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<div class="section" id="api"> |
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<h1>API<a class="headerlink" href="#api" title="Permalink to this headline">¶</a></h1> |
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<div class="toctree-wrapper compound"> |
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<ul> |
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<li class="toctree-l1"><a class="reference internal" href="dscript.commands.html">dscript.commands</a><ul> |
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<li class="toctree-l2"><a class="reference internal" href="dscript.commands.html#dscript-commands-predict">dscript.commands.predict</a></li> |
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<li class="toctree-l2"><a class="reference internal" href="dscript.commands.html#dscript-commands-embed">dscript.commands.embed</a></li> |
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<li class="toctree-l2"><a class="reference internal" href="dscript.commands.html#dscript-commands-train">dscript.commands.train</a></li> |
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<li class="toctree-l2"><a class="reference internal" href="dscript.commands.html#dscript-commands-eval">dscript.commands.eval</a></li> |
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</ul> |
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</li> |
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<li class="toctree-l1"><a class="reference internal" href="dscript.models.html">dscript.models</a><ul> |
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<li class="toctree-l2"><a class="reference internal" href="dscript.models.html#module-dscript.models.embedding">dscript.models.embedding</a></li> |
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<li class="toctree-l2"><a class="reference internal" href="dscript.models.html#module-dscript.models.contact">dscript.models.contact</a></li> |
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<div class="section" id="module-dscript.alphabets"> |
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<span id="dscript-alphabets"></span><h2>dscript.alphabets<a class="headerlink" href="#module-dscript.alphabets" title="Permalink to this headline">¶</a></h2> |
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<dl class="py class"> |
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<dt id="dscript.alphabets.Alphabet"> |
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<em class="property"><span class="pre">class</span> </em><code class="sig-prename descclassname"><span class="pre">dscript.alphabets.</span></code><code class="sig-name descname"><span class="pre">Alphabet</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">chars</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">encoding</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">mask</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">missing</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">255</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/dscript/alphabets.html#Alphabet"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dscript.alphabets.Alphabet" title="Permalink to this definition">¶</a></dt> |
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<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p> |
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<p>From <a class="reference external" href="https://github.com/tbepler/protein-sequence-embedding-iclr2019">Bepler & Berger</a>.</p> |
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<dl class="field-list simple"> |
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<dt class="field-odd">Parameters</dt> |
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<dd class="field-odd"><ul class="simple"> |
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<li><p><strong>chars</strong> (<em>byte str</em>) – List of characters in alphabet</p></li> |
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<li><p><strong>encoding</strong> (<em>np.ndarray</em>) – Mapping of characters to numbers [default: encoding]</p></li> |
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<li><p><strong>mask</strong> (<em>bool</em>) – Set encoding mask [default: False]</p></li> |
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<li><p><strong>missing</strong> (<em>int</em>) – Number to use for a value outside the alphabet [default: 255]</p></li> |
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</ul> |
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</dd> |
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</dl> |
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<dl class="py method"> |
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<dt id="dscript.alphabets.Alphabet.decode"> |
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<code class="sig-name descname"><span class="pre">decode</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/dscript/alphabets.html#Alphabet.decode"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dscript.alphabets.Alphabet.decode" title="Permalink to this definition">¶</a></dt> |
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<dd><p>Decode numeric encoding to byte string of this alphabet</p> |
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<dl class="field-list simple"> |
