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junpenglao committed May 8, 2024
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4 changes: 2 additions & 2 deletions _modules/blackjax/_version.html
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Expand Up @@ -392,8 +392,8 @@ <h1>Source code for blackjax._version</h1><div class="highlight"><pre>
<span class="n">version_tuple</span><span class="p">:</span> <span class="n">VERSION_TUPLE</span></div>


<span class="n">__version__</span> <span class="o">=</span> <span class="n">version</span> <span class="o">=</span> <span class="s1">&#39;0.1.dev1+g1bc6f93&#39;</span>
<span class="n">__version_tuple__</span> <span class="o">=</span> <span class="n">version_tuple</span> <span class="o">=</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="s1">&#39;dev1&#39;</span><span class="p">,</span> <span class="s1">&#39;g1bc6f93&#39;</span><span class="p">)</span>
<span class="n">__version__</span> <span class="o">=</span> <span class="n">version</span> <span class="o">=</span> <span class="s1">&#39;0.1.dev1+g3f92393&#39;</span>
<span class="n">__version_tuple__</span> <span class="o">=</span> <span class="n">version_tuple</span> <span class="o">=</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="s1">&#39;dev1&#39;</span><span class="p">,</span> <span class="s1">&#39;g3f92393&#39;</span><span class="p">)</span>
</pre></div>

</article>
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6 changes: 3 additions & 3 deletions _modules/blackjax/mcmc/proposal.html
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Expand Up @@ -550,7 +550,7 @@ <h1>Source code for blackjax.mcmc.proposal</h1><div class="highlight"><pre>
<span class="sd"> biases the transition away from the trajectory&#39;s initial state.</span>

<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">p_accept</span> <span class="o">=</span> <span class="n">jnp</span><span class="o">.</span><span class="n">clip</span><span class="p">(</span><span class="n">jnp</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">new_proposal</span><span class="o">.</span><span class="n">weight</span> <span class="o">-</span> <span class="n">proposal</span><span class="o">.</span><span class="n">weight</span><span class="p">),</span> <span class="n">a_max</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">p_accept</span> <span class="o">=</span> <span class="n">jnp</span><span class="o">.</span><span class="n">clip</span><span class="p">(</span><span class="n">jnp</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">new_proposal</span><span class="o">.</span><span class="n">weight</span> <span class="o">-</span> <span class="n">proposal</span><span class="o">.</span><span class="n">weight</span><span class="p">),</span> <span class="nb">max</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">do_accept</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">bernoulli</span><span class="p">(</span><span class="n">rng_key</span><span class="p">,</span> <span class="n">p_accept</span><span class="p">)</span>
<span class="n">new_weight</span> <span class="o">=</span> <span class="n">jnp</span><span class="o">.</span><span class="n">logaddexp</span><span class="p">(</span><span class="n">proposal</span><span class="o">.</span><span class="n">weight</span><span class="p">,</span> <span class="n">new_proposal</span><span class="o">.</span><span class="n">weight</span><span class="p">)</span>
<span class="n">new_sum_log_p_accept</span> <span class="o">=</span> <span class="n">jnp</span><span class="o">.</span><span class="n">logaddexp</span><span class="p">(</span>
Expand Down Expand Up @@ -627,7 +627,7 @@ <h1>Source code for blackjax.mcmc.proposal</h1><div class="highlight"><pre>
<span class="sd"> then the new proposal is accepted with probability 1.</span>

<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">p_accept</span> <span class="o">=</span> <span class="n">jnp</span><span class="o">.</span><span class="n">clip</span><span class="p">(</span><span class="n">jnp</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">log_p_accept</span><span class="p">),</span> <span class="n">a_max</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">p_accept</span> <span class="o">=</span> <span class="n">jnp</span><span class="o">.</span><span class="n">clip</span><span class="p">(</span><span class="n">jnp</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">log_p_accept</span><span class="p">),</span> <span class="nb">max</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">do_accept</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">bernoulli</span><span class="p">(</span><span class="n">rng_key</span><span class="p">,</span> <span class="n">p_accept</span><span class="p">)</span>
<span class="n">info</span> <span class="o">=</span> <span class="n">do_accept</span><span class="p">,</span> <span class="n">p_accept</span><span class="p">,</span> <span class="kc">None</span>
<span class="k">return</span> <span class="p">(</span>
Expand Down Expand Up @@ -659,7 +659,7 @@ <h1>Source code for blackjax.mcmc.proposal</h1><div class="highlight"><pre>
<span class="sd"> to the accept/reject step of a current state and new proposal.</span>

