{"id":296,"date":"2024-02-29T07:52:45","date_gmt":"2024-02-29T07:52:45","guid":{"rendered":"https:\/\/metascape.org\/blog\/?p=296"},"modified":"2024-03-02T22:09:17","modified_gmt":"2024-03-02T22:09:17","slug":"frogs-%e5%9f%ba%e5%9b%a0%e8%a1%a8%e5%be%81%e7%9a%84%e5%8d%8e%e4%b8%bd%e8%bd%ac%e8%ba%ab","status":"publish","type":"post","link":"https:\/\/metascape.org\/blog\/?p=296","title":{"rendered":"FRoGS: \u57fa\u56e0\u8868\u5f81\u7684\u534e\u4e3d\u8f6c\u8eab"},"content":{"rendered":"\n<p>\u672c\u6587\u7531ChatGPT\u57fa\u4e8e\u82f1\u6587\u7248\u7ffb\u8bd1\u540e\u7a0d\u52a0\u4fee\u6539, \u4e0d\u51c6\u786e\u4e4b\u5904\u4ee5\u82f1\u6587\u7248\u4e3a\u51c6.<\/p>\n\n\n\n<p>\u5728\u81ea\u7136\u8bed\u8a00\u5904\u7406\uff08NLP\uff09\u7814\u7a76\u7684\u65e9\u671f\u9636\u6bb5\uff0c\u6211\u4eec\u901a\u8fc7\u8ba1\u7b97\u5171\u4eab\u5355\u8bcd\u6765\u91cf\u5316\u6587\u6863\u4e4b\u95f4\u7684\u76f8\u4f3c\u6027\u3002\u7136\u800c\uff0c\u8fd9\u79cd\u7b80\u5355\u7684\u65b9\u6cd5\u5ffd\u7565\u4e86\u540c\u4e49\u8bcd\u5b83\u5c06\u201c\u732b\u201d\u548c\u201c\u5c0f\u732b\u201d\u89c6\u4e3a\u6beb\u65e0\u5173\u8054\u7684\u5b9e\u4f53\uff0c\u5c31\u50cf\u5bf9\u5f85\u201c\u732b\u201d\u548c\u201c\u5ca9\u77f3\u201d\u4e00\u6837\uff08\u56fe1\uff0c\u5de6\u4fa7\uff09\u3002\u7531\u6b64\u4ea7\u751f\u7684\u57fa\u4e8e\u8eab\u4efd(identity)\u7684\u5355\u8bcd\u8868\u793a\uff0c\u5373\u72ec\u70ed(one-hot)\u7f16\u7801\uff0c\u5728\u5e94\u7528\u4e8e\u805a\u7c7b\u6587\u6863\u65f6\u6548\u679c\u5e76\u4e0d\u4f73\u3002\u5e78\u8fd0\u7684\u662f\uff0c\u968f\u7740Word2Vec\u7b49\u6df1\u5ea6\u5b66\u4e60\u6280\u672f\u7684\u51fa\u73b0 [1]\uff0cNLP\u9886\u57df\u5df2\u7ecf\u53d1\u751f\u4e86\u53d8\u9769\u3002\u7531\u4e8eWord2Vec\uff0c\u66fe\u7ecf\u76f8\u8ddd\u751a\u8fdc\u7684\u201c\u732b\u201d\u548c\u201c\u5c0f\u732b\u201d\u4e24\u4e2a\u8bcd\u73b0\u5728\u88ab\u8ba4\u4e3a\u662f\u51e0\u4e4e\u76f8\u540c\u7684\uff08\u56fe1\uff0c\u53f3\u4fa7\uff09\u3002<\/p>\n\n\n<div class=\"wp-block-image\">\n<figure class=\"aligncenter size-large\"><img decoding=\"async\" src=\"https:\/\/metascape.org\/blog\/wp-content\/uploads\/2024\/02\/words.png\" alt=\"\"\/><figcaption class=\"wp-element-caption\">\u56fe1. \u5de6\u4fa7\u662f\u4f7f\u7528\u72ec\u70ed\u7f16\u7801\u8868\u793a\u7684\u60c5\u51b5\uff0c\u201ccat\u201d \u548c \u201ckitty\u201d \u7684\u8ddd\u79bb\u5c31\u50cf \u201ccat\u201d \u548c \u201crock\u201d \u4e00\u6837\u8fdc\u3002\u8fd9\u79cd\u8868\u793a\u65b9\u5f0f\u6ca1\u6709\u610f\u8bc6\u5230 \u201ccat\u201d \u548c \u201ckitty\u201d \u662f\u540c\u4e49\u8bcd\u3002\u53f3\u4fa7\u662f\u4f7f\u7528 Word2Vec \u8868\u793a\u7684\u60c5\u51b5\uff0c\u201ccat\u201d \u548c \u201ckitty\u201d \u975e\u5e38\u63a5\u8fd1\uff0c\u800c\u4e14\u90fd\u4e0e \u201crock\u201d \u76f8\u8ddd\u751a\u8fdc\uff0c\u8fd9\u6b63\u786e\u5730\u63cf\u7ed8\u4e86\u8fd9\u4e9b\u8bcd\u7684\u542b\u4e49\u3002<\/figcaption><\/figure>\n<\/div>\n\n\n<p>\u5728\u57fa\u56e0\u5206\u6790\u4e2d\uff0c\u6211\u4eec\u4e00\u76f4\u9762\u4e34\u7740\u7c7b\u4f3c\u7684\u56f0\u5883\u3002\u5728\u6bd4\u8f83\u57fa\u56e0\u5217\u8868\u65f6\uff0c\u6211\u4eec\u8ba1\u7b97\u5171\u4eab\u7684\u57fa\u56e0\u4e2a\u6570\uff0c\u7c7b\u4f3c\u4e8e\u65e7\u65f6\u7684NLP\u65b9\u6cd5\u3002\u7136\u800c\uff0c\u50cfTLR7\u548cMYD88\u8fd9\u6837\u5728\u5148\u5929\u514d\u75ab\u4fe1\u53f7\u4e2d\u5177\u6709\u975e\u5e38\u76f8\u4f3c\u751f\u7269\u5b66\u4f5c\u7528\u7684\u57fa\u56e0\uff0c\u5f53\u5728\u51fa\u73b0\u5728\u4e0d\u540c\u5217\u8868\u4e2d\u65f6\u88ab\u5f53\u6210\u662f\u5b8c\u5168\u65e0\u5173\u7684\u800c\u88ab\u5ffd\u89c6\u4e86\u3002\u8fd9\u5c31\u50cf\u201c\u732b\u201d\u548c\u201c\u5c0f\u732b\u201d\u66fe\u7ecf\u88ab\u8ba4\u4e3a\u662f\u5b8c\u5168\u4e0d\u540c\u7684\u4e00\u6837\u3002\u76ee\u524d\u4f7f\u7528\u7684\u57fa\u56e0\u5217\u8868\u7684\u76f8\u4f3c\u6027\u7b97\u6cd5\u5f88\u6709\u5c40\u9650\u3002\u5728\u6211\u4eec\u6700\u8fd1\u7684\u300a\u81ea\u7136\u901a\u8baf\u300b\u53d1\u8868\u7684\u7814\u7a76\u4e2d [2]\uff0c\u6211\u4eec\u5c06NLP\u4e0e\u751f\u7269\u4fe1\u606f\u5b66\u8fdb\u884c\u4e86\u7c7b\u6bd4\uff0c\u9996\u5148\u6211\u4eec\u5f15\u5165\u4e86\u57fa\u56e0\u7279\u5f81\u7684\u529f\u80fd\u6027\u8868\u793a(Functional Representation of Gene Signatures &#8212; FRoGS)\uff0c\u4f5c\u4e3a\u57fa\u56e0\u5206\u6790\u7684Word2Vec\u7b49\u6548\u65b9\u6cd5\uff08\u56fe2\uff09\u3002\u7136\u540e\u6211\u4eec\u5229\u7528FRoGS\u7684\u8868\u5f81\u6765\u63ed\u793a\u5316\u5408\u7269\u7684\u9776\u70b9\u3002\u5229\u7528Broad\u7684L1000\u6570\u636e\u96c6,  \u901a\u8fc7\u5c06shRNA\/cDNA\u6270\u52a8\u7684\u57fa\u56e0\u7279\u5f81\u4e0e\u4e2d\u5316\u5408\u7269\u7684\u57fa\u56e0\u7279\u5f81\u8fdb\u884c\u76f8\u4f3c\u6027\u6bd4\u8f83\uff0c\u6211\u4eec\u53d6\u5f97\u4e86\u663e\u8457\u7684\u6210\u679c\u3002\u5177\u4f53\u800c\u8a00\uff0c\u57fa\u4e8eFRoGS\u7684AI\u6a21\u578b\u5728\u8bc6\u522b\u771f\u6b63\u7684\u5316\u5408\u7269\u9776\u70b9\u65b9\u9762\u8868\u73b0\u51fa\u4e8636%\u7684\u53ec\u56de\u7387 (recall)\uff0c\u8d85\u8fc7\u4e86\u4f20\u7edf\u7684\u72ec\u70ed\u7f16\u7801\u65b9\u6cd5\u6240\u80fd\u8fbe\u5230\u76849%\u7684\u53ec\u56de\u7387\u3002<\/p>\n\n\n<div class=\"wp-block-image\">\n<figure class=\"aligncenter size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"585\" height=\"609\" src=\"https:\/\/metascape.org\/blog\/wp-content\/uploads\/2024\/02\/image.png\" alt=\"\" class=\"wp-image-297\" srcset=\"https:\/\/metascape.org\/blog\/wp-content\/uploads\/2024\/02\/image.png 585w, https:\/\/metascape.org\/blog\/wp-content\/uploads\/2024\/02\/image-288x300.png 288w\" sizes=\"auto, (max-width: 585px) 100vw, 585px\" \/><figcaption class=\"wp-element-caption\">\u56fe2. FRoGS\u5411\u91cf\u7684t-SNE\u6295\u5f71\uff0c\u6bcf\u4e2a\u6807\u8bb0\u4ee3\u8868\u4e00\u4e2a\u72ec\u7279\u7684\u4eba\u7c7b\u57fa\u56e0\u3002\u989c\u8272\u8bf4\u660e\u5177\u6709\u76f8\u4f3c\u529f\u80fd\u7684\u57fa\u56e0\u5f80\u5f80\u4f1a\u5f62\u6210\u5c40\u90e8\u805a\u7c7b\u3002<\/figcaption><\/figure>\n<\/div>\n\n\n<p>\u5728\u8fd9\u7bc7\u535a\u5ba2\u4e2d\uff0c\u6211\u4eec\u7528\u4e24\u4e2a\u6d45\u663e\u7684\u4f8b\u5b50\u8fdb\u4e00\u6b65\u5c55\u793a\u4e86FRoGS\u5411\u91cf\u5982\u4f55\u5e2e\u52a9\u5b9e\u73b0\u5f3a\u5927\u7684\u673a\u5668\u5b66\u4e60\u4efb\u52a1\uff0c\u5c06\u57fa\u56e0\u5206\u6790\u63a8\u5411\u4e86\u4f20\u7edf\u72ec\u70ed\u7f16\u7801\u4e0d\u80fd\u591f\u53ca\u7684\u9ad8\u5ea6\u3002<\/p>\n\n\n\n<p>FRoGS\u80fd\u5353\u6709\u6210\u6548\u5730\u5e2e\u52a9\u673a\u5668\u5b66\u4e60\u7684\u8bc0\u7a8d\u5728\u54ea\u91cc\u5462\uff1f\u56e0\u4e3a\u57fa\u56e0\u7684\u529f\u80fd\u9a71\u52a8\u7740\u751f\u7269\u8fc7\u7a0b\u548c\u5b83\u7684\u8868\u578b\u3002 \uff0c\u5b83\u7684\u529f\u80fd\u88ab\u5ffd\u7565\u4e86, AI\u6a21\u578b\u5c31\u5fc5\u987b\u4f7f\u51fa\u6d2a\u8352\u4e4b\u529b\u91cd\u65b0\u53d1\u73b0\u5b83\u4eec\u7684\u529f\u80fd \u624d\u80fd\u6709\u6548\u9884\u6d4b\u5b83\u4eec\u7684\u8868\u578b&#8212; \u800c\u8fd9\u4e2a\u529f\u80fd\u518d\u53d1\u73b0\u7684\u8fc7\u7a0b\u9700\u8981\u5927\u91cf\u7684\u8bad\u7ec3\u6570\u636e\u3002\u4e0d\u5e78\u7684\u662f\uff0c\u8fd9\u6837\u7684\u5927\u91cf\u6570\u636e\u5e76\u4e0d\u603b\u662f\u53ef\u5f97\u5230\uff0c\u4e8e\u662f\u6709\u9650\u7684\u8bad\u7ec3\u6570\u636e\u4e25\u91cd\u5730\u5f71\u54cd\u4e86\u529f\u80fd\u7684\u5b66\u4e60\u4ece\u800c\u5f71\u54cd\u4e86\u6700\u7ec8\u9884\u6d4b\u7684\u51c6\u786e\u6027\u3002FRoGS\u8868\u5f81\u9769\u547d\u6027\u5730\u6539\u53d8\u4e86\u57fa\u56e0\u7684\u8868\u793a\u65b9\u5f0f\u3002\u6bcf\u4e2a\u4eba\u7c7b\u57fa\u56e0\u90fd\u88ab\u7f16\u7801\u4e3a\u4e00\u4e2a\u6709\u610f\u4e49\u7684\u5411\u91cf\uff0c\u65e2\u5305\u542b\u4e86\u5728\u57fa\u56e0\u5728Gene Ontology (GO [3])\u4e2d\u6ce8\u91ca\u7684\u5df2\u77e5\u529f\u80fd\uff0c\u4e5f\u5305\u542b\u4e86\u4ece\u5927\u89c4\u6a21\u8f6c\u5f55\u7ec4\u6570\u636e\u96c6(\u4f8b\u5982ARCHS4 [4])\u4e2d\u8574\u542b\u7684\u6f5c\u5728\u529f\u80fd \u3002FRoGS\u5728AI\u6a21\u578b\u7684\u8f93\u5165\u5411\u91cf\u4e2d\u6ce8\u5165\u529f\u80fd\u4fe1\u606f,  \u6a21\u578b\u65e0\u9700\u6d6a\u8d39\u8d44\u6e90\u53bb\u4ece\u5934\u5f00\u59cb\u5b66\u4e60\u57fa\u56e0\u7684\u529f\u80fd, \u800c\u53ef\u4ee5\u4e13\u6ce8\u4e8e\u5b66\u4e60\u57fa\u56e0\u529f\u80fd\u4e0e\u8868\u578b\u4e4b\u95f4\u590d\u6742\u7684\u5173\u8054\u3002\u8fd9\u6837\u6709\u9650\u7684\u8bad\u7ec3\u6570\u636e\u5168\u90fd\u88ab\u7528\u5728\u4e86\u5200\u5203\u4e0a\u3002<\/p>\n\n\n\n<p><strong>\u793a\u4f8b 1\uff1a\u7ec4\u7ec7\u7279\u5f02\u6027\u57fa\u56e0\u8868\u8fbe<\/strong><\/p>\n\n\n\n<p>\u5728\u6211\u4eec\u7684\u7b2c\u4e00\u4e2a\u793a\u4f8b\u4e2d\uff0c\u6211\u4eec\u5206\u522b\u4f7f\u752897\u300198\u548c100\u4e2a\u5728\u5927\u8111\u3001\u813e\u810f\u548c\u808c\u8089\u4e2d\u7279\u5f02\u6027\u8868\u8fbe\u7684\u57fa\u56e0\u3002\u6211\u4eec\u7684\u76ee\u6807\u662f\u9884\u6d4b\u57fa\u56e0\u8868\u8fbe\u7684\u7ec4\u7ec7\u3002\u4f20\u7edf\u4e0a\uff0c\u72ec\u70ed\u7f16\u7801\u5c06\u8fd9\u4e9b\u57fa\u56e0\u653e\u7f6e\u5728\u9ad8\u7ef4\u7a7a\u95f4\u4e2d\uff0c\u57fa\u56e0\u4e4b\u95f4\u6ca1\u6709\u4efb\u4f55\u7684\u76f8\u4f3c\u6027\u3002\u56e0\u6b64\uff0cAI\u6a21\u578b\u96be\u4ee5\u5b66\u4e60\u6709\u610f\u4e49\u7684\u6a21\u5f0f\uff0c\u5bfc\u81f4\u5206\u7c7b\u51c6\u786e\u7387\u4ec5\u7ea6\u4e3a29%\uff08\u00b13%\uff09\uff08n = 100\u6b21\u6a21\u62df\uff09\u2014\u2014\u7c7b\u4f3c\u4e8e\u968f\u673a\u731c\u6d4b\uff08\u56fe3\uff09\u3002\u7136\u800c\uff0c\u5f53\u6211\u4eec\u4f7f\u7528FRoGS\u5411\u91cf\u8868\u793a\u57fa\u56e0\u65f6\uff0ct-SNE\u56fe\u4e2d\u5df2\u7ecf\u5448\u73b0\u4e86\u7ec4\u7ec7\u7279\u5f02\u6027\u805a\u7c7b\uff08\u56fe4)\uff0c\u8fd9\u6837\u7528\u673a\u5668\u5b66\u4e60\u627e\u51fa\u5206\u7c7b\u7684\u8fb9\u754c\u5c31\u5f88\u76f4\u63a5\u4e86\u3002\u968f\u673a\u68ee\u6797\u6a21\u578b(Random