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<dt class="field-odd">Parameters</dt> |
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<dd class="field-odd"><p><strong>x</strong> (<em>np.ndarray</em>) – Numeric encoding</p> |
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</dd> |
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<dt class="field-even">Returns</dt> |
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<dd class="field-even"><p>Amino acid string</p> |
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</dd> |
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<dt class="field-odd">Return type</dt> |
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<dd class="field-odd"><p>byte str</p> |
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</dd> |
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</dl> |
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</dd></dl> |
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<dl class="py method"> |
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<dt id="dscript.alphabets.Alphabet.encode"> |
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<code class="sig-name descname"><span class="pre">encode</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/dscript/alphabets.html#Alphabet.encode"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dscript.alphabets.Alphabet.encode" title="Permalink to this definition">¶</a></dt> |
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<dd><p>Encode a byte string into alphabet indices</p> |
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<dl class="field-list simple"> |
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<dt class="field-odd">Parameters</dt> |
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<dd class="field-odd"><p><strong>x</strong> (<em>byte str</em>) – Amino acid string</p> |
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</dd> |
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<dt class="field-even">Returns</dt> |
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<dd class="field-even"><p>Numeric encoding</p> |
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</dd> |
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<dt class="field-odd">Return type</dt> |
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<dd class="field-odd"><p>np.ndarray</p> |
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</dd> |
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</dl> |
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</dd></dl> |
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</dd></dl> |
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<dl class="py class"> |
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<dt id="dscript.alphabets.Uniprot21"> |
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<em class="property"><span class="pre">class</span> </em><code class="sig-prename descclassname"><span class="pre">dscript.alphabets.</span></code><code class="sig-name descname"><span class="pre">Uniprot21</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mask</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/dscript/alphabets.html#Uniprot21"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dscript.alphabets.Uniprot21" title="Permalink to this definition">¶</a></dt> |
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<dd><p>Bases: <a class="reference internal" href="#dscript.alphabets.Alphabet" title="dscript.alphabets.Alphabet"><code class="xref py py-class docutils literal notranslate"><span class="pre">dscript.alphabets.Alphabet</span></code></a></p> |
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<p>Uniprot 21 Amino Acid Encoding.</p> |
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<p>From <a class="reference external" href="https://github.com/tbepler/protein-sequence-embedding-iclr2019">Bepler & Berger</a>.</p> |
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</dd></dl> |
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</div> |
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<div class="section" id="module-dscript.fasta"> |
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<span id="dscript-fasta"></span><h2>dscript.fasta<a class="headerlink" href="#module-dscript.fasta" title="Permalink to this headline">¶</a></h2> |
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<dl class="py function"> |
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<dt id="dscript.fasta.parse"> |
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<code class="sig-prename descclassname"><span class="pre">dscript.fasta.</span></code><code class="sig-name descname"><span class="pre">parse</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">f</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">comment</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'#'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/dscript/fasta.html#parse"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dscript.fasta.parse" title="Permalink to this definition">¶</a></dt> |
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<dd><p>Parse a file in <code class="docutils literal notranslate"><span class="pre">.fasta</span></code> format.</p> |
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<dl class="field-list simple"> |
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<dt class="field-odd">Parameters</dt> |
