|
33 | 33 | "url = \"https://dl.dropbox.com/s/lnly9gw8pb1xhir/overfitting.zip\"\n",
|
34 | 34 | "\n",
|
35 | 35 | "\n",
|
36 |
| - "results = requests.get(url);" |
| 36 | + "results = requests.get(url)" |
37 | 37 | ],
|
38 | 38 | "language": "python",
|
39 | 39 | "metadata": {},
|
|
46 | 46 | "input": [
|
47 | 47 | "import StringIO\n",
|
48 | 48 | "z = zipfile.ZipFile(StringIO.StringIO(results.content))\n",
|
49 |
| - "# z.extractall();;" |
| 49 | + "# z.extractall()" |
50 | 50 | ],
|
51 | 51 | "language": "python",
|
52 | 52 | "metadata": {},
|
|
57 | 57 | "cell_type": "code",
|
58 | 58 | "collapsed": false,
|
59 | 59 | "input": [
|
60 |
| - "z.extractall();" |
| 60 | + "z.extractall()" |
61 | 61 | ],
|
62 | 62 | "language": "python",
|
63 | 63 | "metadata": {},
|
|
68 | 68 | "cell_type": "code",
|
69 | 69 | "collapsed": false,
|
70 | 70 | "input": [
|
71 |
| - "z.namelist();" |
| 71 | + "z.namelist()" |
72 | 72 | ],
|
73 | 73 | "language": "python",
|
74 | 74 | "metadata": {},
|
|
88 | 88 | "collapsed": false,
|
89 | 89 | "input": [
|
90 | 90 | "d = z.open('overfitting.csv')\n",
|
91 |
| - "d.readline();" |
| 91 | + "d.readline()" |
92 | 92 | ],
|
93 | 93 | "language": "python",
|
94 | 94 | "metadata": {},
|
|
107 | 107 | "cell_type": "code",
|
108 | 108 | "collapsed": false,
|
109 | 109 | "input": [
|
110 |
| - "import numpy as np;" |
| 110 | + "import numpy as np" |
111 | 111 | ],
|
112 | 112 | "language": "python",
|
113 | 113 | "metadata": {},
|
|
118 | 118 | "cell_type": "code",
|
119 | 119 | "collapsed": false,
|
120 | 120 | "input": [
|
121 |
| - "M = np.fromstring(d.read(), sep=\",\");" |
| 121 | + "M = np.fromstring(d.read(), sep=\",\")" |
122 | 122 | ],
|
123 | 123 | "language": "python",
|
124 | 124 | "metadata": {},
|
|
129 | 129 | "cell_type": "code",
|
130 | 130 | "collapsed": false,
|
131 | 131 | "input": [
|
132 |
| - "len(d.read());" |
| 132 | + "len(d.read())" |
133 | 133 | ],
|
134 | 134 | "language": "python",
|
135 | 135 | "metadata": {},
|
|
167 | 167 | "cell_type": "code",
|
168 | 168 | "collapsed": false,
|
169 | 169 | "input": [
|
170 |
| - "data = np.loadtxt(\"overfitting.csv\", delimiter=\",\", skiprows=1);" |
| 170 | + "data = np.loadtxt(\"overfitting.csv\", delimiter=\",\", skiprows=1)" |
171 | 171 | ],
|
172 | 172 | "language": "python",
|
173 | 173 | "metadata": {},
|
|
193 | 193 | "\n",
|
194 | 194 | "\"\"\"\n",
|
195 | 195 | "\n",
|
196 |
| - "data.shape;" |
| 196 | + "data.shape" |
197 | 197 | ],
|
198 | 198 | "language": "python",
|
199 | 199 | "metadata": {},
|
|
242 | 242 | "testing_labels = data[ix_testing, 2]\n",
|
243 | 243 | "\n",
|
244 | 244 | "print \"training:\", training_data.shape, training_labels.shape\n",
|
245 |
| - "print \"testing: \", testing_data.shape, testing_labels.shape;" |
| 245 | + "print \"testing: \", testing_data.shape, testing_labels.shape" |
246 | 246 | ],
|
247 | 247 | "language": "python",
|
248 | 248 | "metadata": {},
|
|
278 | 278 | "cell_type": "code",
|
279 | 279 | "collapsed": false,
|
280 | 280 | "input": [
|
281 |
| - "figsize(12, 4);" |
| 281 | + "figsize(12, 4)" |
282 | 282 | ],
|
283 | 283 | "language": "python",
|
284 | 284 | "metadata": {},
|
|
290 | 290 | "collapsed": false,
|
291 | 291 | "input": [
|
292 | 292 | "hist(training_data.flatten())\n",
|
293 |
| - "print training_data.shape[0] * training_data.shape[1];" |
| 293 | + "print training_data.shape[0] * training_data.shape[1]" |
294 | 294 | ],
|
295 | 295 | "language": "python",
|
296 | 296 | "metadata": {},
|
|
322 | 322 | "input": [
|
323 | 323 | "import pymc as pm\n",
|
324 | 324 | "\n",
|
325 |
| - "to_include = pm.Bernoulli(\"to_include\", 0.5, size=200);" |
| 325 | + "to_include = pm.Bernoulli(\"to_include\", 0.5, size=200)" |
326 | 326 | ],
|
327 | 327 | "language": "python",
|
328 | 328 | "metadata": {},
|
|
333 | 333 | "cell_type": "code",
|
334 | 334 | "collapsed": false,
|
335 | 335 | "input": [
|
336 |
