Kaggle competition: APTOS 2019 Blindness Detection
<SOS> metric: QuadraticWeightedKappa Kaggle data source: aptos-2019-blindness-detection<compute_test_metric>
%reload_ext autoreload
%autoreload 2
%matplotlib inline
%matplotlib inline
bst = dxgb_evaluate()<predict_on_test>
GlobalParams = collections.namedtuple('GlobalParams', [
'batch_norm_momentum', 'batch_norm_epsilon', 'dropout_rate',
'num_classes', 'width_coefficient', 'depth_coefficient',
'depth_divisor', 'min_depth', 'drop_connect_rate', 'image_size'])
 BlockArgs = collections.namedtuple('BlockArgs', [
'kernel_size', 'num_repeat', 'input_filters', 'output_filters',
'expand_ratio', 'id_skip', 'stride', 'se_ratio'])
 GlobalParams.__new__.__defaults__ =(None,)* len(GlobalParams._fields)
 BlockArgs.__new__.__defaults__ =(None,)* len(BlockArgs._fields)
 def relu_fn(x):

 return x * torch.sigmoid(x)
 def round_filters(filters, global_params):

 multiplier = global_params.width_coefficient
if not multiplier:
return filters
divisor = global_params.depth_divisor
min_depth = global_params.min_depth
filters *= multiplier
min_depth = min_depth or divisor
new_filters = max(min_depth, int(filters + divisor / 2)// divisor * divisor)
 if new_filters < 0.9 * filters:
new_filters += divisor
return int(new_filters)
 def round_repeats(repeats, global_params):

 multiplier = global_params.depth_coefficient
if not multiplier:
return repeats
return int(math.ceil(multiplier * repeats))
def drop_connect(inputs, p, training):

 if not training: return inputs
batch_size = inputs.shape[0]
keep_prob = 1 - p
random_tensor = keep_prob
random_tensor += torch.rand([batch_size, 1, 1, 1], dtype=inputs.dtype, device=inputs.device)
 binary_tensor = torch.floor(random_tensor)
 output = inputs / keep_prob * binary_tensor
return output
def get_same_padding_conv2d(image_size=None):

 if image_size is None:
return Conv2dDynamicSamePadding
else:
return partial(Conv2dStaticSamePadding, image_size=image_size)
 class Conv2dDynamicSamePadding(nn.Conv2d):

 def __init__(self, in_channels, out_channels, kernel_size, stride=1, dilation=1, groups=1, bias=True):
super().__init__(in_channels, out_channels, kernel_size, stride, 0, dilation, groups, bias)
 self.stride = self.stride if len(self.stride)== 2 else [self.stride[0]]*2
def forward(self, x):
ih, iw = x.size() [-2:]
kh, kw = self.weight.size() [-2:]
sh, sw = self.stride
oh, ow = math.ceil(ih / sh), math.ceil(iw / sw)
 pad_h = max(( oh - 1)* self.stride[0] +(kh - 1)* self.dilation[0] + 1 - ih, 0)
 pad_w = max(( ow - 1)* self.stride[1] +(kw - 1)* self.dilation[1] + 1 - iw, 0)
 if pad_h > 0 or pad_w > 0:
x = F.pad(x, [pad_w//2, pad_w - pad_w//2, pad_h//2, pad_h - pad_h//2])
 return F.conv2d(x, self.weight, self.bias, self.stride, self.padding, self.dilation, self.groups)
 class Conv2dStaticSamePadding(nn.Conv2d):

 def __init__(self, in_channels, out_channels, kernel_size, image_size=None, **kwargs):
super().__init__(in_channels, out_channels, kernel_size, **kwargs)
 self.stride = self.stride if len(self.stride)== 2 else [self.stride[0]] * 2
assert image_size is not None
ih, iw = image_size if type(image_size)== list else [image_size, image_size]
kh, kw = self.weight.size() [-2:]
sh, sw = self.stride
oh, ow = math.ceil(ih / sh), math.ceil(iw / sw)
 pad_h = max(( oh - 1)* self.stride[0] +(kh - 1)* self.dilation[0] + 1 - ih, 0)
 pad_w = max(( ow - 1)* self.stride[1] +(kw - 1)* self.dilation[1] + 1 - iw, 0)
 if pad_h > 0 or pad_w > 0:
self.static_padding = nn.ZeroPad2d(( pad_w // 2, pad_w - pad_w // 2, pad_h // 2, pad_h - pad_h // 2))
else:
self.static_padding = Identity()
def forward(self, x):
x = self.static_padding(x)
 x = F.conv2d(x, self.weight, self.bias, self.stride, self.padding, self.dilation, self.groups)
 return x
class Identity(nn.Module):
def __init__(self,):
super(Identity, self ).__init__()
def forward(self, input):
return input
X_train_predictions = dxgb.predict(client, bst, X_train)
 X_test_predictions = dxgb.predict(client, bst, X_test )<compute_test_metric>
def efficientnet_params(model_name):