<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">p_accept</span> <span class="o">=</span> <span class="n">jnp</span><span class="o">.</span><span class="n">clip</span><span class="p">(</span><span class="n">jnp</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">delta_energy</span><span class="p">),</span> <span class="n">a_max</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">p_accept</span> <span class="o">=</span> <span class="n">jnp</span><span class="o">.</span><span class="n">clip</span><span class="p">(</span><span class="n">jnp</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">delta_energy</span><span class="p">),</span> <span class="nb">max</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">do_accept</span> <span class="o">=</span> <span class="n">jnp</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">jnp</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="nb">slice</span><span class="p">))</span> <span class="o">&lt;=</span> <span class="n">delta_energy</span>
<span class="n">slice_next</span> <span class="o">=</span> <span class="nb">slice</span> <span class="o">*</span> <span class="p">(</span><span class="n">jnp</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="n">delta_energy</span><span class="p">)</span> <span class="o">*</span> <span class="n">do_accept</span> <span class="o">+</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">do_accept</span><span class="p">))</span>
<span class="n">info</span> <span class="o">=</span> <span class="n">do_accept</span><span class="p">,</span> <span class="n">p_accept</span><span class="p">,</span> <span class="n">slice_next</span>
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2 changes: 1 addition & 1 deletion examples/howto_custom_gradients.html
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Expand Up @@ -599,7 +599,7 @@ <h3>Using the function with Blackjax<a class="headerlink" href="#using-the-funct
</div>
<div class="cell_output docutils container">
<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>(HMCState(position=1.0, logdensity=Array(-2.5600991, dtype=float32), logdensity_grad=Array(-1.6666666, dtype=float32, weak_type=True)),
HMCState(position=Array(0.8047719, dtype=float32, weak_type=True), logdensity=Array(-2.277532, dtype=float32), logdensity_grad=Array(-1.2365438, dtype=float32, weak_type=True)))
HMCState(position=Array(0.97067314, dtype=float32, weak_type=True), logdensity=Array(-2.512219, dtype=float32), logdensity_grad=Array(-1.5988109, dtype=float32, weak_type=True)))
</pre></div>
</div>
</div>
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10 changes: 5 additions & 5 deletions examples/howto_metropolis_within_gibbs.html
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Expand Up @@ -604,8 +604,8 @@ <h3>Sampling<a class="headerlink" href="#sampling" title="Link to this heading">
</div>
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>CPU times: user 951 ms, sys: 61.8 ms, total: 1.01 s
Wall time: 1.01 s
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>CPU times: user 919 ms, sys: 67.5 ms, total: 986 ms
Wall time: 980 ms
</pre></div>
</div>
</div>
Expand All @@ -622,7 +622,7 @@ <h3>Sampling<a class="headerlink" href="#sampling" title="Link to this heading">
</div>
</div>
<div class="cell_output docutils container">
<img alt="../_images/80afb178ff06ce447f9d6999e3a9d1e66b86f590a85cbcc288811a872af9e9ac.png" src="../_images/80afb178ff06ce447f9d6999e3a9d1e66b86f590a85cbcc288811a872af9e9ac.png" />
<img alt="../_images/aa8f91c89c3588232511e4a3bfb7e0f138ecc96be0bc378d707d58f3bca649b6.png" src="../_images/aa8f91c89c3588232511e4a3bfb7e0f138ecc96be0bc378d707d58f3bca649b6.png" />
</div>
</div>
</section>
Expand Down Expand Up @@ -743,8 +743,8 @@ <h3>Sampling<a class="headerlink" href="#id2" title="Link to this heading">#</a>
</div>
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>CPU times: user 696 ms, sys: 16.8 ms, total: 713 ms
Wall time: 703 ms
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>CPU times: user 705 ms, sys: 36.5 ms, total: 742 ms
Wall time: 733 ms
</pre></div>
</div>
</div>