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<dd class="field-odd"><ul class="simple"> |
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<li><p><strong>f</strong> (<em>_io.TextIOWrapper</em>) – Input file object</p></li> |
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<li><p><strong>comment</strong> (<em>str</em>) – Character used for comments</p></li> |
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</ul> |
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</dd> |
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<dt class="field-even">Returns</dt> |
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<dd class="field-even"><p>names, sequence</p> |
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</dd> |
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<dt class="field-odd">Return type</dt> |
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<dd class="field-odd"><p>list[str], list[str]</p> |
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</dd> |
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</dl> |
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</dd></dl> |
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<dl class="py function"> |
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<dt id="dscript.fasta.parse_directory"> |
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<code class="sig-prename descclassname"><span class="pre">dscript.fasta.</span></code><code class="sig-name descname"><span class="pre">parse_directory</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">directory</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extension</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.seq'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/dscript/fasta.html#parse_directory"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dscript.fasta.parse_directory" title="Permalink to this definition">¶</a></dt> |
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<dd><p>Parse all files in a directory ending with <code class="docutils literal notranslate"><span class="pre">extension</span></code>.</p> |
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<dl class="field-list simple"> |
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<dt class="field-odd">Parameters</dt> |
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<dd class="field-odd"><ul class="simple"> |
|
<li><p><strong>directory</strong> (<em>str</em>) – Input directory</p></li> |
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<li><p><strong>extension</strong> (<em>str</em>) – Extension of all files to read in</p></li> |
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</ul> |
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</dd> |
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<dt class="field-even">Returns</dt> |
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<dd class="field-even"><p>names, sequence</p> |
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</dd> |
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<dt class="field-odd">Return type</dt> |
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<dd class="field-odd"><p>list[str], list[str]</p> |
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</dd> |
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</dl> |
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</dd></dl> |
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|
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<dl class="py function"> |
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<dt id="dscript.fasta.write"> |
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<code class="sig-prename descclassname"><span class="pre">dscript.fasta.</span></code><code class="sig-name descname"><span class="pre">write</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">nam</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seq</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/dscript/fasta.html#write"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dscript.fasta.write" title="Permalink to this definition">¶</a></dt> |
|
<dd><p>Write a file in <code class="docutils literal notranslate"><span class="pre">.fasta</span></code> format.</p> |
|
<dl class="field-list simple"> |
|
<dt class="field-odd">Parameters</dt> |
|
<dd class="field-odd"><ul class="simple"> |
|
<li><p><strong>nam</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – List of names</p></li> |
|
<li><p><strong>seq</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – List of sequences</p></li> |
|
<li><p><strong>f</strong> (<em>_io.TextIOWrapper</em>) – Output file object</p></li> |
|
</ul> |
|
</dd> |
|
</dl> |
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</dd></dl> |
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|
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</div> |
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<div class="section" id="module-dscript.language_model"> |
|
<span id="dscript-language-model"></span><h2>dscript.language_model<a class="headerlink" href="#module-dscript.language_model" title="Permalink to this headline">¶</a></h2> |
|
<dl class="py function"> |
|
<dt id="dscript.language_model.embed_from_directory"> |
|
