{"id":68070,"date":"2026-11-14T20:11:39","date_gmt":"2026-11-14T12:11:39","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=68070"},"modified":"2026-11-14T20:59:59","modified_gmt":"2026-11-14T12:59:59","slug":"scvi-counts-batch-integration-neighbor-controls","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/scvi-counts-batch-integration-neighbor-controls\/","title":{"rendered":"\u7528 scVI \u6574\u5408\u591a\u4e2a\u6837\u672c\uff0c\u600e\u6837\u5224\u65ad\u6279\u6b21\u6d88\u5931\u7684\u540c\u65f6\u8fd8\u7559\u4f4f\u4e86\u751f\u7269\u5dee\u5f02\uff1f"},"content":{"rendered":"<div class=\"ysx-method-guide\" style=\"max-width:820px;min-width:0;margin:0 auto;color:#26374a;line-height:1.86;overflow-wrap:anywhere\">\n<p>\u4e24\u4e2a\u6279\u6b21\u7684\u5355\u7ec6\u80de\u6570\u636e\uff0c\u6574\u5408\u524d\u5728\u56fe\u4e0a\u9694\u5f97\u5f88\u8fdc\uff0c\u6574\u5408\u540e\u4e24\u79cd\u989c\u8272\u7ec8\u4e8e\u4ea4\u7ec7\u8d77\u6765\u3002\u8fd9\u4e2a\u53d8\u5316\u503c\u5f97\u770b\uff0c\u4f46\u5f88\u96be\u53ea\u51ed\u8fd9\u5f20\u56fe\u5224\u65ad\u505a\u5f97\u597d\u4e0d\u597d\u3002\u5982\u679c\u7b2c\u4e8c\u6279\u6837\u672c\u6070\u597d\u591a\u4e86\u4e00\u7c7b\u7ec6\u80de\uff0c\u7406\u60f3\u7ed3\u679c\u5e94\u8be5\u4fdd\u7559\u8fd9\u7c7b\u989d\u5916\u72b6\u6001\u3002\u82e5\u5904\u7406\u7ec4\u5168\u90e8\u6765\u81ea\u7b2c\u4e8c\u6279\uff0c\u771f\u6b63\u7684\u5904\u7406\u6548\u5e94\u4e5f\u53ef\u80fd\u4e0e\u6279\u6b21\u4e00\u540c\u6d88\u5931\u3002\u7528 scvi-tools \u7684 scVI \u6a21\u578b\u6574\u5408\u65f6\uff0c\u6211\u4f1a\u5148\u5199\u4e0b\u54ea\u4e9b\u7fa4\u4f53\u6709\u7406\u7531\u76f8\u4f3c\u3001\u54ea\u4e9b\u5dee\u5f02\u6709\u7406\u7531\u5b58\u5728\uff0c\u518d\u53bb\u770b\u8f93\u51fa\u7684\u4f4e\u7ef4\u8868\u793a\u6709\u6ca1\u6709\u652f\u6301\u8fd9\u4e9b\u9884\u671f\u3002<\/p>\n<h2 style=\"font-size:1.38em;line-height:1.5;margin:1.55em 0 .55em;color:#182d43\">\u5148\u753b\u4e00\u5f20\u6837\u672c\u8bbe\u8ba1\u8868\uff0c\u518d\u767b\u8bb0\u8ba1\u6570\u5c42<\/h2>\n<p>\u5217\u51fa\u6bcf\u4f4d\u4f9b\u4f53\u5c5e\u4e8e\u4ec0\u4e48\u6761\u4ef6\u3001\u5728\u54ea\u4e2a\u5efa\u5e93\u6279\u6b21\uff0c\u4ee5\u53ca\u662f\u5426\u6709\u540c\u4e00\u4f9b\u4f53\u8de8\u6279\u5904\u7406\u7684\u6750\u6599\u3002\u5047\u5b9a\u6709\u7532\u4e59\u4e24\u4e2a\u6279\u6b21\uff0c\u5bf9\u7167\u548c\u5904\u7406\u5728\u4e24\u6279\u4e2d\u90fd\u51fa\u73b0\uff0c\u90a3\u4e48\u53ef\u4ee5\u5206\u522b\u5728\u540c\u4e00\u6761\u4ef6\u3001\u540c\u4e00\u7ec6\u80de\u7c7b\u578b\u5185\u89c2\u5bdf\u6279\u6b21\u504f\u79fb\u3002\u5982\u679c\u7532\u5168\u90e8\u662f\u5bf9\u7167\u3001\u4e59\u5168\u90e8\u662f\u5904\u7406\uff0c\u5355\u51ed\u8fd9\u7ec4\u6570\u636e\u5f88\u96be\u533a\u5206\u4e24\u79cd\u6765\u6e90\u3002\u628a\u5904\u7406\u6807\u7b7e\u6539\u540d\u4e3a\u6279\u6b21\u6807\u7b7e\u4ecd\u7136\u6ca1\u6709\u521b\u9020\u7f3a\u5931\u7684\u5bf9\u7167\u3002\u6700\u6709\u4ef7\u503c\u7684\u9644\u52a0\u6750\u6599\u5e38\u662f\u4e00\u4efd\u8de8\u6279\u91cd\u590d\u6216\u80fd\u5728\u4e24\u6279\u5171\u540c\u627e\u5230\u7684\u53c2\u8003\u6837\u672c\u3002<\/p>\n<p>\u6807\u51c6 