 params_dict = {
'efficientnet-b0':(1.0, 1.0, 224, 0.2),
'efficientnet-b1':(1.0, 1.1, 240, 0.2),
'efficientnet-b2':(1.1, 1.2, 260, 0.3),
'efficientnet-b3':(1.2, 1.4, 300, 0.3),
'efficientnet-b4':(1.4, 1.8, 380, 0.4),
'efficientnet-b5':(1.6, 2.2, 456, 0.4),
'efficientnet-b6':(1.8, 2.6, 528, 0.5),
'efficientnet-b7':(2.0, 3.1, 600, 0.5),
}
return params_dict[model_name]
class BlockDecoder(object):

 @staticmethod
def _decode_block_string(block_string):

 assert isinstance(block_string, str)
 ops = block_string.split('_')
 options = {}
for op in ops:
splits = re.split(r'(\d.*)', op)
 if len(splits)>= 2:
key, value = splits[:2]
options[key] = value
assert(( 's' in options and len(options['s'])== 1)or 
(len(options['s'])== 2 and options['s'][0] == options['s'][1]))
return BlockArgs(
 kernel_size=int(options['k']),
num_repeat=int(options['r']),
input_filters=int(options['i']),
output_filters=int(options['o']),
expand_ratio=int(options['e']),
id_skip=('noskip' not in block_string),
se_ratio=float(options['se'])if 'se' in options else None,
stride=[int(options['s'][0])])
 @staticmethod
def _encode_block_string(block):

 args = [
'r%d' % block.num_repeat,
'k%d' % block.kernel_size,
's%d%d' %(block.strides[0], block.strides[1]),
'e%s' % block.expand_ratio,
'i%d' % block.input_filters,
'o%d' % block.output_filters
]
if 0 < block.se_ratio <= 1:
args.append('se%s' % block.se_ratio)
 if block.id_skip is False:
args.append('noskip')
 return '_'.join(args)
 @staticmethod
def decode(string_list):

 assert isinstance(string_list, list)
 blocks_args = []
for block_string in string_list:
blocks_args.append(BlockDecoder._decode_block_string(block_string))
return blocks_args
@staticmethod
def encode(blocks_args):

 block_strings = []
for block in blocks_args:
block_strings.append(BlockDecoder._encode_block_string(block))
return block_strings
def efficientnet(width_coefficient=None, depth_coefficient=None, dropout_rate=0.2,
drop_connect_rate=0.2, image_size=None, num_classes=1000):

 blocks_args = [
'r1_k3_s11_e1_i32_o16_se0.25', 'r2_k3_s22_e6_i16_o24_se0.25',
'r2_k5_s22_e6_i24_o40_se0.25', 'r3_k3_s22_e6_i40_o80_se0.25',
'r3_k5_s11_e6_i80_o112_se0.25', 'r4_k5_s22_e6_i112_o192_se0.25',
'r1_k3_s11_e6_i192_o320_se0.25',
]
blocks_args = BlockDecoder.decode(blocks_args)
 global_params = GlobalParams(
 batch_norm_momentum=0.99,
batch_norm_epsilon=1e-3,
dropout_rate=dropout_rate,
drop_connect_rate=drop_connect_rate,
num_classes=num_classes,
width_coefficient=width_coefficient,
depth_coefficient=depth_coefficient,
depth_divisor=8,
min_depth=None,
image_size=image_size, 
)
 return blocks_args, global_params
def get_model_params(model_name, override_params):