| - "coef = pm.Uniform(\"coefs\", 0, 1, size=200);" |
| 336 | + "coef = pm.Uniform(\"coefs\", 0, 1, size=200)" |
337 | 337 | ],
|
338 | 338 | "language": "python",
|
339 | 339 | "metadata": {},
|
|
347 | 347 | "@pm.deterministic\n",
|
348 | 348 | "def Z(coef=coef, to_include=to_include, data=training_data):\n",
|
349 | 349 | " ym = np.dot(to_include * training_data, coef)\n",
|
350 |
| - " return ym - ym.mean();" |
| 350 | + " return ym - ym.mean()" |
351 | 351 | ],
|
352 | 352 | "language": "python",
|
353 | 353 | "metadata": {},
|
|
360 | 360 | "input": [
|
361 | 361 | "@pm.deterministic\n",
|
362 | 362 | "def T(z=Z):\n",
|
363 |
| - " return 0.45 * (np.sign(z) + 1.1);" |
| 363 | + " return 0.45 * (np.sign(z) + 1.1)" |
364 | 364 | ],
|
365 | 365 | "language": "python",
|
366 | 366 | "metadata": {},
|
|
375 | 375 | "\n",
|
376 | 376 | "model = pm.Model([to_include, coef, Z, T, obs])\n",
|
377 | 377 | "map_ = pm.MAP(model)\n",
|
378 |
| - "map_.fit();" |
| 378 | + "map_.fit()" |
379 | 379 | ],
|
380 | 380 | "language": "python",
|
381 | 381 | "metadata": {},
|
|
394 | 394 | "cell_type": "code",
|
395 | 395 | "collapsed": false,
|
396 | 396 | "input": [
|
397 |
| - "mcmc = pm.MCMC(model);" |
| 397 | + "mcmc = pm.MCMC(model)" |
398 | 398 | ],
|
399 | 399 | "language": "python",
|
400 | 400 | "metadata": {},
|
|
405 | 405 | "cell_type": "code",
|
406 | 406 | "collapsed": false,
|
407 | 407 | "input": [
|
408 |
| - "mcmc.sample(100000, 90000, 1);" |
| 408 | + "mcmc.sample(100000, 90000, 1)" |
409 | 409 | ],
|
410 | 410 | "language": "python",
|
411 | 411 | "metadata": {},
|
|
432 | 432 | "cell_type": "code",
|
433 | 433 | "collapsed": false,
|
434 | 434 | "input": [
|
435 |
| - "(np.round(T.value) == training_labels).mean();" |
| 435 | + "(np.round(T.value) == training_labels).mean()" |
436 | 436 | ],
|
437 | 437 | "language": "python",
|
438 | 438 | "metadata": {},
|
|
452 | 452 | "collapsed": false,
|
453 | 453 | "input": [
|
454 | 454 | "t_trace = mcmc.trace(\"T\")[:]\n",
|
455 |
| - "(np.round(t_trace[-500:-400, :]).mean(axis=0) == training_labels).mean();" |
| 455 | + "(np.round(t_trace[-500:-400, :]).mean(axis=0) == training_labels).mean()" |
456 | 456 | ],
|
457 | 457 | "language": "python",
|
458 | 458 | "metadata": {},
|
|
471 | 471 | "cell_type": "code",
|
472 | 472 | "collapsed": false,
|
473 | 473 | "input": [
|
474 |
| - "t_mean = np.round(t_trace).mean(axis=1);" |
| 474 | + "t_mean = np.round(t_trace).mean(axis=1)" |
475 | 475 | ],
|
476 | 476 | "language": "python",
|
477 | 477 | "metadata": {},
|
|
483 | 483 | "collapsed": false,
|
484 | 484 | "input": [
|
485 | 485 | "imshow(t_trace[-10000:, :], aspect=\"auto\")\n",
|
486 |
| - "colorbar();" |
| 486 | + "colorbar()" |
487 | 487 | ],
|
488 | 488 | "language": "python",
|
489 | 489 | "metadata": {},
|
|
508 | 508 | "input": [
|
509 | 509 | "figsize(23, 8)\n",
|
510 | 510 | "coef_trace = mcmc.trace(\"coefs\")[:]\n",
|
511 |
| - "imshow(coef_trace[-10000:, :], aspect=\"auto\", cmap=pyplot.cm.RdBu, interpolation=\"none\");" |
| 511 | + "imshow(coef_trace[-10000:, :], aspect=\"auto\", cmap=pyplot.cm.RdBu, interpolation=\"none\")" |
512 | 512 | ],
|
513 | 513 | "language": "python",
|
514 | 514 | "metadata": {},
|
|
531 | 531 | "cell_type": "code",
|
532 | 532 | "collapsed": false,
|
533 | 533 | "input": [
|
534 |
| - "include_trace = mcmc.trace(\"to_include\")[:];" |
| 534 | + "include_trace = mcmc.trace(\"to_include\")[:]" |
535 | 535 | ],
|
536 | 536 | "language": "python",
|
537 | 537 | "metadata": {},
|
|
543 | 543 | "collapsed": false,
|
544 | 544 | "input": [
|
545 | 545 | "figsize(23, 8)\n",
|
546 |
| - "imshow(include_trace[-10000:, :], aspect=\"auto\", interpolation=\"none\");" |
| 546 | + "imshow(include_trace[-10000:, :], aspect=\"auto\", interpolation=\"none\")" |
547 | 547 | ],
|
548 | 548 | "language": "python",
|
549 | 549 | "metadata": {},
|
|
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