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gdp_model.py 179KB

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  225. <path d="M10.3 6.74a.75.75 0 0 1-.04 1.06l-2.908 2.7 2.908 2.7a.75.75 0 1 1-1.02 1.1l-3.5-3.25a.75.75 0 0 1 0-1.1l3.5-3.25a.75.75 0 0 1 1.06.04Zm3.44 1.06a.75.75 0 1 1 1.02-1.1l3.5 3.25a.75.75 0 0 1 0 1.1l-3.5 3.25a.75.75 0 1 1-1.02-1.1l2.908-2.7-2.908-2.7Z"></path><path d="M1.5 4.25c0-.966.784-1.75 1.75-1.75h17.5c.966 0 1.75.784 1.75 1.75v12.5a1.75 1.75 0 0 1-1.75 1.75h-9.69l-3.573 3.573A1.458 1.458 0 0 1 5 21.043V18.5H3.25a1.75 1.75 0 0 1-1.75-1.75ZM3.25 4a.25.25 0 0 0-.25.25v12.5c0 .138.112.25.25.25h2.5a.75.75 0 0 1 .75.75v3.19l3.72-3.72a.749.749 0 0 1 .53-.22h10a.25.25 0 0 0 .25-.25V4.25a.25.25 0 0 0-.25-.25Z"></path>
  226. </svg>
  227. <div>
  228. <div class="color-fg-default h4">Code review</div>
  229. Manage code changes
  230. </div>
  231. </a></li>
  232. <li>
  233. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center pb-lg-3" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Product&quot;,&quot;action&quot;:&quot;click to go to Issues&quot;,&quot;label&quot;:&quot;ref_cta:Issues;&quot;}" href="/features/issues">
  234. <svg aria-hidden="true" height="24" viewBox="0 0 24 24" version="1.1" width="24" data-view-component="true" class="octicon octicon-issue-opened color-fg-subtle mr-3">
  235. <path d="M12 1c6.075 0 11 4.925 11 11s-4.925 11-11 11S1 18.075 1 12 5.925 1 12 1ZM2.5 12a9.5 9.5 0 0 0 9.5 9.5 9.5 9.5 0 0 0 9.5-9.5A9.5 9.5 0 0 0 12 2.5 9.5 9.5 0 0 0 2.5 12Zm9.5 2a2 2 0 1 1-.001-3.999A2 2 0 0 1 12 14Z"></path>
  236. </svg>
  237. <div>
  238. <div class="color-fg-default h4">Issues</div>
  239. Plan and track work
  240. </div>
  241. </a></li>
  242. <li>
  243. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Product&quot;,&quot;action&quot;:&quot;click to go to Discussions&quot;,&quot;label&quot;:&quot;ref_cta:Discussions;&quot;}" href="/features/discussions">
  244. <svg aria-hidden="true" height="24" viewBox="0 0 24 24" version="1.1" width="24" data-view-component="true" class="octicon octicon-comment-discussion color-fg-subtle mr-3">
  245. <path d="M1.75 1h12.5c.966 0 1.75.784 1.75 1.75v9.5A1.75 1.75 0 0 1 14.25 14H8.061l-2.574 2.573A1.458 1.458 0 0 1 3 15.543V14H1.75A1.75 1.75 0 0 1 0 12.25v-9.5C0 1.784.784 1 1.75 1ZM1.5 2.75v9.5c0 .138.112.25.25.25h2a.75.75 0 0 1 .75.75v2.19l2.72-2.72a.749.749 0 0 1 .53-.22h6.5a.25.25 0 0 0 .25-.25v-9.5a.25.25 0 0 0-.25-.25H1.75a.25.25 0 0 0-.25.25Z"></path><path d="M22.5 8.75a.25.25 0 0 0-.25-.25h-3.5a.75.75 0 0 1 0-1.5h3.5c.966 0 1.75.784 1.75 1.75v9.5A1.75 1.75 0 0 1 22.25 20H21v1.543a1.457 1.457 0 0 1-2.487 1.03L15.939 20H10.75A1.75 1.75 0 0 1 9 18.25v-1.465a.75.75 0 0 1 1.5 0v1.465c0 .138.112.25.25.25h5.5a.75.75 0 0 1 .53.22l2.72 2.72v-2.19a.75.75 0 0 1 .75-.75h2a.25.25 0 0 0 .25-.25v-9.5Z"></path>
  246. </svg>
  247. <div>
  248. <div class="color-fg-default h4">Discussions</div>
  249. Collaborate outside of code
  250. </div>
  251. </a></li>
  252. </ul>
  253. </div>
  254. <div class="px-lg-4">
  255. <span class="d-block h4 color-fg-default my-1" id="product-explore-heading">Explore</span>
  256. <ul class="list-style-none f5" aria-labelledby="product-explore-heading">
  257. <li>
  258. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Product&quot;,&quot;action&quot;:&quot;click to go to All features&quot;,&quot;label&quot;:&quot;ref_cta:All features;&quot;}" href="/features">
  259. All features
  260. </a></li>
  261. <li>
  262. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary" target="_blank" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Product&quot;,&quot;action&quot;:&quot;click to go to Documentation&quot;,&quot;label&quot;:&quot;ref_cta:Documentation;&quot;}" href="https://docs.github.com">
  263. Documentation
  264. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-link-external HeaderMenu-external-icon color-fg-subtle">
  265. <path d="M3.75 2h3.5a.75.75 0 0 1 0 1.5h-3.5a.25.25 0 0 0-.25.25v8.5c0 .138.112.25.25.25h8.5a.25.25 0 0 0 .25-.25v-3.5a.75.75 0 0 1 1.5 0v3.5A1.75 1.75 0 0 1 12.25 14h-8.5A1.75 1.75 0 0 1 2 12.25v-8.5C2 2.784 2.784 2 3.75 2Zm6.854-1h4.146a.25.25 0 0 1 .25.25v4.146a.25.25 0 0 1-.427.177L13.03 4.03 9.28 7.78a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042l3.75-3.75-1.543-1.543A.25.25 0 0 1 10.604 1Z"></path>
  266. </svg>
  267. </a></li>
  268. <li>
  269. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary" target="_blank" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Product&quot;,&quot;action&quot;:&quot;click to go to GitHub Skills&quot;,&quot;label&quot;:&quot;ref_cta:GitHub Skills;&quot;}" href="https://skills.github.com/">
  270. GitHub Skills
  271. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-link-external HeaderMenu-external-icon color-fg-subtle">
  272. <path d="M3.75 2h3.5a.75.75 0 0 1 0 1.5h-3.5a.25.25 0 0 0-.25.25v8.5c0 .138.112.25.25.25h8.5a.25.25 0 0 0 .25-.25v-3.5a.75.75 0 0 1 1.5 0v3.5A1.75 1.75 0 0 1 12.25 14h-8.5A1.75 1.75 0 0 1 2 12.25v-8.5C2 2.784 2.784 2 3.75 2Zm6.854-1h4.146a.25.25 0 0 1 .25.25v4.146a.25.25 0 0 1-.427.177L13.03 4.03 9.28 7.78a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042l3.75-3.75-1.543-1.543A.25.25 0 0 1 10.604 1Z"></path>
  273. </svg>
  274. </a></li>
  275. <li>
  276. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary" target="_blank" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Product&quot;,&quot;action&quot;:&quot;click to go to Blog&quot;,&quot;label&quot;:&quot;ref_cta:Blog;&quot;}" href="https://github.blog">
  277. Blog