<code class="sig-prename descclassname"><span class="pre">dscript.language_model.</span></code><code class="sig-name descname"><span class="pre">embed_from_directory</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">directory</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputPath</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">device</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">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">extension</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.seq'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/dscript/language_model.html#embed_from_directory"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dscript.language_model.embed_from_directory" title="Permalink to this definition">¶</a></dt> |
|
<dd><p>Embed all files in a directory in <code class="docutils literal notranslate"><span class="pre">.fasta</span></code> format using pre-trained language model from <a class="reference external" href="https://github.com/tbepler/protein-sequence-embedding-iclr2019">Bepler & Berger</a>.</p> |
|
<dl class="field-list simple"> |
|
<dt class="field-odd">Parameters</dt> |
|
<dd class="field-odd"><ul class="simple"> |
|
<li><p><strong>directory</strong> (<em>str</em>) – Input directory (<code class="docutils literal notranslate"><span class="pre">.fasta</span></code> format)</p></li> |
|
<li><p><strong>outputPath</strong> (<em>str</em>) – Output embedding file (<code class="docutils literal notranslate"><span class="pre">.h5</span></code> format)</p></li> |
|
<li><p><strong>device</strong> (<em>int</em>) – Compute device to use for embeddings [default: 0]</p></li> |
|
<li><p><strong>verbose</strong> (<em>bool</em>) – Print embedding progress</p></li> |
|
<li><p><strong>extension</strong> (<em>str</em>) – Extension of all files to read in</p></li> |
|
</ul> |
|
</dd> |
|
</dl> |
|
</dd></dl> |
|
|
|
<dl class="py function"> |
|
<dt id="dscript.language_model.embed_from_fasta"> |
|
<code class="sig-prename descclassname"><span class="pre">dscript.language_model.</span></code><code class="sig-name descname"><span class="pre">embed_from_fasta</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fastaPath</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputPath</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">device</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">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/dscript/language_model.html#embed_from_fasta"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dscript.language_model.embed_from_fasta" title="Permalink to this definition">¶</a></dt> |
|
<dd><p>Embed sequences using pre-trained language model from <a class="reference external" href="https://github.com/tbepler/protein-sequence-embedding-iclr2019">Bepler & Berger</a>.</p> |
|
<dl class="field-list simple"> |
|
<dt class="field-odd">Parameters</dt> |
|
<dd class="field-odd"><ul class="simple"> |
|
<li><p><strong>fastaPath</strong> (<em>str</em>) – Input sequence file (<code class="docutils literal notranslate"><span class="pre">.fasta</span></code> format)</p></li> |
|
<li><p><strong>outputPath</strong> (<em>str</em>) – Output embedding file (<code class="docutils literal notranslate"><span class="pre">.h5</span></code> format)</p></li> |
|
<li><p><strong>device</strong> (<em>int</em>) – Compute device to use for embeddings [default: 0]</p></li> |
|
<li><p><strong>verbose</strong> (<em>bool</em>) – Print embedding progress</p></li> |
|
</ul> |
|
</dd> |
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</dl> |
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</dd></dl> |
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|
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<dl class="py function"> |
|
<dt id="dscript.language_model.lm_embed"> |
|
<code class="sig-prename descclassname"><span class="pre">dscript.language_model.</span></code><code class="sig-name descname"><span class="pre">lm_embed</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sequence</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_cuda</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/dscript/language_model.html#lm_embed"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dscript.language_model.lm_embed" title="Permalink to this definition">¶</a></dt> |
|
<dd><p>Embed a single sequence using pre-trained language model from <a class="reference external" href="https://github.com/tbepler/protein-sequence-embedding-iclr2019">Bepler & Berger</a>.</p> |
|
<dl class="field-list simple"> |
|
<dt class="field-odd">Parameters</dt> |
|
<dd class="field-odd"><ul class="simple"> |
|
<li><p><strong>sequence</strong> (<em>str</em>) – Input sequence to be embedded</p></li> |
|
<li><p><strong>use_cuda</strong> (<em>bool</em>) – Whether to generate embeddings using GPU device [default: False]</p></li> |
|
</ul> |
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</dd> |
|
<dt class="field-even">Returns</dt> |
|
<dd class="field-even"><p>Embedded sequence</p> |
|
</dd> |
|
<dt class="field-odd">Return type</dt> |
|
<dd class="field-odd"><p>torch.Tensor</p> |
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</dd> |
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</dl> |
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</dd></dl> |
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|
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</div> |
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<div class="section" id="module-dscript.pretrained"> |
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<span id="dscript-pretrained"></span><h2>dscript.pretrained<a class="headerlink" href="#module-dscript.pretrained" title="Permalink to this headline">¶</a></h2> |
