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docs update.
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@Ziaeemehr
Ziaeemehr committed Dec 5, 2023
1 parent 8bd5ae2 commit f85ae87
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128 changes: 0 additions & 128 deletions docs/_modules/examples/00_intro.html
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2 changes: 1 addition & 1 deletion docs/_modules/vbjax/connectome.html
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Expand Up @@ -45,7 +45,7 @@ <h1>Source code for vbjax.connectome</h1><div class="highlight"><pre>


<div class="viewcode-block" id="make_conn_latent_mvnorm">
<a class="viewcode-back" href="../../index.html#vbjax.connectome.make_conn_latent_mvnorm">[docs]</a>
<a class="viewcode-back" href="../../modules.html#vbjax.connectome.make_conn_latent_mvnorm">[docs]</a>
<span class="k">def</span> <span class="nf">make_conn_latent_mvnorm</span><span class="p">(</span><span class="n">SCs</span><span class="p">,</span> <span class="n">nc</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">return_full</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Make a latent multivariate normal distribution over connectomes.</span>
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2 changes: 1 addition & 1 deletion docs/_modules/vbjax/layers.html
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Expand Up @@ -39,7 +39,7 @@ <h1>Source code for vbjax.layers</h1><div class="highlight"><pre>


<div class="viewcode-block" id="make_dense_layers">
<a class="viewcode-back" href="../../index.html#vbjax.layers.make_dense_layers">[docs]</a>
<a class="viewcode-back" href="../../modules.html#vbjax.layers.make_dense_layers">[docs]</a>
<span class="k">def</span> <span class="nf">make_dense_layers</span><span class="p">(</span><span class="n">in_dim</span><span class="p">,</span> <span class="n">latent_dims</span><span class="o">=</span><span class="p">[</span><span class="mi">10</span><span class="p">],</span> <span class="n">out_dim</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">init_scl</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span> <span class="n">extra_in</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
<span class="n">act_fn</span><span class="o">=</span><span class="n">jax</span><span class="o">.</span><span class="n">nn</span><span class="o">.</span><span class="n">leaky_relu</span><span class="p">,</span> <span class="n">key</span><span class="o">=</span><span class="n">jax</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">PRNGKey</span><span class="p">(</span><span class="mi">42</span><span class="p">)):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Make a dense neural network with the given latent layer sizes.&quot;&quot;&quot;</span>
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10 changes: 5 additions & 5 deletions docs/_modules/vbjax/loops.html
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Expand Up @@ -45,7 +45,7 @@ <h1>Source code for vbjax.loops</h1><div class="highlight"><pre>


<div class="viewcode-block" id="heun_step">
<a class="viewcode-back" href="../../index.html#vbjax.loops.heun_step">[docs]</a>
<a class="viewcode-back" href="../../modules.html#vbjax.loops.heun_step">[docs]</a>
<span class="k">def</span> <span class="nf">heun_step</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">dfun</span><span class="p">,</span> <span class="n">dt</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="n">add</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Use a Heun scheme to step state with a right hand sides dfun(.)</span>
<span class="sd"> and additional forcing term add.</span>
Expand All @@ -56,7 +56,7 @@ <h1>Source code for vbjax.loops</h1><div class="highlight"><pre>


<div class="viewcode-block" id="make_sde">
<a class="viewcode-back" href="../../index.html#vbjax.loops.make_sde">[docs]</a>
<a class="viewcode-back" href="../../modules.html#vbjax.loops.make_sde">[docs]</a>
<span class="k">def</span> <span class="nf">make_sde</span><span class="p">(</span><span class="n">dt</span><span class="p">,</span> <span class="n">dfun</span><span class="p">,</span> <span class="n">gfun</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Use a stochastic Heun scheme to integrate autonomous stochastic</span>
<span class="sd"> differential equations (SDEs).</span>
Expand Down Expand Up @@ -123,7 +123,7 @@ <h1>Source code for vbjax.loops</h1><div class="highlight"><pre>


<div class="viewcode-block" id="make_ode">
<a class="viewcode-back" href="../../index.html#vbjax.loops.make_ode">[docs]</a>
<a class="viewcode-back" href="../../modules.html#vbjax.loops.make_ode">[docs]</a>
<span class="k">def</span> <span class="nf">make_ode</span><span class="p">(</span><span class="n">dt</span><span class="p">,</span> <span class="n">dfun</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Use a Heun scheme to integrate autonomous ordinary differential</span>
<span class="sd"> equations (ODEs).</span>
Expand Down Expand Up @@ -173,15 +173,15 @@ <h1>Source code for vbjax.loops</h1><div class="highlight"><pre>


<div class="viewcode-block" id="make_dde">
<a class="viewcode-back" href="../../index.html#vbjax.loops.make_dde">[docs]</a>
<a class="viewcode-back" href="../../modules.html#vbjax.loops.make_dde">[docs]</a>
<span class="k">def</span> <span class="nf">make_dde</span><span class="p">(</span><span class="n">dt</span><span class="p">,</span> <span class="n">nh</span><span class="p">,</span> <span class="n">dfun</span><span class="p">,</span> <span class="n">unroll</span><span class="o">=</span><span class="mi">10</span><span class="p">):</span>
<span class="s2">&quot;Invokes make_sdde w/ gfun 0.&quot;</span>
<span class="k">return</span> <span class="n">make_sdde</span><span class="p">(</span><span class="n">dt</span><span class="p">,</span> <span class="n">nh</span><span class="p">,</span> <span class="n">dfun</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">unroll</span><span class="p">)</span></div>



<div class="viewcode-block" id="make_sdde">
<a class="viewcode-back" href="../../index.html#vbjax.loops.make_sdde">[docs]</a>
<a class="viewcode-back" href="../../modules.html#vbjax.loops.make_sdde">[docs]</a>
<span class="k">def</span> <span class="nf">make_sdde</span><span class="p">(</span><span class="n">dt</span><span class="p">,</span> <span class="n">nh</span><span class="p">,</span> <span class="n">dfun</span><span class="p">,</span> <span class="n">gfun</span><span class="p">,</span> <span class="n">unroll</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">zero_delays</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Use a stochastic Heun scheme to integrate autonomous</span>
<span class="sd"> stochastic delay differential equations (SDEs).</span>
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