  278. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-link-external HeaderMenu-external-icon color-fg-subtle">
  279. <path d="M3.75 2h3.5a.75.75 0 0 1 0 1.5h-3.5a.25.25 0 0 0-.25.25v8.5c0 .138.112.25.25.25h8.5a.25.25 0 0 0 .25-.25v-3.5a.75.75 0 0 1 1.5 0v3.5A1.75 1.75 0 0 1 12.25 14h-8.5A1.75 1.75 0 0 1 2 12.25v-8.5C2 2.784 2.784 2 3.75 2Zm6.854-1h4.146a.25.25 0 0 1 .25.25v4.146a.25.25 0 0 1-.427.177L13.03 4.03 9.28 7.78a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042l3.75-3.75-1.543-1.543A.25.25 0 0 1 10.604 1Z"></path>
  280. </svg>
  281. </a></li>
  282. </ul>
  283. </div>
  284. </div>
  285. </li>
  286. <li class="HeaderMenu-item position-relative flex-wrap flex-justify-between flex-items-center d-block d-lg-flex flex-lg-nowrap flex-lg-items-center js-details-container js-header-menu-item">
  287. <button type="button" class="HeaderMenu-link border-0 width-full width-lg-auto px-0 px-lg-2 py-3 py-lg-2 no-wrap d-flex flex-items-center flex-justify-between js-details-target" aria-expanded="false">
  288. Solutions
  289. <svg opacity="0.5" aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-chevron-down HeaderMenu-icon ml-1">
  290. <path d="M12.78 5.22a.749.749 0 0 1 0 1.06l-4.25 4.25a.749.749 0 0 1-1.06 0L3.22 6.28a.749.749 0 1 1 1.06-1.06L8 8.939l3.72-3.719a.749.749 0 0 1 1.06 0Z"></path>
  291. </svg>
  292. </button>
  293. <div class="HeaderMenu-dropdown dropdown-menu rounded m-0 p-0 py-2 py-lg-4 position-relative position-lg-absolute left-0 left-lg-n3 px-lg-4">
  294. <div class="border-bottom pb-3 mb-3">
  295. <span class="d-block h4 color-fg-default my-1" id="solutions-for-heading">For</span>
  296. <ul class="list-style-none f5" aria-labelledby="solutions-for-heading">
  297. <li>
  298. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Solutions&quot;,&quot;action&quot;:&quot;click to go to Enterprise&quot;,&quot;label&quot;:&quot;ref_cta:Enterprise;&quot;}" href="/enterprise">
  299. Enterprise
  300. </a></li>
  301. <li>
  302. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Solutions&quot;,&quot;action&quot;:&quot;click to go to Teams&quot;,&quot;label&quot;:&quot;ref_cta:Teams;&quot;}" href="/team">
  303. Teams
  304. </a></li>
  305. <li>
  306. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Solutions&quot;,&quot;action&quot;:&quot;click to go to Startups&quot;,&quot;label&quot;:&quot;ref_cta:Startups;&quot;}" href="/enterprise/startups">
  307. Startups
  308. </a></li>
  309. <li>
  310. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary" target="_blank" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Solutions&quot;,&quot;action&quot;:&quot;click to go to Education&quot;,&quot;label&quot;:&quot;ref_cta:Education;&quot;}" href="https://education.github.com">
  311. Education
  312. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-link-external HeaderMenu-external-icon color-fg-subtle">
  313. <path d="M3.75 2h3.5a.75.75 0 0 1 0 1.5h-3.5a.25.25 0 0 0-.25.25v8.5c0 .138.112.25.25.25h8.5a.25.25 0 0 0 .25-.25v-3.5a.75.75 0 0 1 1.5 0v3.5A1.75 1.75 0 0 1 12.25 14h-8.5A1.75 1.75 0 0 1 2 12.25v-8.5C2 2.784 2.784 2 3.75 2Zm6.854-1h4.146a.25.25 0 0 1 .25.25v4.146a.25.25 0 0 1-.427.177L13.03 4.03 9.28 7.78a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042l3.75-3.75-1.543-1.543A.25.25 0 0 1 10.604 1Z"></path>
  314. </svg>
  315. </a></li>
  316. </ul>
  317. </div>
  318. <div class="border-bottom pb-3 mb-3">
  319. <span class="d-block h4 color-fg-default my-1" id="solutions-by-solution-heading">By Solution</span>
  320. <ul class="list-style-none f5" aria-labelledby="solutions-by-solution-heading">
  321. <li>
  322. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Solutions&quot;,&quot;action&quot;:&quot;click to go to CI/CD &amp;amp; Automation&quot;,&quot;label&quot;:&quot;ref_cta:CI/CD &amp;amp; Automation;&quot;}" href="/solutions/ci-cd/">
  323. CI/CD &amp; Automation
  324. </a></li>
  325. <li>
  326. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary" target="_blank" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Solutions&quot;,&quot;action&quot;:&quot;click to go to DevOps&quot;,&quot;label&quot;:&quot;ref_cta:DevOps;&quot;}" href="https://resources.github.com/devops/">
  327. DevOps
  328. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-link-external HeaderMenu-external-icon color-fg-subtle">
  329. <path d="M3.75 2h3.5a.75.75 0 0 1 0 1.5h-3.5a.25.25 0 0 0-.25.25v8.5c0 .138.112.25.25.25h8.5a.25.25 0 0 0 .25-.25v-3.5a.75.75 0 0 1 1.5 0v3.5A1.75 1.75 0 0 1 12.25 14h-8.5A1.75 1.75 0 0 1 2 12.25v-8.5C2 2.784 2.784 2 3.75 2Zm6.854-1h4.146a.25.25 0 0 1 .25.25v4.146a.25.25 0 0 1-.427.177L13.03 4.03 9.28 7.78a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042l3.75-3.75-1.543-1.543A.25.25 0 0 1 10.604 1Z"></path>
  330. </svg>
  331. </a></li>
  332. <li>
  333. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary" target="_blank" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Solutions&quot;,&quot;action&quot;:&quot;click to go to DevSecOps&quot;,&quot;label&quot;:&quot;ref_cta:DevSecOps;&quot;}" href="https://resources.github.com/devops/fundamentals/devsecops/">
  334. DevSecOps
  335. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-link-external HeaderMenu-external-icon color-fg-subtle">
  336. <path d="M3.75 2h3.5a.75.75 0 0 1 0 1.5h-3.5a.25.25 0 0 0-.25.25v8.5c0 .138.112.25.25.25h8.5a.25.25 0 0 0 .25-.25v-3.5a.75.75 0 0 1 1.5 0v3.5A1.75 1.75 0 0 1 12.25 14h-8.5A1.75 1.75 0 0 1 2 12.25v-8.5C2 2.784 2.784 2 3.75 2Zm6.854-1h4.146a.25.25 0 0 1 .25.25v4.146a.25.25 0 0 1-.427.177L13.03 4.03 9.28 7.78a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042l3.75-3.75-1.543-1.543A.25.25 0 0 1 10.604 1Z"></path>