|
<dl class="py function"> |
|
<dt id="dscript.pretrained.get_pretrained"> |
|
<code class="sig-prename descclassname"><span class="pre">dscript.pretrained.</span></code><code class="sig-name descname"><span class="pre">get_pretrained</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">version</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'human_v1'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/dscript/pretrained.html#get_pretrained"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dscript.pretrained.get_pretrained" title="Permalink to this definition">¶</a></dt> |
|
<dd><p>Get pre-trained model object.</p> |
|
<p>See the <a class="reference external" href="https://d-script.readthedocs.io/en/main/data.html#trained-models">documentation</a> for most up-to-date list.</p> |
|
<ul class="simple"> |
|
<li><p><code class="docutils literal notranslate"><span class="pre">lm_v1</span></code> - Language model from <a class="reference external" href="https://github.com/tbepler/protein-sequence-embedding-iclr2019">Bepler & Berger</a>.</p></li> |
|
<li><p><code class="docutils literal notranslate"><span class="pre">human_v1</span></code> - Human trained model from D-SCRIPT manuscript.</p></li> |
|
</ul> |
|
<p>Default: <code class="docutils literal notranslate"><span class="pre">human_v1</span></code></p> |
|
<dl class="field-list simple"> |
|
<dt class="field-odd">Parameters</dt> |
|
<dd class="field-odd"><p><strong>version</strong> (<em>str</em>) – Version of pre-trained model to get</p> |
|
</dd> |
|
<dt class="field-even">Returns</dt> |
|
<dd class="field-even"><p>Pre-trained model</p> |
|
</dd> |
|
<dt class="field-odd">Return type</dt> |
|
<dd class="field-odd"><p>dscript.models.*</p> |
|
</dd> |
|
</dl> |
|
</dd></dl> |
|
|
|
<dl class="py function"> |
|
<dt id="dscript.pretrained.get_state_dict"> |
|
<code class="sig-prename descclassname"><span class="pre">dscript.pretrained.</span></code><code class="sig-name descname"><span class="pre">get_state_dict</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">version</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'human_v1'</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">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/dscript/pretrained.html#get_state_dict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dscript.pretrained.get_state_dict" title="Permalink to this definition">¶</a></dt> |
|
<dd><p>Download a pre-trained model if not already exists on local device.</p> |
|
<dl class="field-list simple"> |
|
<dt class="field-odd">Parameters</dt> |
|
<dd class="field-odd"><ul class="simple"> |
|
<li><p><strong>version</strong> (<em>str</em>) – Version of trained model to download [default: human_1]</p></li> |
|
<li><p><strong>verbose</strong> (<em>bool</em>) – Print model download status on stdout [default: True]</p></li> |
|
</ul> |
|
</dd> |
|
<dt class="field-even">Returns</dt> |
|
<dd class="field-even"><p>Path to state dictionary for pre-trained language model</p> |
|
</dd> |
|
<dt class="field-odd">Return type</dt> |
|
<dd class="field-odd"><p>str</p> |
|
</dd> |
|
</dl> |
|
</dd></dl> |
|
|
|
</div> |
|
<div class="section" id="module-dscript.utils"> |
|
<span id="dscript-utils"></span><h2>dscript.utils<a class="headerlink" href="#module-dscript.utils" title="Permalink to this headline">¶</a></h2> |
|
<dl class="py class"> |
|
<dt id="dscript.utils.PairedDataset"> |
|
<em class="property"><span class="pre">class</span> </em><code class="sig-prename descclassname"><span class="pre">dscript.utils.</span></code><code class="sig-name descname"><span class="pre">PairedDataset</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">X0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">X1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Y</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/dscript/utils.html#PairedDataset"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dscript.utils.PairedDataset" title="Permalink to this definition">¶</a></dt> |
|
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">torch.utils.data.dataset.Dataset</span></code></p> |
|
<p>Dataset to be used by the PyTorch data loader for pairs of sequences and their labels.</p> |
|
<dl class="field-list simple"> |
|
<dt class="field-odd">Parameters</dt> |
|
<dd class="field-odd"><ul class="simple"> |
|
<li><p><strong>X0</strong> – List of first item in the pair</p></li> |
|
<li><p><strong>X1</strong> – List of second item in the pair</p></li> |
|
<li><p><strong>Y</strong> – List of labels</p></li> |
|
</ul> |
|
</dd> |
|
</dl> |
|
</dd></dl> |
|
|
|
<dl class="py function"> |
|
<dt id="dscript.utils.RBF"> |
|
<code class="sig-prename descclassname"><span class="pre">dscript.utils.</span></code><code class="sig-name descname"><span class="pre">RBF</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">D</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sigma</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="reference internal" href="../_modules/dscript/utils.html#RBF"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dscript.utils.RBF" title="Permalink to this definition">¶</a></dt> |
|
<dd><p>Convert distance matrix into similarity matrix using Radial Basis Function (RBF) Kernel.</p> |
|
<p><span class="math notranslate nohighlight">\(RBF(x,x') = \exp{\frac{-(x - x')^{2}}{2\sigma^{2}}}\)</span></p> |
