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naterq pm downstreams #47

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b73ee9b
alpha 01a - documentation and whole refunt
qnater Mar 17, 2025
220d129
01b - documentation and whole refunt
qnater Mar 18, 2025
e8c0f3c
alpha 02a - documentation and whole refunt
qnater Mar 18, 2025
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12 changes: 6 additions & 6 deletions README.md
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Expand Up @@ -152,7 +152,7 @@ ts.load_series(utils.search_path("eeg-alcohol"))
ts.normalize(normalizer="z_score")

# plot a subset of time series
ts.plot(input_data=ts.data, nbr_series=9, nbr_val=100, save_path="./imputegap/assets")
ts.plot(input_data=ts.data, nbr_series=9, nbr_val=100, save_path="./imputegap_assets")

# print a subset of time series
ts.print(nbr_series=6, nbr_val=20)
Expand Down Expand Up @@ -190,7 +190,7 @@ ts.normalize(normalizer="z_score")
ts_m = ts.Contamination.missing_completely_at_random(ts.data, rate_dataset=0.2, rate_series=0.4, block_size=10, seed=True)

# [OPTIONAL] plot the contaminated time series
ts.plot(ts.data, ts_m, nbr_series=9, subplot=True, save_path="./imputegap/assets")
ts.plot(ts.data, ts_m, nbr_series=9, subplot=True, save_path="./imputegap_assets")
```

---
Expand Down Expand Up @@ -236,7 +236,7 @@ imputer.score(ts.data, imputer.recov_data)
ts.print_results(imputer.metrics)

# plot the recovered time series
ts.plot(input_data=ts.data, incomp_data=ts_m, recov_data=imputer.recov_data, nbr_series=9, subplot=True, save_path="./imputegap/assets")
ts.plot(input_data=ts.data, incomp_data=ts_m, recov_data=imputer.recov_data, nbr_series=9, subplot=True, save_path="./imputegap_assets")
```

---
Expand Down Expand Up @@ -275,7 +275,7 @@ imputer.score(ts.data, imputer.recov_data)
ts.print_results(imputer.metrics)

# plot the recovered time series
ts.plot(input_data=ts.data, incomp_data=ts_m, recov_data=imputer.recov_data, nbr_series=9, subplot=True, save_path="./imputegap/assets", display=True)
ts.plot(input_data=ts.data, incomp_data=ts_m, recov_data=imputer.recov_data, nbr_series=9, subplot=True, save_path="./imputegap_assets", display=True)

# save hyperparameters
utils.save_optimization(optimal_params=imputer.parameters, algorithm=imputer.algorithm, dataset="eeg-alcohol", optimizer="ray_tune")
Expand Down Expand Up @@ -343,7 +343,7 @@ ts = TimeSeries()
print(f"ImputeGAP downstream models for forcasting : {ts.downstream_models}")

# load and normalize the timeseries
ts.load_series(utils.search_path("chlorine"))
ts.load_series(utils.search_path("forecast-economy"))
ts.normalize(normalizer="min_max")

# contaminate the time series
Expand All @@ -354,7 +354,7 @@ imputer = Imputation.MatrixCompletion.CDRec(ts_m)
imputer.impute()