  337. </svg>
  338. </a></li>
  339. </ul>
  340. </div>
  341. <div class="">
  342. <span class="d-block h4 color-fg-default my-1" id="solutions-resources-heading">Resources</span>
  343. <ul class="list-style-none f5" aria-labelledby="solutions-resources-heading">
  344. <li>
  345. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Solutions&quot;,&quot;action&quot;:&quot;click to go to Customer Stories&quot;,&quot;label&quot;:&quot;ref_cta:Customer Stories;&quot;}" href="/customer-stories">
  346. Customer Stories
  347. </a></li>
  348. <li>
  349. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary" target="_blank" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Solutions&quot;,&quot;action&quot;:&quot;click to go to White papers, Ebooks, Webinars&quot;,&quot;label&quot;:&quot;ref_cta:White papers, Ebooks, Webinars;&quot;}" href="https://resources.github.com/">
  350. White papers, Ebooks, Webinars
  351. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-link-external HeaderMenu-external-icon color-fg-subtle">
  352. <path d="M3.75 2h3.5a.75.75 0 0 1 0 1.5h-3.5a.25.25 0 0 0-.25.25v8.5c0 .138.112.25.25.25h8.5a.25.25 0 0 0 .25-.25v-3.5a.75.75 0 0 1 1.5 0v3.5A1.75 1.75 0 0 1 12.25 14h-8.5A1.75 1.75 0 0 1 2 12.25v-8.5C2 2.784 2.784 2 3.75 2Zm6.854-1h4.146a.25.25 0 0 1 .25.25v4.146a.25.25 0 0 1-.427.177L13.03 4.03 9.28 7.78a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042l3.75-3.75-1.543-1.543A.25.25 0 0 1 10.604 1Z"></path>
  353. </svg>
  354. </a></li>
  355. <li>
  356. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary" target="_blank" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Solutions&quot;,&quot;action&quot;:&quot;click to go to Partners&quot;,&quot;label&quot;:&quot;ref_cta:Partners;&quot;}" href="https://partner.github.com/">
  357. Partners
  358. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-link-external HeaderMenu-external-icon color-fg-subtle">
  359. <path d="M3.75 2h3.5a.75.75 0 0 1 0 1.5h-3.5a.25.25 0 0 0-.25.25v8.5c0 .138.112.25.25.25h8.5a.25.25 0 0 0 .25-.25v-3.5a.75.75 0 0 1 1.5 0v3.5A1.75 1.75 0 0 1 12.25 14h-8.5A1.75 1.75 0 0 1 2 12.25v-8.5C2 2.784 2.784 2 3.75 2Zm6.854-1h4.146a.25.25 0 0 1 .25.25v4.146a.25.25 0 0 1-.427.177L13.03 4.03 9.28 7.78a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042l3.75-3.75-1.543-1.543A.25.25 0 0 1 10.604 1Z"></path>
  360. </svg>
  361. </a></li>
  362. </ul>
  363. </div>
  364. </div>
  365. </li>
  366. <li class="HeaderMenu-item position-relative flex-wrap flex-justify-between flex-items-center d-block d-lg-flex flex-lg-nowrap flex-lg-items-center js-details-container js-header-menu-item">
  367. <button type="button" class="HeaderMenu-link border-0 width-full width-lg-auto px-0 px-lg-2 py-3 py-lg-2 no-wrap d-flex flex-items-center flex-justify-between js-details-target" aria-expanded="false">
  368. Open Source
  369. <svg opacity="0.5" aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-chevron-down HeaderMenu-icon ml-1">
  370. <path d="M12.78 5.22a.749.749 0 0 1 0 1.06l-4.25 4.25a.749.749 0 0 1-1.06 0L3.22 6.28a.749.749 0 1 1 1.06-1.06L8 8.939l3.72-3.719a.749.749 0 0 1 1.06 0Z"></path>
  371. </svg>
  372. </button>
  373. <div class="HeaderMenu-dropdown dropdown-menu rounded m-0 p-0 py-2 py-lg-4 position-relative position-lg-absolute left-0 left-lg-n3 px-lg-4">
  374. <div class="border-bottom pb-3 mb-3">
  375. <ul class="list-style-none f5" >
  376. <li>
  377. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Open Source&quot;,&quot;action&quot;:&quot;click to go to GitHub Sponsors&quot;,&quot;label&quot;:&quot;ref_cta:GitHub Sponsors;&quot;}" href="/sponsors">
  378. <div>
  379. <div class="color-fg-default h4">GitHub Sponsors</div>
  380. Fund open source developers
  381. </div>
  382. </a></li>
  383. </ul>
  384. </div>
  385. <div class="border-bottom pb-3 mb-3">
  386. <ul class="list-style-none f5" >
  387. <li>
  388. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Open Source&quot;,&quot;action&quot;:&quot;click to go to The ReadME Project&quot;,&quot;label&quot;:&quot;ref_cta:The ReadME Project;&quot;}" href="/readme">
  389. <div>
  390. <div class="color-fg-default h4">The ReadME Project</div>
  391. GitHub community articles
  392. </div>
  393. </a></li>
  394. </ul>
  395. </div>
  396. <div class="">
  397. <span class="d-block h4 color-fg-default my-1" id="open-source-repositories-heading">Repositories</span>
  398. <ul class="list-style-none f5" aria-labelledby="open-source-repositories-heading">
  399. <li>
  400. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Open Source&quot;,&quot;action&quot;:&quot;click to go to Topics&quot;,&quot;label&quot;:&quot;ref_cta:Topics;&quot;}" href="/topics">
  401. Topics
  402. </a></li>
  403. <li>
  404. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Open Source&quot;,&quot;action&quot;:&quot;click to go to Trending&quot;,&quot;label&quot;:&quot;ref_cta:Trending;&quot;}" href="/trending">
  405. Trending
  406. </a></li>
  407. <li>
  408. <a class="HeaderMenu-dropdown-link lh-condensed d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;category&quot;:&quot;Header dropdown (logged out), Open Source&quot;,&quot;action&quot;:&quot;click to go to Collections&quot;,&quot;label&quot;:&quot;ref_cta:Collections;&quot;}" href="/collections">
  409. Collections
  410. </a></li>
  411. </ul>
  412. </div>
  413. </div>
  414. </li>
