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@Lawhy
Lawhy committed Nov 23, 2023
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3 changes: 2 additions & 1 deletion changelog/index.html
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Expand Up @@ -1326,6 +1326,7 @@ <h1 id="changelog">Changelog <img alt="📰" class="twemoji" src="https://cdn.js
<h2 id="unreleased">Unreleased</h2>
<h3 id="added">Added</h3>
<ul class="task-list">
<li class="task-list-item"><label class="task-list-control"><input type="checkbox" disabled checked/><span class="task-list-indicator"></span></label> <strong>Add</strong> empty annotation index warning for BERTMap, related to issue #18.</li>
<li class="task-list-item"><label class="task-list-control"><input type="checkbox" disabled checked/><span class="task-list-indicator"></span></label> <strong>Add</strong> <code>check_consistency()</code> at <code>deeponto.onto.Ontology</code>.</li>
<li class="task-list-item"><label class="task-list-control"><input type="checkbox" disabled checked/><span class="task-list-indicator"></span></label> <strong>Add</strong> a warning message for empty vocab at <code>deeponto.onto.OntologyVerbaliser</code>.</li>
</ul>
Expand Down Expand Up @@ -1511,7 +1512,7 @@ <h2 id="deprecated-before-2023">Deprecated (before 2023)</h2>
<small>

Last update:
<span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">November 13, 2023</span>
<span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">November 23, 2023</span>

<br>
Created:
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62 changes: 33 additions & 29 deletions deeponto/align/bertmap/index.html
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Expand Up @@ -1802,7 +1802,9 @@ <h2 id="deeponto.align.bertmap.pipeline.BERTMapPipeline" class="doc doc-heading"
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<span class="normal">214</span></pre></div></td><td class="code"><div><pre><span></span><code><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">src_onto</span><span class="p">:</span> <span class="n">Ontology</span><span class="p">,</span> <span class="n">tgt_onto</span><span class="p">:</span> <span class="n">Ontology</span><span class="p">,</span> <span class="n">config</span><span class="p">:</span> <span class="n">CfgNode</span><span class="p">):</span>
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;Initialise the BERTMap or BERTMapLt model.</span>

<span class="sd"> Args:</span>
Expand Down Expand Up @@ -1838,6 +1840,8 @@ <h2 id="deeponto.align.bertmap.pipeline.BERTMapPipeline" class="doc doc-heading"
<span class="c1"># build the annotation thesaurus</span>
<span class="bp">self</span><span class="o">.</span><span class="n">src_annotation_index</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">src_onto</span><span class="o">.</span><span class="n">build_annotation_index</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">annotation_property_iris</span><span class="p">,</span> <span class="n">apply_lowercasing</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">tgt_annotation_index</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">tgt_onto</span><span class="o">.</span><span class="n">build_annotation_index</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">annotation_property_iris</span><span class="p">,</span> <span class="n">apply_lowercasing</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="k">if</span> <span class="p">(</span><span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">src_annotation_index</span><span class="p">)</span> <span class="ow">or</span> <span class="p">(</span><span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">tgt_annotation_index</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">&quot;No class annotations found in input ontologies; unable to produce alignment.&quot;</span><span class="p">)</span>

<span class="c1"># provided mappings if any</span>
<span class="bp">self</span><span class="o">.</span><span class="n">known_mappings</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">known_mappings</span>
Expand Down Expand Up @@ -1981,9 +1985,7 @@ <h3 id="deeponto.align.bertmap.pipeline.BERTMapPipeline.load_or_construct" class

<details class="quote">
<summary>Source code in <code>src/deeponto/align/bertmap/pipeline.py</code></summary>
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;Load existing data or construct a new one.</span>

<span class="sd"> An auxlirary function that checks the existence of a data file and loads it if it exists.</span>
Expand Down Expand Up @@ -2032,9 +2036,7 @@ <h3 id="deeponto.align.bertmap.pipeline.BERTMapPipeline.load_text_semantics_corp

<details class="quote">
<summary>Source code in <code>src/deeponto/align/bertmap/pipeline.py</code></summary>
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Expand All @@ -2055,7 +2057,9 @@ <h3 id="deeponto.align.bertmap.pipeline.BERTMapPipeline.load_text_semantics_corp
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;Load or construct text semantics corpora.</span>

<span class="sd"> See [`TextSemanticsCorpora`][deeponto.align.bertmap.text_semantics.TextSemanticsCorpora].</span>
Expand Down Expand Up @@ -2107,9 +2111,7 @@ <h3 id="deeponto.align.bertmap.pipeline.BERTMapPipeline.load_finetune_data" clas

<details class="quote">
<summary>Source code in <code>src/deeponto/align/bertmap/pipeline.py</code></summary>
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Expand All @@ -2131,7 +2133,9 @@ <h3 id="deeponto.align.bertmap.pipeline.BERTMapPipeline.load_finetune_data" clas
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<span class="w"> </span><span class="sa">r</span><span class="sd">&quot;&quot;&quot;Load or construct fine-tuning data from text semantics corpora.</span>

<span class="sd"> Steps of constructing fine-tuning data from text semantics:</span>
Expand Down Expand Up @@ -2184,9 +2188,7 @@ <h3 id="deeponto.align.bertmap.pipeline.BERTMapPipeline.load_bert_synonym_classi

<details class="quote">
<summary>Source code in <code>src/deeponto/align/bertmap/pipeline.py</code></summary>
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Expand All @@ -2209,7 +2211,9 @@ <h3 id="deeponto.align.bertmap.pipeline.BERTMapPipeline.load_bert_synonym_classi
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;Load the BERT model from a pre-trained or a local checkpoint.</span>

<span class="sd"> - If loaded from pre-trained, it means to start training from a pre-trained model such as `bert-uncased`.</span>
Expand Down Expand Up @@ -2258,9 +2262,7 @@ <h3 id="deeponto.align.bertmap.pipeline.BERTMapPipeline.load_best_checkpoint" cl

<details class="quote">
<summary>Source code in <code>src/deeponto/align/bertmap/pipeline.py</code></summary>
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Expand All @@ -2279,7 +2281,9 @@ <h3 id="deeponto.align.bertmap.pipeline.BERTMapPipeline.load_best_checkpoint" cl
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;Find the best checkpoint by searching for trainer states in each checkpoint file.&quot;&quot;&quot;</span>
<span class="n">best_checkpoint</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>

Expand Down Expand Up @@ -2329,17 +2333,17 @@ <h3 id="deeponto.align.bertmap.pipeline.BERTMapPipeline.load_bertmap_config" cla

<details class="quote">
<summary>Source code in <code>src/deeponto/align/bertmap/pipeline.py</code></summary>
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<span class="k">def</span> <span class="nf">load_bertmap_config</span><span class="p">(</span><span class="n">config_file</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Load the BERTMap configuration in `.yaml`. If the file</span>
<span class="sd"> is not provided, use the default configuration.</span>
Expand Down Expand Up @@ -2377,11 +2381,11 @@ <h3 id="deeponto.align.bertmap.pipeline.BERTMapPipeline.save_bertmap_config" cla

<details class="quote">
<summary>Source code in <code>src/deeponto/align/bertmap/pipeline.py</code></summary>
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<span class="k">def</span> <span class="nf">save_bertmap_config</span><span class="p">(</span><span class="n">config</span><span class="p">:</span> <span class="n">CfgNode</span><span class="p">,</span> <span class="n">config_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Save the BERTMap configuration in `.yaml`.&quot;&quot;&quot;</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">config_file</span><span class="p">,</span> <span class="s2">&quot;w&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">c</span><span class="p">:</span>
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