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diff --git a/genindex.html b/genindex.html
@@ -97,6 +97,12 @@ <h2 id="C">C</h2>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="multidms.plot.html#multidms.plot.color_gradient_hex">color_gradient_hex() (in module multidms.plot)</a>
 </li>
+      <li><a href="multidms.html#multidms.Model.conditional_loss">conditional_loss (multidms.Model property)</a>
+
+      <ul>
+        <li><a href="multidms.model.html#multidms.model.Model.conditional_loss">(multidms.model.Model property)</a>
+</li>
+      </ul></li>
       <li><a href="multidms.html#multidms.Data.conditions">conditions (multidms.Data property)</a>
 
       <ul>
@@ -183,6 +189,12 @@ <h2 id="G">G</h2>
 
       <ul>
         <li><a href="multidms.model.html#multidms.model.Model.get_condition_params">(multidms.model.Model method)</a>
+</li>
+      </ul></li>
+      <li><a href="multidms.model_collection.html#multidms.model_collection.ModelCollection.get_conditional_loss_df">get_conditional_loss_df() (multidms.model_collection.ModelCollection method)</a>
+
+      <ul>
+        <li><a href="multidms.html#multidms.ModelCollection.get_conditional_loss_df">(multidms.ModelCollection method)</a>
 </li>
       </ul></li>
       <li><a href="multidms.html#multidms.Model.get_df_loss">get_df_loss() (multidms.Model method)</a>

diff --git a/multidms.html b/multidms.html
@@ -587,6 +587,12 @@ <h2>multidms<a class="headerlink" href="#multidms" title="Link to this heading">
 without ridge or lasso penalties included.</p>
 </dd></dl>
 
+<dl class="py property">
+<dt class="sig sig-object py" id="multidms.Model.conditional_loss">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">conditional_loss</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></em><a class="headerlink" href="#multidms.Model.conditional_loss" title="Link to this definition">¶</a></dt>
+<dd><p>Compute loss individually for each condition.</p>
+</dd></dl>
+
 <dl class="py property">
 <dt class="sig sig-object py" id="multidms.Model.variants_df">
 <em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">variants_df</span></span><a class="headerlink" href="#multidms.Model.variants_df" title="Link to this definition">¶</a></dt>
@@ -660,7 +666,7 @@ <h2>multidms<a class="headerlink" href="#multidms" title="Link to this heading">
 
 <dl class="py method">
 <dt class="sig sig-object py" id="multidms.Model.get_df_loss">
-<span class="sig-name descname"><span class="pre">get_df_loss</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">error_if_unknown</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="headerlink" href="#multidms.Model.get_df_loss" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">get_df_loss</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">error_if_unknown</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>, <em class="sig-param"><span class="n"><span class="pre">conditional</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="headerlink" href="#multidms.Model.get_df_loss" title="Link to this definition">¶</a></dt>
 <dd><p>Get the loss of the model on a given data frame.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -673,13 +679,15 @@ <h2>multidms<a class="headerlink" href="#multidms" title="Link to this heading">
 then by default we do not include those variants
 in the loss calculation. If <cite>True</cite>, raise an error.</p></li>
 <li><p><strong>verbose</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – If True, print the number of valid and invalid variants.</p></li>
+<li><p><strong>conditional</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – If True, return the loss for each condition as a dictionary.
+If False, return the total loss.</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>
 <dd class="field-even"><p>The loss of the model on the given data frame.</p>
 </dd>
 <dt class="field-odd">Return type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)">float</a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)">float</a> or <a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)">dict</a></p>
 </dd>
 </dl>
 </dd></dl>
@@ -990,6 +998,21 @@ <h2>multidms<a class="headerlink" href="#multidms" title="Link to this heading">
 </dl>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="multidms.ModelCollection.get_conditional_loss_df">
+<span class="sig-name descname"><span class="pre">get_conditional_loss_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">query</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#multidms.ModelCollection.get_conditional_loss_df" title="Link to this definition">¶</a></dt>
+<dd><p>return a long form dataframe with columns
+“dataset_name”, “scale_coeff_lasso_shift”,
+“split” (“training” or “validation”),
+“loss” (actual value), and “condition”.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>query</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – The query to apply to the fit_models dataframe
+before formatting the loss dataframe. The default is None.</p>
+</dd>
+</dl>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="multidms.ModelCollection.mut_param_heatmap">
 <span class="sig-name descname"><span class="pre">mut_param_heatmap</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">query</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">mut_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'shift'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">aggregate_func</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'mean'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">inner_merge_dataset_muts</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">times_seen_threshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">phenotype_as_effect</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="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#multidms.ModelCollection.mut_param_heatmap" title="Link to this definition">¶</a></dt>
@@ -1189,6 +1212,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <li class="toctree-l2"><a class="reference internal" href="multidms.model.html#multidms.model.Model.data"><code class="docutils literal notranslate"><span class="pre">Model.data</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="multidms.model.html#multidms.model.Model.model_components"><code class="docutils literal notranslate"><span class="pre">Model.model_components</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="multidms.model.html#multidms.model.Model.loss"><code class="docutils literal notranslate"><span class="pre">Model.loss</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="multidms.model.html#multidms.model.Model.conditional_loss"><code class="docutils literal notranslate"><span class="pre">Model.conditional_loss</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="multidms.model.html#multidms.model.Model.variants_df"><code class="docutils literal notranslate"><span class="pre">Model.variants_df</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="multidms.model.html#multidms.model.Model.get_variants_df"><code class="docutils literal notranslate"><span class="pre">Model.get_variants_df()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="multidms.model.html#multidms.model.Model.mutations_df"><code class="docutils literal notranslate"><span class="pre">Model.mutations_df</span></code></a></li>
@@ -1225,6 +1249,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <li class="toctree-l2"><a class="reference internal" href="multidms.model_collection.html#multidms.model_collection.ModelCollection.all_mutations"><code class="docutils literal notranslate"><span class="pre">ModelCollection.all_mutations</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="multidms.model_collection.html#multidms.model_collection.ModelCollection.split_apply_combine_muts"><code class="docutils literal notranslate"><span class="pre">ModelCollection.split_apply_combine_muts()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="multidms.model_collection.html#multidms.model_collection.ModelCollection.add_validation_loss"><code class="docutils literal notranslate"><span class="pre">ModelCollection.add_validation_loss()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="multidms.model_collection.html#multidms.model_collection.ModelCollection.get_conditional_loss_df"><code class="docutils literal notranslate"><span class="pre">ModelCollection.get_conditional_loss_df()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="multidms.model_collection.html#multidms.model_collection.ModelCollection.mut_param_heatmap"><code class="docutils literal notranslate"><span class="pre">ModelCollection.mut_param_heatmap()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="multidms.model_collection.html#multidms.model_collection.ModelCollection.mut_param_traceplot"><code class="docutils literal notranslate"><span class="pre">ModelCollection.mut_param_traceplot()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="multidms.model_collection.html#multidms.model_collection.ModelCollection.shift_sparsity"><code class="docutils literal notranslate"><span class="pre">ModelCollection.shift_sparsity()</span></code></a></li>