Forest)\u7684\u51c6\u786e\u7387\u98d9\u5347\u81f3\u7ea680%\uff08\u00b15%\uff09\uff08n = 100\u6b21\u6a21\u62df\uff09\uff0c\u5c55\u793a\u4e86FRoGS\u4f7f\u5f97AI\u6a21\u578b\u5373\u4f7f\u5728\u6709\u9650\u6570\u636e\u60c5\u51b5\u4e0b\u4e5f\u5177\u6709\u5f3a\u5927\u7684\u5b66\u4e60\u80fd\u529b\uff08\u56fe4\uff09\u3002<\/p>\n\n\n<div class=\"wp-block-image\">\n<figure class=\"aligncenter size-large\"><img decoding=\"async\" src=\"https:\/\/github.com\/chenhcs\/FRoGS\/blob\/main\/demo\/tsne_onehot.png?raw=true\" alt=\"\"\/><figcaption class=\"wp-element-caption\">\u56fe3. \u4f7f\u7528\u5176\u72ec\u70ed\u8868\u793a\u7684\u57fa\u56e0\u7684t-SNE\u6295\u5f71\u3002\u57fa\u56e0\u7684\u4f4d\u7f6e\u662f\u968f\u673a\u7684\uff0c\u4e0d\u9002\u5408\u7528\u4e8e\u673a\u5668\u5b66\u4e60\u3002\u4e09\u7c7b\u57fa\u56e0\u65e0\u6cd5\u533a\u5206\u3002<\/figcaption><\/figure>\n<\/div>\n\n<div class=\"wp-block-image\">\n<figure class=\"aligncenter size-large\"><img decoding=\"async\" src=\"https:\/\/github.com\/chenhcs\/FRoGS\/blob\/main\/demo\/tsne_FRoGS.png?raw=true\" alt=\"\"\/><figcaption class=\"wp-element-caption\">\u56fe4. \u4f7f\u7528\u5176FRoGS\u8868\u793a\u7684\u57fa\u56e0\u7684t-SNE\u6295\u5f71\u3002\u5177\u6709\u76f8\u540c\u7ec4\u7ec7\u8868\u8fbe\u6a21\u5f0f\u7684\u57fa\u56e0\u5f80\u5f80\u4f1a\u805a\u96c6\u5728\u4e00\u8d77\uff0c\u4ece\u800c\u5e2e\u52a9\u6211\u4eec\u8bad\u7ec3\u51fa\u5177\u6709\u826f\u597d\u51c6\u786e\u6027\u7684\u5206\u7c7b\u5668\u3002<\/figcaption><\/figure>\n<\/div>\n\n\n<p><strong>\u793a\u4f8b 2\uff1a\u57fa\u56e0\u5217\u8868\u548c\u529f\u80fd\u7279\u5f81<\/strong><\/p>\n\n\n\n<p>\u6211\u4eec\u7684\u6570\u636e\u96c6\u5305\u62ec\u4e0e\u52a8\u8109\u3001\u5fc3\u810f\u548c\u5927\u8111\u5206\u522b\u76f8\u5173\u768435\u300124\u548c122\u4e2a\u57fa\u56e0\u5217\u8868\u3002\u6bcf\u4e2a\u57fa\u56e0\u5217\u8868\u5185\u542b\u7ea6100\u4e2a\u57fa\u56e0\u3002\u5728\u72ec\u70ed\u7f16\u7801\u65b9\u6cd5\u4e2d\uff0c\u57fa\u56e0\u5217\u8868\u88ab\u8868\u793a\u4e3a\u5176\u7ec4\u6210\u6210\u5458\u57fa\u56e0\u72ec\u70ed\u5411\u91cf\u7684\u603b\u548c\u3002\u867d\u7136\u8fd9\u4e9b\u57fa\u56e0\u5217\u8868\u4e5f\u5c55\u793a\u4e86\u4e00\u4e9b\u805a\u7c7b\u6a21\u5f0f\uff08\u56fe5\uff09\uff0c\u4f46\u4e0eFRoGS\u57fa\u56e0\u7279\u5f81\u5d4c\u5165\u5f62\u6210\u7684\u660e\u663e\u805a\u7c7b\u76f8\u6bd4\uff0c\u5b83\u4eec\u76f8\u5f62\u89c1\u7ecc\uff08\u56fe6\uff09\u3002\u56e0\u6b64\uff0c\u7528\u4e8e\u9884\u6d4b\u7684\u5206\u7c7b\u51c6\u786e\u7387\u4e3a\u72ec\u70ed\u5411\u91cf\u4e3a85%\uff08\u00b14%\uff09\uff08n = 100\u6b21\u6a21\u62df\uff09\uff0c\u800cFRoGS\u5411\u91cf\u4e3a100.0%\uff08\u00b10.4%\uff09\uff08n = 100\u6b21\u6a21\u62df\uff09\u3002<\/p>\n\n\n<div class=\"wp-block-image\">\n<figure class=\"aligncenter size-large\"><img decoding=\"async\" src=\"https:\/\/github.com\/chenhcs\/FRoGS\/blob\/main\/demo\/tsne_signature_onehot.png?raw=true\" alt=\"\"\/><figcaption