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j-c-gibson committed Dec 2, 2024
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8 changes: 4 additions & 4 deletions dev/notebooks/model_solver.html
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Expand Up @@ -698,7 +698,7 @@ <h3>Random parameters<a class="headerlink" href="#random-parameters" title="Perm
</div>
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Expand Down Expand Up @@ -859,7 +859,7 @@ <h3>Fixed parameters<a class="headerlink" href="#id3" title="Permalink to this h
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Expand Down Expand Up @@ -968,7 +968,7 @@ <h3>Random parameters<a class="headerlink" href="#id4" title="Permalink to this
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Expand Down Expand Up @@ -1017,7 +1017,7 @@ <h2>Summary<a class="headerlink" href="#summary" title="Permalink to this headin
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Expand Up @@ -544,53 +544,6 @@ <h2>Unknown initial conditions<a class="headerlink" href="#unknown-initial-condi
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<div class="output traceback highlight-ipythontb notranslate"><div class="highlight"><pre><span></span><span class="gt">---------------------------------------------------------------------------</span>
<span class="ne">AttributeError</span><span class="g g-Whitespace"> </span>Traceback (most recent call last)
<span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="n">line</span> <span class="mi">8</span>
<span class="g g-Whitespace"> </span><span class="mi">4</span> <span class="n">theta</span> <span class="o">=</span> <span class="p">[</span><span class="mf">20.0</span><span class="p">]</span>
<span class="g g-Whitespace"> </span><span class="mi">6</span> <span class="n">initialState</span> <span class="o">=</span> <span class="p">[</span><span class="mf">0.0</span><span class="p">,</span> <span class="mf">20.0</span><span class="p">]</span>
<span class="ne">----&gt; </span><span class="mi">8</span> <span class="n">obj</span> <span class="o">=</span> <span class="n">SquareLoss</span><span class="p">(</span><span class="n">theta</span><span class="o">=</span><span class="n">theta</span><span class="p">,</span>
<span class="g g-Whitespace"> </span><span class="mi">9</span> <span class="n">ode</span><span class="o">=</span><span class="n">model</span><span class="p">,</span>
<span class="g g-Whitespace"> </span><span class="mi">10</span> <span class="n">t0</span><span class="o">=</span><span class="n">t</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">x0</span><span class="o">=</span><span class="n">initialState</span><span class="p">,</span>
<span class="g g-Whitespace"> </span><span class="mi">11</span> <span class="n">t</span><span class="o">=</span><span class="n">t</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">y</span><span class="o">=</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
<span class="g g-Whitespace"> </span><span class="mi">12</span> <span class="n">state_name</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;y&#39;</span><span class="p">],</span> <span class="n">target_state</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;v&#39;</span><span class="p">])</span>

<span class="nn">File /opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/pygom/loss/ode_loss.py:27,</span> in <span class="ni">SquareLoss.__init__</span><span class="nt">(self, theta, ode, x0, t0, t, y, state_name, state_weight, target_param, target_state)</span>
<span class="g g-Whitespace"> </span><span class="mi">25</span> <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">theta</span><span class="p">,</span> <span class="n">ode</span><span class="p">,</span> <span class="n">x0</span><span class="p">,</span> <span class="n">t0</span><span class="p">,</span> <span class="n">t</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">state_name</span><span class="p">,</span>
<span class="g g-Whitespace"> </span><span class="mi">26</span> <span class="n">state_weight</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">target_param</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">target_state</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="ne">---&gt; </span><span class="mi">27</span> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">theta</span><span class="p">,</span> <span class="n">ode</span><span class="p">,</span> <span class="n">x0</span><span class="p">,</span> <span class="n">t0</span><span class="p">,</span> <span class="n">t</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">state_name</span><span class="p">,</span> <span class="n">state_weight</span><span class="p">,</span>
<span class="g g-Whitespace"> </span><span class="mi">28</span> <span class="kc">None</span><span class="p">,</span> <span class="n">target_param</span><span class="p">,</span> <span class="n">target_state</span><span class="p">)</span>