  415. <li class="HeaderMenu-item position-relative flex-wrap flex-justify-between flex-items-center d-block d-lg-flex flex-lg-nowrap flex-lg-items-center js-details-container js-header-menu-item">
  416. <a class="HeaderMenu-link no-underline px-0 px-lg-2 py-3 py-lg-2 d-block d-lg-inline-block" data-analytics-event="{&quot;category&quot;:&quot;Header menu top item (logged out)&quot;,&quot;action&quot;:&quot;click to go to Pricing&quot;,&quot;label&quot;:&quot;ref_cta:Pricing;&quot;}" href="/pricing">Pricing</a>
  417. </li>
  418. </ul>
  419. </nav>
  420. <div class="d-lg-flex flex-items-center mb-3 mb-lg-0 text-center text-lg-left ml-3" style="">
  421. <qbsearch-input class="search-input" data-scope="repo:WGLab/GDP" data-custom-scopes-path="/search/custom_scopes" data-delete-custom-scopes-csrf="iBbX4yXKX-8bD1N7QnvNgA8P3XHucdwZsl73EbQTqCCf2TiDaOYc8NB56asoHxejN_l_E4UrzwiOFVKhrWdQvw" data-max-custom-scopes="10" data-header-redesign-enabled="false" data-initial-value="" data-blackbird-suggestions-path="/search/suggestions" data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations" data-current-repository="WGLab/GDP" data-current-org="WGLab" data-current-owner="" data-logged-in="false">
  422. <div
  423. class="search-input-container search-with-dialog position-relative d-flex flex-row flex-items-center mr-4 rounded"
  424. data-action="click:qbsearch-input#searchInputContainerClicked"
  425. >
  426. <button
  427. type="button"
  428. class="header-search-button placeholder input-button form-control d-flex flex-1 flex-self-stretch flex-items-center no-wrap width-full py-0 pl-2 pr-0 text-left border-0 box-shadow-none"
  429. data-target="qbsearch-input.inputButton"
  430. placeholder="Search or jump to..."
  431. data-hotkey=s,/
  432. autocapitalize="off"
  433. data-action="click:qbsearch-input#handleExpand"
  434. >
  435. <div class="mr-2 color-fg-muted">
  436. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-search">
  437. <path d="M10.68 11.74a6 6 0 0 1-7.922-8.982 6 6 0 0 1 8.982 7.922l3.04 3.04a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215ZM11.5 7a4.499 4.499 0 1 0-8.997 0A4.499 4.499 0 0 0 11.5 7Z"></path>
  438. </svg>
  439. </div>
  440. <span class="flex-1" data-target="qbsearch-input.inputButtonText">Search or jump to...</span>
  441. <div class="d-flex" data-target="qbsearch-input.hotkeyIndicator">
  442. <svg xmlns="http://www.w3.org/2000/svg" width="22" height="20" aria-hidden="true" class="mr-1"><path fill="none" stroke="#979A9C" opacity=".4" d="M3.5.5h12c1.7 0 3 1.3 3 3v13c0 1.7-1.3 3-3 3h-12c-1.7 0-3-1.3-3-3v-13c0-1.7 1.3-3 3-3z"></path><path fill="#979A9C" d="M11.8 6L8 15.1h-.9L10.8 6h1z"></path></svg>
  443. </div>
  444. </button>
  445. <input type="hidden" name="type" class="js-site-search-type-field">
  446. <div class="Overlay--hidden " data-modal-dialog-overlay>
  447. <modal-dialog data-action="close:qbsearch-input#handleClose cancel:qbsearch-input#handleClose" data-target="qbsearch-input.searchSuggestionsDialog" role="dialog" id="search-suggestions-dialog" aria-modal="true" aria-labelledby="search-suggestions-dialog-header" data-view-component="true" class="Overlay Overlay--width-large Overlay--height-auto">
  448. <h1 id="search-suggestions-dialog-header" class="sr-only">Search code, repositories, users, issues, pull requests...</h1>
  449. <div class="Overlay-body Overlay-body--paddingNone">
  450. <div data-view-component="true"> <div class="search-suggestions position-fixed width-full color-shadow-large border color-fg-default color-bg-default overflow-hidden d-flex flex-column query-builder-container"
  451. style="border-radius: 12px;"
  452. data-target="qbsearch-input.queryBuilderContainer"
  453. hidden
  454. >
  455. <!-- '"` --><!-- </textarea></xmp> --></option></form><form id="query-builder-test-form" action="" accept-charset="UTF-8" method="get">
  456. <query-builder data-target="qbsearch-input.queryBuilder" id="query-builder-query-builder-test" data-filter-key=":" data-view-component="true" class="QueryBuilder search-query-builder">
  457. <div class="FormControl FormControl--fullWidth">
  458. <label id="query-builder-test-label" for="query-builder-test" class="FormControl-label sr-only">
  459. Search
  460. </label>
  461. <div
  462. class="QueryBuilder-StyledInput width-fit "
  463. data-target="query-builder.styledInput"
  464. >
  465. <span id="query-builder-test-leadingvisual-wrap" class="FormControl-input-leadingVisualWrap QueryBuilder-leadingVisualWrap">
  466. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-search FormControl-input-leadingVisual">
  467. <path d="M10.68 11.74a6 6 0 0 1-7.922-8.982 6 6 0 0 1 8.982 7.922l3.04 3.04a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215ZM11.5 7a4.499 4.499 0 1 0-8.997 0A4.499 4.499 0 0 0 11.5 7Z"></path>
  468. </svg>
  469. </span>
  470. <div data-target="query-builder.styledInputContainer" class="QueryBuilder-StyledInputContainer">
  471. <div
  472. aria-hidden="true"
  473. class="QueryBuilder-StyledInputContent"
  474. data-target="query-builder.styledInputContent"
  475. ></div>
  476. <div class="QueryBuilder-InputWrapper">
  477. <div aria-hidden="true" class="QueryBuilder-Sizer" data-target="query-builder.sizer"></div>
  478. <input id="query-builder-test" name="query-builder-test" value="" autocomplete="off" type="text" role="combobox" spellcheck="false" aria-expanded="false" aria-describedby="validation-c761a23e-0a8e-499e-acea-ef0d0dd8e626" data-target="query-builder.input" data-action="
  479. input:query-builder#inputChange
  480. blur:query-builder#inputBlur
  481. keydown:query-builder#inputKeydown
