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<title>spCellEval Methods</title>
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<span class="text-xl font-bold tracking-tight text-white">spCellEval</span>
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<a href="index.html#about" class="text-gray-300 hover:text-indigo-400 transition-colors">About</a>
<a href="results.html" class="text-gray-300 hover:text-indigo-400 transition-colors">Results</a>
<a href="methods.html" class="text-indigo-300 font-semibold">Methods</a>
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<section class="text-center text-white mb-10">
<h1 class="text-4xl md:text-5xl font-extrabold tracking-tight">Methods</h1>
<p class="mt-4 max-w-3xl mx-auto text-gray-300">
This page summarizes the algorithmic families included in spCellEval and the criteria used to assess method performance across datasets.
</p>
</section>
<section class="grid grid-cols-1 md:grid-cols-4 gap-6 mb-8">
<div class="bg-white/10 rounded-xl p-6 card-hover">
<i class="fas fa-user-check text-indigo-300 text-2xl mb-3"></i>
<h2 class="text-white font-semibold text-lg mb-2">Supervised</h2>
<p class="text-indigo-100 text-sm">Learns explicit labels and generally achieves strongest recovery when high-quality annotations are available.</p>
</div>
<div class="bg-white/10 rounded-xl p-6 card-hover">
<i class="fas fa-project-diagram text-indigo-300 text-2xl mb-3"></i>
<h2 class="text-white font-semibold text-lg mb-2">Prior-Knowledge Based</h2>
<p class="text-indigo-100 text-sm">Uses marker panels and biological priors for robust cell typing when labels are scarce.</p>
</div>
<div class="bg-white/10 rounded-xl p-6 card-hover">
<i class="fas fa-layer-group text-indigo-300 text-2xl mb-3"></i>
<h2 class="text-white font-semibold text-lg mb-2">Unsupervised</h2>
<p class="text-indigo-100 text-sm">Identifies structure in large cohorts and supports exploratory phenotyping in novel tissues.</p>
</div>
<div class="bg-white/10 rounded-xl p-6 card-hover">
<i class="fas fa-plug-circle-check text-indigo-300 text-2xl mb-3"></i>
<h2 class="text-white font-semibold text-lg mb-2">Pre-trained</h2>
<p class="text-indigo-100 text-sm">Enables rapid cell typing in novel tissues using pre-existing models.</p>
</div>
</section>
<section class="bg-white rounded-xl shadow-sm overflow-hidden mb-8">
<div class="border-b border-gray-100 px-6 py-4">
<h2 class="text-xl font-semibold text-gray-800">Method Papers</h2>
<p class="text-gray-500 text-sm">Open the primary paper or publication page for each method in the benchmark.</p>
</div>
<div id="methodPaperGrid" class="p-6 space-y-8"></div>
</section>
<!--
<section class="bg-white rounded-xl shadow-sm overflow-hidden mb-8">
<div class="border-b border-gray-100 px-6 py-4">
<h2 class="text-xl font-semibold text-gray-800">Method Comparison Snapshot</h2>
<p class="text-gray-500 text-sm">Illustrative examples of method profiles used in the benchmark.</p>
</div>
<div class="p-4 overflow-x-auto">
<table class="w-full border-collapse min-w-[760px]">
<thead class="sticky-header">
<tr>
<th class="method-cell py-3 px-4 text-left font-semibold text-gray-700 border-b text-sm">Method</th>
<th class="py-3 px-4 text-left font-semibold text-gray-700 border-b text-sm">Family</th>
<th class="py-3 px-4 text-left font-semibold text-gray-700 border-b text-sm">Strength</th>
<th class="py-3 px-4 text-left font-semibold text-gray-700 border-b text-sm">Best Use Case</th>
</tr>
</thead>
<tbody>
<tr class="border-b hover:bg-gray-50">
<td class="method-cell py-3 px-4 text-sm font-medium text-gray-900">scimap</td>
<td class="py-3 px-4 text-sm text-gray-700">Prior-knowledge / Gating</td>
<td class="py-3 px-4 text-sm text-gray-700">Marker-aware interpretability</td>
<td class="py-3 px-4 text-sm text-gray-700">Marker-guided discovery workflows</td>
</tr>
<tr class="border-b hover:bg-gray-50">
<td class="method-cell py-3 px-4 text-sm font-medium text-gray-900">Phenograph</td>
<td class="py-3 px-4 text-sm text-gray-700">Unsupervised</td>
<td class="py-3 px-4 text-sm text-gray-700">Community detection in high-dimensional space</td>
<td class="py-3 px-4 text-sm text-gray-700">Discovery of novel cell states</td>
</tr>
<tr class="hover:bg-gray-50">
<td class="method-cell py-3 px-4 text-sm font-medium text-gray-900">Leiden + UMAP</td>
<td class="py-3 px-4 text-sm text-gray-700">Clustering + Visualization</td>
<td class="py-3 px-4 text-sm text-gray-700">Scalable exploratory segmentation</td>
<td class="py-3 px-4 text-sm text-gray-700">Initial stratification before supervision</td>
</tr>
</tbody>
</table>
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</section> -->
<section class="bg-gradient-to-r from-indigo-700 to-teal-700 rounded-xl p-8 text-center">
<h2 class="text-2xl font-bold text-white">Need Full Quantitative Results?</h2>
<p class="mt-2 text-indigo-100">Explore the full metric matrix and ranking tables on the homepage Results section.</p>
<a href="results.html" class="inline-block mt-5 px-6 py-3 bg-white text-indigo-700 font-semibold rounded-lg hover:bg-gray-100 transition-colors">Open Results</a>
</section>
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"XGBoost": "https://doi.org/10.1145/2939672.2939785",
"Logistic Regression": "https://doi.org/10.1038/nmeth.3904",
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"MAPS": "https://doi.org/10.1038/s41467-023-44188-w",
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"Leiden": "https://doi.org/10.1038/s41598-019-41695-z",
"CellLENS_Lite": "https://doi.org/10.1038/s41590-025-02163-1",
"CellLENS_Full": "https://doi.org/10.1038/s41590-025-02163-1",
"FuseSOM": "https://doi.org/10.1093/bioadv/vbad141",
"Starling": "https://doi.org/10.1038/s41467-024-55214-w",
"FlowSOM Meta Clusters": "https://doi.org/10.1002/cyto.a.22625",
"Scyan": "https://doi.org/10.1093/bib/bbad260",
"Tacit": "https://doi.org/10.1038/s41467-025-58874-4",
"Tribus": "https://doi.org/10.1093/bioinformatics/btaf082",
"Astir": "https://doi.org/10.1016/j.cels.2021.08.012",
"Nimbus": "https://doi.org/10.1038/s41592-025-02826-9",
"Deepcelltypes": "https://doi.org/10.1101/2024.11.02.621624",
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