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495<section class="tex2jax_ignore mathjax_ignore" id="neural-models">
496<h1><strong>Neural ModelS</strong><a class="headerlink" href="#neural-models" title="Link to this heading">#</a></h1>
497<p>NeMoS (Neural ModelS) is a statistical modeling framework optimized for systems neuroscience and powered by <a class="reference external" href="https://jax.readthedocs.io/en/latest/">
497JAX</a>.
498It streamlines the process of defining and selecting models, through a collection of easy-to-use methods for feature design.</p>
499<p>The core of NeMoS includes GPU-accelerated, well-tested implementations of standard statistical models for systems neuroscience.</p>
500<p>We provide:</p>
501<ul class="simple">
502<li><p>A <a class="reference internal" href="api/generated/glm/nemos.glm.GLM.html#nemos.glm.GLM" title="nemos.glm.GLM"><code class="xref py py-class docutils literal notranslate"><span class="pre">GLM</span></code></a> for single neurons and a <a class="reference internal" href="api/generated/glm/nemos.glm.PopulationGLM.html#nemos.glm.PopulationGLM" title="nemos.glm.PopulationGLM"><code class="xref py py-class docutils literal notranslate"><span class="pre">PopulationGLM</span></code></a>, with a choice of <a class="reference internal" href="api/observation_models.html#observation-models"><span class="std std-ref">observation models</span></a> (<a class="reference internal" href="api/generated/observation_models/nemos.observation_models.PoissonObservations.html#nemos.observation_models.PoissonObservations" title="nemos.observation_models.PoissonObservations"><code class="xref py py-class docutils literal notranslate"><span class="pre">Poisson</span></code></a>, <a class="reference internal" href="api/generated/observation_models/nemos.observation_models.NegativeBinomialObservations.html#nemos.observation_models.NegativeBinomialObservations" title="nemos.observation_models.NegativeBinomialObservations"><code class="xref py py-class docutils literal notranslate"><span class="pre">Negative</span> <span class="pre">Binomial</span></code></a>, <a class="reference internal" href="api/generated/observation_models/nemos.observation_models.GammaObservations.html#nemos.observation_models.GammaObservations" title="nemos.observation_models.GammaObservations"><code class="xref py py-class docutils literal notranslate"><span class="pre">Gamma</span></code></a>, <a class="reference internal" href="api/generated/observation_models/nemos.observation_models.GaussianObservations.html#nemos.observation_models.GaussianObservations" title="nemos.observation_models.GaussianObservations"><code class="xref py py-class docutils literal notranslate"><span class="pre">Gaussian</span></code></a>, <a class="reference internal" href="api/generated/observation_models/nemos.observation_models.BernoulliObservations.html#nemos.observation_models.BernoulliObservations" title="nemos.observation_models.BernoulliObservations"><code class="xref py py-class docutils literal notranslate"><span class="pre">Bernoulli</span></code></a>) and a <a class="reference internal" href="api/generated/glm/nemos.glm.ClassifierGLM.html#nemos.glm.ClassifierGLM" title="nemos.glm.ClassifierGLM"><code class="xref py py-class docutils literal notranslate"><span class="pre">ClassifierGLM</span></code></a> for categorical responses.</p></li>
503<li><p>A composable <a class="reference internal" href="api/basis.html#nemos-basis"><span class="std std-ref">basis module</span></a> for constructing and transforming model features.</p></li>
