STRIDE | Species Tree Root Inference from Gene Duplication Events | Genomics library

import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
import torchvision
from PIL import Image
import matplotlib.pyplot as plt

class Model_Down(nn.Module):
    """
    Convolutional (Downsampling) Blocks.

    nd = Number of Filters
    kd = Kernel size

    """
    def __init__(self,in_channels, nd = 128, kd = 3, padding = 1, stride = 2):
        super(Model_Down,self).__init__()
        self.padder = nn.ReflectionPad2d(padding)
        self.conv1 = nn.Conv2d(in_channels = in_channels, out_channels = nd, kernel_size = kd, stride = stride)
        self.bn1 = nn.BatchNorm2d(nd)

        self.conv2 = nn.Conv2d(in_channels = nd, out_channels = nd, kernel_size = kd, stride = 1)
        self.bn2 = nn.BatchNorm2d(nd)

        self.relu = nn.LeakyReLU()

    def forward(self, x):
        x = self.padder(x)
        x = self.conv1(x)
        x = self.bn1(x)
        x = self.relu(x)
        x = self.padder(x)
        x = self.conv2(x)
        x = self.bn2(x)
        x = self.relu(x)
        return x

import torch
import torch.nn as nn
import torch.nn.functional as F


class double_conv(nn.Module):
    '''(conv => BN => ReLU) * 2'''
    def __init__(self, in_ch, out_ch):
        super(double_conv, self).__init__()
        self.conv = nn.Sequential(
            nn.Conv2d(in_ch, out_ch, 3, padding=1),
            nn.BatchNorm2d(out_ch),
            nn.ReLU(inplace=True),
            nn.Conv2d(out_ch, out_ch, 3, padding=1),
            nn.BatchNorm2d(out_ch),
            nn.ReLU(inplace=True)
        )

    def forward(self, x):
        x = self.conv(x)
        return x


class inconv(nn.Module):
    def __init__(self, in_ch, out_ch):
        super(inconv, self).__init__()
        self.conv = double_conv(in_ch, out_ch)

    def forward(self, x):
        x = self.conv(x)
        return x


class down(nn.Module):
    def __init__(self, in_ch, out_ch):
        super(down, self).__init__()
        self.mpconv = nn.Sequential(
            nn.MaxPool2d(2),
            double_conv(in_ch, out_ch)
        )

    def forward(self, x):
        x = self.mpconv(x)
        return x


class up(nn.Module):
    def __init__(self, in_ch, out_ch, bilinear=True):
        super(up, self).__init__()

        #  would be a nice idea if the upsampling could be learned too,
        #  but my machine do not have enough memory to handle all those weights
        if bilinear:
            self.up = nn.Upsample(scale_factor=2, mode='bilinear', align_corners=True)
        else:
            self.up = nn.ConvTranspose2d(in_ch//2, in_ch//2, 2, stride=2)

        self.conv = double_conv(in_ch, out_ch)

    def forward(self, x1, x2):
        x1 = self.up(x1)
        diffX = x1.size()[2] - x2.size()[2]
        diffY = x1.size()[3] - x2.size()[3]
        x2 = F.pad(x2, (diffX // 2, int(diffX / 2),
                        diffY // 2, int(diffY / 2)))
        x = torch.cat([x2, x1], dim=1)
        x = self.conv(x)
        return x


class outconv(nn.Module):
    def __init__(self, in_ch, out_ch):
        super(outconv, self).__init__()
        self.conv = nn.Conv2d(in_ch, out_ch, 1)

    def forward(self, x):
        x = self.conv(x)
        return x


class UNet(nn.Module):
    def __init__(self, n_channels, n_classes):
        super(UNet, self).__init__()
        self.inc = inconv(n_channels, 64)
        self.down1 = down(64, 128)
        self.down2 = down(128, 256)
        self.down3 = down(256, 512)
        self.down4 = down(512, 512)
        self.up1 = up(1024, 256)
        self.up2 = up(512, 128)
        self.up3 = up(256, 64)
        self.up4 = up(128, 64)
        self.outc = outconv(64, n_classes)

    def forward(self, x):
        self.x1 = self.inc(x)
        self.x2 = self.down1(self.x1)
        self.x3 = self.down2(self.x2)
        self.x4 = self.down3(self.x3)
        self.x5 = self.down4(self.x4)
        self.x6 = self.up1(self.x5, self.x4)
        self.x7 = self.up2(self.x6, self.x3)
        self.x8 = self.up3(self.x7, self.x2)
        self.x9 = self.up4(self.x8, self.x1)
        self.y = self.outc(self.x9)
        return self.y