Structure Optimization for Large Gene Networks Based on Greedy Strategy

<div>An example of the second step of our method, in which the Hubs of the pruned network are identified and relevant edges are added to them. Note that the relationships are added if their weight exceeds the <span class="nowrap"><svg height="14.8173pt" id="M3" style="vertical-align:-5.52897pt" version="1.1" viewbox="-0.0498162 -9.28833 20.9394 14.8173" width="20.9394pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g transform="matrix(.013,0,0,-0.013,0,0)"><path d="M620 675H597C578 656 570 650 541 650H144C112 650 104 653 94 675H72C59 618 42 552 23 493L53 491C71 534 88 564 105 585C124 608 144 615 238 615H290L197 121C182 40 174 34 88 28L82 0H361L367 28C275 34 266 38 281 121L374 615H441C522 615 543 608 553 583C562 560 566 531 565 493L597 494C603 551 612 629 620 675Z" id="g113-85"></path></g><g transform="matrix(.013,0,0,-0.013,8.285,0)"><path d="M499 88L487 113C459 86 422 65 413 65C403 65 403 74 409 98L461 318C487 426 460 448 431 448C408 448 383 441 352 424C305 398 223 344 157 257H155L243 674C249 702 249 712 240 712C227 712 170 680 87 673L82 648H117C155 648 162 644 150 590L23 -4L30 -12C55 -4 81 3 105 8C113 53 131 150 143 187C199 281 323 387 372 387C390 387 393 369 380 311L328 86C313 19 319 -12 347 -12C379 -12 442 24 499 88Z" id="g113-105"></path></g><g transform="matrix(.0091,0,0,-0.0091,14.928,3.132)"><path d="M563 583C563 664 501 710 433 710C381 710 334 692 285 648C212 582 178 506 149 350L74 -56C49 -190 36 -222 24 -226L30 -257C52 -256 95 -247 121 -229C131 -222 134 -206 165 -21L219 303C254 510 296 665 397 665C447 665 481 626 481 572C481 512 446 457 390 420C367 405 351 400 323 397L302 349C398 338 466 285 466 197C466 117 419 45 306 45C268 45 224 59 198 74L186 50C197 20 228 -14 274 -14C318 -14 359 3 401 26C478 68 554 144 554 225C554 322 493 367 412 396C490 446 563 500 563 583Z" id="g50-224"></path></g></svg>;</span> in this example, <span class="nowrap"><svg height="14.8173pt" id="M4" style="vertical-align:-5.52897pt" version="1.1" viewbox="-0.0498162 -9.28833 51.3646 14.8173" width="51.3646pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g transform="matrix(.013,0,0,-0.013,0,0)"><path d="M620 675H597C578 656 570 650 541 650H144C112 650 104 653 94 675H72C59 618 42 552 23 493L53 491C71 534 88 564 105 585C124 608 144 615 238 615H290L197 121C182 40 174 34 88 28L82 0H361L367 28C275 34 266 38 281 121L374 615H441C522 615 543 608 553 583C562 560 566 531 565 493L597 494C603 551 612 629 620 675Z" id="g113-85"></path></g><g transform="matrix(.013,0,0,-0.013,8.285,0)"><path d="M499 88L487 113C459 86 422 65 413 65C403 65 403 74 409 98L461 318C487 426 460 448 431 448C408 448 383 441 352 424C305 398 223 344 157 257H155L243 674C249 702 249 712 240 712C227 712 170 680 87 673L82 648H117C155 648 162 644 150 590L23 -4L30 -12C55 -4 81 3 105 8C113 53 131 150 143 187C199 281 323 387 372 387C390 387 393 369 380 311L328 86C313 19 319 -12 347 -12C379 -12 442 24 499 88Z" id="g113-105"></path></g><g transform="matrix(.0091,0,0,-0.0091,14.928,3.132)"><path d="M563 583C563 664 501 710 433 710C381 710 334 692 285 648C212 582 178 506 149 350L74 -56C49 -190 36 -222 24 -226L30 -257C52 -256 95 -247 121 -229C131 -222 134 -206 165 -21L219 303C254 510 296 665 397 665C447 665 481 626 481 572C481 512 446 457 390 420C367 405 351 400 323 397L302 349C398 338 466 285 466 197C466 117 419 45 306 45C268 45 224 59 198 74L186 50C197 20 228 -14 274 -14C318 -14 359 3 401 26C478 68 554 144 554 225C554 322 493 367 412 396C490 446 563 500 563 583Z" id="g50-224"></path></g><g transform="matrix(.013,0,0,-0.013,24.42,0)"><path d="M531 285V335L57 550V494L473 310L57 127V71L531 285ZM531 -40V10H57V-40H531Z" id="g117-94"></path></g><g transform="matrix(.013,0,0,-0.013,35.683,0)"><path d="M241 635C89 635 35 457 35 312C35 153 89 -12 240 -12C390 -12 443 166 443 312C443 466 390 635 241 635ZM238 602C329 602 354 454 354 312C354 172 330 22 240 22C152 22 124 173 124 313S148 602 238 602Z" id="g113-49"></path></g><g transform="matrix(.013,0,0,-0.013,41.923,0)"><path d="M113 -12C146 -12 170 11 170 46C170 78 146 103 114 103S58 78 58 46C58 11 82 -12 113 -12Z" id="g113-47"></path></g><g transform="matrix(.013,0,0,-0.013,44.887,0)"><path d="M447 623H65C61 580 56 530 47 475H76C100 541 106 550 172 550H388C308 376 196 170 91 -1L98 -12L172 -2C268 204 360 408 455 611L447 623Z" id="g113-56"></path></g></svg>.</span></div>

Computational and Mathematical Methods in Medicine

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Figure 3

Figure 3: Structure Optimization for Large Gene Networks Based on Greedy Strategy 