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29.9652%;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 29.9652% !important;\">\n<section style=\"margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;line-height: 0;\">\n<section>\n<section style=\"display: inline-block;vertical-align: middle;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 0;\">\n<section style=\"width: 111px;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1.75em;text-indent: 0em;\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;height: auto;width: 111px;\"><img decoding=\"async\" data-ratio=\"1\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-07-06_\u76f4\u51fb\u70ed\u70b9\uff01\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u4e4bLASSO,randomForest\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\/1_Xkz3aJGClianeaJMFaPKsbDRmfsHNw.png\" 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flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;border-left: 3px solid rgb(219, 219, 219);border-bottom-left-radius: 0px;padding-left: 8px;align-self: flex-start;flex: 0 0 auto;\">\n<section style=\"color: rgba(0, 0, 0, 0.5);text-align: justify;font-size: 14px;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;letter-spacing: 0.578px;\">\u5c0f\u679c\u4eca\u5929\u7ed9\u5927\u5bb6\u5e26\u6765\u7684\u5206\u4eab\u7edd\u5bf9\u662f\u751f\u4fe1\u70ed\u70b9\u5206\u6790\u5185\u5bb9\uff0c\u57fa\u4e8e\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u751f\u5b58\u8d44\u6599\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\uff0c\u6700\u7ec8\u5c06\u4e09\u79cd\u7b97\u6cd5\u83b7\u5f97\u7684\u4ea4\u53c9\u57fa\u56e0\u4f5c\u4e3a\u6211\u4eec\u7684\u7279\u5f81\u57fa\u56e0\u3002<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u63a5\u4e0b\u6765\u8ddf\u7740\u5c0f\u679c\u5f00\u542f\u4eca\u5929\u7684\u5b66\u4e60\u4e4b\u65c5\u5427\uff01\u5173\u6ce8\u5c0f\u679c\u56de\u590d111\u9886\u53d6\u76f8\u5173\u6587\u4ef6\u54df\uff01<\/span><span style=\"text-align: center;letter-spacing: 0.034em;\"><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">1. \u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u7b5b\u9009<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5c0f\u4f19\u4f34\u4eec\u662f\u4e0d\u662f\u5728\u60f3\u5230\u5e95\u662f\u90a3\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\uff1f\u4e0d\u6025\uff01\u5c0f\u679c\u6765\u6162\u6162\u544a\u8bc9\u5927\u5bb6\uff0c\u4eca\u5929\u5c0f\u679c\u5c06\u5229\u7528LASSO\u56de\u5f52\uff0c\u968f\u673a\u68ee\u6797\u548cxgboost\u4e09\u79cd\u7b97\u6cd5\u8fdb\u884c\u751f\u5b58\u8d44\u6599\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\uff0c\u8fd9\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7684\u7b97\u6cd5\u539f\u7406\u5c0f\u679c\u5728\u8fd9\u91cc\u4e0d\u505a\u8fc7\u591a\u7684\u4ecb\u7ecd\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u4eec\u53ef\u4ee5\u81ea\u884c\u67e5\u8be2\u5b66\u4e60\uff0c\u4eca\u5929\u5c0f\u679c\u5c06\u901a\u8fc7\u5b9e\u64cd\uff0c\u8ba9\u5927\u5bb6\u8f7b\u677e\u638c\u63e1\u5982\u4f55\u5229\u7528\u8fd9\u4e09\u79cd\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\uff0c\u5176\u5b9e\u5206\u6790\u975e\u5e38\u7b80\u5355\uff0c\u53ea\u9700\u8981\u8f93\u5165\u5e26\u6709\u751f\u5b58\u4fe1\u606f\u7684\u8868\u8fbe\u77e9\u9635\u6587\u4ef6\uff0c\u5c31\u53ef\u4ee5\u5f88\u8f7b\u677e\u7684\u5b8c\u6210\u8be5\u5206\u6790\uff0c\u5bf9\u5c0f\u767d\u4e5f\u5f88\u9002\u7528\uff0c\u8bdd\u4e0d\u591a\u8bf4\uff0c\u9a6c\u4e0a\u8ddf\u7740\u5c0f\u679c\u5f00\u59cb\u4eca\u5929\u7684\u5b9e\u64cd\u5427\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">2. \u51c6\u5907\u9700\u8981\u7684R\u5305<\/span><\/em><\/strong><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u5b89\u88c5\u9700\u8981\u7684R\u5305<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"ggplot2\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"tidyverse\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"ggvenn\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"glmnet\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"survival\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"xgboost\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"randomForestSRC\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">#\u52a0\u8f7d\u9700\u8981\u7684R\u5305 <\/span><\/code><code><span class=\"code-snippet_outer\">library(randomForestSRC)<\/span><\/code><code><span class=\"code-snippet_outer\">library(tidyverse)<\/span><\/code><code><span class=\"code-snippet_outer\">library(ggplot2)<\/span><\/code><code><span class=\"code-snippet_outer\">library(ggvenn)<\/span><\/code><code><span class=\"code-snippet_outer\">library(glmnet)<\/span><\/code><code><span class=\"code-snippet_outer\">library(survival)<\/span><\/code><code><span class=\"code-snippet_outer\">library(xgboost)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">3. \u6570\u636e\u51c6\u5907<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">exp_surv.txt<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">#\u751f\u5b58\u4fe1\u606f\u52a0\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u6587\u4ef6\uff0c\u884c\u540d\u4e3a\u6837\u672c\u4fe1\u606f\uff0c\u7b2c\u4e00\u5217\u4e3aOS.time(\u751f\u5b58\u65f6\u95f4),\u7b2c\u4e8c\u5217\u4e3aOS(\u751f\u5b58\u72b6\u6001),\u5176\u4ed6\u5217\u4e3a\u57fa\u56e0\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.24548736462093862\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-07-06_\u76f4\u51fb\u70ed\u70b9\uff01\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u4e4bLASSO,randomForest\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\/2_4UhN3ZHByrTJz96diaw3libaGnoxhg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3UxF8pzNoKPofjKOrn0yypCxiaHnd4UhN3ZHByrTJz96diaw3libaGnoxhg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" \/><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\"><br \/><\/span><\/em><\/strong><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\"><br \/><\/span><\/em><\/strong><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">4 . LASSO\u56de\u5f52\u5206\u6790<\/span><\/em><\/strong><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u8bfb\u53d6\u751f\u5b58\u4fe1\u606f\u7684\u57fa\u56e0\u8868\u8fbe\u77e9\u9635<\/span><\/code><code><span class=\"code-snippet_outer\">train<-read.table(<span class=\"code-snippet__string\">\"exp_surv.txt\"<\/span>,header=T,sep=<span class=\"code-snippet__string\">\"t\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u63d0\u53d6\u57fa\u56e0\u8868\u8fbe\u77e9\u9635<\/span><\/code><code><span class=\"code-snippet_outer\">x1 <- as.matrix(train[, <span class=\"code-snippet__number\">3<\/span>:ncol(train)])<\/span><\/code><code><span class=\"code-snippet_outer\">x2 <- as.matrix(Surv(train$OS.time, train$OS))<\/span><\/code><code><span class=\"code-snippet_outer\">cvfit = cv.glmnet(x1, x2,<\/span><\/code><code><span class=\"code-snippet_outer\"> nfold=<span class=\"code-snippet__number\">10<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> family = <span class=\"code-snippet__string\">\"cox\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> )<\/span><\/code><code><span class=\"code-snippet_outer\">#\u7ed8\u5236lamba\u56fe<\/span><\/code><code><span class=\"code-snippet_outer\">pdf(<span class=\"code-snippet__string\">\"lambda.pdf\"<\/span>,width = <span class=\"code-snippet__number\">10<\/span>,height = <span class=\"code-snippet__number\">8<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">plot(cvfit)<\/span><\/code><code><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><code><span class=\"code-snippet_outer\">#\u6b64\u5904\u4f7f\u7528`lambda min`<\/span><\/code><code><span class=\"code-snippet_outer\">cvfit$lambda.min #\u6700\u4f73lambda\u503c<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.07942238267148015\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-07-06_\u76f4\u51fb\u70ed\u70b9\uff01\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u4e4bLASSO,randomForest\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\/3_8kic2UHSadrRsrecK2cAZUrRfanMIg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3UBIuE7FowpgCGfGnibJYblFiaRyz8kic2UHSadrRsrecK2cAZUrRfanMIg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" \/><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">fit <- glmnet(x1, x2,<\/span><\/code><code><span class=\"code-snippet_outer\"> family = <span class=\"code-snippet__string\">\"cox\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u7528\u5305\u81ea\u5e26\u7684\u51fd\u6570\u7ed8\u5236lasso\u56de\u5f52\u56fe<\/span><\/code><code><span class=\"code-snippet_outer\">pdf(<span class=\"code-snippet__string\">\"lasso.pdf\"<\/span>,width = <span class=\"code-snippet__number\">10<\/span>,height = <span class=\"code-snippet__number\">8<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">plot(fit)<\/span><\/code><code><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><code><span class=\"code-snippet_outer\">#\u6700\u5c0f\u503c\u4e00\u4e2a\u6807\u51c6\u8bef\u65f6\u5404\u53d8\u91cf\u7684\u7cfb\u6570\u503c<\/span><\/code><code><span class=\"code-snippet_outer\">coef.min = coef(cvfit, s = <span class=\"code-snippet__string\">\"lambda.min\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u975e\u96f6\u7cfb\u6570<\/span><\/code><code><span class=\"code-snippet_outer\">active.min = which(coef.min != <span class=\"code-snippet__number\">0<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u975e\u96f6\u53d8\u91cf\uff0c\u57fa\u56e0\u540d<\/span><\/code><code><span class=\"code-snippet_outer\">geneids <- rownames(coef.min)[active.min]<\/span><\/code><code><span class=\"code-snippet_outer\">#\u63d0\u53d6\u9009\u4e2d\u7684\u57fa\u56e0\u5bf9\u5e94\u7684coefficient\uff0c\u56de\u5f52\u7cfb\u6570<\/span><\/code><code><span class=\"code-snippet_outer\">index.min = coef.min[active.min]<\/span><\/code><code><span class=\"code-snippet_outer\">#\u6309\u5217\u5408\u5e76\u4e24\u4e2a\u53d8\u91cf<\/span><\/code><code><span class=\"code-snippet_outer\">combine <- cbind(geneids, index.min)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u5c06\u6570\u636e\u8f6c\u6362\u4e3a\u6570\u636e\u6846<\/span><\/code><code><span class=\"code-snippet_outer\">lasso.result<-as.data.frame(combine)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u5c06index.min\u6570\u636e\u7c7b\u578b\u6539\u4e3a\u6570\u503c\u578b\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">lasso.result$index.min<-as.numeric(lasso.result$index.min)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.19133574007220217\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-07-06_\u76f4\u51fb\u70ed\u70b9\uff01\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u4e4bLASSO,randomForest\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\/4_bdGjYFyMjUrKGQJTK6HBDaLTauulsA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3Uqt9PxY9QwTIq8se0fGfFVfWfbdGjYFyMjUrKGQJTK6HBDaLTauulsA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" \/><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">#\u901a\u8fc7LASSO\u56de\u5f52\u7b5b\u9009\u7684\u7279\u5f81\u57fa\u56e0\u6587\u4ef6\uff0c\u7b2c\u4e00\u5217\u8868\u793a\u57fa\u56e0\u540d\uff0c\u7b2c\u4e8c\u5217\u8868\u793acoefficient\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">5.