# compute print the downstream results
downstream_config = {"task": "forecast", "model": "prophet"}
downstream_config = {"task": "forecast", "model": "hw-add"}
imputer.score(ts.data, imputer.recov_data, downstream=downstream_config)
ts.print_results(imputer.downstream_metrics, algorithm=imputer.algorithm)
```
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2 changes: 1 addition & 1 deletion build/lib/imputegap/runner_explainer.py
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Expand Up @@ -9,7 +9,7 @@
ts_1.load_series(utils.search_path("eeg-alcohol"))

# 3. call the explanation of your dataset with a specific algorithm to gain insight on the Imputation results
shap_values, shap_details = Explainer.shap_explainer(input_data=ts_1.data, extractor="pycatch22", pattern="mcar", missing_rate=0.25, limit_ratio=1, split_ratio=0.7, file_name="eeg-alcohol", algorithm="cdrec")
shap_values, shap_details = Explainer.shap_explainer(input_data=ts_1.data, extractor="pycatch22", pattern="mcar", missing_rate=0.25, rate_dataset=1, training_ratio=0.7, file_name="eeg-alcohol", algorithm="cdrec")

# [OPTIONAL] print the results with the impact of each feature.
Explainer.print(shap_values, shap_details)
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4 changes: 2 additions & 2 deletions docs/generation/build/html/downstream.html
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Expand Up @@ -282,7 +282,7 @@ <h1>Downstream Evaluation<a class="headerlink" href="#downstream-evaluation" tit
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;ImputeGAP downstream models for forcasting : </span><span class="si">{</span><span class="n">ts</span><span class="o">.</span><span class="n">downstream_models</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>

<span class="c1"># load and normalize the timeseries</span>
<span class="n">ts</span><span class="o">.</span><span class="n">load_series</span><span class="p">(</span><span class="n">utils</span><span class="o">.</span><span class="n">search_path</span><span class="p">(</span><span class="s2">&quot;chlorine&quot;</span><span class="p">))</span>
<span class="n">ts</span><span class="o">.</span><span class="n">load_series</span><span class="p">(</span><span class="n">utils</span><span class="o">.</span><span class="n">search_path</span><span class="p">(</span><span class="s2">&quot;forecast-economy&quot;</span><span class="p">))</span>
<span class="n">ts</span><span class="o">.</span><span class="n">normalize</span><span class="p">(</span><span class="n">normalizer</span><span class="o">=</span><span class="s2">&quot;min_max&quot;</span><span class="p">)</span>

<span class="c1"># contaminate the time series</span>
Expand All @@ -293,7 +293,7 @@ <h1>Downstream Evaluation<a class="headerlink" href="#downstream-evaluation" tit
<span class="n">imputer</span><span class="o">.</span><span class="n">impute</span><span class="p">()</span>

<span class="c1"># compute print the downstream results</span>
<span class="n">downstream_config</span> <span class="o">=</span> <span class="p">{</span><span class="s2">&quot;task&quot;</span><span class="p">:</span> <span class="s2">&quot;forecast&quot;</span><span class="p">,</span> <span class="s2">&quot;model&quot;</span><span class="p">:</span> <span class="s2">&quot;prophet&quot;</span><span class="p">}</span>
<span class="n">downstream_config</span> <span class="o">=</span> <span class="p">{</span><span class="s2">&quot;task&quot;</span><span class="p">:</span> <span class="s2">&quot;forecast&quot;</span><span class="p">,</span> <span class="s2">&quot;model&quot;</span><span class="p">:</span> <span class="s2">&quot;hw-add&quot;</span><span class="p">}</span>
<span class="n">imputer</span><span class="o">.</span><span class="n">score</span><span class="p">(</span><span class="n">ts</span><span class="o">.</span><span class="n">data</span><span class="p">,</span> <span class="n">imputer</span><span class="o">.</span><span class="n">recov_data</span><span class="p">,</span> <span class="n">downstream</span><span class="o">=</span><span class="n">downstream_config</span><span class="p">)</span>
<span class="n">ts</span><span class="o">.</span><span class="n">print_results</span><span class="p">(</span><span class="n">imputer</span><span class="o">.</span><span class="n">downstream_metrics</span><span class="p">,</span> <span class="n">algorithm</span><span class="o">=</span><span class="n">imputer</span><span class="o">.</span><span class="n">algorithm</span><span class="p">)</span>
</pre></div>
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10 changes: 8 additions & 2 deletions docs/generation/build/html/genindex.html
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Expand Up @@ -454,13 +454,15 @@ <h2>C</h2>
</li>
<li><a href="imputegap.evaluation.html#id10">compute_mae() (imputegap.recovery.evaluation.Evaluation method)</a>, <a href="imputegap.evaluation.html#imputegap.recovery.evaluation.Evaluation.compute_mae">[1]</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="imputegap.evaluation.html#id12">compute_mi() (imputegap.recovery.evaluation.Evaluation method)</a>, <a href="imputegap.evaluation.html#imputegap.recovery.evaluation.Evaluation.compute_mi">[1]</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="imputegap.evaluation.html#id14">compute_rmse() (imputegap.recovery.evaluation.Evaluation method)</a>, <a href="imputegap.evaluation.html#imputegap.recovery.evaluation.Evaluation.compute_rmse">[1]</a>
</li>
<li><a href="imputegap.utils.html#imputegap.tools.utils.config_contamination">config_contamination() (in module imputegap.tools.utils)</a>
</li>
<li><a href="imputegap.utils.html#imputegap.tools.utils.config_forecaster">config_forecaster() (in module imputegap.tools.utils)</a>
</li>
<li><a href="imputegap.utils.html#imputegap.tools.utils.config_impute_algorithm">config_impute_algorithm() (in module imputegap.tools.utils)</a>
</li>
Expand Down Expand Up @@ -832,6 +834,10 @@ <h2>L</h2>
<li><a href="imputegap.utils.html#imputegap.tools.utils.list_of_datasets">list_of_datasets() (in module imputegap.tools.utils)</a>
</li>
<li><a href="imputegap.utils.html#imputegap.tools.utils.list_of_downstreams">list_of_downstreams() (in module imputegap.tools.utils)</a>
</li>
<li><a href="imputegap.utils.html#imputegap.tools.utils.list_of_downstreams_darts">list_of_downstreams_darts() (in module imputegap.tools.utils)</a>
</li>
<li><a href="imputegap.utils.html#imputegap.tools.utils.list_of_downstreams_sktime">list_of_downstreams_sktime() (in module imputegap.tools.utils)</a>
</li>
<li><a href="imputegap.utils.html#imputegap.tools.utils.list_of_optimizers">list_of_optimizers() (in module imputegap.tools.utils)</a>
</li>
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6 changes: 3 additions & 3 deletions docs/generation/build/html/imputegap.explainer.html
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Expand Up @@ -540,7 +540,7 @@ <h4>Returns<a class="headerlink" href="#id12" title="Link to this heading">¶</a