504<li><p>Multiple <a class="reference internal" href="api/regularizers.html#regularizers"><span class="std std-ref">regularization schemes</span></a>: <a class="reference internal" href="api/generated/regularizer/nemos.regularizer.Ridge.html#nemos.regularizer.Ridge" title="nemos.regularizer.Ridge"><code class="xref py py-class docutils literal notranslate"><span class="pre">Ridge</span></code></a>, <a class="reference internal" href="api/generated/regularizer/nemos.regularizer.Lasso.html#nemos.regularizer.Lasso" title="nemos.regularizer.Lasso"><code class="xref py py-class docutils literal notranslate"><span class="pre">Lasso</span></code></a>, <a class="reference internal" href="api/generated/regularizer/nemos.regularizer.GroupLasso.html#nemos.regularizer.GroupLasso" title="nemos.regularizer.GroupLasso"><code class="xref py py-class docutils literal notranslate"><span class="pre">GroupLasso</span></code></a>, and <a class="reference internal" href="api/generated/regularizer/nemos.regularizer.ElasticNet.html#nemos.regularizer.ElasticNet" title="nemos.regularizer.ElasticNet"><code class="xref py py-class docutils literal notranslate"><span class="pre">ElasticNet</span></code></a>.</p></li>
505</ul>
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510<div class="sd-card-body docutils">
511<div class="sd-card-title sd-font-weight-bold docutils">
512<span class="iconify" data-icon="mdi:hammer-wrench"></span>   <strong>Installation Instructions</strong></div>
513<hr class="docutils" />
514<p class="sd-card-text">Run the following <code class="docutils literal notranslate"><span class="pre">pip</span></code> command in your virtual environment.</p>
515<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">nemos</span>
516</pre></div>
517</div>
518</div>
519<a class="sd-stretched-link sd-hide-link-text reference external" href="installation.html"><span>Install</span></a></div>
520</div>
521<div class="sd-col sd-d-flex-row docutils">
522<div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm sd-card-hover docutils">
523<div class="sd-card-body docutils">
524<div class="sd-card-title sd-font-weight-bold docutils">
525<span class="iconify" data-icon="mdi:clock-fast"></span>   <strong>Getting Started</strong></div>
526<hr class="docutils" />
527<p class="sd-card-text">New to NeMoS? Get the ball rolling with our quickstart.</p>
528</div>
529<a class="sd-stretched-link sd-hide-link-text reference external" href="quickstart.html"><span>Quickstart</span></a></div>
530</div>
531<div class="sd-col sd-d-flex-row docutils">
532<div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm sd-card-hover docutils">
533<div class="sd-card-body docutils">
534<div class="sd-card-title sd-font-weight-bold docutils">
535<span class="iconify" data-icon="mdi:book-open-variant-outline"></span>   <strong>Background</strong></div>
536<hr class="docutils" />
537<p class="sd-card-text">Refresh your theoretical knowledge before diving into data analysis with our notes.</p>
538</div>
539<a class="sd-stretched-link sd-hide-link-text reference external" href="background/README.html"><span>Background</span></a></div>
540</div>
541<div class="sd-col sd-d-flex-row docutils">
542<div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm sd-card-hover docutils">
543<div class="sd-card-body docutils">
544<div class="sd-card-title sd-font-weight-bold docutils">
545<span class="iconify" data-icon="mdi:lightbulb-on-10"></span>   <strong>How-to Guide</strong></div>
546<hr class="docutils" />
547<p class="sd-card-text">Already familiar with the concepts? Learn how you to process and analyze your data with NeMoS.</p>
548<div class="card-footer-content">
549<p class="sd-card-text"><em>Requires familiarity with the theory.</em></p>
550</div>
551</div>
552<a class="sd-stretched-link sd-hide-link-text reference external" href="how_to_guide/README.html"><span>How-to-Guide</span></a></div>
553</div>
554<div class="sd-col sd-d-flex-row docutils">
555<div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm sd-card-hover docutils">
556<div class="sd-card-body docutils">
557<div class="sd-card-title sd-font-weight-bold docutils">
558<span class="iconify" data-icon="mdi:brain"></span>   <strong>Neural Modeling</strong></div>
559<hr class="docutils" />