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8 changes: 4 additions & 4 deletions examples/howto_sample_multiple_chains.html
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Expand Up @@ -524,8 +524,8 @@ <h3>Using <code class="docutils literal notranslate"><span class="pre">jax.vmap<
</div>
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>CPU times: user 13.8 s, sys: 508 ms, total: 14.3 s
Wall time: 14.3 s
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>CPU times: user 14.9 s, sys: 201 ms, total: 15.1 s
Wall time: 15.1 s
</pre></div>
</div>
</div>
Expand Down Expand Up @@ -629,8 +629,8 @@ <h3>Back to our example<a class="headerlink" href="#back-to-our-example" title="
</div>
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>CPU times: user 17.7 s, sys: 60.1 ms, total: 17.8 s
Wall time: 5.69 s
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>CPU times: user 17.9 s, sys: 76.3 ms, total: 18 s
Wall time: 5.62 s
</pre></div>
</div>
</div>
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4 changes: 2 additions & 2 deletions examples/howto_use_aesara.html
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Expand Up @@ -655,7 +655,7 @@ <h1>Use with Aesara models<a class="headerlink" href="#use-with-aesara-models" t
|Elemwise{sigmoid,no_inplace} [id FD]
</pre></div>
</div>
<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;ipykernel.iostream.OutStream at 0x7fa9e50c05b0&gt;
<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;ipykernel.iostream.OutStream at 0x7fe2f43185b0&gt;
</pre></div>
</div>
</div>
Expand Down Expand Up @@ -757,7 +757,7 @@ <h1>Use with Aesara models<a class="headerlink" href="#use-with-aesara-models" t
</div>
</div>
<div class="cell_output docutils container">
<img alt="../_images/4a6ec46b1cf51a550920214e7085fffccebffa359d663ff67223ec290a9ae507.png" src="../_images/4a6ec46b1cf51a550920214e7085fffccebffa359d663ff67223ec290a9ae507.png" />
<img alt="../_images/baffa78b233e62eaae0b452fedc34dd869b6a850dcf567c3bb47d0bcc867b97c.png" src="../_images/baffa78b233e62eaae0b452fedc34dd869b6a850dcf567c3bb47d0bcc867b97c.png" />
</div>
</div>
</section>
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24 changes: 12 additions & 12 deletions examples/howto_use_numpyro.html
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Expand Up @@ -526,8 +526,8 @@ <h1>Use with Numpyro models<a class="headerlink" href="#use-with-numpyro-models"
</div>
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>\Average acceptance rate: 0.93
There were 0.00% divergent transitions
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>\Average acceptance rate: 0.86
There were 0.10% divergent transitions
</pre></div>
</div>
</div>
Expand All @@ -551,7 +551,7 @@ <h1>Use with Numpyro models<a class="headerlink" href="#use-with-numpyro-models"
</div>
</div>
<div class="cell_output docutils container">
<img alt="../_images/5e9dacb1cc8432322d836df7671d6f1d06adbfd64dab4d9e339ef9c9cc642a65.png" src="../_images/5e9dacb1cc8432322d836df7671d6f1d06adbfd64dab4d9e339ef9c9cc642a65.png" />
<img alt="../_images/c1b5ae4d60046bbc7df177257e50d8886674d8e044040b7097299f2b53263d7c.png" src="../_images/c1b5ae4d60046bbc7df177257e50d8886674d8e044040b7097299f2b53263d7c.png" />
</div>
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Relative treatment effect for school 0: 0.31
Relative treatment effect for school 1: 0.56
Relative treatment effect for school 2: 0.07
Relative treatment effect for school 3: -0.11
Relative treatment effect for school 4: 0.60
Relative treatment effect for school 5: 0.47
Relative treatment effect for school 6: 0.23
Relative treatment effect for school 7: -0.16
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Relative treatment effect for school 0: 0.32
Relative treatment effect for school 1: 0.41
Relative treatment effect for school 2: -0.27
Relative treatment effect for school 3: -0.27
Relative treatment effect for school 4: 0.09
Relative treatment effect for school 5: -0.01
Relative treatment effect for school 6: 0.33
Relative treatment effect for school 7: 0.12
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