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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> 506<div class="sd-container-fluid sd-sphinx-override sd-mb-4 docutils"> 507<div class="sd-row sd-row-cols-1 sd-row-cols-xs-1 sd-row-cols-sm-2 sd-row-cols-md-3 sd-row-cols-lg-3 docutils"> 508<div class="sd-col sd-d-flex-row docutils"> 509<div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm sd-card-hover docut
509ils"> 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> Â <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> Â <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> Â <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> Â <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> Â <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"> 568<div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm sd-card-hover docutils"> 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> Â <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 Academyâs Lessons</a> | <a class="reference external" href="https://www.youtube.com/watch?v=NFeGW5ljUoI&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> 603</section> 604 605 606 </article> 607 608 609 610 611 612 <footer class="prev-next-footer d-print-none"> 613 614<div class="prev-next-area"> 615 <a class="right-next" 616 href="quickstart.html" 617 title="next page"> 618 <div class="prev-next-info"> 619 <p class="prev-next-subtitle">next</p> 620 <p class="prev-next-title">Quickstart</p> 621 </div> 622 <i class="fa-solid fa-angle-right"></i> 623 </a> 624</div> 625 </footer> 626 627 </div> 628 629 630 631 632 </div> 633 <footer class="bd-footer-content"> 634 635 </footer> 636 637 </main> 638 </div> 639 </div> 640 641 <!-- Scripts loaded after <body> so the DOM is not blocked --> 642
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643 644 645<footer class="footer" style="border-top: 1px solid #ccc; padding-top: 10px"> 646 <div class="container"> 647 <div id="credits" style="width: 50%; float: left"> 648 <p> 649 © Copyright 2024, <a href="https://www.simonsfoundation.org/people/edoardo-balzani/">nemos authors</a>.<br/> 650 Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> and the <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/">PyData Theme</a>.<br/> 651 </p> 652 </div> 653 <div id="version" style="color: #999; float: right; margin: 15px">v0.2.10</div> 654 </div> 655 </div> 656</footer> 657 </body> 658</html>
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