 if model_name.startswith('efficientnet'):
w, d, s, p = efficientnet_params(model_name)
 blocks_args, global_params = efficientnet(
 width_coefficient=w, depth_coefficient=d, dropout_rate=p, image_size=s)
 else:
raise NotImplementedError('model name is not pre-defined: %s' % model_name)
 if override_params:
global_params = global_params._replace(**override_params)
 return blocks_args, global_params
url_map = {
'efficientnet-b0': 'http://storage.googleapis.com/public-models/efficientnet-b0-08094119.pth',
'efficientnet-b1': 'http://storage.googleapis.com/public-models/efficientnet-b1-dbc7070a.pth',
'efficientnet-b2': 'http://storage.googleapis.com/public-models/efficientnet-b2-27687264.pth',
'efficientnet-b3': 'http://storage.googleapis.com/public-models/efficientnet-b3-c8376fa2.pth',
'efficientnet-b4': 'http://storage.googleapis.com/public-models/efficientnet-b4-e116e8b3.pth',
'efficientnet-b5': 'http://storage.googleapis.com/public-models/efficientnet-b5-586e6cc6.pth',
}
def load_pretrained_weights(model, model_name, load_fc=True):

 state_dict = model_zoo.load_url(url_map[model_name])
 if load_fc:
model.load_state_dict(state_dict)
 else:
state_dict.pop('_fc.weight')
 state_dict.pop('_fc.bias')
 res = model.load_state_dict(state_dict, strict=False)
 assert str(res.missing_keys)== str(['_fc.weight', '_fc.bias']), 'issue loading pretrained weights'
print('Loaded pretrained weights for {}'.format(model_name))
class MBConvBlock(nn.Module):

 def __init__(self, block_args, global_params):
super().__init__()
self._block_args = block_args
self._bn_mom = 1 - global_params.batch_norm_momentum
self._bn_eps = global_params.batch_norm_epsilon
self.has_se =(self._block_args.se_ratio is not None)and(0 < self._block_args.se_ratio <= 1)
 self.id_skip = block_args.id_skip
Conv2d = get_same_padding_conv2d(image_size=global_params.image_size)
 inp = self._block_args.input_filters
oup = self._block_args.input_filters * self._block_args.expand_ratio
if self._block_args.expand_ratio != 1:
self._expand_conv = Conv2d(in_channels=inp, out_channels=oup, kernel_size=1, bias=False)
 self._bn0 = nn.BatchNorm2d(num_features=oup, momentum=self._bn_mom, eps=self._bn_eps)
 k = self._block_args.kernel_size
s = self._block_args.stride
self._depthwise_conv = Conv2d(
 in_channels=oup, out_channels=oup, groups=oup,
kernel_size=k, stride=s, bias=False)
 self._bn1 = nn.BatchNorm2d(num_features=oup, momentum=self._bn_mom, eps=self._bn_eps)
 if self.has_se:
num_squeezed_channels = max(1, int(self._block_args.input_filters * self._block_args.se_ratio))
self._se_reduce = Conv2d(in_channels=oup, out_channels=num_squeezed_channels, kernel_size=1)
 self._se_expand = Conv2d(in_channels=num_squeezed_channels, out_channels=oup, kernel_size=1)
 final_oup = self._block_args.output_filters
self._project_conv = Conv2d(in_channels=oup, out_channels=final_oup, kernel_size=1, bias=False)
 self._bn2 = nn.BatchNorm2d(num_features=final_oup, momentum=self._bn_mom, eps=self._bn_eps)
 def forward(self, inputs, drop_connect_rate=None):

 x = inputs
if self._block_args.expand_ratio != 1:
x = relu_fn(self._bn0(self._expand_conv(inputs)))
 x = relu_fn(self._bn1(self._depthwise_conv(x)))
 if self.has_se:
x_squeezed = F.adaptive_avg_pool2d(x, 1)
 x_squeezed = self._se_expand(relu_fn(self._se_reduce(x_squeezed)))
 x = torch.sigmoid(x_squeezed)* x
x = self._bn2(self._project_conv(x))
input_filters, output_filters = self._block_args.input_filters, self._block_args.output_filters
if self.id_skip and self._block_args.stride == 1 and input_filters == output_filters:
if drop_connect_rate:
x = drop_connect(x, p=drop_connect_rate, training=self.training)
 x = x + inputs
return x
class EfficientNet(nn.Module):