  482. focus:query-builder#inputFocus
  483. " data-view-component="true" class="FormControl-input QueryBuilder-Input FormControl-medium" />
  484. </div>
  485. </div>
  486. <span class="sr-only" id="query-builder-test-clear">Clear</span>
  487. <button role="button" id="query-builder-test-clear-button" aria-labelledby="query-builder-test-clear query-builder-test-label" data-target="query-builder.clearButton" data-action="
  488. click:query-builder#clear
  489. focus:query-builder#clearButtonFocus
  490. blur:query-builder#clearButtonBlur
  491. " variant="small" hidden="hidden" type="button" data-view-component="true" class="Button Button--iconOnly Button--invisible Button--medium mr-1 px-2 py-0 d-flex flex-items-center rounded-1 color-fg-muted"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-x-circle-fill Button-visual">
  492. <path d="M2.343 13.657A8 8 0 1 1 13.658 2.343 8 8 0 0 1 2.343 13.657ZM6.03 4.97a.751.751 0 0 0-1.042.018.751.751 0 0 0-.018 1.042L6.94 8 4.97 9.97a.749.749 0 0 0 .326 1.275.749.749 0 0 0 .734-.215L8 9.06l1.97 1.97a.749.749 0 0 0 1.275-.326.749.749 0 0 0-.215-.734L9.06 8l1.97-1.97a.749.749 0 0 0-.326-1.275.749.749 0 0 0-.734.215L8 6.94Z"></path>
  493. </svg>
  494. </button>
  495. </div>
  496. <template id="search-icon">
  497. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-search">
  498. <path d="M10.68 11.74a6 6 0 0 1-7.922-8.982 6 6 0 0 1 8.982 7.922l3.04 3.04a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215ZM11.5 7a4.499 4.499 0 1 0-8.997 0A4.499 4.499 0 0 0 11.5 7Z"></path>
  499. </svg>
  500. </template>
  501. <template id="code-icon">
  502. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-code">
  503. <path d="m11.28 3.22 4.25 4.25a.75.75 0 0 1 0 1.06l-4.25 4.25a.749.749 0 0 1-1.275-.326.749.749 0 0 1 .215-.734L13.94 8l-3.72-3.72a.749.749 0 0 1 .326-1.275.749.749 0 0 1 .734.215Zm-6.56 0a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042L2.06 8l3.72 3.72a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215L.47 8.53a.75.75 0 0 1 0-1.06Z"></path>
  504. </svg>
  505. </template>
  506. <template id="file-code-icon">
  507. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-file-code">
  508. <path d="M4 1.75C4 .784 4.784 0 5.75 0h5.586c.464 0 .909.184 1.237.513l2.914 2.914c.329.328.513.773.513 1.237v8.586A1.75 1.75 0 0 1 14.25 15h-9a.75.75 0 0 1 0-1.5h9a.25.25 0 0 0 .25-.25V6h-2.75A1.75 1.75 0 0 1 10 4.25V1.5H5.75a.25.25 0 0 0-.25.25v2.5a.75.75 0 0 1-1.5 0Zm1.72 4.97a.75.75 0 0 1 1.06 0l2 2a.75.75 0 0 1 0 1.06l-2 2a.749.749 0 0 1-1.275-.326.749.749 0 0 1 .215-.734l1.47-1.47-1.47-1.47a.75.75 0 0 1 0-1.06ZM3.28 7.78 1.81 9.25l1.47 1.47a.751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018l-2-2a.75.75 0 0 1 0-1.06l2-2a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042Zm8.22-6.218V4.25c0 .138.112.25.25.25h2.688l-.011-.013-2.914-2.914-.013-.011Z"></path>
  509. </svg>
  510. </template>
  511. <template id="history-icon">
  512. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-history">
  513. <path d="m.427 1.927 1.215 1.215a8.002 8.002 0 1 1-1.6 5.685.75.75 0 1 1 1.493-.154 6.5 6.5 0 1 0 1.18-4.458l1.358 1.358A.25.25 0 0 1 3.896 6H.25A.25.25 0 0 1 0 5.75V2.104a.25.25 0 0 1 .427-.177ZM7.75 4a.75.75 0 0 1 .75.75v2.992l2.028.812a.75.75 0 0 1-.557 1.392l-2.5-1A.751.751 0 0 1 7 8.25v-3.5A.75.75 0 0 1 7.75 4Z"></path>
  514. </svg>
  515. </template>
  516. <template id="repo-icon">
  517. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-repo">
  518. <path d="M2 2.5A2.5 2.5 0 0 1 4.5 0h8.75a.75.75 0 0 1 .75.75v12.5a.75.75 0 0 1-.75.75h-2.5a.75.75 0 0 1 0-1.5h1.75v-2h-8a1 1 0 0 0-.714 1.7.75.75 0 1 1-1.072 1.05A2.495 2.495 0 0 1 2 11.5Zm10.5-1h-8a1 1 0 0 0-1 1v6.708A2.486 2.486 0 0 1 4.5 9h8ZM5 12.25a.25.25 0 0 1 .25-.25h3.5a.25.25 0 0 1 .25.25v3.25a.25.25 0 0 1-.4.2l-1.45-1.087a.249.249 0 0 0-.3 0L5.4 15.7a.25.25 0 0 1-.4-.2Z"></path>
  519. </svg>
  520. </template>
  521. <template id="bookmark-icon">
  522. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-bookmark">
  523. <path d="M3 2.75C3 1.784 3.784 1 4.75 1h6.5c.966 0 1.75.784 1.75 1.75v11.5a.75.75 0 0 1-1.227.579L8 11.722l-3.773 3.107A.751.751 0 0 1 3 14.25Zm1.75-.25a.25.25 0 0 0-.25.25v9.91l3.023-2.489a.75.75 0 0 1 .954 0l3.023 2.49V2.75a.25.25 0 0 0-.25-.25Z"></path>
  524. </svg>
  525. </template>
  526. <template id="plus-circle-icon">
  527. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-plus-circle">
  528. <path d="M8 0a8 8 0 1 1 0 16A8 8 0 0 1 8 0ZM1.5 8a6.5 6.5 0 1 0 13 0 6.5 6.5 0 0 0-13 0Zm7.25-3.25v2.5h2.5a.75.75 0 0 1 0 1.5h-2.5v2.5a.75.75 0 0 1-1.5 0v-2.5h-2.5a.75.75 0 0 1 0-1.5h2.5v-2.5a.75.75 0 0 1 1.5 0Z"></path>
  529. </svg>
  530. </template>
  531. <template id="circle-icon">
  532. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-dot-fill">
  533. <path d="M8 4a4 4 0 1 1 0 8 4 4 0 0 1 0-8Z"></path>
  534. </svg>
  535. </template>
  536. <template id="trash-icon">
  537. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-trash">
  538. <path d="M11 1.75V3h2.25a.75.75 0 0 1 0 1.5H2.75a.75.75 0 0 1 0-1.5H5V1.75C5 .784 5.784 0 6.75 0h2.5C10.216 0 11 .784 11 1.75ZM4.496 6.675l.66 6.6a.25.25 0 0 0 .249.225h5.19a.25.25 0 0 0 .249-.225l.66-6.6a.75.75 0 0 1 1.492.149l-.66 6.6A1.748 1.748 0 0 1 10.595 15h-5.19a1.75 1.75 0 0 1-1.741-1.575l-.66-6.6a.75.75 0 1 1 1.492-.15ZM6.5 1.75V3h3V1.75a.25.25 0 0 0-.25-.25h-2.5a.25.25 0 0 0-.25.25Z"></path>
  539. </svg>
  540. </template>
  541. <template id="team-icon">
  542. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-people">
