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data_df_sample_submission = pd.read_csv('.. /input/hpa-single-cell-image-classification/sample_submission.csv') test_files = os.listdir(".. /input/hpa-single-cell-image-classification/test") color_list = ["_red.png", "_green.png", "_yellow.png", "_blue.png"] test_files_names = [re.sub(r'|'.join(map(re.escape, color_l...
cnn.add(layer = tf.keras.layers.Dense(units = 108, activation='relu'))
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PATH_TEST = ".. /input/hpa-single-cell-image-classification/test" MODEL_PATH = ".. /input/models-hpa/" MODELS_LIST_EFFNET = [ "efficientnet-b4_rgby_lr_0.001_ADAM_steplr_g085_focal1_g1.0_resize640_mediumaug_3.pth", "efficientnet-b4_rgby_lr_0.0015_ADAM_focal1_g1.0_resize640_10pcTest_HEAVY_AUG_E3_F0.pth", "efficientnet-b4...
cnn.add(layer = tf.keras.layers.Dropout(0.5))
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class CFG: debug=False verbose = False num_workers=8 model_name_effnet = 'efficientnet-b4' model_name_resnest = 'resnest101' size=640 seed=2002 classes = 19 color_mode = "rgby" resnest = True effnet = True extra_model_for_labels = True extra_model_is_tf = True only_green_extra_model = True color_mode_image_level = "rgb...
cnn.add(layer = tf.keras.layers.Dense(units = 108, activation='relu'))
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Compose, OneOf, Normalize, Resize, RandomResizedCrop, RandomCrop, HorizontalFlip, VerticalFlip, RandomBrightness, RandomContrast, RandomBrightnessContrast, Rotate, ShiftScaleRotate, Cutout, IAAAdditiveGaussianNoise, Transpose, HueSaturationValue, CoarseDropout ) dataset_mean = [0.0994, 0.0466, 0.0606, 0.0879] dataset...
cnn.add(layer = tf.keras.layers.Dense(units = 10, activation = 'softmax'))
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def load_RGBY_image(image_id, path, mode="cam", image_size=None): if mode == "green_model": green = read_img_scale255(image_id, "green",path, image_size) stacked_images = np.transpose(np.array([green, green, green]),(1,2,0)) return stacked_images if mode=="cam": red = read_img(image_id, "red", path, image_size) green...
cnn.compile(optimizer = 'adam', loss = 'sparse_categorical_crossentropy', metrics = ['accuracy'] )
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def build_decoder(with_labels=True, target_size=(300, 300), ext='jpg'): def decode(path): if CFG.color_mode_image_level == "ggg": file_bytes = tf.io.read_file(path + "_green.png") if ext == 'png': img = tf.image.decode_png(file_bytes, channels=3) elif ext in ['jpg', 'jpeg']: img = tf.image.decode_jpeg(file_bytes, cha...
model_train = cnn.fit(x = X_train, y = y_train, validation_data =(X_val, y_val), epochs = 25 )
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class Yield_Images_Dataset(Dataset): def __init__(self, csv_file, root=PATH_TEST, transform=None): self.images_df = csv_file self.transform = transform self.root = root def __len__(self): return len(self.images_df) def __getitem__(self, idx): if torch.is_tensor(idx): idx = idx.tolist() _id = self.images_df["ID"].iloc[...
y_pred = np.argmax(cnn.predict(testing), axis = -1 )
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NUCLEI_MODEL_URL, TWO_CHANNEL_CELL_MODEL_URL) NORMALIZE = {"mean": [124 / 255, 117 / 255, 104 / 255], "std": [1 /(0.0167 * 255)] * 3} class CellSegmentator(object): def __init__( self, nuclei_model="./nuclei_model.pth", cell_model="./cell_model.pth", model_width_height=None, device="cuda", multi_channel_model=Tru...
predictions = pd.DataFrame({"ImageId" : list(range(1, len(y_pred)+1)) , "Label" : y_pred} )
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<define_variables><EOS>
predictions.to_csv('predictions.csv', index = False )
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<SOS> metric: categorizationaccuracy Kaggle data source: digit-recognizer<choose_model_class>
import pandas as pd import numpy as np import tensorflow as tf
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NUC_MODEL = ".. /input/hpacellsegmentatormodelweights/dpn_unet_nuclei_v1.pth" CELL_MODEL = ".. /input/hpacellsegmentatormodelweights/dpn_unet_cell_3ch_v1.pth" segmentator_even_faster = CellSegmentator( NUC_MODEL, CELL_MODEL, device="cuda", multi_channel_model=True, padding=True, return_without_scale_restore=True )<cre...
train=pd.read_csv('/kaggle/input/digit-recognizer/train.csv') print("Training Dataset Shape:",train.shape) train.head()
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yield_ims_1728 = Yield_Images_Dataset(predict_df_1728) yield_ims_2048 = Yield_Images_Dataset(predict_df_2048) yield_ims_3072 = Yield_Images_Dataset(predict_df_3072) yield_ims_4096 = Yield_Images_Dataset(predict_df_4096) dataloader_ims_seg_1728 = DataLoader(yield_ims_1728, batch_size=24, shuffle=False, num_workers=0...
