The.Algorithm.Design.Manual.Springer-Verlag.1998
The.Algorithm.Design.Manual.Springer-Verlag.1998 The.Algorithm.Design.Manual.Springer-Verlag.1998
Genetic Algorithms Algorithms Mon Jun 2 23:33:50 EDT 1997 file:///E|/BOOK/BOOK3/NODE98.HTM (2 of 2) [19/1/2003 1:29:38]
War Story: Annealing Arrays Next: Parallel Algorithms Up: Combinatorial Search and Heuristic Previous: Genetic Algorithms War Story: Annealing Arrays The war story of Section reported how we used advanced data structures to simulate a new method for sequencing DNA. Our method, interactive sequencing by hybridization (SBH), involved building arrays of specific oligonucleotides on demand. Although the simulation results were very promising to us, most biologists we encountered were suspicious. They needed to see our technique proven in the lab before they would take it seriously. But we got lucky. A biochemist at Oxford University, got interested in our technique, and moreover he had in his laboratory the equipment we needed to test it out. The Southern Array Maker [Sou96], manufactured by Beckman Instruments, could prepare discrete oligonucleotide sequences in 64 parallel rows across a polypropylene substrate. The device constructs arrays by appending single characters to each cell along specific rows and columns of arrays. Figure shows how to construct an array of all purine (A or G) 4-mers by building the prefixes along rows and the suffixes along columns. This technology provided an ideal environment for testing the feasibility of interactive SBH in a laboratory, because with proper programming it gave an inexpensive way to fabricate a wide variety of oligonucleotide arrays on demand. Figure: A prefix-suffix array of all purine 4-mers. But we had to provide the proper programming. Fabricating complicated arrays requires solving a difficult combinatorial problem. We were given as input a set S of n strings (representing oligonucleotides) to fabricate an array (where m=64 on the Southern apparatus). We had to produce a schedule of row and column commands to realize the set of strings S. We proved that the problem of designing dense arrays was NP-complete, but that didn't really matter. My student Ricky Bradley and I had to solve it anyway. file:///E|/BOOK/BOOK3/NODE99.HTM (1 of 4) [19/1/2003 1:29:40]
- Page 243 and 244: Modeling Graph Problems good line s
- Page 245 and 246: Minimum Spanning Trees ● Prim's A
- Page 247 and 248: Prim's Algorithm inserted edge (x,y
- Page 249 and 250: Kruskal's Algorithm a tree of weigh
- Page 251 and 252: Dijkstra's Algorithm Next: All-Pair
- Page 253 and 254: All-Pairs Shortest Path Next: War S
- Page 255 and 256: War Story: Nothing but Nets Next: W
- Page 257 and 258: War Story: Nothing but Nets ``You a
- Page 259 and 260: War Story: Dialing for Documents Ne
- Page 261 and 262: War Story: Dialing for Documents If
- Page 263 and 264: War Story: Dialing for Documents CO
- Page 265 and 266: Exercises Next: Implementation Chal
- Page 267 and 268: Exercises Prove the statement or gi
- Page 269 and 270: Backtracking report it. kth element
- Page 271 and 272: Constructing All Subsets Next: Cons
- Page 273 and 274: Constructing All Paths in a Graph N
- Page 275 and 276: Search Pruning Next: Bandwidth Mini
- Page 277 and 278: Bandwidth Minimization immediately
- Page 279 and 280: War Story: Covering Chessboards Nex
- Page 281 and 282: War Story: Covering Chessboards att
- Page 283 and 284: Heuristic Methods Mon Jun 2 23:33:5
- Page 285 and 286: Simulated Annealing Return S then u
- Page 287 and 288: Traveling Salesman Problem Next: Ma
- Page 289 and 290: Independent Set Next: Circuit Board
- Page 291 and 292: Neural Networks Next: Genetic Algor
- Page 293: Genetic Algorithms Next: War Story:
- Page 297 and 298: War Story: Annealing Arrays optimal
- Page 299 and 300: Parallel Algorithms Next: War Story
- Page 301 and 302: War Story: Going Nowhere Fast Next:
- Page 303 and 304: Exercises Next: Implementation Chal
- Page 305 and 306: Problems and Reductions Next: Simpl
- Page 307 and 308: Simple Reductions Next: Hamiltonian
- Page 309 and 310: Hamiltonian Cycles Next: Independen
- Page 311 and 312: Independent Set and Vertex Cover pr
- Page 313 and 314: Clique and Independent Set These la
- Page 315 and 316: Satisfiability Mon Jun 2 23:33:50 E
- Page 317 and 318: The Theory of NP-Completeness Next:
- Page 319 and 320: 3-Satisfiability where for , , , an
- Page 321 and 322: Integer Programming Next: Vertex Co
- Page 323 and 324: Integer Programming possible IP ins
- Page 325 and 326: Vertex Cover reduction for the 3-SA
- Page 327 and 328: Other NP-Complete Problems hard. Th
- Page 329 and 330: The Art of Proving Hardness easiest
- Page 331 and 332: War Story: Hard Against the Clock N
- Page 333 and 334: War Story: Hard Against the Clock I
- Page 335 and 336: Approximation Algorithms Next: Appr
- Page 337 and 338: Approximating Vertex Cover Next: Th
- Page 339 and 340: The Euclidean Traveling Salesman Ne
- Page 341 and 342: The Euclidean Traveling Salesman Ne
- Page 343 and 344: Exercises 1. Prove that the low deg
Genetic <strong>Algorithm</strong>s<br />
<strong>Algorithm</strong>s<br />
Mon Jun 2 23:33:50 EDT 1997<br />
file:///E|/BOOK/BOOK3/NODE98.HTM (2 of 2) [19/1/2003 1:29:38]