  543. <path d="M2 5.5a3.5 3.5 0 1 1 5.898 2.549 5.508 5.508 0 0 1 3.034 4.084.75.75 0 1 1-1.482.235 4 4 0 0 0-7.9 0 .75.75 0 0 1-1.482-.236A5.507 5.507 0 0 1 3.102 8.05 3.493 3.493 0 0 1 2 5.5ZM11 4a3.001 3.001 0 0 1 2.22 5.018 5.01 5.01 0 0 1 2.56 3.012.749.749 0 0 1-.885.954.752.752 0 0 1-.549-.514 3.507 3.507 0 0 0-2.522-2.372.75.75 0 0 1-.574-.73v-.352a.75.75 0 0 1 .416-.672A1.5 1.5 0 0 0 11 5.5.75.75 0 0 1 11 4Zm-5.5-.5a2 2 0 1 0-.001 3.999A2 2 0 0 0 5.5 3.5Z"></path>
  544. </svg>
  545. </template>
  546. <template id="project-icon">
  547. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-project">
  548. <path d="M1.75 0h12.5C15.216 0 16 .784 16 1.75v12.5A1.75 1.75 0 0 1 14.25 16H1.75A1.75 1.75 0 0 1 0 14.25V1.75C0 .784.784 0 1.75 0ZM1.5 1.75v12.5c0 .138.112.25.25.25h12.5a.25.25 0 0 0 .25-.25V1.75a.25.25 0 0 0-.25-.25H1.75a.25.25 0 0 0-.25.25ZM11.75 3a.75.75 0 0 1 .75.75v7.5a.75.75 0 0 1-1.5 0v-7.5a.75.75 0 0 1 .75-.75Zm-8.25.75a.75.75 0 0 1 1.5 0v5.5a.75.75 0 0 1-1.5 0ZM8 3a.75.75 0 0 1 .75.75v3.5a.75.75 0 0 1-1.5 0v-3.5A.75.75 0 0 1 8 3Z"></path>
  549. </svg>
  550. </template>
  551. <template id="pencil-icon">
  552. <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-pencil">
  553. <path d="M11.013 1.427a1.75 1.75 0 0 1 2.474 0l1.086 1.086a1.75 1.75 0 0 1 0 2.474l-8.61 8.61c-.21.21-.47.364-.756.445l-3.251.93a.75.75 0 0 1-.927-.928l.929-3.25c.081-.286.235-.547.445-.758l8.61-8.61Zm.176 4.823L9.75 4.81l-6.286 6.287a.253.253 0 0 0-.064.108l-.558 1.953 1.953-.558a.253.253 0 0 0 .108-.064Zm1.238-3.763a.25.25 0 0 0-.354 0L10.811 3.75l1.439 1.44 1.263-1.263a.25.25 0 0 0 0-.354Z"></path>
  554. </svg>
  555. </template>
  556. <div class="position-relative">
  557. <ul
  558. role="listbox"
  559. class="ActionListWrap QueryBuilder-ListWrap"
  560. aria-label="Suggestions"
  561. data-action="
  562. combobox-commit:query-builder#comboboxCommit
  563. mousedown:query-builder#resultsMousedown
  564. "
  565. data-target="query-builder.resultsList"
  566. data-persist-list=false
  567. id="query-builder-test-results"
  568. ></ul>
  569. </div>
  570. <div class="FormControl-inlineValidation" id="validation-c761a23e-0a8e-499e-acea-ef0d0dd8e626" hidden="hidden">
  571. <span class="FormControl-inlineValidation--visual">
  572. <svg aria-hidden="true" height="12" viewBox="0 0 12 12" version="1.1" width="12" data-view-component="true" class="octicon octicon-alert-fill">
  573. <path d="M4.855.708c.5-.896 1.79-.896 2.29 0l4.675 8.351a1.312 1.312 0 0 1-1.146 1.954H1.33A1.313 1.313 0 0 1 .183 9.058ZM7 7V3H5v4Zm-1 3a1 1 0 1 0 0-2 1 1 0 0 0 0 2Z"></path>
  574. </svg>
  575. </span>
  576. <span></span>
  577. </div> </div>
  578. <div data-target="query-builder.screenReaderFeedback" aria-live="polite" aria-atomic="true" class="sr-only"></div>
  579. </query-builder></form>
  580. <div class="d-flex flex-row color-fg-muted px-3 text-small color-bg-default search-feedback-prompt">
  581. <a target="_blank" href="https://docs.github.com/en/search-github/github-code-search/understanding-github-code-search-syntax" data-view-component="true" class="Link color-fg-accent text-normal ml-2">
  582. Search syntax tips
  583. </a> <div class="d-flex flex-1"></div>
  584. </div>
  585. </div>
  586. </div>
  587. </div>
  588. </modal-dialog></div>
  589. </div>
  590. <div data-action="click:qbsearch-input#retract" class="dark-backdrop position-fixed" hidden data-target="qbsearch-input.darkBackdrop"></div>
  591. <div class="color-fg-default">
  592. <div class="Overlay--hidden Overlay-backdrop--center" data-modal-dialog-overlay>
  593. <modal-dialog data-target="qbsearch-input.feedbackDialog" data-action="close:qbsearch-input#handleDialogClose cancel:qbsearch-input#handleDialogClose" role="dialog" id="feedback-dialog" aria-modal="true" aria-disabled="true" aria-labelledby="feedback-dialog-title" aria-describedby="feedback-dialog-description" data-view-component="true" class="Overlay Overlay-whenNarrow Overlay--size-medium Overlay--motion-scaleFade">
  594. <div data-view-component="true" class="Overlay-header">
  595. <div class="Overlay-headerContentWrap">
  596. <div class="Overlay-titleWrap">
  597. <h1 class="Overlay-title " id="feedback-dialog-title">
  598. Provide feedback
  599. </h1>
  600. </div>
  601. <div class="Overlay-actionWrap">
  602. <button data-close-dialog-id="feedback-dialog" aria-label="Close" type="button" data-view-component="true" class="close-button Overlay-closeButton"><svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-x">
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  724. <div id="start-of-content" class="show-on-focus"></div>
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  741. <include-fragment class="js-notification-shelf-include-fragment" data-base-src="https://github.com/notifications/beta/shelf"></include-fragment>
  742. <div
