Kaggle competition: Plant Pathology 2020 - FGVC7
<SOS> metric: MCAUC Kaggle data source: plant-pathology-2020-fgvc7<train_model>
import numpy as np
import pandas as pd
import os
import random, re, math
import tensorflow as tf, tensorflow.keras.backend as K
from tensorflow.keras.layers import Dense
from tensorflow.keras.models import Model
from tensorflow.keras import optimizers
from kaggle_datasets import KaggleDatasets
from tensorflow.keras.models import Sequential
import tensorflow.keras.layers as L
from tensorflow.keras.applications import ResNet152V2, InceptionResNetV2, InceptionV3, Xception, VGG19
from tensorflow.keras.layers import Dense, GlobalAveragePooling2D
from tensorflow.keras.preprocessing.image import ImageDataGenerator
from sklearn.model_selection import train_test_split
import matplotlib.pyplot as plt
X = np.asarray([outputs[i][0] for i in range(len(outputs)) ])
 X = X[...,0]
reg = LinearRegression().fit(X.T, val_y)
 print(reg.score(X.T, val_y),reg.coef_ )<find_best_params>
!pip install efficientnet
pred_val_y = np.sum([outputs[i][0] * reg.coef_[i] for i in range(len(outputs)) ], axis = 0)
 thresholds = []
for thresh in np.arange(0.1, 0.501, 0.01):
thresh = np.round(thresh, 2)
 res = metrics.f1_score(val_y,(pred_val_y > thresh ).astype(int))
thresholds.append([thresh, res])
 print("F1 score at threshold {0} is {1}".format(thresh, res))
thresholds.sort(key=lambda x: x[1], reverse=True)
 best_thresh = thresholds[0][0]
print("Best threshold: ", best_thresh )<save_to_csv>
AUTO = tf.data.experimental.AUTOTUNE
try:
tpu = tf.distribute.cluster_resolver.TPUClusterResolver()
print('Running on TPU ', tpu.master())
 except ValueError:
tpu = None
if tpu:
tf.config.experimental_connect_to_cluster(tpu)
 tf.tpu.experimental.initialize_tpu_system(tpu)
 strategy = tf.distribute.experimental.TPUStrategy(tpu)
 else:
strategy = tf.distribute.get_strategy()
print("REPLICAS: ", strategy.num_replicas_in_sync)
 GCS_DS_PATH = KaggleDatasets().get_gcs_path()
pred_test_y = np.sum([outputs[i][1] * reg.coef_[i] for i in range(len(outputs)) ], axis = 0)
 pred_test_y =(pred_test_y > best_thresh ).astype(int)
 test_df = pd.read_csv(".. /input/test.csv", usecols=["qid"])
 out_df = pd.DataFrame({"qid":test_df["qid"].values})
 out_df['prediction'] = pred_test_y
out_df.to_csv("submission.csv", index=False )<import_modules>
img = plt.imread('.. /input/plant-pathology-2020-fgvc7/images/Train_0.jpg')
 print(img.shape)
 plt.imshow(img )
tqdm.pandas(desc='Progress')
<define_variables>
path='.. /input/plant-pathology-2020-fgvc7/'
train = pd.read_csv(path + 'train.csv')
 test = pd.read_csv(path + 'test.csv')
 sub = pd.read_csv(path + 'sample_submission.csv')
 train_paths = train.image_id.apply(lambda x: GCS_DS_PATH + '/images/' + x + '.jpg' ).values
test_paths = test.image_id.apply(lambda x: GCS_DS_PATH + '/images/' + x + '.jpg' ).values
train_labels = train.loc[:, 'healthy':].values
embed_size = 300
max_features = 120000
maxlen = 70
batch_size = 512
n_epochs = 5
n_splits = 5
SEED = 1029<set_options>
nb_classes = 4
BATCH_SIZE = 8 * strategy.num_replicas_in_sync
img_size = 768
EPOCHS = 40
SEED = 12345
AUG_BATCH = BATCH_SIZE
IMAGE_SIZE = [img_size, img_size]
def seed_everything(seed=1029):
random.seed(seed)
 os.environ['PYTHONHASHSEED'] = str(seed)
 np.random.seed(seed)
 torch.manual_seed(seed)
 torch.cuda.manual_seed(seed)
 torch.backends.cudnn.deterministic = True
seed_everything()<features_selection>
def mixup(image, label, PROBABILITY = 1.0):
DIM = IMAGE_SIZE[0]
CLASSES = nb_classes
imgs = []; labs = []
for j in range(AUG_BATCH):
P = tf.cast(tf.random.uniform([],0,1)<=PROBABILITY, tf.float32)
 k = tf.cast(tf.random.uniform([],0,AUG_BATCH),tf.int32)
 a = tf.random.uniform([],0,1)*P
img1 = image[j,]
img2 = image[k,]
imgs.append(( 1-a)*img1 + a*img2)