<span class="nn">File /opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/pygom/loss/base_loss.py:101,</span> in <span class="ni">BaseLoss.__init__</span><span class="nt">(self, theta, ode, x0, t0, t, y, state_name, state_weight, spread_param, target_param, target_state)</span>
<span class="g g-Whitespace"> </span><span class="mi">89</span> <span class="bp">self</span><span class="o">.</span><span class="n">_ode</span> <span class="o">=</span> <span class="n">ode</span>
<span class="g g-Whitespace"> </span><span class="mi">91</span> <span class="c1"># We are making a shitty check here because I screwed up (sort of)</span>
<span class="g g-Whitespace"> </span><span class="mi">92</span> <span class="c1"># Should have been a base class where we do not have the target_param</span>
<span class="g g-Whitespace"> </span><span class="mi">93</span> <span class="c1"># and target_state and another class extending it. The only problem of</span>
<span class="p">(</span><span class="o">...</span><span class="p">)</span>
<span class="g g-Whitespace"> </span><span class="mi">99</span> <span class="c1"># Basically, it will require a lot of work to make things sync and</span>
<span class="g g-Whitespace"> </span><span class="mi">100</span> <span class="c1"># that is too much effort and time which I do not have</span>
<span class="ne">--&gt; </span><span class="mi">101</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_ode</span><span class="o">.</span><span class="n">parameters</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="g g-Whitespace"> </span><span class="mi">102</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_ode</span><span class="o">.</span><span class="n">num_param</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
<span class="g g-Whitespace"> </span><span class="mi">103</span> <span class="c1"># note that this is necessary because we want to make sure that</span>
<span class="g g-Whitespace"> </span><span class="mi">104</span> <span class="c1"># it is possible to only estimate part of the full parameter set</span>
<span class="g g-Whitespace"> </span><span class="mi">105</span> <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">&quot;Set the parameters of the ode first&quot;</span><span class="p">)</span>

<span class="nn">File /opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/pygom/model/base_ode_model.py:166,</span> in <span class="ni">BaseOdeModel.parameters</span><span class="nt">(self)</span>
<span class="g g-Whitespace"> </span><span class="mi">156</span> <span class="nd">@property</span>
<span class="g g-Whitespace"> </span><span class="mi">157</span> <span class="k">def</span> <span class="nf">parameters</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="g g-Whitespace"> </span><span class="mi">158</span><span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="g g-Whitespace"> </span><span class="mi">159</span><span class="sd"> Returns</span>
<span class="g g-Whitespace"> </span><span class="mi">160</span><span class="sd"> -------</span>
<span class="sd"> (...)</span>
<span class="g g-Whitespace"> </span><span class="mi">164</span><span class="sd"> </span>
<span class="g g-Whitespace"> </span><span class="mi">165</span><span class="sd"> &quot;&quot;&quot;</span>
<span class="ne">--&gt; </span><span class="mi">166</span> <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_parameters</span>

<span class="ne">AttributeError</span>: &#39;SimulateOde&#39; object has no attribute &#39;_parameters&#39;
</pre></div>
</div>
</div>
</div>
<p>And we use the <code class="xref py py-func docutils literal notranslate"><span class="pre">costIV()</span></code> function to let the solver know we are considering an initial value problem:</p>
<div class="cell docutils container">
Expand All @@ -601,13 +554,16 @@ <h2>Unknown initial conditions<a class="headerlink" href="#unknown-initial-condi
</div>
</div>
<div class="cell_output docutils container">
<div class="output traceback highlight-ipythontb notranslate"><div class="highlight"><pre><span></span><span class="gt">---------------------------------------------------------------------------</span>
<span class="ne">NameError</span><span class="g g-Whitespace"> </span>Traceback (most recent call last)
<span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span> <span class="n">line</span> <span class="mi">1</span>
<span class="ne">----&gt; </span><span class="mi">1</span> <span class="n">thetaHat</span> <span class="o">=</span> <span class="n">minimize</span><span class="p">(</span><span class="n">fun</span><span class="o">=</span><span class="n">obj</span><span class="o">.</span><span class="n">costIV</span><span class="p">,</span> <span class="n">x0</span><span class="o">=</span><span class="n">theta</span><span class="p">)</span>
<span class="g g-Whitespace"> </span><span class="mi">2</span> <span class="nb">print</span><span class="p">(</span><span class="n">thetaHat</span><span class="p">)</span>