class=\"wp-element-caption\"><strong>\u56fe5. <\/strong>\u4f7f\u7528\u5176\u7ec4\u6210\u57fa\u56e0\u6210\u5458\u7684\u805a\u5408\u72ec\u70ed\u8868\u793a\u7684\u57fa\u56e0\u5217\u8868\u7684t-SNE\u6295\u5f71\u3002\u5177\u6709\u76f8\u540c\u7ec4\u7ec7\u8868\u8fbe\u6a21\u5f0f\u7684\u57fa\u56e0\u5f80\u5f80\u4f1a\u805a\u96c6\u5728\u4e00\u8d77\uff0c\u4ece\u800c\u5bfc\u81f4\u5177\u6709\u826f\u597d\u51c6\u786e\u6027\u7684\u5206\u7c7b\u5668\u3002\u8fd9\u53cd\u6620\u4e86\u5f53\u524d\u57fa\u4e8e\u57fa\u56e0\u8eab\u4efd\u7684\u65b9\u6cd5\u7684\u6027\u80fd\u3002<\/figcaption><\/figure>\n<\/div>\n\n<div class=\"wp-block-image\">\n<figure class=\"aligncenter size-large\"><img decoding=\"async\" src=\"https:\/\/github.com\/chenhcs\/FRoGS\/blob\/main\/demo\/tsne_signature_FRoGS.png?raw=true\" alt=\"\"\/><figcaption class=\"wp-element-caption\"><strong>\u56fe6. <\/strong>\u4f7f\u7528\u5176FRoGS\u8868\u793a\u7684\u57fa\u56e0\u5217\u8868\u7684t-SNE\u6295\u5f71\u3002\u5177\u6709\u76f8\u540c\u7ec4\u7ec7\u8868\u8fbe\u6a21\u5f0f\u7684\u57fa\u56e0\u5f62\u6210\u7d27\u5bc6\u4e14\u72ec\u7279\u7684\u805a\u7c7b\uff0c\u4ece\u800c\u5bfc\u81f4\u5177\u6709\u51fa\u8272\u51c6\u786e\u6027\u7684\u5206\u7c7b\u5668\u3002\u8fd9\u663e\u793a\u4e86\u5728\u751f\u7269\u4fe1\u606f\u5b66\u673a\u5668\u5b66\u4e60\u5e94\u7528\u4e2d\u5229\u7528FRoGS\u7684\u5f3a\u5927\u80fd\u529b\u3002<\/figcaption><\/figure>\n<\/div>\n\n\n<p><strong>\u7ed3\u8bba<\/strong><\/p>\n\n\n\n<p>FRoGS\u6807\u5fd7\u7740\u751f\u7269\u4fe1\u606f\u5b66\u7684\u4e00\u4e2a\u65b0\u8df3\u8dc3\uff0c\u7c7b\u4f3c\u4e8eWord2Vec\u5bf9NLP\u7684\u5f71\u54cd\u3002\u4f5c\u4e3a\u7814\u7a76\u4eba\u5458\uff0c\u8ba9\u6211\u4eec\u62e5\u62b1\u8fd9\u4e00\u8d77\u63a2\u7d22FRoGS\u5728\u4e0d\u540c\u751f\u7269\u95ee\u9898\u4e2d\u7684\u5e94\u7528\u6f5c\u529b\u3002\u8bf7\u8bbf\u95ee\u6211\u4eec\u7684GitHub\u4ee3\u7801\u5e93[5]\uff0c\u5728\u60a8\u7684\u4e0b\u4e00\u4e2a\u673a\u5668\u5b66\u4e60\u5c1d\u8bd5\u4e2d\u53d1\u6398FRoGS\u7684\u53d8\u9769\u6027\u80fd\u529b\u3002<\/p>\n\n\n\n<p><strong>\u5f15\u6587<\/strong><\/p>\n\n\n\n<ol class=\"wp-block-list\">\n<li><a href=\"https:\/\/en.wikipedia.org\/wiki\/Word2vec\">Word2vec &#8211; Wikipedia<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.nature.com\/articles\/s41467-024-46089-y\">Chen et al. Drug target prediction through deep learning functional representation of gene signatures. Nature Communications. (2024) 15:1853.<\/a>   <\/li>\n\n\n\n<li><a href=\"https:\/\/www.geneontology.org\/\">Gene Ontology Resource<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/maayanlab.cloud\/archs4\/\">ARCHS4 (maayanlab.cloud)<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/github.com\/chenhcs\/FRoGS\/tree\/main\">GitHub &#8211; chenhcs\/FRoGS: Functional Embedding of Gene Signatures<\/a><\/li>\n<\/ol>\n\n\n\n<p><\/p>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u672c\u6587\u7531ChatGPT\u57fa\u4e8e\u82f1\u6587\u7248\u7ffb\u8bd1\u540e\u7a0d\u52a0\u4fee\u6539, \u4e0d\u51c6\u786e\u4e4b\u5904\u4ee5\u82f1\u6587\u7248\u4e3a\u51c6. \u5728\u81ea\u7136\u8bed\u8a00\u5904\u7406\uff08NLP\uff09\u7814\u7a76\u7684\u65e9\u671f\u9636\u6bb5\uff0c\u6211\u4eec\u901a\u8fc7\u8ba1\u7b97\u5171\u4eab\u5355\u8bcd\u6765\u91cf\u5316\u6587\u6863\u4e4b\u95f4\u7684\u76f8\u4f3c\u6027\u3002\u7136\u800c\uff0c\u8fd9\u79cd\u7b80\u5355\u7684\u65b9\u6cd5\u5ffd\u7565\u4e86\u540c\u4e49\u8bcd\u5b83\u5c06\u201c\u732b\u201d\u548c