\u968f\u673a\u68ee\u6797\u5206\u6790<\/span><\/em><\/strong><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">fit <- rfsrc(Surv(OS.time,OS)~., data = train,<\/span><\/code><code><span class=\"code-snippet_outer\"> ntree = <span class=\"code-snippet__number\">1000<\/span>, nodesize = <span class=\"code-snippet__number\">14<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> splitrule = <span class=\"code-snippet__string\">'logrank'<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> importance = T,<\/span><\/code><code><span class=\"code-snippet_outer\"> proximity = T,<\/span><\/code><code><span class=\"code-snippet_outer\"> forest = T)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u7ed8\u5236OBB\u56fe\u548cVIP\u56fe<\/span><\/code><code><span class=\"code-snippet_outer\">pdf(<span class=\"code-snippet__string\">\"forest.pdf\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">plot(fit)<\/span><\/code><code><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><code><span class=\"code-snippet_outer\">#\u7b5b\u9009\u7279\u5f81\u57fa\u56e0<\/span><\/code><code><span class=\"code-snippet_outer\">rftop<-var.select(fit)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u5c06\u6570\u636e\u7c7b\u578b\u8f6c\u5316\u4e3a\u6570\u636e\u6846<\/span><\/code><code><span class=\"code-snippet_outer\">rftop2<-data.frame(<\/span><\/code><code><span class=\"code-snippet_outer\"> Feature=rftop$topvars,<\/span><\/code><code><span class=\"code-snippet_outer\"> vimp=rftop$varselect[rftop$topvars,<span class=\"code-snippet__number\">2<\/span>])<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.16967509025270758\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_YrcP4Q4nchfRMickwGvCiaM8aqf9zg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3UQiaPr0SiahiaEDSp6cwEQ8arZehrgYrcP4Q4nchfRMickwGvCiaM8aqf9zg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u6ce8\uff1a\u901a\u8fc7\u968f\u673a\u68ee\u6797\u7b97\u6cd5\u7b5b\u9009\u7684\u7279\u5f81\u57fa\u56e0\uff0c\u7b2c\u4e00\u5217\u8868\u793a\u57fa\u56e0\u540d\uff0c\u7b2c\u4e8c\u5217\u4e3aVIP\u503c\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">6.xgboost\u7b97\u6cd5<\/span><\/em><\/strong><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">x_label<-ifelse(train$OS==<span class=\"code-snippet__number\">1<\/span>,train$OS.time,-train$OS.time)<\/span><\/code><code><span class=\"code-snippet_outer\">x_train<-as.matrix(train[,c(<span class=\"code-snippet__number\">3<\/span>:ncol(train))])<\/span><\/code><code><span class=\"code-snippet_outer\">x_val<-xgb.DMatrix(x_train,<\/span><\/code><code><span class=\"code-snippet_outer\"> label=x_label)<\/span><\/code><code><span class=\"code-snippet_outer\">xgb_param<-<span class=\"code-snippet__built_in\">list<\/span>(<span class=\"code-snippet__string\">\"objective\"<\/span>=<span class=\"code-snippet__string\">\"survival:cox\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"eval_metric\"<\/span>=<span class=\"code-snippet__string\">\"cox-nloglik\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">xgb.model<-xgb.train(params=xgb_param,<\/span><\/code><code><span class=\"code-snippet_outer\"> data=x_val,<\/span><\/code><code><span class=\"code-snippet_outer\"> nrounds=<span class=\"code-snippet__number\">100<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> eta=<span class=\"code-snippet__number\">0.1<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> watchlist=<span class=\"code-snippet__built_in\">list<\/span>(val2=x_val))<\/span><\/code><code><span class=\"code-snippet_outer\">e<-data.frame(xgb.model$evaluation_log)<\/span><\/code><code><span class=\"code-snippet_outer\">ggplot(aes(x=iter,y=val2_cox_nloglik),data=e)+<\/span><\/code><code><span class=\"code-snippet_outer\">geom_point(color=<span class=\"code-snippet__string\">\"pink\"<\/span>,size=<span class=\"code-snippet__number\">3<\/span>)+<\/span><\/code><code><span class=\"code-snippet_outer\">geom_line()+<\/span><\/code><code><span class=\"code-snippet_outer\">theme_bw()<\/span><\/code><code><span class=\"code-snippet_outer\">ggsave(<span class=\"code-snippet__string\">\"train_error.pdf\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u7b5b\u9009VIP\u503c\u6392\u540d\u524d\u5341\u7684\u57fa\u56e0\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">imp<-xgb.importance(feature_names=colnames(x_train),model=xgb.model)<\/span><\/code><code><span class=\"code-snippet_outer\">top_10<-imp[<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">10<\/span>,<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">2<\/span>]<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3724007561436673\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-07-06_\u76f4\u51fb\u70ed\u70b9\uff01\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u4e4bLASSO,randomForest\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\/6_YHwjcqcKpH2KZOiaBKwOmZtPiaA90w.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3UoL1qpKiakdp9hNhg8EATWLK1evvYHwjcqcKpH2KZOiaBKwOmZtPiaA90w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"529\" style=\"\" \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u6ce8\uff1a\u901a\u8fc7xgboost\u7b97\u6cd5\u7b5b\u9009\u7684VIP\u503c\u6392\u524d\u5341\u7684\u57fa\u56e0\uff0c\u7b2c\u4e00\u5217\u8868\u793a\u57fa\u56e0\u540d\uff0c\u7b2c\u4e8c\u5217\u8868\u793aVIP\u503c\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u7ed8\u5236venn\u56fe\u7b5b\u9009\u4e09\u79cd\u7b97\u6cd5\u83b7\u5f97\u7684\u4ea4\u53c9\u57fa\u56e0<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">gene<-<span class=\"code-snippet__built_in\">list<\/span>(LASSO=geneids,<\/span><\/code><code><span class=\"code-snippet_outer\"> RF=rftop2$Feature\uff0c<\/span><\/code><code><span class=\"code-snippet_outer\">Xgboost=top_10$Feature)<\/span><\/code><code><span class=\"code-snippet_outer\">ggvenn(gene,<\/span><\/code><code><span class=\"code-snippet_outer\"> fill_color=c(<span class=\"code-snippet__string\">\"#0073C2FF\"<\/span>,<span class=\"code-snippet__string\">\"#EFC000FF\"<\/span>,\u201d#CD534CFF\u201d),<\/span><\/code><code><span class=\"code-snippet_outer\"> stroke_size=<span class=\"code-snippet__number\">0.5<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> set_name_size=<span class=\"code-snippet__number\">4<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">ggsave(<span class=\"code-snippet__string\">\"venn.pdf\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">7.