-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathsimulation_clib.h
More file actions
521 lines (466 loc) · 26.7 KB
/
simulation_clib.h
File metadata and controls
521 lines (466 loc) · 26.7 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
void estimate_stable_expression(int NUM_NODES,int NUM_EDGES,\
int ITER_FOR_ODE,\
int TOTAL_EULER_STEPS,\
double EULER_STEP_SIZE,\
long double CONVERGENCE_PROXIMITY,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,\
const double *DNR_arrv,\
const int *node_type_arrv,\
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
const double *IC_arr,double *exp_arr,\
double *fX_arr);
void cluster_solutions(char *WORK_DIR, \
char *FNAME_STATES, char *FNAME_LIMITCYCLES, \
char *FNAME_SUMMARY,\
const int MODEL_NO,\
int NUM_NODES,int NUM_EDGES,\
int NUM_RANDOM_ICS,int ITER_FOR_ODE,\
double EULER_SIM_TIME,\
double EULER_STEP_SIZE,\
long double CONVERGENCE_PROXIMITY,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,\
const double *DNR_arrv,\
const int *node_type_arrv,\
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
double *fX_arr_norm,\
double EXP_arr[][NUM_NODES]);
int find_states(char *WORK_DIR, char *FNAME_STATES, const int MODEL_NO,\
int NUM_NODES, int NUM_RANDOM_ICS,\
long double CONVERGENCE_PROXIMITY,\
double *fX_arr_norm,\
double EXP_arr[][NUM_NODES],\
bool fX_arr_bool[NUM_RANDOM_ICS]);
int find_limitcycles(char *WORK_DIR, char *FNAME_LIMITCYCLES, \
const int MODEL_NO,\
int NUM_NODES,int NUM_EDGES,\
int NUM_RANDOM_ICS,int ITER_FOR_ODE,\
double EULER_SIM_TIME,\
double EULER_STEP_SIZE,\
long double CONVERGENCE_PROXIMITY,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,\
const double *DNR_arrv,\
const int *node_type_arrv,\
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
double *fX_arr_norm,\
double EXP_arr[][NUM_NODES],\
bool fX_arr_bool[NUM_RANDOM_ICS]);
void write_limitcycle(FILE *fh_LCs, int MODEL_NO, int NUM_NODES,\
int count_LC, int SIZE_OF_PERIOD, int SIZE_OF_LIMIT_CYCLE,\
double **LC_exp_arr);
void cal_euler_approximation(int NUM_NODES,int NUM_EDGES,\
int TOTAL_EULER_STEPS,double EULER_STEP_SIZE,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,const double *DNR_arrv,\
const int *node_type_arrv,\
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
double const *curr_exp_arrv,\
double *next_exp_arr,
double *fX_arr);
int detect_limitcycle(int NUM_NODES,int NUM_EDGES,\
int SIM_STEPS,double SIM_STEP_SIZE,\
long double CONVERGENCE_PROXIMITY,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,const double *DNR_arrv,\
const int *node_type_arrv,\
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
double *start_exp_arr,\
double *LC_start_exp_arr);
int cal_period(int NUM_NODES,\
int MAX_PERIODS,\
int count_min_exp,\
int *min_idx_arr,\
double min_exp_arr[][NUM_NODES],\
double *LC_start_exp_arr);
double cal_limitcycle(int NUM_NODES,int NUM_EDGES,\
int SIM_STEPS,double SIM_STEP_SIZE,\
long double CONVERGENCE_PROXIMITY,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,const double *DNR_arrv,\
const int *node_type_arrv,\
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
double *start_exp_arr,\
double **EXP_arr);
void cal_fX(int NUM_NODES,int NUM_EDGES,\
double EULER_STEP_SIZE,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,
const double *DNR_arrv,\
const int *node_type_arrv,\
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
double const *curr_exp_arr,\
double *fX_arr);
void cal_fX2(int NUM_NODES,int NUM_EDGES,\
double EULER_STEP_SIZE,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,
const double *DNR_arrv,\
const int *node_type_arrv,\
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
double const *curr_exp_arr,\
double *fX_arr);
void cal_ode(int NUM_NODES,int NUM_EDGES,\
int TOTAL_EULER_STEPS,\
double EULER_STEP_SIZE,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,const double *DNR_arrv,\
const int *node_type_arrv,\
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
double const *curr_exp_arrv);
void cal_EXPrange(int NUM_NODES,int NUM_EDGES,const double *MPR_arrv,\
const double *DNR_arrv,const int *edge_source_arrv,\
const int *edge_target_arrv,const int *edge_type_arrv,\
const double *FCH_arrv,double *minEXP_arr, double *maxEXP_arr);
void set_ICs(int NUM_NODES, const double *minEXP_arr, \