|
<dl class="field-list simple"> |
|
<dt class="field-odd">Parameters</dt> |
|
<dd class="field-odd"><ul class="simple"> |
|
<li><p><strong>D</strong> (<em>np.ndarray</em>) – Distance matrix</p></li> |
|
<li><p><strong>sigma</strong> (<em>float</em>) – Bandwith of RBF Kernel [default: <span class="math notranslate nohighlight">\(\sqrt{\text{max}(D)}\)</span>]</p></li> |
|
</ul> |
|
</dd> |
|
<dt class="field-even">Returns</dt> |
|
<dd class="field-even"><p>Similarity matrix</p> |
|
</dd> |
|
<dt class="field-odd">Return type</dt> |
|
<dd class="field-odd"><p>np.ndarray</p> |
|
</dd> |
|
</dl> |
|
</dd></dl> |
|
|
|
<dl class="py function"> |
|
<dt id="dscript.utils.collate_paired_sequences"> |
|
<code class="sig-prename descclassname"><span class="pre">dscript.utils.</span></code><code class="sig-name descname"><span class="pre">collate_paired_sequences</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/dscript/utils.html#collate_paired_sequences"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dscript.utils.collate_paired_sequences" title="Permalink to this definition">¶</a></dt> |
|
<dd><p>Collate function for PyTorch data loader.</p> |
|
</dd></dl> |
|
|
|
<dl class="py function"> |
|
<dt id="dscript.utils.gpu_mem"> |
|
<code class="sig-prename descclassname"><span class="pre">dscript.utils.</span></code><code class="sig-name descname"><span class="pre">gpu_mem</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">device</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/dscript/utils.html#gpu_mem"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dscript.utils.gpu_mem" title="Permalink to this definition">¶</a></dt> |
|
<dd><p>Get current memory usage for GPU.</p> |
|
<dl class="field-list simple"> |
|
<dt class="field-odd">Parameters</dt> |
|
<dd class="field-odd"><p><strong>device</strong> (<em>int</em>) – GPU device number</p> |
|
</dd> |
|
<dt class="field-even">Returns</dt> |
|
<dd class="field-even"><p>memory used, memory total</p> |
|
</dd> |
|
<dt class="field-odd">Return type</dt> |
|
<dd class="field-odd"><p>int, int</p> |
|
</dd> |
|
</dl> |
|
</dd></dl> |
|
|
|
<dl class="py function"> |
|
<dt id="dscript.utils.log"> |
|
<code class="sig-prename descclassname"><span class="pre">dscript.utils.</span></code><code class="sig-name descname"><span class="pre">log</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="pre">msg</span></em>, <em class="sig-param"><span class="pre">file=<_io.TextIOWrapper</span> <span class="pre">name='<stderr>'</span> <span class="pre">mode='w'</span> <span class="pre">encoding='UTF-8'></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/dscript/utils.html#log"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dscript.utils.log" title="Permalink to this definition">¶</a></dt> |
|
<dd><p>Log datetime-stamped message to file</p> |
|
<dl class="field-list simple"> |
|
<dt class="field-odd">Parameters</dt> |
|
<dd class="field-odd"><ul class="simple"> |
|
<li><p><strong>msg</strong> – Message to log</p></li> |
|
<li><p><strong>f</strong> – Writable file object to log message to</p></li> |
|
</ul> |
|
</dd> |
|
</dl> |
|
</dd></dl> |
|
|
|
<dl class="py function"> |
|
<dt id="dscript.utils.plot_PR_curve"> |
|
<code class="sig-prename descclassname"><span class="pre">dscript.utils.</span></code><code class="sig-name descname"><span class="pre">plot_PR_curve</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">phat</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">saveFile</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="reference internal" href="../_modules/dscript/utils.html#plot_PR_curve"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dscript.utils.plot_PR_curve" title="Permalink to this definition">¶</a></dt> |
|
<dd><p>Plot precision-recall curve.</p> |
|
<dl class="field-list simple"> |
|
<dt class="field-odd">Parameters</dt> |
|
<dd class="field-odd"><ul class="simple"> |
|
<li><p><strong>y</strong> (<em>np.ndarray</em>) – Labels</p></li> |
|
<li><p><strong>phat</strong> (<em>np.ndarray</em>) – Predicted probabilities</p></li> |
|
<li><p><strong>saveFile</strong> (<em>str</em>) – File for plot of curve to be saved to</p></li> |
|
</ul> |
|
</dd> |
|
</dl> |
|
</dd></dl> |
|
|
|
<dl class="py function"> |
|
<dt id="dscript.utils.plot_ROC_curve"> |
|
<code class="sig-prename descclassname"><span class="pre">dscript.utils.</span></code><code class="sig-name descname"><span class="pre">plot_ROC_curve</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">phat</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">saveFile</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="reference internal" href="../_modules/dscript/utils.html#plot_ROC_curve"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dscript.utils.plot_ROC_curve" title="Permalink to this definition">¶</a></dt> |
|
<dd><p>Plot receiver operating characteristic curve.</p> |
|
<dl class="field-list simple"> |
|
<dt class="field-odd">Parameters</dt> |
|
<dd class="field-odd"><ul class="simple"> |
|
<li><p><strong>y</strong> (<em>np.ndarray</em>) – Labels</p></li> |
|
<li><p><strong>phat</strong> (<em>np.ndarray</em>) – Predicted probabilities</p></li> |
|
<li><p><strong>saveFile</strong> (<em>str</em>) – File for plot of curve to be saved to</p></li> |
|
</ul> |
|
</dd> |
|
</dl> |
|
</dd></dl> |
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