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For every patient i, this"," function returns the index of the first patient who died after i, after"," sorting the patients w.r.t. time of death."," Refer to the definition of"," Cox proportional hazards log likelihood for details: https://goo.gl/k4TsEM",""," Parameters"," ----------"," X: numpy.ndarray"," m*n matrix of expression data"," T: numpy.ndarray"," m sized vector of time of death"," O: numpy.ndarray"," m sized vector of observed status (1 - censoring status)",""," Returns"," -------"," X: numpy.ndarray"," m*n matrix of expression data sorted w.r.t time of death"," T: numpy.ndarray"," m sized sorted vector of time of death"," O: numpy.ndarray"," m sized vector of observed status sorted w.r.t time of death"," at_risk: numpy.ndarray"," m sized vector of starting index of risk groups"," Output Examples"," ------"," (array([[ 0. , 0. , 0. , ..., 0. ,"," -0.53219468, 0.12068921],"," [ 0. , 0. , 0. , ..., 0. ,"," 0.33331188, 0.12068921],"," [ 1. , 0. , 0. , ..., 0. ,"," 0.61579785, 0.12068921],"," ...,"," [ 1. , 0. , 0. , ..., 0. ,"," 0.18626446, 0.12068921],"," [ 0. , 1. , 0. , ..., 0. ,"," 1.80174805, 0.12068921],"," [ 1. , 0. , 0. , ..., 0. ,"," 0.08993093, 0.12068921]]), array([ 6., 33., 181., 279., 315., 327., 359., 705.,"," 734., 1322.]), array([ 0., 0., 0., 0., 0., 0., 0., 0., 0., 1.]), array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9], dtype=int32))"," \"\"\""," tmp = list(T)"," T = np.asarray(tmp).astype('float64')"," order = np.argsort(T)"," sorted_T = T[order]"," at_risk = np.asarray([list(sorted_T).index(x) for x in sorted_T]).astype('int32')"," T = np.asarray(sorted_T)"," O = O[order]"," X = X[order]"," return X, T, O, at_risk","","def activation(x,method):","\tif method=='relu':","\t\treturn tf.nn.relu(x)","\telif method=='sigmoid':","\t\treturn tf.nn.sigmoid(x)","\telif method=='tanh':","\t\treturn tf.nn.tanh(x)","\telse:","\t\tprint(\"Activation method can only be on of these, relu, sigmoid and tanh\")","\t\treturn False","","","def inference(features,hidden_nodes,activation_type,keep_prob,isTrain):"," \"\"\" Build the survival model for further inference"," Args:"," features: the survival co-variants data,"," hidden_nodes: a list, # of nodes in each hidden layer, eg: [20,30,20]"," activation_type: activation function, suggested default relu","\tkeep_prob: dropout keep_probability","\tisTrain: if or not training optimization process"," Returns:"," output: the output value of the neural network"," \"\"\""," def f_train(h,k_p):","\t #add dropout to training optimization process","\t return tf.nn.dropout(h,k_p)"," def f_nontrain(h):","\t #doesn't add dropout","\t return h"," pre_hidden_units=0 #keep previous layer nodes number"," for i,hidden_units in enumerate(hidden_nodes):"," layer_index=i+1"," if layer_index==1:"," with tf.name_scope(\"hidden\"+str(layer_index)):"," weights=tf.Variable(tf.truncated_normal([FEATURE_SIZE, hidden_units], dtype=tf.float32)/20,name=\"weights\") # divided by 20 to generate smaller ouptut at initial, otherwise exp(output) will be inf"," #biases1=tf.Variable(tf.zeros([hidden_units]),name=\"biases\")"," #hidden1=tf.nn.relu(tf.matmul(features,weights1)+biases1)","\t\thidden=activation(tf.matmul(features,weights),activation_type)"," #hidden=tf.nn.relu(tf.matmul(features,weights))","\t\thidden_dropout=tf.cond(isTrain,lambda: f_train(hidden,keep_prob),lambda: f_nontrain(hidden))"," pre_hidden_units=hidden_units"," else:"," with tf.name_scope(\"hidden\"+str(layer_index)):"," weights=tf.Variable(tf.truncated_normal([pre_hidden_units, hidden_units], dtype=tf.float32)/20,name=\"weights\") # divided by 20 to generate smaller ouptut at initial, otherwise exp(output) will be inf"," #biases1=tf.Variable(tf.zeros([hidden_units]),name=\"biases\")"," #hidden1=tf.nn.relu(tf.matmul(features,weights1)+biases1)","\t\thidden=activation(tf.matmul(hidden_dropout,weights),activation_type)","\t\t#if add_dropout:","\t #\t\thidden_dropout=tf.nn.dropout(hidden,keep_prob)","\t#\telse:","\t#\t\thidden_dropout=hidden","\t\t#hidden=tf.nn.relu(tf.matmul(hidden,weights))","\t\thidden_dropout=tf.cond(isTrain,lambda: f_train(hidden,keep_prob),lambda: f_nontrain(hidden))"," pre_hidden_units=hidden_units","",""," with tf.name_scope('output'):"," weights2=tf.Variable(tf.truncated_normal([hidden_units,NUM_CLASSES],dtype=tf.float32)/20,name=\"weights\")"," #biases2=tf.Variable(tf.zeros([NUM_CLASSES]),name='biases')"," #output=tf.matmul(hidden1,weights2)+biases2"," output=tf.matmul(hidden_dropout,weights2)",""," return output","","def inference_linear(features):"," #theata=tf.Variable(tf.truncated_normal([FEATURE_SIZE,1],dtype=tf.float32)/20,name=\"theta\")"," #keep the name scope the same as in NN (for group lasso and sparse_group_lasso weights filtering)"," with tf.name_scope(\"hidden1\"):","\tweights=tf.Variable(tf.truncated_normal([FEATURE_SIZE, 1], dtype=tf.float32)/20,name=\"weights\")"," output=tf.matmul(features,weights)"," #output=tf.matmul(features,theata)"," return output","","#def loss(inf_output,at_risk,censors,groups,batch_size,alpha,penaltyLambda):","# \"\"\" Calculate the loss based on observed survival data and the predicted ones.","#","# Args:","# inf_weights1: the weights1 of the first hidden layer from inference","# inf_output: the inference output","# at_risk: ","# censors: censor status of the patients ([batch_size])","# batch_size: number of samples/patients data used for each training/validation/testing","# groups: corresponding group id for each feature ([feature_size])","# Returns:","# loss","# \"\"\"","# groups_size=len(set(groups)) # number of groups","#","#","# partial_sum=tf.reverse(cumsum(tf.reverse(tf.exp(inf_output),axis=[-2]),batch_size),axis=[-2])+1","# psum_at_risk=tf.gather(partial_sum,tf.reshape(at_risk,[-1])) # at_risk out of boundary?","# log_at_risk=tf.log(tf.gather(partial_sum,tf.reshape(at_risk,[-1]))+1e-50)","# diff=tf.reshape(tf.subtract(inf_output,log_at_risk),[-1])*(1-censors) #Only use non-censored data for difference calculation","#","# all_variables=tf.get_collection(tf.GraphKeys.TRAINABLE_VARIABLES)","# all_weights=[x for x in all_variables if re.search(\"weights\",x.name)]","# weights1=[x for x in all_weights if re.search(\"hidden1/weights\",x.name)][0]","#","#","# # group lasso regularization for the