import torch import torch.nn as nn import torch.nn.functional as F import math from fastai.layers import * from fastai.core import * ############################################################################################################################################## # utility functions def _conv1d(in_planes,out_planes,kernel_size=3, stride=1, dilation=1, act="relu", bn=True, drop_p=0): lst=[] if(drop_p>0): lst.append(nn.Dropout(drop_p)) lst.append(nn.Conv1d(in_planes, out_planes, kernel_size=kernel_size, stride=stride, padding=(kernel_size-1)//2, dilation=dilation, bias=not(bn))) if(bn): lst.append(nn.BatchNorm1d(out_planes)) if(act=="relu"): lst.append(nn.ReLU(True)) if(act=="elu"): lst.append(nn.ELU(True)) if(act=="prelu"): lst.append(nn.PReLU(True)) return nn.Sequential(*lst) def _fc(in_planes,out_planes, act="relu", bn=True): lst = [nn.Linear(in_planes, out_planes, bias=not(bn))] if(bn): lst.append(nn.BatchNorm1d(out_planes)) if(act=="relu"): lst.append(nn.ReLU(True)) if(act=="elu"): lst.append(nn.ELU(True)) if(act=="prelu"): lst.append(nn.PReLU(True)) return nn.Sequential(*lst) def cd_adaptiveconcatpool(relevant, irrelevant, module): mpr, mpi = module.mp.attrib(relevant,irrelevant) apr, api = module.ap.attrib(relevant,irrelevant) return torch.cat([mpr, apr], 1), torch.cat([mpi, api], 1) def attrib_adaptiveconcatpool(self,relevant,irrelevant): return cd_adaptiveconcatpool(relevant,irrelevant,self) class AdaptiveConcatPool1d(nn.Module): "Layer that concats `AdaptiveAvgPool1d` and `AdaptiveMaxPool1d`." def __init__(self, sz:Optional[int]=None): "Output will be 2*sz or 2 if sz is None" super().__init__() sz = sz or 1 self.ap,self.mp = nn.AdaptiveAvgPool1d(sz), nn.AdaptiveMaxPool1d(sz) def forward(self, x): return torch.cat([self.mp(x), self.ap(x)], 1) def attrib(self,relevant,irrelevant): return attrib_adaptiveconcatpool(self,relevant,irrelevant) class SqueezeExcite1d(nn.Module): '''squeeze excite block as used for example in LSTM FCN''' def __init__(self,channels,reduction=16): super().__init__() channels_reduced = channels//reduction self.w1 = torch.nn.Parameter(torch.randn(channels_reduced,channels).unsqueeze(0)) self.w2 = torch.nn.Parameter(torch.randn(channels, channels_reduced).unsqueeze(0)) def forward(self, x): #input is bs,ch,seq z=torch.mean(x,dim=2,keepdim=True)#bs,ch intermed = F.relu(torch.matmul(self.w1,z))#(1,ch_red,ch * bs,ch,1) = (bs, ch_red, 1) s=F.sigmoid(torch.matmul(self.w2,intermed))#(1,ch,ch_red * bs, ch_red, 1=bs, ch, 1 return s*x #bs,ch,seq * bs, ch,1 = bs,ch,seq def weight_init(m): '''call weight initialization for model n via n.apply(weight_init)''' if isinstance(m, nn.Conv1d) or isinstance(m, nn.Linear): nn.init.kaiming_normal_(m.weight) if m.bias is not None: nn.init.zeros_(m.bias) if isinstance(m, nn.BatchNorm1d): nn.init.constant_(m.weight,1) nn.init.constant_(m.bias,0) if isinstance(m,SqueezeExcite1d): stdv1=math.sqrt(2./m.w1.size[0]) nn.init.normal_(m.w1,0.,stdv1) stdv2=math.sqrt(1./m.w2.size[1]) nn.init.normal_(m.w2,0.,stdv2) def create_head1d(nf:int, nc:int, lin_ftrs:Optional[Collection[int]]=None, ps:Floats=0.5, bn_final:bool=False, bn:bool=True, act="relu", concat_pooling=True): "Model head that takes `nf` features, runs through `lin_ftrs`, and about `nc` classes; added bn and act here" lin_ftrs = [2*nf if concat_pooling else nf, nc] if lin_ftrs is None else [2*nf if concat_pooling else nf] + lin_ftrs + [nc] #was [nf, 512,nc] ps = listify(ps) if len(ps)==1: ps = [ps[0]/2] * (len(lin_ftrs)-2) + ps actns = [nn.ReLU(inplace=True) if act=="relu" else nn.ELU(inplace=True)] * (len(lin_ftrs)-2) + [None] layers = [AdaptiveConcatPool1d() if concat_pooling else nn.MaxPool1d(2), Flatten()] for ni,no,p,actn in zip(lin_ftrs[:-1],lin_ftrs[1:],ps,actns): layers += bn_drop_lin(ni,no,bn,p,actn) if bn_final: layers.append(nn.BatchNorm1d(lin_ftrs[-1], momentum=0.01)) return nn.Sequential(*layers) ############################################################################################################################################## # basic convolutional architecture class basic_conv1d(nn.Sequential): '''basic conv1d''' def __init__(self, filters=[128,128,128,128],kernel_size=3, stride=2, dilation=1, pool=0, pool_stride=1, squeeze_excite_reduction=0, num_classes=2, input_channels=8, act="relu", bn=True, headless=False,split_first_layer=False,drop_p=0.,lin_ftrs_head=None, ps_head=0.5, bn_final_head=False, bn_head=True, act_head="relu", concat_pooling=True): layers = [] if(isinstance(kernel_size,int)): kernel_size = [kernel_size]*len(filters) for i in range(len(filters)): layers_tmp = [] layers_tmp.append(_conv1d(input_channels if i==0 else filters[i-1],filters[i],kernel_size=kernel_size[i],stride=(1 if (split_first_layer is True and i==0) else stride),dilation=dilation,act="none" if ((headless is True and i==len(filters)-1) or (split_first_layer is True and i==0)) else act, bn=False if (headless is True and i==len(filters)-1) else bn,drop_p=(0. if i==0 else drop_p))) if((split_first_layer is True and i==0)): layers_tmp.append(_conv1d(filters[0],filters[0],kernel_size=1,stride=1,act=act, bn=bn,drop_p=0.)) #layers_tmp.append(nn.Linear(filters[0],filters[0],bias=not(bn))) #layers_tmp.append(_fc(filters[0],filters[0],act=act,bn=bn)) if(pool>0 and i0): layers_tmp.append(SqueezeExcite1d(filters[i],squeeze_excite_reduction)) layers.append(nn.Sequential(*layers_tmp)) #head #layers.append(nn.AdaptiveAvgPool1d(1)) #layers.append(nn.Linear(filters[-1],num_classes)) #head #inplace=True leads to a runtime error see ReLU+ dropout https://discuss.pytorch.org/t/relu-dropout-inplace/13467/5 self.headless = headless if(headless is True): head = nn.Sequential(nn.AdaptiveAvgPool1d(1),Flatten()) else: head=create_head1d(filters[-1], nc=num_classes, lin_ftrs=lin_ftrs_head, ps=ps_head, bn_final=bn_final_head, bn=bn_head, act=act_head, concat_pooling=concat_pooling) layers.append(head) super().__init__(*layers) def get_layer_groups(self): return (self[2],self[-1]) def get_output_layer(self): if self.headless is False: return self[-1][-1] else: return None def set_output_layer(self,x): if self.headless is False: self[-1][-1] = x ############################################################################################ # convenience functions for basic convolutional architectures def fcn(filters=[128]*5,num_classes=2,input_channels=8): filters_in = filters + [num_classes] return basic_conv1d(filters=filters_in,kernel_size=3,stride=1,pool=2,pool_stride=2,input_channels=input_channels,act="relu",bn=True,headless=True) def fcn_wang(num_classes=2,input_channels=8,lin_ftrs_head=None, ps_head=0.5, bn_final_head=False, bn_head=True, act_head="relu", concat_pooling=True): return basic_conv1d(filters=[128,256,128],kernel_size=[8,5,3],stride=1,pool=0,pool_stride=2, num_classes=num_classes,input_channels=input_channels,act="relu",bn=True,lin_ftrs_head=lin_ftrs_head, ps_head=ps_head, bn_final_head=bn_final_head, bn_head=bn_head, act_head=act_head, concat_pooling=concat_pooling) def schirrmeister(num_classes=2,input_channels=8,lin_ftrs_head=None, ps_head=0.5, bn_final_head=False, bn_head=True, act_head="relu", concat_pooling=True): return basic_conv1d(filters=[25,50,100,200],kernel_size=10, stride=3, pool=3, pool_stride=1, num_classes=num_classes, input_channels=input_channels, act="relu", bn=True, headless=False,split_first_layer=True,drop_p=0.5,lin_ftrs_head=lin_ftrs_head, ps_head=ps_head, bn_final_head=bn_final_head, bn_head=bn_head, act_head=act_head, concat_pooling=concat_pooling) def sen(filters=[128]*5,num_classes=2,input_channels=8,squeeze_excite_reduction=16,drop_p=0.,lin_ftrs_head=None, ps_head=0.5, bn_final_head=False, bn_head=True, act_head="relu", concat_pooling=True): return basic_conv1d(filters=filters,kernel_size=3,stride=2,pool=0,pool_stride=0,input_channels=input_channels,act="relu",bn=True,num_classes=num_classes,squeeze_excite_reduction=squeeze_excite_reduction,drop_p=drop_p,lin_ftrs_head=lin_ftrs_head, ps_head=ps_head, bn_final_head=bn_final_head, bn_head=bn_head, act_head=act_head, concat_pooling=concat_pooling) def basic1d(filters=[128]*5,kernel_size=3, stride=2, dilation=1, pool=0, pool_stride=1, squeeze_excite_reduction=0, num_classes=2, input_channels=8, act="relu", bn=True, headless=False,drop_p=0.,lin_ftrs_head=None, ps_head=0.5, bn_final_head=False, bn_head=True, act_head="relu", concat_pooling=True): return basic_conv1d(filters=filters,kernel_size=kernel_size, stride=stride, dilation=dilation, pool=pool, pool_stride=pool_stride, squeeze_excite_reduction=squeeze_excite_reduction, num_classes=num_classes, input_channels=input_channels, act=act, bn=bn, headless=headless,drop_p=drop_p,lin_ftrs_head=lin_ftrs_head, ps_head=ps_head, bn_final_head=bn_final_head, bn_head=bn_head, act_head=act_head, concat_pooling=concat_pooling)