 def __init__(self, blocks_args=None, global_params=None):
super().__init__()
assert isinstance(blocks_args, list), 'blocks_args should be a list'
assert len(blocks_args)> 0, 'block args must be greater than 0'
self._global_params = global_params
self._blocks_args = blocks_args
Conv2d = get_same_padding_conv2d(image_size=global_params.image_size)
 bn_mom = 1 - self._global_params.batch_norm_momentum
bn_eps = self._global_params.batch_norm_epsilon
in_channels = 3
out_channels = round_filters(32, self._global_params)
 self._conv_stem = Conv2d(in_channels, out_channels, kernel_size=3, stride=2, bias=False)
 self._bn0 = nn.BatchNorm2d(num_features=out_channels, momentum=bn_mom, eps=bn_eps)
 self._blocks = nn.ModuleList([])
 for block_args in self._blocks_args:
block_args = block_args._replace(
 input_filters=round_filters(block_args.input_filters, self._global_params),
output_filters=round_filters(block_args.output_filters, self._global_params),
num_repeat=round_repeats(block_args.num_repeat, self._global_params)
)
 self._blocks.append(MBConvBlock(block_args, self._global_params))
if block_args.num_repeat > 1:
block_args = block_args._replace(input_filters=block_args.output_filters, stride=1)
 for _ in range(block_args.num_repeat - 1):
self._blocks.append(MBConvBlock(block_args, self._global_params))
in_channels = block_args.output_filters
out_channels = round_filters(1280, self._global_params)
 self._conv_head = Conv2d(in_channels, out_channels, kernel_size=1, bias=False)
 self._bn1 = nn.BatchNorm2d(num_features=out_channels, momentum=bn_mom, eps=bn_eps)
 self._dropout = self._global_params.dropout_rate
self._fc = nn.Linear(out_channels, self._global_params.num_classes)
 def extract_features(self, inputs):

 x = relu_fn(self._bn0(self._conv_stem(inputs)))
 for idx, block in enumerate(self._blocks):
drop_connect_rate = self._global_params.drop_connect_rate
if drop_connect_rate:
drop_connect_rate *= float(idx)/ len(self._blocks)
 x = block(x, drop_connect_rate=drop_connect_rate)
 x = relu_fn(self._bn1(self._conv_head(x)))
 return x
def forward(self, inputs):

 x = self.extract_features(inputs)
 x = F.adaptive_avg_pool2d(x, 1 ).squeeze(-1 ).squeeze(-1)
 if self._dropout:
x = F.dropout(x, p=self._dropout, training=self.training)
 x = self._fc(x)
 return x
@classmethod
def from_name(cls, model_name, override_params=None):
cls._check_model_name_is_valid(model_name)
 blocks_args, global_params = get_model_params(model_name, override_params)
 return EfficientNet(blocks_args, global_params)
 @classmethod
def from_pretrained(cls, model_name, num_classes=1000):
model = EfficientNet.from_name(model_name, override_params={'num_classes': num_classes})
 return model
@classmethod
def get_image_size(cls, model_name):
cls._check_model_name_is_valid(model_name)
 _, _, res, _ = efficientnet_params(model_name)
 return res
@classmethod
def _check_model_name_is_valid(cls, model_name, also_need_pretrained_weights=False):