input-hidden1 weights","# rg=0.0","# group_index=0","# for group_id in range(groups_size):","# this_group_mask=[i for i,x in enumerate(groups) if x== group_id]","# rg += tf.sqrt(tf.nn.l2_loss(tf.gather(weights1,tf.to_int64(this_group_mask))))","#","#","#","# loss = - (tf.reduce_sum(diff)) + alpha*penaltyLambda*rg+(1-alpha)*tf.reduce_sum(penaltyLambda*tf.abs(inf_weights1))","#","# return loss","","#def loss(inf_output,at_risk,censors,groups,batch_size,alpha,scale,reg_type=\"lasso\"):","# \"\"\" Calculate the loss based on observed survival data and the predicted ones.","#","# Args:","# inf_output: the inference output","# at_risk: #TODO","# censors: censor status of the patients ([batch_size])","# batch_size: number of samples/patients data used for each training/validation/testing","# groups: corresponding group id for each feature ([feature_size])","# alpha: adjust the proportion of group penalty","# scale: scale used for regularization adjust (float)","# Returns:","# loss","# \"\"\"","# groups_size=len(set(groups)) # number of groups","#","#","# #TODO: consider the situation of Tied times","# partial_sum=tf.reverse(cumsum(tf.reverse(tf.exp(inf_output),axis=[-2]),batch_size),axis=[-2])+1","# #psum_at_risk=tf.gather(partial_sum,tf.reshape(at_risk,[-1])) # at_risk out of boundary?","# log_at_risk=tf.log(tf.gather(partial_sum,tf.reshape(at_risk,[-1]))+1e-50)","# diff=tf.reshape(tf.subtract(inf_output,log_at_risk),[-1])*(1-censors) #Only use non-censored data for difference calculation","#","# if reg_type==\"lasso\":","# reg=lasso(scale)","# elif reg_type==\"l2\":","# reg=l2(scale)","# elif reg_type=='group_lasso':","# reg=group_lasso(alpha,scale,groups)","# elif reg_type=='sparse_group_lasso':","# reg=sparse_group_lasso(alpha,scale,groups)","#","# loss=-(tf.reduce_sum(diff))+reg","#","# return loss","","def loss(inf_output,censors,groups,batch_size,alpha,scale,delta,reg_type=\"lasso\"):"," \"\"\" Calculate the loss based on observed survival data and the predicted ones.",""," Args:"," inf_output: the inference output"," censors: censor status of the patients ([batch_size])"," batch_size: number of samples/patients data used for each training/validation/testing"," groups: corresponding group id for each feature ([feature_size])"," alpha: adjust the proportion of group penalty"," scale: scale used for regularization adjust (float)"," delta: a small value added in log transformed value to avoid log(0)"," Returns:"," loss (negative sum of log parital likelihood+regularizer)"," \"\"\""," #groups_size=len(set(groups)) # number of groups","",""," #TODO: consider the situation of Tied times"," hazard=tf.squeeze(tf.exp(inf_output)) # samples are ordered by dates in increasing way during batch fetching"," hazard_condition_sum=tf.reverse(tf.cumsum(tf.reverse(hazard,[0])),[0]) #for given i, get sum of theta_j where dates_j\u003e=dates_i"," log_sum=tf.log(hazard_condition_sum+delta)"," diff=tf.subtract(tf.squeeze(inf_output),log_sum)*(1-censors) # only consider events Ci==1",""," if reg_type==\"lasso\":"," reg=lasso(scale)"," elif reg_type==\"l2\":"," reg=l2(scale)"," elif reg_type=='group_lasso':"," reg=group_lasso(alpha,scale,groups)"," elif reg_type=='sparse_group_lasso':"," reg=sparse_group_lasso(alpha,scale,groups)"," elif reg_type=='none':"," reg=0",""," loss=-(tf.reduce_sum(diff))+reg",""," return loss","","def hazard(inf_output):"," \"\"\" Calculate the survival hazard value",""," Args:"," inf_output: the inference output"," Returns:"," \tGDP-CPH hazard"," \"\"\"",""," hazard=tf.squeeze(tf.exp(inf_output)) "," return hazard","","","#or l1","def lasso(scale):"," all_variables=tf.get_collection(tf.GraphKeys.TRAINABLE_VARIABLES)"," all_weights=[x for x in all_variables if re.search(\"weights\",x.name)]"," rg=0.0"," regularizer = tf.contrib.layers.l1_regularizer(scale=scale)"," rg=tf.contrib.layers.apply_regularization(regularizer, all_weights)"," return rg","","def l2(scale):"," all_variables=tf.get_collection(tf.GraphKeys.TRAINABLE_VARIABLES)"," all_weights=[x for x in all_variables if re.search(\"weights\",x.name)]"," regularizer = tf.contrib.layers.l2_regularizer(scale=scale)"," rg=tf.contrib.layers.apply_regularization(regularizer, all_weights)"," return rg","","def group_lasso(alpha,scale,groups):"," #groups_size=len(set(groups)) # number of groups"," all_variables=tf.get_collection(tf.GraphKeys.TRAINABLE_VARIABLES)"," all_weights=[x for x in all_variables if re.search(\"weights\",x.name)]"," weights1=[x for x in all_weights if re.search(\"hidden1/weights\",x.name)][0] #only the input-hidden1 weights were grouped"," weights_others=[x for x in all_weights if not re.search(\"hidden1/weights\",x.name)]",""," # group lasso regularization for the input-hidden1 weights"," regularizer = tf.contrib.layers.l2_regularizer(scale=scale)"," rg=0.0"," group_index=0"," for group_id in list(set(groups)):"," this_group_mask=[i for i,x in enumerate(groups) if x== group_id]"," pl=len(this_group_mask)"," rg+=math.sqrt(pl)*tf.sqrt(regularizer(tf.gather(weights1,tf.to_int64(this_group_mask))))"," #rg+=math.sqrt(pl)*tf.contrib.layers.l2_regularizer(tf.gather(weights1,tf.to_int64(this_group_mask)))"," #rg += tf.sqrt(tf.nn.l2_loss(tf.gather(weights1,tf.to_int64(this_group_mask))))"," regularizer2 = tf.contrib.layers.l1_regularizer(scale=scale)"," if(alpha==1):","\t#for the case of linear regression, and there are no other weights","\tpass"," else:","\trg=rg*alpha+(1-alpha)*tf.contrib.layers.apply_regularization(regularizer2, weights_others)"," return rg","","","def 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