\u7ed3\u679c\u6587\u4ef6<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><strong><span style=\"font-size: 14px;\">1. lambda.pdf<\/span><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8be5\u7ed3\u679c\u56fe\u7247\u4e3aLASSO\u56de\u5f52lambda\u56fe\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.786697247706422\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_tFtCp55AaCuUYMBvXclIrRic8iakQg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3Ut2czc4tDMJf6JJqG2GkqegAfuiatFtCp55AaCuUYMBvXclIrRic8iakQg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"436\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p style=\"white-space: normal;\"><strong><span style=\"font-size: 14px;\"><br \/><\/span><\/strong><\/p>\n<p style=\"white-space: normal;\"><strong><span style=\"font-size: 14px;\">2. lasso.pdf<\/span><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8be5\u7ed3\u679c\u56fe\u7247LASSO\u56de\u5f52\u4e3a10\u6298\u4ea4\u53c9\u9a8c\u8bc1\u56fe\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.7911025145067698\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-07-06_\u76f4\u51fb\u70ed\u70b9\uff01\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u4e4bLASSO,randomForest\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\/8_T7j8hP8XsLjySq6cxrJoo0x3s5tJ6Q.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3UVVoOWGsJo6NebclcNicjia9QmaT7j8hP8XsLjySq6cxrJoo0x3s5tJ6Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"517\" style=\"\" \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><strong><span style=\"font-size: 14px;\">3. forest.pdf<\/span><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8be5\u7ed3\u679c\u56fe\u7247\u4e3a\u968f\u673a\u68ee\u6797OBB\u56fe\u548cVIP\u56fe\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.9567567567567568\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_g1z9LiaDxJr5WPtlCRJVOe5xFmsXyA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3Uod4fURaPNO4W1dysiccsB7fS8icg1z9LiaDxJr5WPtlCRJVOe5xFmsXyA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"370\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><strong><span style=\"font-size: 14px;\">4. train_error.pdf<\/span><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8be5\u7ed3\u679c\u56fe\u7247\u4e3axgboost\u7b97\u6cd5cox\u98ce\u9669\u6bd4\u4f8b\u56de\u5f52\u7684\u8d1f\u504f\u5bf9\u6570\u968f\u7740\u8fed\u4ee3\u6b21\u6570\u7684\u53d8\u5316\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.9442970822281167\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-07-06_\u76f4\u51fb\u70ed\u70b9\uff01\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u4e4bLASSO,randomForest\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\/10_GBiciaMmMb2DrM0s8YaAppFXaIuoIw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3UYG3JZGoSA1aubr8elgjKW5KVaMGBiciaMmMb2DrM0s8YaAppFXaIuoIw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"377\" style=\"\" \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><strong><span style=\"font-size: 14px;\">5. venn.pdf<\/span><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8be5\u7ed3\u679c\u56fe\u7247\u4e3a\u4e09\u79cd\u7b97\u6cd5\u7279\u5f81\u57fa\u56e0\u7684venn\u56fe\uff0c\u5c06\u4ea4\u53c9\u57fa\u56e0\u7b5b\u9009\u4e3a\u5019\u9009\u57fa\u56e0\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.9624664879356568\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_qeavOpmukvNf7Bv5B6K6fz4rxCib1w.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3Uf3w9ibCDK81S03UUdiczQoxcqExqeavOpmukvNf7Bv5B6K6fz4rxCib1w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"373\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u6700\u7ec8\u5c0f\u679c\u987a\u5229\u5b8c\u6210\u4e86\u5229\u7528 lassso\u56de\u5f52,\u968f\u673a\u68ee\u6797\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u4e86\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\u3002<\/span><span style=\"font-size: 14px;\">\u673a\u5668\u5b66\u4e60\u76f8\u5173\u5176\u4ed6\u5206\u6790\u5185\u5bb9\u6b22\u8fce\u5c1d\u8bd5\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u4e91\u5e73\u53f0\u751f\u7269\u4fe1\u606f\u5206\u6790\u5c0f\u5de5\u5177\uff0c\u96f6\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u4e91\u5e73\u53f0\u7f51\u5740\uff1ahttp:\/\/www.biocloudservice.com\/home.html\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-cropselx1=\"0\" data-cropselx2=\"578\" data-cropsely1=\"0\" data-cropsely2=\"322\" data-galleryid=\"\" data-ratio=\"0.7193195625759417\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-07-06_\u76f4\u51fb\u70ed\u70b9\uff01\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u4e4bLASSO,randomForest\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\/12_oRxs73HBHUoxCtAqBPQnq1AXricRvg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxenwVZiaibuOTpj6MMDUj2LoPdS6tic40bbGQV7QyM6QOQY8EFoRxs73HBHUoxCtAqBPQnq1AXricRvg\/640?wx_fmt=png'\" data-type=\"jpeg\" data-w=\"823\" style=\"width: 578px;height: 416px;\" \/><\/p>\n<section style=\"margin-bottom: 0px;font-size: 16px;letter-spacing: 0.578px;white-space: normal;caret-color: rgba(0, 0, 0, 0);\">\n<section>\n<section style=\"margin-top: 0.5em;\">\n<section style=\"padding: 0.5em;border-width: 1px;border-style: solid;box-shadow: rgb(226, 226, 226) 0px 16px 1px -13px;border-color: rgb(0, 150, 136);\">\n<section style=\"text-align: left;\">\n<section style=\"color: rgb(255, 129, 36);text-align: justify;\">\n<section style=\"margin-bottom: 8px;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u70b9\u51fb<strong><span style=\"color: rgb(0, 150, 136);\">\u201c\u9605\u8bfb\u539f\u6587\u201d<\/span><\/strong>\u7acb\u523b\u62e5\u6709<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: 8px;font-size: 32px;color: rgb(0, 150, 136);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u2193\u2193\u2193 <\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"display: none;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<p><\/content><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u76f4\u51fb\u70ed\u70b9\uff01\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u4e4bLASSO,randomForest\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009 […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/54587"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=54587"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/54587\/revisions"}],"predecessor-version":[{"id":54600,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/54587\/revisions\/54600"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=54587"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=54587"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=54587"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}

