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"# make sure, you have activated the proper environment\n",
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"conda activate reinvent_shared.v2.1\n",
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"conda activate reinvent_shared.v.3.0\n",
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"\n",
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"# start tensorboard\n",
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"tensorboard --logdir progress.log\n",
@@ -584,7 +584,7 @@
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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": "3.7.6"
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"version": "3.7.3"
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}
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},
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"nbformat": 4,

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