diff --git a/multidms.model.html b/multidms.model.html
@@ -237,6 +237,12 @@
 without ridge or lasso penalties included.</p>
 </dd></dl>
 
+<dl class="py property">
+<dt class="sig sig-object py" id="multidms.model.Model.conditional_loss">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">conditional_loss</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></em><a class="headerlink" href="#multidms.model.Model.conditional_loss" title="Link to this definition">¶</a></dt>
+<dd><p>Compute loss individually for each condition.</p>
+</dd></dl>
+
 <dl class="py property">
 <dt class="sig sig-object py" id="multidms.model.Model.variants_df">
 <em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">variants_df</span></span><a class="headerlink" href="#multidms.model.Model.variants_df" title="Link to this definition">¶</a></dt>
@@ -310,7 +316,7 @@
 
 <dl class="py method">
 <dt class="sig sig-object py" id="multidms.model.Model.get_df_loss">
-<span class="sig-name descname"><span class="pre">get_df_loss</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">error_if_unknown</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="headerlink" href="#multidms.model.Model.get_df_loss" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">get_df_loss</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">error_if_unknown</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>, <em class="sig-param"><span class="n"><span class="pre">conditional</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="headerlink" href="#multidms.model.Model.get_df_loss" title="Link to this definition">¶</a></dt>
 <dd><p>Get the loss of the model on a given data frame.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -323,13 +329,15 @@
 then by default we do not include those variants
 in the loss calculation. If <cite>True</cite>, raise an error.</p></li>
 <li><p><strong>verbose</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – If True, print the number of valid and invalid variants.</p></li>
+<li><p><strong>conditional</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – If True, return the loss for each condition as a dictionary.
+If False, return the total loss.</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>
 <dd class="field-even"><p>The loss of the model on the given data frame.</p>
 </dd>
 <dt class="field-odd">Return type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)">float</a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)">float</a> or <a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)">dict</a></p>
 </dd>
 </dl>
 </dd></dl>

diff --git a/multidms.model_collection.html b/multidms.model_collection.html
@@ -266,6 +266,21 @@
 </dl>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="multidms.model_collection.ModelCollection.get_conditional_loss_df">
+<span class="sig-name descname"><span class="pre">get_conditional_loss_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">query</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#multidms.model_collection.ModelCollection.get_conditional_loss_df" title="Link to this definition">¶</a></dt>
+<dd><p>return a long form dataframe with columns
+“dataset_name”, “scale_coeff_lasso_shift”,
+“split” (“training” or “validation”),
+“loss” (actual value), and “condition”.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>query</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – The query to apply to the fit_models dataframe
+before formatting the loss dataframe. The default is None.</p>
+</dd>
+</dl>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="multidms.model_collection.ModelCollection.mut_param_heatmap">
 <span class="sig-name descname"><span class="pre">mut_param_heatmap</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">query</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">mut_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'shift'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">aggregate_func</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'mean'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">inner_merge_dataset_muts</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">times_seen_threshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">phenotype_as_effect</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="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#multidms.model_collection.ModelCollection.mut_param_heatmap" title="Link to this definition">¶</a></dt>

diff --git a/objects.inv b/objects.inv
diff --git a/searchindex.js b/searchindex.js