{"id":54587,"date":"2024-06-16T14:20:14","date_gmt":"2024-06-16T06:20:14","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=54587"},"modified":"2024-06-16T14:20:14","modified_gmt":"2024-06-16T06:20:14","slug":"%e7%9b%b4%e5%87%bb%e7%83%ad%e7%82%b9%ef%bc%81%e7%94%9f%e4%bf%a1%e6%96%87%e7%ab%a0%e5%bf%85%e5%a4%87%e4%b9%8blassorandomforest%e5%92%8cxgboost%e4%b8%89%e7%a7%8d%e6%9c%ba%e5%99%a8%e5%ad%a6%e4%b9%a0-2","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=54587","title":{"rendered":"\u76f4\u51fb\u70ed\u70b9\uff01\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u4e4bLASSO,randomForest\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009"},"content":{"rendered":"

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powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u63a5\u4e0b\u6765\u8ddf\u7740\u5c0f\u679c\u5f00\u542f\u4eca\u5929\u7684\u5b66\u4e60\u4e4b\u65c5\u5427\uff01\u5173\u6ce8\u5c0f\u679c\u56de\u590d111\u9886\u53d6\u76f8\u5173\u6587\u4ef6\u54df\uff01<\/span><span style=\"text-align: center;letter-spacing: 0.034em;\"><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">1. \u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u7b5b\u9009<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5c0f\u4f19\u4f34\u4eec\u662f\u4e0d\u662f\u5728\u60f3\u5230\u5e95\u662f\u90a3\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\uff1f\u4e0d\u6025\uff01\u5c0f\u679c\u6765\u6162\u6162\u544a\u8bc9\u5927\u5bb6\uff0c\u4eca\u5929\u5c0f\u679c\u5c06\u5229\u7528LASSO\u56de\u5f52\uff0c\u968f\u673a\u68ee\u6797\u548cxgboost\u4e09\u79cd\u7b97\u6cd5\u8fdb\u884c\u751f\u5b58\u8d44\u6599\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\uff0c\u8fd9\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7684\u7b97\u6cd5\u539f\u7406\u5c0f\u679c\u5728\u8fd9\u91cc\u4e0d\u505a\u8fc7\u591a\u7684\u4ecb\u7ecd\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u4eec\u53ef\u4ee5\u81ea\u884c\u67e5\u8be2\u5b66\u4e60\uff0c\u4eca\u5929\u5c0f\u679c\u5c06\u901a\u8fc7\u5b9e\u64cd\uff0c\u8ba9\u5927\u5bb6\u8f7b\u677e\u638c\u63e1\u5982\u4f55\u5229\u7528\u8fd9\u4e09\u79cd\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\uff0c\u5176\u5b9e\u5206\u6790\u975e\u5e38\u7b80\u5355\uff0c\u53ea\u9700\u8981\u8f93\u5165\u5e26\u6709\u751f\u5b58\u4fe1\u606f\u7684\u8868\u8fbe\u77e9\u9635\u6587\u4ef6\uff0c\u5c31\u53ef\u4ee5\u5f88\u8f7b\u677e\u7684\u5b8c\u6210\u8be5\u5206\u6790\uff0c\u5bf9\u5c0f\u767d\u4e5f\u5f88\u9002\u7528\uff0c\u8bdd\u4e0d\u591a\u8bf4\uff0c\u9a6c\u4e0a\u8ddf\u7740\u5c0f\u679c\u5f00\u59cb\u4eca\u5929\u7684\u5b9e\u64cd\u5427\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">2. \u51c6\u5907\u9700\u8981\u7684R\u5305<\/span><\/em><\/strong><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u5b89\u88c5\u9700\u8981\u7684R\u5305<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"ggplot2\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"tidyverse\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"ggvenn\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"glmnet\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"survival\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"xgboost\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"randomForestSRC\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">#\u52a0\u8f7d\u9700\u8981\u7684R\u5305 <\/span><\/code><code><span class=\"code-snippet_outer\">library(randomForestSRC)<\/span><\/code><code><span class=\"code-snippet_outer\">library(tidyverse)<\/span><\/code><code><span class=\"code-snippet_outer\">library(ggplot2)<\/span><\/code><code><span class=\"code-snippet_outer\">library(ggvenn)<\/span><\/code><code><span class=\"code-snippet_outer\">library(glmnet)<\/span><\/code><code><span class=\"code-snippet_outer\">library(survival)<\/span><\/code><code><span class=\"code-snippet_outer\">library(xgboost)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">3. \u6570\u636e\u51c6\u5907<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">exp_surv.txt<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">#\u751f\u5b58\u4fe1\u606f\u52a0\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u6587\u4ef6\uff0c\u884c\u540d\u4e3a\u6837\u672c\u4fe1\u606f\uff0c\u7b2c\u4e00\u5217\u4e3aOS.time(\u751f\u5b58\u65f6\u95f4),\u7b2c\u4e8c\u5217\u4e3aOS(\u751f\u5b58\u72b6\u6001),\u5176\u4ed6\u5217\u4e3a\u57fa\u56e0\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.24548736462093862\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-07-06_\u76f4\u51fb\u70ed\u70b9\uff01\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u4e4bLASSO,randomForest\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\/2_4UhN3ZHByrTJz96diaw3libaGnoxhg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3UxF8pzNoKPofjKOrn0yypCxiaHnd4UhN3ZHByrTJz96diaw3libaGnoxhg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" \/><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\"><br \/><\/span><\/em><\/strong><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\"><br \/><\/span><\/em><\/strong><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">4 . LASSO\u56de\u5f52\u5206\u6790<\/span><\/em><\/strong><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u8bfb\u53d6\u751f\u5b58\u4fe1\u606f\u7684\u57fa\u56e0\u8868\u8fbe\u77e9\u9635<\/span><\/code><code><span