\u201c\u5c0f\u732b\u201d\u89c6\u4e3a\u6beb\u65e0\u5173\u8054\u7684\u5b9e\u4f53\uff0c\u5c31\u50cf\u5bf9\u5f85\u201c\u732b\u201d\u548c\u201c\u5ca9\u77f3\u201d\u4e00\u6837\uff08\u56fe1\uff0c\u5de6\u4fa7\uff09\u3002\u7531\u6b64\u4ea7\u751f\u7684\u57fa\u4e8e\u8eab\u4efd(identity)\u7684\u5355\u8bcd\u8868\u793a\uff0c\u5373\u72ec\u70ed(one-hot)\u7f16\u7801\uff0c\u5728\u5e94\u7528\u4e8e\u805a\u7c7b\u6587\u6863\u65f6\u6548\u679c\u5e76\u4e0d\u4f73\u3002\u5e78\u8fd0\u7684\u662f\uff0c\u968f\u7740Word2Vec\u7b49\u6df1\u5ea6\u5b66\u4e60\u6280\u672f\u7684\u51fa\u73b0 [1]\uff0cNLP\u9886\u57df\u5df2\u7ecf\u53d1\u751f\u4e86\u53d8\u9769\u3002\u7531\u4e8eWord2Vec\uff0c\u66fe\u7ecf\u76f8\u8ddd\u751a\u8fdc\u7684\u201c\u732b\u201d\u548c\u201c\u5c0f\u732b\u201d\u4e24\u4e2a\u8bcd\u73b0\u5728\u88ab\u8ba4\u4e3a\u662f\u51e0\u4e4e\u76f8\u540c\u7684\uff08\u56fe1\uff0c\u53f3\u4fa7\uff09\u3002 \u5728\u57fa\u56e0\u5206\u6790\u4e2d\uff0c\u6211\u4eec\u4e00\u76f4\u9762\u4e34\u7740\u7c7b\u4f3c\u7684\u56f0\u5883\u3002\u5728\u6bd4\u8f83\u57fa\u56e0\u5217\u8868\u65f6\uff0c\u6211\u4eec\u8ba1\u7b97\u5171\u4eab\u7684\u57fa\u56e0\u4e2a\u6570\uff0c\u7c7b\u4f3c\u4e8e\u65e7\u65f6\u7684NLP\u65b9\u6cd5\u3002\u7136\u800c\uff0c\u50cfTLR7\u548cMYD88\u8fd9\u6837\u5728\u5148\u5929\u514d\u75ab\u4fe1\u53f7\u4e2d\u5177\u6709\u975e\u5e38\u76f8\u4f3c\u751f\u7269\u5b66\u4f5c\u7528\u7684\u57fa\u56e0\uff0c\u5f53\u5728\u51fa\u73b0\u5728\u4e0d\u540c\u5217\u8868\u4e2d\u65f6\u88ab\u5f53\u6210\u662f\u5b8c\u5168\u65e0\u5173\u7684\u800c\u88ab\u5ffd\u89c6\u4e86\u3002\u8fd9\u5c31\u50cf\u201c\u732b\u201d\u548c\u201c\u5c0f\u732b\u201d\u66fe\u7ecf\u88ab\u8ba4\u4e3a\u662f\u5b8c\u5168\u4e0d\u540c\u7684\u4e00\u6837\u3002\u76ee\u524d\u4f7f\u7528\u7684\u57fa\u56e0\u5217\u8868\u7684\u76f8\u4f3c\u6027\u7b97\u6cd5\u5f88\u6709\u5c40\u9650\u3002\u5728\u6211\u4eec\u6700\u8fd1\u7684\u300a\u81ea\u7136\u901a\u8baf\u300b\u53d1\u8868\u7684\u7814\u7a76\u4e2d [2]\uff0c\u6211\u4eec\u5c06NLP\u4e0e\u751f\u7269\u4fe1\u606f\u5b66\u8fdb\u884c\u4e86\u7c7b\u6bd4\uff0c\u9996\u5148\u6211\u4eec\u5f15\u5165\u4e86\u57fa\u56e0\u7279\u5f81\u7684\u529f\u80fd\u6027\u8868\u793a(Functional Representation of Gene Signatures &#8212; FRoGS)\uff0c\u4f5c\u4e3a\u57fa\u56e0\u5206\u6790\u7684Word2Vec\u7b49\u6548\u65b9\u6cd5\uff08\u56fe2\uff09\u3002\u7136\u540e\u6211\u4eec\u5229\u7528FRoGS\u7684\u8868\u5f81\u6765\u63ed\u793a\u5316\u5408\u7269\u7684\u9776\u70b9\u3002\u5229\u7528Broad\u7684L1000\u6570\u636e\u96c6, \u901a\u8fc7\u5c06shRNA\/cDNA\u6270\u52a8\u7684\u57fa\u56e0\u7279\u5f81\u4e0e\u4e2d\u5316\u5408\u7269\u7684\u57fa\u56e0\u7279\u5f81\u8fdb\u884c\u76f8\u4f3c\u6027\u6bd4\u8f83\uff0c\u6211\u4eec\u53d6\u5f97\u4e86\u663e\u8457\u7684\u6210\u679c\u3002\u5177\u4f53\u800c\u8a00\uff0c\u57fa\u4e8eFRoGS\u7684AI\u6a21\u578b\u5728\u8bc6\u522b\u771f\u6b63\u7684\u5316\u5408\u7269\u9776\u70b9\u65b9\u9762\u8868\u73b0\u51fa\u4e8636%\u7684\u53ec\u56de\u7387 (recall)\uff0c\u8d85\u8fc7\u4e86\u4f20\u7edf\u7684\u72ec\u70ed\u7f16\u7801\u65b9\u6cd5\u6240\u80fd\u8fbe\u5230\u76849%\u7684\u53ec\u56de\u7387\u3002 \u5728\u8fd9\u7bc7\u535a\u5ba2\u4e2d\uff0c\u6211\u4eec\u7528\u4e24\u4e2a\u6d45\u663e\u7684\u4f8b\u5b50\u8fdb\u4e00\u6b65\u5c55\u793a\u4e86FRoGS\u5411\u91cf\u5982\u4f55\u5e2e\u52a9\u5b9e\u73b0\u5f3a\u5927\u7684\u673a\u5668\u5b66\u4e60\u4efb\u52a1\uff0c\u5c06\u57fa\u56e0\u5206\u6790\u63a8\u5411\u4e86\u4f20\u7edf\u72ec\u70ed\u7f16\u7801\u4e0d\u80fd\u591f\u53ca\u7684\u9ad8\u5ea6\u3002 FRoGS\u80fd\u5353\u6709\u6210\u6548\u5730\u5e2e\u52a9\u673a\u5668\u5b66\u4e60\u7684\u8bc0\u7a8d\u5728\u54ea\u91cc\u5462\uff1f\u56e0\u4e3a\u57fa\u56e0\u7684\u529f\u80fd\u9a71\u52a8\u7740\u751f\u7269\u8fc7\u7a0b\u548c\u5b83\u7684\u8868\u578b\u3002 \uff0c\u5b83\u7684\u529f\u80fd\u88ab\u5ffd\u7565\u4e86, AI\u6a21\u578b\u5c31\u5fc5\u987b\u4f7f\u51fa\u6d2a\u8352\u4e4b\u529b\u91cd\u65b0\u53d1\u73b0\u5b83\u4eec\u7684\u529f\u80fd \u624d\u80fd\u6709\u6548\u9884\u6d4b\u5b83\u4eec\u7684\u8868\u578b&#8212; \u800c\u8fd9\u4e2a\u529f\u80fd\u518d\u53d1\u73b0\u7684\u8fc7\u7a0b\u9700\u8981\u5927\u91cf\u7684\u8bad\u7ec3\u6570\u636e\u3002\u4e0d\u5e78\u7684\u662f\uff0c\u8fd9\u6837\u7684\u5927\u91cf\u6570\u636e\u5e76\u4e0d\u603b\u662f\u53ef\u5f97\u5230\uff0c\u4e8e\u662f\u6709\u9650\u7684\u8bad\u7ec3\u6570\u636e\u4e25\u91cd\u5730\u5f71\u54cd\u4e86\u529f\u80fd\u7684\u5b66\u4e60\u4ece\u800c\u5f71\u54cd\u4e86\u6700\u7ec8\u9884\u6d4b\u7684\u51c6\u786e\u6027\u3002FRoGS\u8868\u5f81\u9769\u547d\u6027\u5730\u6539\u53d8\u4e86\u57fa\u56e0\u7684\u8868\u793a\u65b9\u5f0f\u3002\u6bcf\u4e2a\u4eba\u7c7b\u57fa\u56e0\u90fd\u88ab\u7f16\u7801\u4e3a\u4e00\u4e2a\u6709\u610f\u4e49\u7684\u5411\u91cf\uff0c\u65e2\u5305\u542b\u4e86\u5728\u57fa\u56e0\u5728Gene Ontology (GO [3])\u4e2d\u6ce8\u91ca\u7684\u5df2\u77e5\u529f\u80fd\uff0c\u4e5f\u5305\u542b\u4e86\u4ece\u5927\u89c4\u6a21\u8f6c\u5f55\u7ec4\u6570\u636e\u96c6(\u4f8b\u5982ARCHS4 [4])\u4e2d\u8574\u542b\u7684\u6f5c\u5728\u529f\u80fd \u3002FRoGS\u5728AI\u6a21\u578b\u7684\u8f93\u5165\u5411\u91cf\u4e2d\u6ce8\u5165\u529f\u80fd\u4fe1\u606f, \u6a21\u578b\u65e0\u9700\u6d6a\u8d39\u8d44\u6e90\u53bb\u4ece\u5934\u5f00\u59cb\u5b66\u4e60\u57fa\u56e0\u7684\u529f\u80fd, \u800c\u53ef\u4ee5\u4e13\u6ce8\u4e8e\u5b66\u4e60\u57fa\u56e0\u529f\u80fd\u4e0e\u8868\u578b\u4e4b\u95f4\u590d\u6742\u7684\u5173\u8054\u3002\u8fd9\u6837\u6709\u9650\u7684\u8bad\u7ec3\u6570\u636e\u5168\u90fd\u88ab\u7528\u5728\u4e86\u5200\u5203\u4e0a\u3002 \u793a\u4f8b 1\uff1a\u7ec4\u7ec7\u7279\u5f02\u6027\u57fa\u56e0\u8868\u8fbe \u5728\u6211\u4eec\u7684\u7b2c\u4e00\u4e2a\u793a\u4f8b\u4e2d\uff0c\u6211\u4eec\u5206\u522b\u4f7f\u752897\u300198\u548c100\u4e2a\u5728\u5927\u8111\u3001\u813e\u810f\u548c\u808c\u8089\u4e2d\u7279\u5f02\u6027\u8868\u8fbe\u7684\u57fa\u56e0\u3002\u6211\u4eec\u7684\u76ee\u6807\u662f\u9884\u6d4b\u57fa\u56e0\u8868\u8fbe\u7684\u7ec4\u7ec7\u3002\u4f20\u7edf\u4e0a\uff0c\u72ec\u70ed\u7f16\u7801\u5c06\u8fd9\u4e9b\u57fa\u56e0\u653e\u7f6e\u5728\u9ad8\u7ef4\u7a7a\u95f4\u4e2d\uff0c\u57fa\u56e0\u4e4b\u95f4\u6ca1\u6709\u4efb\u4f55\u7684\u76f8\u4f3c\u6027\u3002\u56e0\u6b64\uff0cAI\u6a21\u578b\u96be\u4ee5\u5b66\u4e60\u6709\u610f\u4e49\u7684\u6a21\u5f0f\uff0c\u5bfc\u81f4\u5206\u7c7b\u51c6\u786e\u7387\u4ec5\u7ea6\u4e3a29%\uff08\u00b13%\uff09\uff08n = 