<dl class="py method">
<dt class="sig sig-object py" id="imputegap.recovery.explainer.Explainer.shap_explainer">
<span class="sig-name descname"><span class="pre">shap_explainer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">algorithm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'cdrec'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">params</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extractor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pycatch'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pattern</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'mcar'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">missing_rate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.4</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">block_size</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">offset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">limit_ratio</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">split_ratio</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.6</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'ts'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">display</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="modules/imputegap/recovery/explainer.html#Explainer.shap_explainer"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#imputegap.recovery.explainer.Explainer.shap_explainer" title="Link to this definition">¶</a></dt>
<span class="sig-name descname"><span class="pre">shap_explainer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">algorithm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'cdrec'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">params</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extractor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pycatch'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pattern</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'mcar'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">missing_rate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.4</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">block_size</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">offset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rate_dataset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">training_ratio</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.6</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'ts'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">display</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="modules/imputegap/recovery/explainer.html#Explainer.shap_explainer"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#imputegap.recovery.explainer.Explainer.shap_explainer" title="Link to this definition">¶</a></dt>
<dd><p>Handle parameters and set variables to launch the SHAP model.</p>
<section id="id13">
<h4>Parameters<a class="headerlink" href="#id13" title="Link to this heading">¶</a></h4>
Expand All @@ -563,9 +563,9 @@ <h4>Parameters<a class="headerlink" href="#id13" title="Link to this heading">¶
</dd>
<dt>seed<span class="classifier">bool, optional</span></dt><dd><p>Whether to use a seed for reproducibility (default is True).</p>
</dd>
<dt>limit_ratio<span class="classifier">flaot, optional</span></dt><dd><p>Limitation on the number of series for the model (default is 1).</p>
<dt>rate_dataset<span class="classifier">flaot, optional</span></dt><dd><p>Limitation on the number of series for the model (default is 1).</p>
</dd>
<dt>split_ratio<span class="classifier">flaot, optional</span></dt><dd><p>Limitation on the training series for the model (default is 0.6).</p>
<dt>training_ratio<span class="classifier">flaot, optional</span></dt><dd><p>Limitation on the training series for the model (default is 0.6).</p>
</dd>
<dt>file_name<span class="classifier">str, optional</span></dt><dd><p>Name of the dataset file (default is ‘ts’).</p>
</dd>
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3 changes: 3 additions & 0 deletions docs/generation/build/html/imputegap.html
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Expand Up @@ -417,11 +417,14 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
<li class="toctree-l2"><a class="reference internal" href="imputegap.utils.html#submodule-documentation">Submodule Documentation</a></li>
<li class="toctree-l2"><a class="reference internal" href="imputegap.utils.html#module-imputegap.tools.utils">imputegap.tools.utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="imputegap.utils.html#imputegap.tools.utils.config_contamination"><code class="docutils literal notranslate"><span class="pre">config_contamination()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="imputegap.utils.html#imputegap.tools.utils.config_forecaster"><code class="docutils literal notranslate"><span class="pre">config_forecaster()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="imputegap.utils.html#imputegap.tools.utils.config_impute_algorithm"><code class="docutils literal notranslate"><span class="pre">config_impute_algorithm()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="imputegap.utils.html#imputegap.tools.utils.display_title"><code class="docutils literal notranslate"><span class="pre">display_title()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="imputegap.utils.html#imputegap.tools.utils.list_of_algorithms"><code class="docutils literal notranslate"><span class="pre">list_of_algorithms()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="imputegap.utils.html#imputegap.tools.utils.list_of_datasets"><code class="docutils literal notranslate"><span class="pre">list_of_datasets()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="imputegap.utils.html#imputegap.tools.utils.list_of_downstreams"><code class="docutils literal notranslate"><span class="pre">list_of_downstreams()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="imputegap.utils.html#imputegap.tools.utils.list_of_downstreams_darts"><code class="docutils literal notranslate"><span class="pre">list_of_downstreams_darts()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="imputegap.utils.html#imputegap.tools.utils.list_of_downstreams_sktime"><code class="docutils literal notranslate"><span class="pre">list_of_downstreams_sktime()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="imputegap.utils.html#imputegap.tools.utils.list_of_optimizers"><code class="docutils literal notranslate"><span class="pre">list_of_optimizers()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="imputegap.utils.html#imputegap.tools.utils.list_of_patterns"><code class="docutils literal notranslate"><span class="pre">list_of_patterns()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="imputegap.utils.html#imputegap.tools.utils.load_parameters"><code class="docutils literal notranslate"><span class="pre">load_parameters()</span></code></a></li>
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