 if len(label.shape)==1:
lab1 = tf.one_hot(label[j],CLASSES)
 lab2 = tf.one_hot(label[k],CLASSES)
 else:
lab1 = label[j,]
lab2 = label[k,]
labs.append(( 1-a)*float(lab1)+ a*float(lab2))
image2 = tf.reshape(tf.stack(imgs),(AUG_BATCH,DIM,DIM,3))
label2 = tf.reshape(tf.stack(labs),(AUG_BATCH,CLASSES))
return image2,label2
def load_glove(word_index):
EMBEDDING_FILE = '.. /input/embeddings/glove.840B.300d/glove.840B.300d.txt'
def get_coefs(word,*arr): return word, np.asarray(arr, dtype='float32')[:300]
embeddings_index = dict(get_coefs(*o.split(" ")) for o in open(EMBEDDING_FILE))
all_embs = np.stack(embeddings_index.values())
 emb_mean,emb_std = -0.005838499,0.48782197
embed_size = all_embs.shape[1]
nb_words = min(max_features, len(word_index))
embedding_matrix = np.random.normal(emb_mean, emb_std,(nb_words, embed_size))
for word, i in word_index.items() :
if i >= max_features: continue
embedding_vector = embeddings_index.get(word)
 if embedding_vector is not None: embedding_matrix[i] = embedding_vector
return embedding_matrix
def load_fasttext(word_index):
EMBEDDING_FILE = '.. /input/embeddings/wiki-news-300d-1M/wiki-news-300d-1M.vec'
def get_coefs(word,*arr): return word, np.asarray(arr, dtype='float32')
 embeddings_index = dict(get_coefs(*o.split(" ")) for o in open(EMBEDDING_FILE)if len(o)>100)
 all_embs = np.stack(embeddings_index.values())
 emb_mean,emb_std = all_embs.mean() , all_embs.std()
embed_size = all_embs.shape[1]
nb_words = min(max_features, len(word_index))
embedding_matrix = np.random.normal(emb_mean, emb_std,(nb_words, embed_size))
for word, i in word_index.items() :
if i >= max_features: continue
embedding_vector = embeddings_index.get(word)
 if embedding_vector is not None: embedding_matrix[i] = embedding_vector
return embedding_matrix
def load_para(word_index):
EMBEDDING_FILE = '.. /input/embeddings/paragram_300_sl999/paragram_300_sl999.txt'
def get_coefs(word,*arr): return word, np.asarray(arr, dtype='float32')
 embeddings_index = dict(get_coefs(*o.split(" ")) for o in open(EMBEDDING_FILE, encoding="utf8", errors='ignore')if len(o)>100)
 all_embs = np.stack(embeddings_index.values())
 emb_mean,emb_std = -0.0053247833,0.49346462
embed_size = all_embs.shape[1]
nb_words = min(max_features, len(word_index))
embedding_matrix = np.random.normal(emb_mean, emb_std,(nb_words, embed_size))
for word, i in word_index.items() :
if i >= max_features: continue
embedding_vector = embeddings_index.get(word)
 if embedding_vector is not None: embedding_matrix[i] = embedding_vector
return embedding_matrix<load_from_csv>
def decode_image(filename, label=None, image_size=(img_size, img_size)) :
bits = tf.io.read_file(filename)
 image = tf.image.decode_jpeg(bits, channels=3)
 image = tf.cast(image, tf.float32)/ 255.0
image = tf.image.resize(image, image_size)
 if label is None:
return image
else:
return image, label
def data_augment(image, label=None, seed=2020):
image = tf.image.random_flip_left_right(image, seed=seed)
 image = tf.image.random_flip_up_down(image, seed=seed)
 image = tf.image.random_brightness(image, max_delta=0.05, seed=seed)
 image = tf.image.random_contrast(image, lower=0.7, upper=1.3, seed=seed)
 if label is None:
return image
else:
return image, label
df_train = pd.read_csv(".. /input/train.csv")
 df_test = pd.read_csv(".. /input/test.csv")
 df = pd.concat([df_train ,df_test],sort=True )<feature_engineering>
train_dataset =(
 tf.data.Dataset 
.from_tensor_slices(( train_paths, train_labels)) 
.map(decode_image, num_parallel_calls=AUTO)
.map(data_augment, num_parallel_calls=AUTO)
.repeat() 
.shuffle(512)
.batch(BATCH_SIZE)
.map(mixup)
.prefetch(AUTO)
 )
def build_vocab(texts):
sentences = texts.apply(lambda x: x.split() ).values
vocab = {}
for sentence in sentences:
for word in sentence:
try:
vocab[word] += 1
except KeyError:
vocab[word] = 1
return vocab
vocab = build_vocab(df['question_text'] )<define_variables>
test_dataset =(
 tf.data.Dataset 
.from_tensor_slices(test_paths)
.map(decode_image, num_parallel_calls=AUTO)
.batch(BATCH_SIZE)
 )
sin = len(df_train[df_train["target"]==0])
 insin = len(df_train[df_train["target"]==1])
 persin =(sin/(sin+insin)) *100
perinsin =(insin/(sin+insin)) *100
print("
print("<feature_engineering>
LR_START = 0.00001
LR_MAX = 0.0001 * strategy.num_replicas_in_sync
LR_MIN = 0.00001
T_max = EPOCHS
LR_RAMPUP_EPOCHS = 25
LR_SUSTAIN_EPOCHS = 3
LR_EXP_DECAY =.8
def lrfn(epoch):
if epoch < LR_RAMPUP_EPOCHS:
lr =(LR_MAX - LR_START)/ LR_RAMPUP_EPOCHS * epoch + LR_START
elif epoch < LR_RAMPUP_EPOCHS + LR_SUSTAIN_EPOCHS:
lr = LR_MAX
else:
lr =(LR_MAX - LR_MIN)* LR_EXP_DECAY**(epoch - LR_RAMPUP_EPOCHS - LR_SUSTAIN_EPOCHS)+ LR_MIN
return lr
lr_callback = tf.keras.callbacks.LearningRateScheduler(lrfn, verbose=True)
 rng = [i for i in range(EPOCHS)]
y = [lrfn(x)for x in rng]
plt.plot(rng, y)
 print("Learning rate schedule: {:.3g} to {:.3g} to {:.3g}".format(y[0], max(y), y[-1]))
def build_vocab(texts):
sentences = texts.apply(lambda x: x.split() ).values
vocab = {}
for sentence in sentences:
for word in sentence:
try:
vocab[word] += 1
except KeyError:
vocab[word] = 1
return vocab
def known_contractions(embed):
known = []
for contract in contraction_mapping:
if contract in embed:
known.append(contract)
 return known
def clean_contractions(text, mapping):
specials = ["’", "‘", "´", "`"]
for s in specials:
text = text.replace(s, "'")
 text = ' '.join([mapping[t] if t in mapping else t for t in text.split(" ")])
 return text
def correct_spelling(x, dic):
for word in dic.keys() :
x = x.replace(word, dic[word])
 return x
def unknown_punct(embed, punct):
unknown = ''
for p in punct:
if p not in embed:
unknown += p
unknown += ' '
return unknown
def clean_numbers(x):
x = re.sub('[0-9]{5,}', '
x = re.sub('[0-9]{4}', '
x = re.sub('[0-9]{3}', '
x = re.sub('[0-9]{2}', '
return x
def clean_special_chars(text, punct, mapping):
for p in mapping:
text = text.replace(p, mapping[p])
 for p in punct:
text = text.replace(p, f' {p} ')
 specials = {'\u200b': ' ', '…': '...', '\ufeff': '', 'करना': '', 'है': ''}
for s in specials:
text = text.replace(s, specials[s])
 return text
def add_lower(embedding, vocab):
count = 0
for word in vocab:
if word in embedding and word.lower() not in embedding:
embedding[word.lower() ] = embedding[word]
count += 1
print(f"Added {count} words to embedding" )<feature_engineering>
def get_model1() :
base_model = efn.EfficientNetB7(input_shape=(img_size, img_size, 3), weights='noisy-student', include_top=False, pooling='avg')
 x = base_model.output
predictions = Dense(nb_classes, activation="softmax" )(x)
 return Model(inputs=base_model.input, outputs=predictions )
def add_features(df):
df['question_text'] = df['question_text'].progress_apply(lambda x:str(x))
df['total_length'] = df['question_text'].progress_apply(len)
 df['capitals'] = df['question_text'].progress_apply(lambda comment: sum(1 for c in comment if c.isupper()))
df['caps_vs_length'] = df.progress_apply(lambda row: float(row['capitals'])/float(row['total_length']),
axis=1)
 df['num_words'] = df.question_text.str.count('\S+')
 df['num_unique_words'] = df['question_text'].progress_apply(lambda comment: len(set(w for w in comment.split())))
 df['words_vs_unique'] = df['num_unique_words'] / df['num_words']
return df
def load_and_prec() :
train_df = pd.read_csv(".. /input/train.csv")
 test_df = pd.read_csv(".. /input/test.csv")
 print("Train shape : ",train_df.shape)
 print("Test shape : ",test_df.shape)
 train_df["question_text"] = train_df["question_text"].apply(lambda x: x.lower())