class=\"code-snippet_outer\">train<-read.table(<span class=\"code-snippet__string\">\"exp_surv.txt\"<\/span>,header=T,sep=<span class=\"code-snippet__string\">\"t\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u63d0\u53d6\u57fa\u56e0\u8868\u8fbe\u77e9\u9635<\/span><\/code><code><span class=\"code-snippet_outer\">x1 <- as.matrix(train[, <span class=\"code-snippet__number\">3<\/span>:ncol(train)])<\/span><\/code><code><span class=\"code-snippet_outer\">x2 <- as.matrix(Surv(train$OS.time, train$OS))<\/span><\/code><code><span class=\"code-snippet_outer\">cvfit = cv.glmnet(x1, x2,<\/span><\/code><code><span class=\"code-snippet_outer\"> nfold=<span class=\"code-snippet__number\">10<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> family = <span class=\"code-snippet__string\">\"cox\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> )<\/span><\/code><code><span class=\"code-snippet_outer\">#\u7ed8\u5236lamba\u56fe<\/span><\/code><code><span class=\"code-snippet_outer\">pdf(<span class=\"code-snippet__string\">\"lambda.pdf\"<\/span>,width = <span class=\"code-snippet__number\">10<\/span>,height = <span class=\"code-snippet__number\">8<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">plot(cvfit)<\/span><\/code><code><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><code><span class=\"code-snippet_outer\">#\u6b64\u5904\u4f7f\u7528`lambda min`<\/span><\/code><code><span class=\"code-snippet_outer\">cvfit$lambda.min #\u6700\u4f73lambda\u503c<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.07942238267148015\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-07-06_\u76f4\u51fb\u70ed\u70b9\uff01\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u4e4bLASSO,randomForest\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\/3_8kic2UHSadrRsrecK2cAZUrRfanMIg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3UBIuE7FowpgCGfGnibJYblFiaRyz8kic2UHSadrRsrecK2cAZUrRfanMIg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" \/><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">fit <- glmnet(x1, x2,<\/span><\/code><code><span class=\"code-snippet_outer\"> family = <span class=\"code-snippet__string\">\"cox\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u7528\u5305\u81ea\u5e26\u7684\u51fd\u6570\u7ed8\u5236lasso\u56de\u5f52\u56fe<\/span><\/code><code><span class=\"code-snippet_outer\">pdf(<span class=\"code-snippet__string\">\"lasso.pdf\"<\/span>,width = <span class=\"code-snippet__number\">10<\/span>,height = <span class=\"code-snippet__number\">8<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">plot(fit)<\/span><\/code><code><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><code><span class=\"code-snippet_outer\">#\u6700\u5c0f\u503c\u4e00\u4e2a\u6807\u51c6\u8bef\u65f6\u5404\u53d8\u91cf\u7684\u7cfb\u6570\u503c<\/span><\/code><code><span class=\"code-snippet_outer\">coef.min = coef(cvfit, s = <span class=\"code-snippet__string\">\"lambda.min\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u975e\u96f6\u7cfb\u6570<\/span><\/code><code><span class=\"code-snippet_outer\">active.min = which(coef.min != <span class=\"code-snippet__number\">0<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u975e\u96f6\u53d8\u91cf\uff0c\u57fa\u56e0\u540d<\/span><\/code><code><span class=\"code-snippet_outer\">geneids <- rownames(coef.min)[active.min]<\/span><\/code><code><span class=\"code-snippet_outer\">#\u63d0\u53d6\u9009\u4e2d\u7684\u57fa\u56e0\u5bf9\u5e94\u7684coefficient\uff0c\u56de\u5f52\u7cfb\u6570<\/span><\/code><code><span class=\"code-snippet_outer\">index.min = coef.min[active.min]<\/span><\/code><code><span class=\"code-snippet_outer\">#\u6309\u5217\u5408\u5e76\u4e24\u4e2a\u53d8\u91cf<\/span><\/code><code><span class=\"code-snippet_outer\">combine <- cbind(geneids, index.min)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u5c06\u6570\u636e\u8f6c\u6362\u4e3a\u6570\u636e\u6846<\/span><\/code><code><span class=\"code-snippet_outer\">lasso.result<-as.data.frame(combine)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u5c06index.min\u6570\u636e\u7c7b\u578b\u6539\u4e3a\u6570\u503c\u578b\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">lasso.result$index.min<-as.numeric(lasso.result$index.min)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.19133574007220217\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-07-06_\u76f4\u51fb\u70ed\u70b9\uff01\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u4e4bLASSO,randomForest\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\/4_bdGjYFyMjUrKGQJTK6HBDaLTauulsA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3Uqt9PxY9QwTIq8se0fGfFVfWfbdGjYFyMjUrKGQJTK6HBDaLTauulsA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" \/><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">#\u901a\u8fc7LASSO\u56de\u5f52\u7b5b\u9009\u7684\u7279\u5f81\u57fa\u56e0\u6587\u4ef6\uff0c\u7b2c\u4e00\u5217\u8868\u793a\u57fa\u56e0\u540d\uff0c\u7b2c\u4e8c\u5217\u8868\u793acoefficient\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">5.