const double *maxEXP_arr, double *IC_arr);
double eval_shiftedHill_fn (double x, double x0, double nx, double lamda);
double randu(double minV, double maxV);
double cal_norm (double *curr_exp, int NUM_NODES);
double sum_delta (double *curr_exp, double *next_exp, int NUM_NODES);
bool is_element(int key, const int *arr, int size);
double **allocate_LCmemory(int LC_SIZE, int NUM_NODES);
void free_LCmemory(double ** EXP_arr, int LC_SIZE, int NUM_NODES);
void read_config(char *WORK_DIR, char* fname_cfg);
void print_config();
/********-------------- common stochastic simulation -------- ***********/
/*------------------------------- START --------------------------------*/
void write_state_expressions(FILE *fh_states, int MODEL_NO, \
int NUM_NODES, double *exp_arr);
void cal_fX_gnw(int NUM_NODES,int NUM_EDGES,\
double EULER_STEP_SIZE,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,
const double *DNR_arrv,\
const int *node_type_arrv,\
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
double const *curr_exp_arr,\
double *fX_arr,\
double *fX2_arr);
/********-------------- common stochastic simulation -------- ***********/
/*------------------------------- END --------------------------------*/
/*--- probing models using stochastic simulation with GNW constant noise --*/
/*------------------------------- START -----------------------------------*/
void simulate_network_cnoise_gnw(char *WORK_DIR,\
char *FNAME_STATES, \
char *FNAME_LIMITCYCLES, \
char *FNAME_SUMMARY, \
const int MODEL_NO,\
int NUM_NODES,\
int NUM_EDGES,\
int NUM_RANDOM_ICS,\
int ITER_FOR_ODE,\
double EULER_SIM_TIME,\
double EULER_STEP_SIZE,\
long double CONVERGENCE_PROXIMITY,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,\
const double *DNR_arrv,\
const int *node_type_arrv,\
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
double *EXP_dict_arrv);
void estimate_stable_expression_cnoise_gnw(int NUM_NODES,int NUM_EDGES,\
int ITER_FOR_ODE,int TOTAL_EULER_STEPS,\
double EULER_STEP_SIZE,\
long double CONVERGENCE_PROXIMITY,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,\
const double *DNR_arrv,\
const int *node_type_arrv,
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
const double *IC_arr, double *exp_arr,\
double *fX_arr,\
double NOISE);
void cal_euler_approximation_cnoise_gnw(int NUM_NODES,int NUM_EDGES,\
int TOTAL_EULER_STEPS,double EULER_STEP_SIZE,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,\
const double *DNR_arrv,\
const int *node_type_arrv,\
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
double const *curr_exp_arrv,\
double *next_exp_arr,\
double *fX_arr,\
double NOISE);
/*--- probing models using stochastic simulation with GNW constant noise --*/
/*------------------------------- END ----------------------------------*/
/********----- stochastic simulation with constant noise ---- ***********/
/*------------------------------- START --------------------------------*/
void find_solutions_stochastic(char *WORK_DIR, const int MODEL_NO,\
int NUM_NODES,int NUM_EDGES,\
int NUM_RANDOM_ICS,int ITER_FOR_ODE,\
double EULER_SIM_TIME,\
double EULER_STEP_SIZE,\
long double CONVERGENCE_PROXIMITY,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,\
const double *DNR_arrv,\
const int *node_type_arrv,\
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
double *EXP_dict_arrv,\
double *NOISE_strength,\
double *NOISE_strength_shot,\
double NOISE, double NOISE_SHOT);
void estimate_stable_expression_stochastic(int NUM_NODES,int NUM_EDGES,\
int ITER_FOR_ODE,int TOTAL_EULER_STEPS,\
double EULER_STEP_SIZE,\
long double CONVERGENCE_PROXIMITY,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,\
const double *DNR_arrv,\
const int *node_type_arrv,
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
const double *IC_arr, \
double *exp_arr,\
double *fX_arr,\
double *NOISE_strength,\
double *NOISE_strength_shot,\
double NOISE,\
double NOISE_SHOT);
void cal_euler_approximation_stochastic (int NUM_NODES,\
int NUM_EDGES,\
int TOTAL_EULER_STEPS,\
double EULER_STEP_SIZE,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,\
const double *DNR_arrv,\
const int *node_type_arrv,\
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
double const *curr_exp_arrv,\
double *next_exp_arr,\
double *fX_arr,\