100\u6b21\u6a21\u62df\uff09\u2014\u2014\u7c7b\u4f3c\u4e8e\u968f\u673a\u731c\u6d4b\uff08\u56fe3\uff09\u3002\u7136\u800c\uff0c\u5f53\u6211\u4eec\u4f7f\u7528FRoGS\u5411\u91cf\u8868\u793a\u57fa\u56e0\u65f6\uff0ct-SNE\u56fe\u4e2d\u5df2\u7ecf\u5448\u73b0\u4e86\u7ec4\u7ec7\u7279\u5f02\u6027\u805a\u7c7b\uff08\u56fe4)\uff0c\u8fd9\u6837\u7528\u673a\u5668\u5b66\u4e60\u627e\u51fa\u5206\u7c7b\u7684\u8fb9\u754c\u5c31\u5f88\u76f4\u63a5\u4e86\u3002\u968f\u673a\u68ee\u6797\u6a21\u578b(Random Forest)\u7684\u51c6\u786e\u7387\u98d9\u5347\u81f3\u7ea680%\uff08\u00b15%\uff09\uff08n = 100\u6b21\u6a21\u62df\uff09\uff0c\u5c55\u793a\u4e86FRoGS\u4f7f\u5f97AI\u6a21\u578b\u5373\u4f7f\u5728\u6709\u9650\u6570\u636e\u60c5\u51b5\u4e0b\u4e5f\u5177\u6709\u5f3a\u5927\u7684\u5b66\u4e60\u80fd\u529b\uff08\u56fe4\uff09\u3002 \u793a\u4f8b 2\uff1a\u57fa\u56e0\u5217\u8868\u548c\u529f\u80fd\u7279\u5f81 \u6211\u4eec\u7684\u6570\u636e\u96c6\u5305\u62ec\u4e0e\u52a8\u8109\u3001\u5fc3\u810f\u548c\u5927\u8111\u5206\u522b\u76f8\u5173\u768435\u300124\u548c122\u4e2a\u57fa\u56e0\u5217\u8868\u3002\u6bcf\u4e2a\u57fa\u56e0\u5217\u8868\u5185\u542b\u7ea6100\u4e2a\u57fa\u56e0\u3002\u5728\u72ec\u70ed\u7f16\u7801\u65b9\u6cd5\u4e2d\uff0c\u57fa\u56e0\u5217\u8868\u88ab\u8868\u793a\u4e3a\u5176\u7ec4\u6210\u6210\u5458\u57fa\u56e0\u72ec\u70ed\u5411\u91cf\u7684\u603b\u548c\u3002\u867d\u7136\u8fd9\u4e9b\u57fa\u56e0\u5217\u8868\u4e5f\u5c55\u793a\u4e86\u4e00\u4e9b\u805a\u7c7b\u6a21\u5f0f\uff08\u56fe5\uff09\uff0c\u4f46\u4e0eFRoGS\u57fa\u56e0\u7279\u5f81\u5d4c\u5165\u5f62\u6210\u7684\u660e\u663e\u805a\u7c7b\u76f8\u6bd4\uff0c\u5b83\u4eec\u76f8\u5f62\u89c1\u7ecc\uff08\u56fe6\uff09\u3002\u56e0\u6b64\uff0c\u7528\u4e8e\u9884\u6d4b\u7684\u5206\u7c7b\u51c6\u786e\u7387\u4e3a\u72ec\u70ed\u5411\u91cf\u4e3a85%\uff08\u00b14%\uff09\uff08n = 100\u6b21\u6a21\u62df\uff09\uff0c\u800cFRoGS\u5411\u91cf\u4e3a100.0%\uff08\u00b10.4%\uff09\uff08n &hellip; <a href=\"https:\/\/metascape.org\/blog\/?p=296\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[46,5],"tags":[48,49,47,3],"class_list":["post-296","post","type-post","status-publish","format-standard","hentry","category-machine-learning","category-news","tag-deep-learning","tag-embedding","tag-gene-signature","tag-news"],"_links":{"self":[{"href":"https:\/\/metascape.org\/blog\/index.php?rest_route=\/wp\/v2\/posts\/296","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/metascape.org\/blog\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/metascape.org\/blog\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/metascape.org\/blog\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/metascape.org\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=296"}],"version-history":[{"count":6,"href":"https:\/\/metascape.org\/blog\/index.php?rest_route=\/wp\/v2\/posts\/296\/revisions"}],"predecessor-version":[{"id":305,"href":"https:\/\/metascape.org\/blog\/index.php?rest_route=\/wp\/v2\/posts\/296\/revisions\/305"}],"wp:attachment":[{"href":"https:\/\/metascape.org\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=296"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/metascape.org\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=296"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/metascape.org\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=296"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}