 test_df["question_text"] = test_df["question_text"].apply(lambda x: x.lower())
 train_df["question_text"] = train_df["question_text"].progress_apply(lambda x: clean_text(x))
test_df["question_text"] = test_df["question_text"].apply(lambda x: clean_text(x))
train_df["question_text"] = train_df["question_text"].progress_apply(lambda x: clean_numbers(x))
test_df["question_text"] = test_df["question_text"].apply(lambda x: clean_numbers(x))
train_df["question_text"] = train_df["question_text"].progress_apply(lambda x: replace_typical_misspell(x))
test_df["question_text"] = test_df["question_text"].apply(lambda x: replace_typical_misspell(x))
train_X = train_df["question_text"].fillna("_
test_X = test_df["question_text"].fillna("_
train = add_features(train_df)
 test = add_features(test_df)
 features = train[['caps_vs_length', 'words_vs_unique']].fillna(0)
 test_features = test[['caps_vs_length', 'words_vs_unique']].fillna(0)
 ss = StandardScaler()
ss.fit(np.vstack(( features, test_features)))
 features = ss.transform(features)
 test_features = ss.transform(test_features)
 tokenizer = Tokenizer(num_words=max_features)
 tokenizer.fit_on_texts(list(train_X))
train_X = tokenizer.texts_to_sequences(train_X)
 test_X = tokenizer.texts_to_sequences(test_X)
 train_X = pad_sequences(train_X, maxlen=maxlen)
 test_X = pad_sequences(test_X, maxlen=maxlen)
 train_y = train_df['target'].values
np.random.seed(SEED)
 trn_idx = np.random.permutation(len(train_X))
train_X = train_X[trn_idx]
train_y = train_y[trn_idx]
features = features[trn_idx]
return train_X, test_X, train_y, features, test_features, tokenizer.word_index 
<train_model>
def get_model2() :
base_model = efn.EfficientNetB6(input_shape=(img_size, img_size, 3), weights='imagenet', include_top=False, pooling='avg')
 x = base_model.output
predictions = Dense(nb_classes, activation="softmax" )(x)
 return Model(inputs=base_model.input, outputs=predictions )
x_train, x_test, y_train, features, test_features, word_index = load_and_prec() 
<save_model>
def get_model3() :
model = tf.keras.Sequential([
ResNet152V2(input_shape=(img_size, img_size, 3), weights='imagenet', include_top=False),
L.GlobalAveragePooling2D() ,
L.Dense(train_labels.shape[1], activation='softmax')
 ])
 return model
np.save("x_train",x_train)
 np.save("x_test",x_test)
 np.save("y_train",y_train)
 np.save("features",features)
 np.save("test_features",test_features)
 np.save("word_index.npy",word_index )<load_pretrained>
def get_model4() :
model = tf.keras.Sequential([
InceptionResNetV2(input_shape=(img_size, img_size, 3), weights='imagenet', include_top=False),
L.GlobalAveragePooling2D() ,
L.Dense(train_labels.shape[1], activation='softmax')
 ])
 return model
x_train = np.load("x_train.npy")
 x_test = np.load("x_test.npy")
 y_train = np.load("y_train.npy")
 features = np.load("features.npy")
 test_features = np.load("test_features.npy")
 word_index = np.load("word_index.npy" ).item()<normalization>
with strategy.scope() :
model1 = get_model1()
model1.compile(optimizer='adam', loss=tf.keras.losses.CategoricalCrossentropy() ,metrics=['categorical_accuracy'] )
seed_everything()
glove_embeddings = load_glove(word_index)
 paragram_embeddings = load_para(word_index)
 fasttext_embeddings = load_fasttext(word_index)
 embedding_matrix = np.mean([glove_embeddings, paragram_embeddings, fasttext_embeddings], axis=0)
 del glove_embeddings, paragram_embeddings, fasttext_embeddings
gc.collect()
np.shape(embedding_matrix )<split>
%%time
model1.fit(
 train_dataset,
steps_per_epoch=train_labels.shape[0] // BATCH_SIZE,
callbacks=[lr_callback],
epochs=EPOCHS
)
<choose_model_class><EOS> 
%%time
probs1 = model1.predict(test_dataset, verbose=1)
 probs_avg = probs1
sub.loc[:, 'healthy':] = probs_avg
sub.to_csv('submission.csv', index=False)
 sub.head()