double *NOISE_strength,\
double *NOISE_strength_shot,\
double NOISE, double NOISE_SHOT );
/********----- stochastic simulation with constant noise ---- ***********/
/*------------------------------- END --------------------------------*/
/********----- stochastic simulation with annealing ---- *****************/
/*************------------START-------------****************************/
void estimate_stable_expression_stochastic_anneal_network(\
char *FNAME_STATES, \
const int MODEL_NO,\
int NUM_NODES,int NUM_EDGES,\
int ITER_FOR_ODE,int TOTAL_EULER_STEPS,\
double EULER_STEP_SIZE,\
long double CONVERGENCE_PROXIMITY,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,\
const double *DNR_arrv,\
const int *node_type_arrv,
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
const double *IC_arr, double *exp_arr,\
double *fX_arr,\
double *NOISE_strength,\
double *NOISE_strength_shot,\
double NOISE, double NOISE_SHOT,\
double SCALING);
void find_solutions_stochastic_annealing(char *WORK_DIR, const int MODEL_NO,\
int NUM_NODES,int NUM_EDGES,\
int NUM_RANDOM_ICS,int ITER_FOR_ODE,\
double EULER_SIM_TIME,\
double EULER_STEP_SIZE,\
long double CONVERGENCE_PROXIMITY,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,\
const double *DNR_arrv,\
const int *node_type_arrv,\
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
double *EXP_dict_arrv,\
double *NOISE_strength,\
double *NOISE_strength_shot,\
double NOISE, double NOISE_SHOT,\
double SCALING);
void estimate_stable_expression_stochastic_annealing (const int MODEL_NO,\
int NUM_NODES,int NUM_EDGES,\
int ITER_FOR_ODE,\
int TOTAL_EULER_STEPS,\
double EULER_STEP_SIZE,\
long double CONVERGENCE_PROXIMITY,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,\
const double *DNR_arrv,\
const int *node_type_arrv,
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
const double *IC_arr, \
double *exp_arr,\
double *fX_arr,\
double *NOISE_strength,\
double *NOISE_strength_shot,\
double NOISE, double NOISE_SHOT,\
double SCALING);
void cal_rk_approximation(int NUM_NODES,int NUM_EDGES,\
double RK_TOLERANCE,\
double *ptr_TOTAL_TIME,\
double *ptr_RK_STEP_SIZE,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,const double *DNR_arrv,\
const int *node_type_arrv,\
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
double const *curr_exp_arrv,\
double *next_exp_arr,double *fX_arr);
/********----- stochastic simulation with annealing ---- *****************/
/*************------------END-------------*****************************/
/*** functions for stochastic annealing with GeneNetworkWeaver(GNW) ****/
/*************------------START-------------****************************/
void stochastic_anneal_network_gnw(char *WORK_DIR,
char *FNAME_STATES, \
char *FNAME_LIMITCYCLES, \
char *FNAME_SUMMARY, \
const int MODEL_NO,\
int NUM_NODES,int NUM_EDGES,\
int NUM_RANDOM_ICS,int ITER_FOR_ODE,\
double EULER_SIM_TIME,\
double EULER_STEP_SIZE,\
long double CONVERGENCE_PROXIMITY,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,\
const double *DNR_arrv,\
const int *node_type_arrv,\
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
double *EXP_dict_arrv,\
double NOISE, double SCALING);
void estimate_stable_expression_stochastic_anneal_network_gnw(\
char *FNAME_STATES, \
const int MODEL_NO,\
int NUM_NODES,int NUM_EDGES,\
int ITER_FOR_ODE,int TOTAL_EULER_STEPS,\
double EULER_STEP_SIZE,\
long double CONVERGENCE_PROXIMITY,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,\
const double *DNR_arrv,\
const int *node_type_arrv,
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
const double *IC_arr, double *exp_arr,\
double *fX_arr,\
double NOISE, \
double SCALING);
void cal_euler_approximation_stochastic_gnw (int NUM_NODES,int NUM_EDGES,\
int TOTAL_EULER_STEPS,double EULER_STEP_SIZE,\
double TRANS_RATE_FACTOR,\
const double *MPR_arrv,\
const double *DNR_arrv,\
const int *node_type_arrv,\
const int *edge_source_arrv,\
const int *edge_target_arrv,\
const int *edge_type_arrv,\
const double *TSH_arrv,\
const int *HCO_arrv,\
const double *FCH_arrv,\
double const *curr_exp_arrv,\
double *next_exp_arr,\
double *fX_arr,\
double NOISE);
/*****----- functions for stochastic annealing with gnew ----- ********/
/*************------------END -------------*****************************/