scVI \u7684\u8868\u8fbe\u89c2\u6d4b\u6a21\u578b\u4ee5\u8ba1\u6570\u4e3a\u57fa\u7840\u3002\u5efa\u7acb\u5bf9\u8c61\u65f6\uff0c\u5148\u8bc1\u5b9e\u4f60\u4f20\u5165\u7684\u5c42\u786e\u5b9e\u4fdd\u5b58\u672a\u5bf9\u6570\u5316\u7684\u5206\u5b50\u8ba1\u6570\u3002\u5982\u679c\u4e3b\u77e9\u9635\u5df2\u505a\u603b\u91cf\u5f52\u4e00\u5316\u3001\u53d6\u5bf9\u6570\u6216\u6807\u51c6\u5316\uff0c\u5c31\u4ece\u53ef\u4fe1\u7684\u8ba1\u6570\u5c42\u767b\u8bb0\uff0c\u4e0d\u80fd\u4ec5\u4ec5\u56e0\u4e3a\u6587\u4ef6\u91cc\u6709\u4e00\u4e2a\u53eb counts \u7684\u540d\u79f0\u5c31\u8ba4\u5b9a\u5b83\u5408\u9002\u3002\u6bd4\u8f83\u4e24\u4e2a\u5bf9\u8c61\u65f6\uff0c\u8fd8\u8981\u7528\u4e00\u81f4\u7684\u57fa\u56e0\u7f16\u53f7\u5bf9\u9f50\u7279\u5f81\u3002\u5bf9\u7f3a\u5931\u4e8e\u67d0\u4e00\u7248\u6ce8\u91ca\u7684\u57fa\u56e0\u76f4\u63a5\u8865\u96f6\uff0c\u4f1a\u628a\u672a\u6d4b\u91cf\u8bef\u5199\u6210\u6ca1\u6709\u8868\u8fbe\u3002<a style=\"color:#28569b;text-decoration:underline;text-underline-offset:2px\" href=\"https:\/\/docs.scvi-tools.org\/en\/stable\/user_guide\/models\/scvi.html\">scVI \u6a21\u578b\u53ca\u8f93\u5165\u8bf4\u660e<\/a><\/p>\n<h2 style=\"font-size:1.38em;line-height:1.5;margin:1.55em 0 .55em;color:#182d43\">\u540c\u65f6\u4fdd\u7559\u539f\u6765\u7684\u7a7a\u95f4\u548c\u6a21\u578b\u5b66\u5230\u7684\u7a7a\u95f4<\/h2>\n<p>\u4e0b\u9762\u5047\u5b9a\u5bf9\u8c61\u7684\u8ba1\u6570\u5c42\u548c\u6279\u6b21\u5217\u5df2\u7ecf\u786e\u8ba4\u3002\u57fa\u7840\u793a\u4f8b\u628a\u6a21\u578b\u5b66\u4e60\u5230\u7684\u5750\u6807\u5199\u8fdb\u5355\u72ec\u7684\u4f4e\u7ef4\u8868\u793a\uff0c\u518d\u7528\u8fd9\u7ec4\u5750\u6807\u5efa\u7acb\u65b0\u7684\u90bb\u5c45\u56fe\u3002\u6ce8\u610f\u5206\u522b\u7ed9\u90bb\u5c45\u56fe\u548c\u5750\u6807\u8d77\u540d\u5b57\uff0c\u5426\u5219\u5bf9\u7167\u6574\u5408\u524d\u540e\u65f6\uff0c\u5b8c\u5168\u53ef\u80fd\u65e0\u610f\u4e2d\u4e24\u6b21\u4f7f\u7528\u540c\u4e00\u5f20\u56fe\u3002\u6570\u636e\u4e2d\u7684\u5177\u4f53\u6279\u6b21\u5217\u540d\u9700\u8981\u66ff\u6362\u6210\u4f60\u8bbe\u8ba1\u8868\u4e2d\u6838\u5b9e\u8fc7\u7684\u5b57\u6bb5\u3002<\/p>\n<pre style=\"max-width:100%;box-sizing:border-box;overflow-x:auto;margin:18px 0;padding:14px 16px;background:#f3f6fa;color:#1a293c;border:1px solid #d8e1ea;border-radius:8px;line-height:1.55;white-space:pre;overflow-wrap:normal;word-break:normal\"><code class=\"language-python\">import scanpy as sc\r\nimport scvi\r\n\r\nscvi.model.SCVI.setup_anndata(adata, layer=&quot;counts&quot;, batch_key=&quot;batch&quot;)\r\nmodel = scvi.model.SCVI(adata)\r\nmodel.train()\r\nadata.obsm[&quot;X_scVI&quot;] = model.get_latent_representation()\r\nsc.pp.neighbors(adata, use_rep=&quot;X_scVI&quot;, key_added=&quot;scvi_neighbors&quot;)\r\n<\/code><\/pre>\n<p>\u4f4e\u7ef4\u5750\u6807\u9002\u5408\u5efa\u7acb\u90bb\u5c45\u5173\u7cfb\u3001\u805a\u7c7b\u548c\u63a2\u7d22\u56fe\u8c31\u3002\u67d0\u4e2a\u5750\u6807\u7684\u6b63\u8d1f\u503c\u6ca1\u6709\u201c\u67d0\u4e2a\u57fa\u56e0\u8868\u8fbe\u591a\u5c11\u5206\u5b50\u201d\u7684\u5355\u4f4d\u3002\u8981\u6838\u5b9e\u67d0\u4e2a\u6dcb\u5df4\u7ec6\u80de\u6807\u8bb0\u662f\u5426\u5728\u539f\u59cb\u6837\u672c\u4e2d\u68c0\u51fa\uff0c\u5e94\u56de\u5230\u5bf9\u5e94\u7684\u57fa\u56e0\u8868\u8fbe\u5c42\u3002\u82e5\u4f7f\u7528\u6a21\u578b\u4f30\u8ba1\u7684\u6807\u51c6\u5316\u8868\u8fbe\uff0c\u5219\u8981\u6ce8\u660e\u53d6\u503c\u7684\u65b9\u6cd5\u548c\u6761\u4ef6\uff0c\u4e24\u79cd\u56fe\u56de\u7b54\u7684\u4fa7\u91cd\u70b9\u4e0d\u540c\u3002\u4f5c\u8005\u7684\u80ba\u90e8\u56fe\u8c31\u6574\u5408\u6559\u7a0b\u628a\u4f4e\u7ef4\u8868\u793a\u53d6\u51fa\u540e\u53e6\u5efa\u90bb\u5c45\u56fe\uff0c\u53ef\u4ee5\u5bf9\u7167\u67e5\u770b\u6bcf\u4e00\u6b65\u843d\u5728\u54ea\u4e2a\u5bf9\u8c61\u91cc\u3002<a style=\"color:#28569b;text-decoration:underline;text-underline-offset:2px\" href=\"https:\/\/docs.scvi-tools.org\/en\/stable\/tutorials\/notebooks\/scrna\/harmonization.html\">scvi-tools \u56fe\u8c31\u6574\u5408\u793a\u4f8b<\/a><\/p>\n<h2 style=\"font-size:1.38em;line-height:1.5;margin:1.55em 0 .55em;color:#182d43\">\u505a\u4e00\u6b21\u6709\u5206\u6bcd\u7684\u90bb\u5c45\u68c0\u67e5<\/h2>\n<p>\u5047\u8bbe\u67d0\u7c7b\u7ec6\u80de\u5728\u7532\u6279\u6709\u4e5d\u5341\u4e2a\u3001\u4e59\u6279\u6709\u5341\u4e2a\u3002\u5bf9\u7532\u6279\u4e00\u4e2a\u7ec6\u80de\u68c0\u67e5\u5341\u4e2a\u8fd1\u90bb\uff0c\u4e5d\u7532\u4e00\u4e59\u4e0e\u8fd9\u4e00\u7c7b\u7ec6\u80de\u7684\u6765\u6e90\u6bd4\u4f8b\u76f8\u5f53\u3002\u82e5\u673a\u68b0\u8981\u6c42\u4e94\u7532\u4e94\u4e59\uff0c\u4f1a\u628a\u672c\u6765\u5c31\u4e0d\u5747\u8861\u7684\u91c7\u6837\u8bf4\u6210\u201c\u4ecd\u6709\u6279\u6b21\u201d\u3002\u6362\u4e00\u7c7b\u7ec6\u80de\uff0c\u4e24\u6279\u5404\u6709\u4e94\u5341\u4e2a\uff0c\u5982\u679c\u7edd\u5927\u591a\u6570\u7ec6\u80de\u7684\u5341\u4e2a\u8fd1\u90bb\u5168\u6765\u81ea\u81ea\u8eab\u6279\u6b21\uff0c\u5c31\u503c\u5f97\u8ffd\u67e5\u3002\u4e0b\u9762\u7684\u6570\u503c\u662f\u6559\u5b66\u7b97\u4f8b\uff0c\u5341\u4e2a\u90bb\u5c45\u4e0d\u662f\u63a8\u8350\u7ed9\u6240\u6709\u9879\u76ee\u7684\u56fa\u5b9a\u8bbe\u7f6e\u3002<\/p>\n<div class=\"guide-table\" style=\"max-width:100%;overflow-x:auto;margin:18px 0\">\n<table style=\"display:table;width:100%;max-width:100%;min-width:0;table-layout:fixed;border-collapse:collapse;font-size:.92em;line-height:1.6\">\n<thead>\n<tr>\n<th scope=\"col\" style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;background:#edf4ff;color:#1e293b;vertical-align:top;text-align:left;padding:6px;border:1px solid #c4cfdb\">\u540c\u4e00\u79cd\u7ec6\u80de\u7684\u6765\u6e90<\/th>\n<th