\u968f\u673a\u68ee\u6797\u5206\u6790<\/span><\/em><\/strong><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">fit <- rfsrc(Surv(OS.time,OS)~., data = train,<\/span><\/code><code><span class=\"code-snippet_outer\"> ntree = <span class=\"code-snippet__number\">1000<\/span>, nodesize = <span class=\"code-snippet__number\">14<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> splitrule = <span class=\"code-snippet__string\">'logrank'<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> importance = T,<\/span><\/code><code><span class=\"code-snippet_outer\"> proximity = T,<\/span><\/code><code><span class=\"code-snippet_outer\"> forest = T)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u7ed8\u5236OBB\u56fe\u548cVIP\u56fe<\/span><\/code><code><span class=\"code-snippet_outer\">pdf(<span class=\"code-snippet__string\">\"forest.pdf\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">plot(fit)<\/span><\/code><code><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><code><span class=\"code-snippet_outer\">#\u7b5b\u9009\u7279\u5f81\u57fa\u56e0<\/span><\/code><code><span class=\"code-snippet_outer\">rftop<-var.select(fit)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u5c06\u6570\u636e\u7c7b\u578b\u8f6c\u5316\u4e3a\u6570\u636e\u6846<\/span><\/code><code><span class=\"code-snippet_outer\">rftop2<-data.frame(<\/span><\/code><code><span class=\"code-snippet_outer\"> Feature=rftop$topvars,<\/span><\/code><code><span class=\"code-snippet_outer\"> vimp=rftop$varselect[rftop$topvars,<span class=\"code-snippet__number\">2<\/span>])<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.16967509025270758\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_YrcP4Q4nchfRMickwGvCiaM8aqf9zg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3UQiaPr0SiahiaEDSp6cwEQ8arZehrgYrcP4Q4nchfRMickwGvCiaM8aqf9zg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u6ce8\uff1a\u901a\u8fc7\u968f\u673a\u68ee\u6797\u7b97\u6cd5\u7b5b\u9009\u7684\u7279\u5f81\u57fa\u56e0\uff0c\u7b2c\u4e00\u5217\u8868\u793a\u57fa\u56e0\u540d\uff0c\u7b2c\u4e8c\u5217\u4e3aVIP\u503c\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">6.xgboost\u7b97\u6cd5<\/span><\/em><\/strong><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">x_label<-ifelse(train$OS==<span class=\"code-snippet__number\">1<\/span>,train$OS.time,-train$OS.time)<\/span><\/code><code><span class=\"code-snippet_outer\">x_train<-as.matrix(train[,c(<span class=\"code-snippet__number\">3<\/span>:ncol(train))])<\/span><\/code><code><span class=\"code-snippet_outer\">x_val<-xgb.DMatrix(x_train,<\/span><\/code><code><span class=\"code-snippet_outer\"> label=x_label)<\/span><\/code><code><span class=\"code-snippet_outer\">xgb_param<-<span class=\"code-snippet__built_in\">list<\/span>(<span class=\"code-snippet__string\">\"objective\"<\/span>=<span class=\"code-snippet__string\">\"survival:cox\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"eval_metric\"<\/span>=<span class=\"code-snippet__string\">\"cox-nloglik\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">xgb.model<-xgb.train(params=xgb_param,<\/span><\/code><code><span class=\"code-snippet_outer\"> data=x_val,<\/span><\/code><code><span class=\"code-snippet_outer\"> nrounds=<span class=\"code-snippet__number\">100<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> eta=<span class=\"code-snippet__number\">0.1<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> watchlist=<span class=\"code-snippet__built_in\">list<\/span>(val2=x_val))<\/span><\/code><code><span class=\"code-snippet_outer\">e<-data.frame(xgb.model$evaluation_log)<\/span><\/code><code><span class=\"code-snippet_outer\">ggplot(aes(x=iter,y=val2_cox_nloglik),data=e)+<\/span><\/code><code><span class=\"code-snippet_outer\">geom_point(color=<span class=\"code-snippet__string\">\"pink\"<\/span>,size=<span class=\"code-snippet__number\">3<\/span>)+<\/span><\/code><code><span class=\"code-snippet_outer\">geom_line()+<\/span><\/code><code><span class=\"code-snippet_outer\">theme_bw()<\/span><\/code><code><span class=\"code-snippet_outer\">ggsave(<span class=\"code-snippet__string\">\"train_error.pdf\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u7b5b\u9009VIP\u503c\u6392\u540d\u524d\u5341\u7684\u57fa\u56e0\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">imp<-xgb.importance(feature_names=colnames(x_train),model=xgb.model)<\/span><\/code><code><span class=\"code-snippet_outer\">top_10<-imp[<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">10<\/span>,<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">2<\/span>]<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3724007561436673\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-07-06_\u76f4\u51fb\u70ed\u70b9\uff01\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u4e4bLASSO,randomForest\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\/6_YHwjcqcKpH2KZOiaBKwOmZtPiaA90w.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3UoL1qpKiakdp9hNhg8EATWLK1evvYHwjcqcKpH2KZOiaBKwOmZtPiaA90w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"529\" style=\"\" \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u6ce8\uff1a\u901a\u8fc7xgboost\u7b97\u6cd5\u7b5b\u9009\u7684VIP\u503c\u6392\u524d\u5341\u7684\u57fa\u56e0\uff0c\u7b2c\u4e00\u5217\u8868\u793a\u57fa\u56e0\u540d\uff0c\u7b2c\u4e8c\u5217\u8868\u793aVIP\u503c\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u7ed8\u5236venn\u56fe\u7b5b\u9009\u4e09\u79cd\u7b97\u6cd5\u83b7\u5f97\u7684\u4ea4\u53c9\u57fa\u56e0<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">gene<-<span class=\"code-snippet__built_in\">list<\/span>(LASSO=geneids,<\/span><\/code><code><span class=\"code-snippet_outer\"> RF=rftop2$Feature\uff0c<\/span><\/code><code><span class=\"code-snippet_outer\">Xgboost=top_10$Feature)<\/span><\/code><code><span class=\"code-snippet_outer\">ggvenn(gene,<\/span><\/code><code><span class=\"code-snippet_outer\"> fill_color=c(<span class=\"code-snippet__string\">\"#0073C2FF\"<\/span>,<span class=\"code-snippet__string\">\"#EFC000FF\"<\/span>,\u201d#CD534CFF\u201d),<\/span><\/code><code><span class=\"code-snippet_outer\"> stroke_size=<span class=\"code-snippet__number\">0.5<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> set_name_size=<span class=\"code-snippet__number\">4<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">ggsave(<span class=\"code-snippet__string\">\"venn.pdf\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">7.