<span class="ne">NameError</span>: name &#39;obj&#39; is not defined
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> message: Optimization terminated successfully.
success: True
status: 0
fun: 4.987646893079144e-16
x: [ 1.500e+01]
nit: 4
jac: [ 1.122e-10]
hess_inv: [[ 5.556e-02]]
nfev: 10
njev: 5
</pre></div>
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Expand All @@ -627,16 +583,7 @@ <h2>Unknown initial conditions<a class="headerlink" href="#unknown-initial-condi
</div>
</div>
<div class="cell_output docutils container">
<div class="output traceback highlight-ipythontb notranslate"><div class="highlight"><pre><span></span><span class="gt">---------------------------------------------------------------------------</span>
<span class="ne">NameError</span><span class="g g-Whitespace"> </span>Traceback (most recent call last)
<span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">5</span><span class="p">],</span> <span class="n">line</span> <span class="mi">1</span>
<span class="ne">----&gt; </span><span class="mi">1</span> <span class="n">model</span><span class="o">.</span><span class="n">initial_values</span> <span class="o">=</span> <span class="p">([</span><span class="mf">0.0</span><span class="p">]</span> <span class="o">+</span> <span class="n">thetaHat</span><span class="p">[</span><span class="s1">&#39;x&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">tolist</span><span class="p">(),</span> <span class="n">t</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="g g-Whitespace"> </span><span class="mi">3</span> <span class="n">solution</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">integrate</span><span class="p">(</span><span class="n">t</span><span class="p">[</span><span class="mi">1</span><span class="p">::])</span>
<span class="g g-Whitespace"> </span><span class="mi">5</span> <span class="n">f</span><span class="p">,</span> <span class="n">axarr</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="n">layout</span><span class="o">=</span><span class="s1">&#39;constrained&#39;</span><span class="p">)</span>

<span class="ne">NameError</span>: name &#39;thetaHat&#39; is not defined
</pre></div>
</div>
<img alt="../../_images/cf4c2431c9cf94cb48b4994873671e352a515b97d47b2070dc7d4683ab1c43fa.png" src="../../_images/cf4c2431c9cf94cb48b4994873671e352a515b97d47b2070dc7d4683ab1c43fa.png" />
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</section>
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Expand Up @@ -810,9 +810,8 @@ <h2>Fitting an SIR model (with only Infected known)<a class="headerlink" href="#
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Generation 6
tolerance = 1108.75380
acceptance rate = 33.83%
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Generation 7

Generation 7
tolerance = 936.24091
acceptance rate = 32.51%
</pre></div>
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Expand Up @@ -553,7 +553,7 @@ <h2>Gradient calculations<a class="headerlink" href="#gradient-calculations" tit
</div>
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>33.8 ms ± 372 μs per loop (mean ± std. dev. of 7 runs, 10 loops each)
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>33 ms ± 358 μs per loop (mean ± std. dev. of 7 runs, 10 loops each)
</pre></div>
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Expand All @@ -565,7 +565,7 @@ <h2>Gradient calculations<a class="headerlink" href="#gradient-calculations" tit
</div>
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>259 ms ± 1.29 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>257 ms ± 1.23 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
</pre></div>
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