 num_models = 4 if also_need_pretrained_weights else 8
valid_models = ['efficientnet_b'+str(i)for i in range(num_models)]
if model_name.replace('-','_')not in valid_models:
raise ValueError('model_name should be one of: ' + ', '.join(valid_models))
print("\033[1;37;40m\033[2;37:40mdata category \t\t\trmse-score\033[0m")
 print('train test split \t\t\033[0;37;41m {0:.2f} \033[0m'.format(np.sqrt(mean_squared_error(y_test, X_test_predictions))))
print('train split \t\t\t\033[0;37;41m {0:.2f} \033[0m
'.format(np.sqrt(mean_squared_error(y_train, X_train_predictions))))<drop_column>
md_ef = EfficientNet.from_pretrained('efficientnet-b5', num_classes=1 )
%%time
df_test = load_data(data_test_file_path, train_data='N')
 df_test = calculate_coordinates_distance(df_test, train_data='N')
 df_test_key = df_test.key
df_test = df_test.drop(['key', 'pickup_datetime'], axis=1 )<predict_on_test>
def get_df() :
base_image_dir = os.path.join('.. ', 'input/aptos2019-blindness-detection/')
 train_dir = os.path.join(base_image_dir,'train_images/')
 df = pd.read_csv(os.path.join(base_image_dir, 'train.csv'))
df['path'] = df['id_code'].map(lambda x: os.path.join(train_dir,'{}.png'.format(x)))
 df = df.drop(columns=['id_code'])
 df = df.sample(frac=1 ).reset_index(drop=True)
 test_df = pd.read_csv('.. /input/aptos2019-blindness-detection/sample_submission.csv')
 return df, test_df
df, test_df = get_df()
test_predictions = dxgb.predict(client, bst, df_test )<save_to_csv>
bs = 32
sz = 224
tfms = get_transforms(do_flip=True,flip_vert=True )
submission_predictions = pd.DataFrame({'key': df_test_key.compute() , 'fare_amount': test_predictions.compute() })
 submission_predictions.to_csv('submission.csv', index=False )<define_variables>
def qk(y_pred, y):
return torch.tensor(cohen_kappa_score(torch.round(y_pred), y, weights='quadratic'), device='cuda:0' )
TRAIN_PATH = '.. /input/train.csv'
traintypes = {'fare_amount': 'float32',
'pickup_datetime': 'str',
'pickup_longitude': 'float32',
'pickup_latitude': 'float32',
'dropoff_longitude': 'float32',
'dropoff_latitude': 'float32',
'passenger_count': 'uint8'}
cols = list(traintypes.keys() )<load_from_csv>
learn = Learner(data,
md_ef,
metrics = [qk],
model_dir="models" ).to_fp16()
learn.data.add_test(ImageList.from_df(test_df,
'.. /input/aptos2019-blindness-detection',
folder='test_images',
suffix='.png'))
with open(TRAIN_PATH)as file:
n_rows = len(file.readlines())
 print(f'Exact number of rows: {n_rows}' )<define_variables>
learn.fit_one_cycle(10, 1e-3 )
chunksize = 5_000_000
total_chunk = n_rows // chunksize + 1
print(f'Chunk size: {chunksize:,}
Total chunks required: {total_chunk}' )<feature_engineering>
learn.load('abcdef');
df_list = []
i=0
for df_chunk in pd.read_csv(TRAIN_PATH, usecols=cols, dtype=traintypes, chunksize=chunksize):
i = i+1
print(f'DataFrame Chunk {i:02d}/{total_chunk}')
 df_chunk['pickup_datetime'] = df_chunk['pickup_datetime'].str.slice(0, 16)
 df_chunk['pickup_datetime'] = pd.to_datetime(df_chunk['pickup_datetime'], utc=True, format='%Y-%m-%d %H:%M')
 df_list.append(df_chunk )<load_from_csv>
class OptimizedRounder(object):
def __init__(self):
self.coef_ = 0
def _kappa_loss(self, coef, X, y):
X_p = np.copy(X)
 for i, pred in enumerate(X_p):
if pred < coef[0]:
X_p[i] = 0
elif pred >= coef[0] and pred < coef[1]:
X_p[i] = 1
elif pred >= coef[1] and pred < coef[2]:
X_p[i] = 2
elif pred >= coef[2] and pred < coef[3]:
X_p[i] = 3
else:
X_p[i] = 4
ll = metrics.cohen_kappa_score(y, X_p, weights='quadratic')
 return -ll
def fit(self, X, y):
loss_partial = partial(self._kappa_loss, X=X, y=y)
 initial_coef = [0.5, 1.5, 2.5, 3.5]
self.coef_ = sp.optimize.minimize(loss_partial, initial_coef, method='nelder-mead')
 print(-loss_partial(self.coef_['x']))
def predict(self, X, coef):
X_p = np.copy(X)
 for i, pred in enumerate(X_p):
if pred < coef[0]:
X_p[i] = 0
elif pred >= coef[0] and pred < coef[1]:
X_p[i] = 1
elif pred >= coef[1] and pred < coef[2]:
X_p[i] = 2
elif pred >= coef[2] and pred < coef[3]:
X_p[i] = 3
else:
X_p[i] = 4
return X_p
def coefficients(self):
return self.coef_['x']
<count_missing_values><EOS> 
def run_subm(learn=learn, coefficients=[0.5, 1.5, 2.5, 3.5]):
opt = OptimizedRounder()
preds,y = learn.get_preds(DatasetType.Test)
 tst_pred = opt.predict(preds, coefficients)
 test_df.diagnosis = tst_pred.astype(int)
 test_df.to_csv('submission.csv',index=False)
 print('done' )