560<p class="sd-card-text">Explore fully worked examples to learn how to analyze neural recordings from scratch.</p>
561<div class="card-footer-content">
562<p class="sd-card-text"><em>Requires familiarity with the theory.</em></p>
563</div>
564</div>
565<a class="sd-stretched-link sd-hide-link-text reference external" href="tutorials/README.html"><span>Tutorials</span></a></div>
566</div>
567<div class="sd-col sd-d-flex-row docutils">
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569<div class="sd-card-body docutils">
570<div class="sd-card-title sd-font-weight-bold docutils">
571<span class="iconify" data-icon="mdi:cog"></span>   <strong>API Reference</strong></div>
572<hr class="docutils" />
573<p class="sd-card-text">Access a detailed description of each module and function, including parameters and functionality.</p>
574</div>
575<a class="sd-stretched-link sd-hide-link-text reference external" href="api/index.html"><span>API Reference</span></a></div>
576</div>
577</div>
578</div>
579<div style="text-align: center;">
580<p><strong>Learning Resources:</strong> <a class="reference external" href="https://compneuro.neuromatch.io/tutorials/W1D3_GeneralizedLinearModels/student/W1D3_Tutorial1.html"><span class="iconify" data-icon="mdi:book-open-variant-outline"></span> Neuromatch Academy’s Lessons</a> | <a class="reference external" href="https://www.youtube.com/watch?v=NFeGW5ljUoI&amp;t=424s"><span class="iconify" data-icon="mdi:youtube"></span>
580 Cosyne 2018 Tutorial</a> <br>
581<strong>Useful Links:</strong> <a class="reference internal" href="getting_help.html"><span class="std std-doc"><span class="iconify" data-icon="mdi:chat-question"></span> Getting Help</span></a> | <a class="reference external" href="https://github.com/flatironinstitute/nemos/issues"><span class="iconify" data-icon="mdi:alert-circle-outline"></span> Issue Tracker</a> | <a class="reference external" href="https://github.com/flatironinstitute/nemos/blob/main/CONTRIBUTING.md"><span class="iconify" data-icon="mdi:order-bool-ascending-variant"></span> Contributing Guidelines</a></p>
582</div>
583<section id="license">
584<h2><span class="iconify" data-icon="mdi:scale-balance" style="width: 1em"></span>  <strong>License</strong><a class="headerlink" href="#license" title="Link to this heading">#</a></h2>
585<p>Open source, <a class="reference external" href="https://github.com/flatironinstitute/nemos/blob/main/LICENSE">licensed under MIT</a>.</p>
586</section>
587<section id="cite-us">
588<h2><span class="iconify" data-icon="mdi:lead-pencil" style="width: 1em"></span>  <strong>Cite Us</strong><a class="headerlink" href="#cite-us" title="Link to this heading">#</a></h2>
589<p>If you use NeMoS in academic work, please cite the software. See the <a class="reference internal" href="citation.html#citation-doc"><span class="std std-ref">Citation Guide and Bibliography</span></a> for more details.</p>
590</section>
591<section id="support">
592<h2><strong>Support</strong><a class="headerlink" href="#support" title="Link to this heading">#</a></h2>
593<p>This package is supported by:</p>
594<ul class="simple">
595<li><p>The Center for Computational Neuroscience, in the Flatiron Institute of the Simons Foundation.</p></li>
596<li><p>The NIH BRAIN Initiative (1RF1MH133778).</p></li>
597</ul>
598<a class="reference external image-reference" href="https://www.simonsfoundation.org/flatiron/center-for-computational-neuroscience/"><img alt="Flatiron Center for Computational Neuroscience logo White." class="only-dark" src="_images/logo_flatiron_white.svg" style="width: 200px;" />
599</a>
600<a class="reference external image-reference" href="https://www.simonsfoundation.org/flatiron/center-for-computational-neuroscience/"><img alt="Flatiron Center for Computational Neuroscience logo." class="only-light" src="_images/CCN-logo-wText.png" style="width: 200px;" />
601</a>
602</section>
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