DeepVISP (Deep learning for viral integration sites prediction)

  Visualization of the kernel-specific motifs of the first convolutional layer in DeepVISP and distribution of PWMs of each motif.

The visualizations are based on the benchmark data set. First, we need the output of the first convolutional layer given the DNA sequences. This output is called activations. You can think of a kernel as a position-weight matrix (PWM) and activations are the result of sliding with the kernel over an input sequence, one position at a time. The result is a vector of numbers and the position of the maximum activation shows to which subsequence the kernel is most similar. If the maximum activation is above a certain threshold we can extract the corresponding subsequence of the length of the kernel from the input starting at that position. If we do this for all input sequences we get a number of subsequences, all of the same length, and we can compute a PWM. In addition, we drew the heatmaps to show the distributions of the PWMs for each motif.

Motifs score. Motifs logo. Distribution of the PWMs.


Kernel 238
score = 0.032


Kernel 182
score = 0.032


Kernel 6
score = 0.022


Kernel 75
score = 0.022


Kernel 215
score = 0.022


Kernel 86
score = 0.021


Kernel 155
score = 0.021


Kernel 12
score = 0.021


Kernel 90
score = 0.020


Kernel 224
score = 0.020


Kernel 163
score = 0.019


Kernel 88
score = 0.018


Kernel 56
score = 0.018


Kernel 203
score = 0.018


Kernel 206
score = 0.018


Kernel 124
score = 0.018


Kernel 147
score = 0.017


Kernel 98
score = 0.017


Kernel 118
score = 0.017


Kernel 111
score = 0.017


Kernel 177
score = 0.017


Kernel 119
score = 0.017


Kernel 144
score = 0.016


Kernel 28
score = 0.016


Kernel 217
score = 0.016


Kernel 253
score = 0.016


Kernel 187
score = 0.016


Kernel 57
score = 0.015


Kernel 130
score = 0.015


Kernel 62
score = 0.014


Kernel 116
score = 0.014


Kernel 176
score = 0.014


Kernel 212
score = 0.014


Kernel 110
score = 0.014


Kernel 27
score = 0.014


Kernel 172
score = 0.014


Kernel 225
score = 0.014


Kernel 117
score = 0.014


Kernel 228
score = 0.014


Kernel 59
score = 0.014


Kernel 67
score = 0.014


Kernel 128
score = 0.013


Kernel 159
score = 0.013


Kernel 240
score = 0.013


Kernel 186
score = 0.013


Kernel 242
score = 0.013


Kernel 135
score = 0.013


Kernel 181
score = 0.013


Kernel 33
score = 0.012


Kernel 87
score = 0.012


Kernel 145
score = 0.012


Kernel 4
score = 0.012


Kernel 50
score = 0.012


Kernel 34
score = 0.012


Kernel 36
score = 0.012


Kernel 143
score = 0.012


Kernel 114
score = 0.012


Kernel 161
score = 0.012


Kernel 48
score = 0.012


Kernel 15
score = 0.011


Kernel 209
score = 0.011


Kernel 221
score = 0.011


Kernel 39
score = 0.011


Kernel 141
score = 0.011


Kernel 190
score = 0.010


Kernel 46
score = 0.010


Kernel 250
score = 0.010


Kernel 180
score = 0.010


Kernel 55
score = 0.010


Kernel 140
score = 0.010


Kernel 249
score = 0.010


Kernel 107
score = 0.010


Kernel 233
score = 0.010


Kernel 197
score = 0.009


Kernel 136
score = 0.009


Kernel 231
score = 0.009


Kernel 208
score = 0.009


Kernel 219
score = 0.009


Kernel 195
score = 0.009


Kernel 105
score = 0.009


Kernel 101
score = 0.009


Kernel 226
score = 0.009


Kernel 92
score = 0.009


Kernel 99
score = 0.009


Kernel 254
score = 0.009


Kernel 198
score = 0.009


Kernel 213
score = 0.009


Kernel 227
score = 0.009


Kernel 153
score = 0.009


Kernel 183
score = 0.009


Kernel 255
score = 0.009


Kernel 152
score = 0.009


Kernel 64
score = 0.009


Kernel 165
score = 0.009


Kernel 171
score = 0.008


Kernel 200
score = 0.008


Kernel 132
score = 0.008


Kernel 237
score = 0.008


Kernel 3
score = 0.008


Kernel 76
score = 0.008


Kernel 142
score = 0.008


Kernel 113
score = 0.008


Kernel 104
score = 0.008


Kernel 94
score = 0.008


Kernel 178
score = 0.007


Kernel 158
score = 0.007


Kernel 164