\u7ed3\u679c\u6587\u4ef6<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><strong><span style=\"font-size: 14px;\">1. lambda.pdf<\/span><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8be5\u7ed3\u679c\u56fe\u7247\u4e3aLASSO\u56de\u5f52lambda\u56fe\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.786697247706422\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_tFtCp55AaCuUYMBvXclIrRic8iakQg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3Ut2czc4tDMJf6JJqG2GkqegAfuiatFtCp55AaCuUYMBvXclIrRic8iakQg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"436\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p style=\"white-space: normal;\"><strong><span style=\"font-size: 14px;\"><br \/><\/span><\/strong><\/p>\n<p style=\"white-space: normal;\"><strong><span style=\"font-size: 14px;\">2. lasso.pdf<\/span><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8be5\u7ed3\u679c\u56fe\u7247LASSO\u56de\u5f52\u4e3a10\u6298\u4ea4\u53c9\u9a8c\u8bc1\u56fe\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.7911025145067698\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-07-06_\u76f4\u51fb\u70ed\u70b9\uff01\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u4e4bLASSO,randomForest\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\/8_T7j8hP8XsLjySq6cxrJoo0x3s5tJ6Q.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3UVVoOWGsJo6NebclcNicjia9QmaT7j8hP8XsLjySq6cxrJoo0x3s5tJ6Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"517\" style=\"\" \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><strong><span style=\"font-size: 14px;\">3. forest.pdf<\/span><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8be5\u7ed3\u679c\u56fe\u7247\u4e3a\u968f\u673a\u68ee\u6797OBB\u56fe\u548cVIP\u56fe\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.9567567567567568\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_g1z9LiaDxJr5WPtlCRJVOe5xFmsXyA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3Uod4fURaPNO4W1dysiccsB7fS8icg1z9LiaDxJr5WPtlCRJVOe5xFmsXyA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"370\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><strong><span style=\"font-size: 14px;\">4. train_error.pdf<\/span><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8be5\u7ed3\u679c\u56fe\u7247\u4e3axgboost\u7b97\u6cd5cox\u98ce\u9669\u6bd4\u4f8b\u56de\u5f52\u7684\u8d1f\u504f\u5bf9\u6570\u968f\u7740\u8fed\u4ee3\u6b21\u6570\u7684\u53d8\u5316\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.9442970822281167\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-07-06_\u76f4\u51fb\u70ed\u70b9\uff01\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u4e4bLASSO,randomForest\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\/10_GBiciaMmMb2DrM0s8YaAppFXaIuoIw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3UYG3JZGoSA1aubr8elgjKW5KVaMGBiciaMmMb2DrM0s8YaAppFXaIuoIw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"377\" style=\"\" \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><strong><span style=\"font-size: 14px;\">5. venn.pdf<\/span><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8be5\u7ed3\u679c\u56fe\u7247\u4e3a\u4e09\u79cd\u7b97\u6cd5\u7279\u5f81\u57fa\u56e0\u7684venn\u56fe\uff0c\u5c06\u4ea4\u53c9\u57fa\u56e0\u7b5b\u9009\u4e3a\u5019\u9009\u57fa\u56e0\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.9624664879356568\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_qeavOpmukvNf7Bv5B6K6fz4rxCib1w.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3Uf3w9ibCDK81S03UUdiczQoxcqExqeavOpmukvNf7Bv5B6K6fz4rxCib1w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"373\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u6700\u7ec8\u5c0f\u679c\u987a\u5229\u5b8c\u6210\u4e86\u5229\u7528 lassso\u56de\u5f52,\u968f\u673a\u68ee\u6797\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u4e86\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\u3002<\/span><span style=\"font-size: 14px;\">\u673a\u5668\u5b66\u4e60\u76f8\u5173\u5176\u4ed6\u5206\u6790\u5185\u5bb9\u6b22\u8fce\u5c1d\u8bd5\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u4e91\u5e73\u53f0\u751f\u7269\u4fe1\u606f\u5206\u6790\u5c0f\u5de5\u5177\uff0c\u96f6\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u4e91\u5e73\u53f0\u7f51\u5740\uff1ahttp:\/\/www.biocloudservice.com\/home.html\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-cropselx1=\"0\" data-cropselx2=\"578\" data-cropsely1=\"0\" data-cropsely2=\"322\" data-galleryid=\"\" data-ratio=\"0.7193195625759417\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-07-06_\u76f4\u51fb\u70ed\u70b9\uff01\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u4e4bLASSO,randomForest\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\/12_oRxs73HBHUoxCtAqBPQnq1AXricRvg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxenwVZiaibuOTpj6MMDUj2LoPdS6tic40bbGQV7QyM6QOQY8EFoRxs73HBHUoxCtAqBPQnq1AXricRvg\/640?wx_fmt=png'\" data-type=\"jpeg\" data-w=\"823\" style=\"width: 578px;height: 416px;\" \/><\/p>\n<section style=\"margin-bottom: 0px;font-size: 16px;letter-spacing: 0.578px;white-space: normal;caret-color: rgba(0, 0, 0, 0);\">\n<section>\n<section style=\"margin-top: 0.5em;\">\n<section style=\"padding: 0.5em;border-width: 1px;border-style: solid;box-shadow: rgb(226, 226, 226) 0px 16px 1px -13px;border-color: rgb(0, 150, 136);\">\n<section style=\"text-align: left;\">\n<section style=\"color: rgb(255, 129, 36);text-align: justify;\">\n<section style=\"margin-bottom: 8px;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u70b9\u51fb<strong><span style=\"color: rgb(0, 150, 136);\">\u201c\u9605\u8bfb\u539f\u6587\u201d<\/span><\/strong>\u7acb\u523b\u62e5\u6709<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: 8px;font-size: 32px;color: rgb(0, 150, 136);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u2193\u2193\u2193 <\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"display: none;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<p><\/content><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u76f4\u51fb\u70ed\u70b9\uff01\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u4e4bLASSO,randomForest\u548cxgboost\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u7279\u5f81\u57fa\u56e0\u7b5b\u9009 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