Commit 8125cbec authored by SOLIMAN Sylvain's avatar SOLIMAN Sylvain
Browse files

Comet Bernot to the rescue

parent b53b382f
......@@ -13,15 +13,7 @@
"metadata": {},
"outputs": [],
"source": [
"load(library:examples/lotka_volterra/LVi.bc)."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"load(library:examples/lotka_volterra/LVi.bc).\n",
"list_model."
]
},
......@@ -179,13 +171,100 @@
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"---\n",
"\n",
"Let us now consider a bigger model coming from L. Mendoza (Biosystems 2006), and made Boolean by the same author with Remy et al. (Dynamical Roles and Functionality of Feedback Circuits, Springer 2006).\n",
"Let us now look at a slightly bigger model of the Circadian Clock by J.-P. Comet and G. Bernot"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"load(library:examples/circadian_cycle/bernot_comet.bc).\n",
"list_model."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Question 4\n",
"\n",
"Using Biocham commands of your choice, what do you observe as the behavior of this model?"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Question 5\n",
"\n",
"Now try PAC learning on that model, choosing yourself the number of initial states and simulation lenght.\n",
"Are you satisfied with the result?"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"---\n",
"\n",
"Let us now consider an even bigger model coming from L. Mendoza (Biosystems 2006), and made Boolean by the same author with Remy et al. (Dynamical Roles and Functionality of Feedback Circuits, Springer 2006).\n",
"\n",
"![Th Lymphocite differentiation](RemyEtAl06.png)\n",
"\n",
......@@ -239,7 +318,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## Question 4\n",
"## Question 6\n",
"\n",
"Why do we have 6 stable states instead of 3?\n",
"\n",
......@@ -264,7 +343,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## Question 5\n",
"## Question 7\n",
"\n",
"If one hopes for traces that would present all events with equal probability, what would be the approximate total number of samples needed to learn our 12-species model for $h = 0.1$?"
]
......@@ -289,7 +368,7 @@
"source": [
"For time reasons, we will only use 10000 samples total.\n",
"\n",
"## Question 6\n",
"## Question 8\n",
"\n",
"Compare the three following models, and especially the last two ones:\n",
"\n",
......@@ -327,7 +406,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## Question 7\n",
"## Question 9\n",
"\n",
"Keeping the total number of samples at 10000, can you find a threshold after which models learnt are of better quality?"
]
......@@ -380,7 +459,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## Question 9\n",
"## Question 10\n",
"\n",
"In order to reduce the number of samples needed for a given $h$, one solution is to use some prior knowledge.\n",
"\n",
......
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