score = 0.007


Kernel 112
score = 0.007


Kernel 13
score = 0.007


Kernel 162
score = 0.007


Kernel 126
score = 0.007


Kernel 24
score = 0.007


Kernel 61
score = 0.007


Kernel 42
score = 0.007


Kernel 127
score = 0.007


Kernel 192
score = 0.007


Kernel 73
score = 0.007


Kernel 194
score = 0.007


Kernel 80
score = 0.007


Kernel 16
score = 0.007


Kernel 95
score = 0.007


Kernel 54
score = 0.006


Kernel 97
score = 0.006


Kernel 252
score = 0.006


Kernel 167
score = 0.006


Kernel 199
score = 0.006


Kernel 85
score = 0.006


Kernel 5
score = 0.006


Kernel 29
score = 0.006


Kernel 89
score = 0.006


Kernel 230
score = 0.006


Kernel 37
score = 0.006


Kernel 96
score = 0.006


Kernel 108
score = 0.006


Kernel 9
score = 0.006


Kernel 220
score = 0.006


Kernel 191
score = 0.006


Kernel 204
score = 0.006


Kernel 214
score = 0.006


Kernel 174
score = 0.006


Kernel 222
score = 0.006


Kernel 148
score = 0.006


Kernel 150
score = 0.006


Kernel 201
score = 0.006


Kernel 11
score = 0.006


Kernel 134
score = 0.006


Kernel 205
score = 0.005


Kernel 154
score = 0.005


Kernel 151
score = 0.005


Kernel 139
score = 0.005


Kernel 236
score = 0.005


Kernel 10
score = 0.005


Kernel 1
score = 0.005


Kernel 211
score = 0.005


Kernel 223
score = 0.005


Kernel 63
score = 0.005


Kernel 7
score = 0.005


Kernel 17
score = 0.005


Kernel 72
score = 0.005


Kernel 14
score = 0.005


Kernel 202
score = 0.005


Kernel 21
score = 0.005


Kernel 44
score = 0.005


Kernel 184
score = 0.005


Kernel 137
score = 0.005


Kernel 125
score = 0.005


Kernel 23
score = 0.005


Kernel 121
score = 0.004


Kernel 18
score = 0.004


Kernel 245
score = 0.004


Kernel 84
score = 0.004


Kernel 109
score = 0.004


Kernel 235
score = 0.004


Kernel 58
score = 0.004


Kernel 71
score = 0.004


Kernel 83
score = 0.004


Kernel 0
score = 0.004


Kernel 20
score = 0.004


Kernel 149
score = 0.004


Kernel 248
score = 0.004


Kernel 106
score = 0.004


Kernel 51
score = 0.004


Kernel 122
score = 0.004


Kernel 241
score = 0.004


Kernel 26
score = 0.004


Kernel 82
score = 0.004


Kernel 91
score = 0.004


Kernel 38
score = 0.003


Kernel 129
score = 0.003


Kernel 246
score = 0.003


Kernel 70
score = 0.003


Kernel 22
score = 0.003


Kernel 102
score = 0.003


Kernel 69
score = 0.003


Kernel 189
score = 0.003


Kernel 229
score = 0.003


Kernel 251
score = 0.003


Kernel 207
score = 0.003


Kernel 239
score = 0.003


Kernel 79
score = 0.003


Kernel 234
score = 0.003


Kernel 210
score = 0.003


Kernel 32
score = 0.003


Kernel 169
score = 0.003


Kernel 218
score = 0.003


Kernel 68
score = 0.002


Kernel 8
score = 0.002


Kernel 173
score = 0.002


Kernel 166
score = 0.002


Kernel 168
score = 0.002


Kernel 244
score = 0.002


Kernel 65
score = 0.002


Kernel 45
score = 0.002


Kernel 19
score = 0.002


Kernel 185
score = 0.002


Kernel 74
score = 0.002


Kernel 115
score = 0.002


Kernel 232
score = 0.002


Kernel 81
score = 0.002


Kernel 123
score = 0.002


Kernel 146
score = 0.002


Kernel 138
score = 0.002


Kernel 156
score = 0.002


Kernel 188
score = 0.001


Kernel 120
score = 0.001


Kernel 247
score = 0.001


Kernel 175
score = 0.001


Kernel 193
score = 0.001


Kernel 60
score = 0.001


Kernel 133
score = 0.001


Kernel 2
score = 0.001


Kernel 31
score = 0.001


Kernel 43
score = 0.001


Kernel 179
score = 0.001


Kernel 170
score = 0.001


Kernel 243
score = 0.001


Kernel 40
score = 0.001


Kernel 66
score = 0.001


Kernel 216
score = 0.001


Kernel 78
score = 0.001


Kernel 41
score = 0.001


Kernel 30
score = 0.001


Kernel 47
score = 0.001


Kernel 103
score = 0.001


Kernel 53
score = 0.001


Kernel 77
score = 0.001


Kernel 49
score = 0.000


Kernel 196
score = 0.000


Kernel 160
score = 0.000


Kernel 157
score = 0.000


Kernel 25
score = 0.000


Kernel 100
score = 0.000


Kernel 35
score = 0.000


Kernel 93
score = 0.000


Kernel 131
score = 0.000


Kernel 52
score = 0.000