-
Notifications
You must be signed in to change notification settings - Fork 0
/
felsenstein_test16.c
118 lines (101 loc) · 2.96 KB
/
felsenstein_test16.c
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
#include <stdint.h>
#include <stdlib.h>
#include <math.h>
#include <stdio.h>
#include <string.h>
#include "felsenstein_lin.h"
int main() {
int i = 0;
int j = 1;
int N = 16;
int L = 5;
uint8_t* msa = (uint8_t*) malloc(sizeof(u_int8_t)*N*L);
for(int i = 0; i < L; i++) {
for(int j = 0; j < N; j++) {
if (j < N / 2) {
msa[j*L + i] = 1;
} else {
msa[j*L + i] = 2;
}
}
}
c_float_t t1 = 0.2;
c_float_t phi1 = exp(-t1);
c_float_t t2 = 0.2;
c_float_t phi2 = exp(-t2);
Node* nodes = (Node*) malloc(sizeof(Node)*(2*N - 1));
for(int n = 0; n < N - 1; n++) {
nodes[n].seq_id = -n - 1;
nodes[n].left = nodes + 2*n + 1;
nodes[n].right = nodes + 2*n + 2;
nodes[n].phi_left = phi1;
nodes[n].phi_right = phi2;
}
for(int n = N - 1; n < 2*N - 1; n++) {
nodes[n].left = NULL;
nodes[n].right = NULL;
nodes[n].seq_id = n - N + 1;
}
c_float_t* x = (c_float_t*) malloc(sizeof(c_float_t)*(N_COL*A + A*A));
for(int idx = 0; idx < N_COL*A + A*A; idx++) {
x[idx] = (c_float_t)rand() / (c_float_t)RAND_MAX;
x[idx] = 0;
}
c_float_t* grad = (c_float_t*) malloc(sizeof(c_float_t)*(N_COL*A + A*A));
Node* root = &nodes[0];
Constants* consts = malloc(sizeof(Constants));
consts->phylo_tree = root;
consts->msa = msa;
consts->L = L;
consts->i = i;
consts->j = j;
initialize_constants(consts);
Buffer* buffer = malloc(sizeof(Buffer));
buffer->left = malloc(sizeof(NodeBuffer));
initialize_buffer(buffer->left, consts);
buffer->right = malloc(sizeof(NodeBuffer));
initialize_buffer(buffer->right, consts);
c_float_t fx = calculate_fx_grad(x, grad, consts, buffer);
printf("log fx= %e\n", log(fx));
c_float_t epsilon = 1e-9;
int pos = 0;
for(int l = 0; l < N_COL; l++) {
for(int c = 0; c < A; c++) {
calculate_fx_grad(x, grad, consts, buffer);
c_float_t target_grad = grad[pos];
x[pos] += epsilon;
c_float_t fx_fwd = calculate_fx_grad(x, grad, consts, buffer);
x[pos] -= 2*epsilon;
c_float_t fx_rev = calculate_fx_grad(x, grad, consts, buffer);
x[pos] += epsilon;
printf("v|i=%d|c=%d %e / %e\n", l, c, target_grad, (fx_fwd - fx_rev) / (2*epsilon));
pos++;
}
}
for(int c = 0; c < A; c++) {
for(int d = 0; d < A; d++) {
calculate_fx_grad(x, grad, consts, buffer);
c_float_t target_grad = grad[pos];
x[pos] += epsilon;
c_float_t fx_fwd = calculate_fx_grad(x, grad, consts, buffer);
x[pos] -= 2*epsilon;
c_float_t fx_rev = calculate_fx_grad(x, grad, consts, buffer);
x[pos] += epsilon;
printf("w|c=%d|d=%d %e / %e\n", c, d, target_grad, (fx_fwd - fx_rev) / (2*epsilon));
pos++;
}
}
// cleanup
free(x);
free(grad);
deinitialize_buffer(buffer->left);
deinitialize_buffer(buffer->right);
free(buffer->left);
free(buffer->right);
free(buffer);
deinitialize_constants(consts);
free(consts->msa);
free(consts->phylo_tree);
free(consts);
free(nodes);
}