scope=\"col\" style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;background:#edf4ff;color:#1e293b;vertical-align:top;text-align:left;padding:6px;border:1px solid #c4cfdb\">\u67d0\u4e2a\u7ec6\u80de\u5468\u56f4\u7684\u5341\u4e2a\u90bb\u5c45<\/th>\n<th scope=\"col\" style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;background:#edf4ff;color:#1e293b;vertical-align:top;text-align:left;padding:6px;border:1px solid #c4cfdb\">\u53ef\u4ee5\u8fdb\u4e00\u6b65\u95ee\u4ec0\u4e48<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u7532\u4e5d\u5341\u3001\u4e59\u5341<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u4e5d\u7532\u3001\u4e00\u4e59<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u4e0d\u540c\u4f9b\u4f53\u7684\u591a\u4e2a\u7ec6\u80de\u662f\u5426\u4e5f\u7b26\u5408\u8fd9\u4e2a\u6765\u6e90\u6bd4\u4f8b<\/td>\n<\/tr>\n<tr>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u7532\u4e94\u5341\u3001\u4e59\u4e94\u5341<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u5341\u7532\u3001\u96f6\u4e59<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u540c\u6761\u4ef6\u4e0b\u662f\u5426\u4ecd\u6309\u6279\u6b21\u9694\u79bb\uff0c\u6216\u6709\u771f\u5b9e\u4e9a\u578b\u5dee\u522b<\/td>\n<\/tr>\n<tr>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u53ea\u6709\u4e59\u6279\u89c2\u6d4b\u5230<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u5168\u90e8\u6765\u81ea\u4e59<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u80fd\u5426\u7528\u72ec\u7acb\u6750\u6599\u786e\u5b9a\u8fd9\u4e2a\u72b6\u6001\u662f\u5426\u53ea\u5728\u4e59\u51fa\u73b0<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n<figure class=\"guide-figure\" style=\"margin:24px 0 28px\"><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2026\/11\/scvi-counts-batch-integration-neighbor-controls-guide.png?resize=1200%2C840&#038;ssl=1\" alt=\"\u5341\u4e2a\u8fd1\u90bb\uff0c\u51e0\u4e2a\u8be5\u6765\u81ea\u53e6\u4e00\u6279\u3002\u6559\u5b66\u7b97\u4f8b\uff5c\u5148\u67e5\u540c\u4e00\u7ec6\u80de\u7c7b\u578b\u7684\u6765\u6e90\u6bd4\u4f8b\uff0c\u518d\u89e3\u91ca\u5c40\u90e8\u6df7\u5408\u300290\u223610\uff0c\u4e5d\u7532\u4e00\u4e59\uff0c\u540c\u7c7b\u7ec6\u80de\u672c\u6765\u5c31\u5931\u8861\uff0c\u8fd9\u4e2a\u90bb\u57df\u7b26\u5408\u603b\u4f53\u6bd4\u4f8b\u300250\u223650\uff0c\u5341\u7532\u96f6\u4e59\uff0c\u5728\u591a\u4e2a\u7ec6\u80de\u3001\u591a\u4e2a\u4f9b\u4f53\u4e2d\u6838\u67e5\u662f\u5426\u4ecd\u6309\u6279\u6b21\u9694\u79bb\u3002\u53ea\u6709\u4e59\uff0c\u540c\u7c7b\u4ec5\u5728\u4e59\u6279\u51fa\u73b0\uff0c\u56de\u770b\u72ec\u7acb\u6837\u672c\u4e0e\u8868\u8fbe\u6807\u8bb0\uff0c\u4fdd\u7559\u72b6\u6001\u5dee\u5f02\u3002\" width=\"1200\" height=\"840\" style=\"display:block;width:100%;height:auto;border-radius:10px\"><figcaption style=\"font-size:14px;line-height:1.6;margin:9px 2px 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