test=pd.read_csv('/kaggle/input/digit-recognizer/test.csv') print('Test Dataset Shape:',test.shape) test.head()
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cell_masks_df = cell_masks_df.set_index('ID') cell_masks_df = cell_masks_df.reindex(index=data_df['ID']) cell_masks_df = cell_masks_df.reset_index()<set_options>
x=x.reshape(-1,28,28,1) test=test.values.reshape(-1,28,28,1) x=x/255 test=test/255 y=to_categorical(y )
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del sizes_list del even_faster_outputs del output_ids del segmentator_even_faster del yield_ims_1728 del yield_ims_2048 del yield_ims_3072 del yield_ims_4096 del dataloader_ims_seg_1728 del dataloader_ims_seg_2048 del dataloader_ims_seg_3072 del dataloader_ims_seg_4096 del dataloaders_all_sizes libc = ctypes.CDLL("libc...
train_datagen=ImageDataGenerator( rotation_range=10, width_shift_range=0.2, height_shift_range=0.2, zoom_range=0.2, fill_mode='nearest' )
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libc = ctypes.CDLL("libc.so.6") libc.malloc_trim(0) gc.collect() torch.cuda.empty_cache() torch.cuda.empty_cache() torch.cuda.empty_cache() torch.cuda.empty_cache()<prepare_x_and_y>
ensem=10 model=[0]*ensem for i in range(ensem): model[i]=Sequential() model[i].add(Conv2D(filters=32,kernel_size=(3,3),padding='same',activation='relu',input_shape=(28,28,1))) model[i].add(BatchNormalization()) model[i].add(Conv2D(filters=32,kernel_size=(3,3),padding='same',activation='relu')) model[i].add(BatchNorma...
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X_test = data_df["ID"]<train_model>
callback=tf.keras.callbacks.EarlyStopping(monitor='accuracy',min_delta=0,patience=5,mode='auto',restore_best_weights=True,verbose=0) lrs=tf.keras.callbacks.LearningRateScheduler(lambda x: 1e-3 * 0.95 ** x, verbose=0) history=[0]*ensem for i in range(ensem): train_x,valid_x,train_y,valid_y=train_test_split(x,y,test_si...
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<create_dataframe><EOS>
prediction=np.zeros(( test.shape[0],10)) for i in range(ensem): prediction=prediction+model[i].predict(test) prediction=np.argmax(prediction,axis = 1) prediction=pd.Series(prediction,name="Label") submission = pd.concat([pd.Series(range(1,28001),name="ImageId"),prediction],axis=1) submission.to_csv("digit_recognize...
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<SOS> metric: categorizationaccuracy Kaggle data source: digit-recognizer<set_options>
import numpy as np import pandas as pd import matplotlib.pyplot as plt from sklearn.model_selection import train_test_split import tensorflow as tf from kerastuner import HyperModel from kerastuner.tuners import RandomSearch from tensorflow.python.keras.callbacks import ModelCheckpoint import seaborn as sns from pylab ...
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def swish(x, beta=1.0): return x * torch.sigmoid(beta*x) def get_all_cams(batch_cam_scaled, model, scales, ims_per_batch): bs = ims_per_batch with torch.no_grad() : ori_w, ori_h = CFG.size, CFG.size strided_up_size =(CFG.size, CFG.size) all_scale_cams = torch.from_numpy(np.zeros(( bs, len(scales), 19, CFG.size, CFG.s...
rcParams['figure.figsize'] = 15, 15 NUM_CLASSES = 10 INPUT_SHAPE =(28, 28, 1 )
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label_names = [ '0-Nucleoplasm', '1-Nuclear membrane', '2-Nucleoli', '3-Nucleoli fibrillar center', '4-Nuclear speckles', '5-Nuclear bodies', '6-Endoplasmic reticulum', '7-Golgi apparatus', '8-Intermediate filaments', '9-Actin filaments', '10-Microtubules', '11-Mitotic spindle', '12-Centrosome', '13-Plasma membrane', '...
train = pd.read_csv('.. /input/digit-recognizer/train.csv') test = pd.read_csv('.. /input/digit-recognizer/test.csv') X = train.iloc[:, 1:] y = train.iloc[:, 0]
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def encode_binary_mask(mask: np.ndarray)-> t.Text: if mask.dtype != np.bool: raise ValueError( "encode_binary_mask expects a binary mask, received dtype == %s" % mask.dtype) mask = np.squeeze(mask) if len(mask.shape)!= 2: raise ValueError( "encode_binary_mask expects a 2d mask, received shape == %s" % mask.shape)...
X /= 256 test /= 256 X = X.values.reshape(( -1,)+ INPUT_SHAPE) test = test.values.reshape(( -1,)+ INPUT_SHAPE )
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def resize_mask(mask): resized_mask = resize_full_mask(mask, CFG.size) cell_masks = [] for i in range(1, np.max(mask)+1): cell_masks.append(( resized_mask == i)) return cell_masks def resize_full_mask(mask, size): resized_mask = cv2.resize(mask,(size,size),interpolation=cv2.INTER_NEAREST_EXACT) return resized_mask <...
class CNNHyperModel(HyperModel): def __init__(self, input_shape, num_classes): self.input_shape = input_shape self.num_classes = num_classes def build(self, hp): model = tf.keras.models.Sequential() model.add(tf.keras.layers.Conv2D(8, 3, padding='same', dilation_rate=(3, 3), \ activation='relu', input_shape=self.input_...
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def get_pred_string(mask_probas, cell_masks_fullsize_enc): assert len(mask_probas)== len(cell_masks_fullsize_enc), "Probas have different length than masks" string = "" for enc_mask, mask_proba in zip(cell_masks_fullsize_enc, mask_probas): for cls, proba in enumerate(mask_proba): string += str(cls)+ " " + str(proba)+ "...
hypermodel = CNNHyperModel(input_shape=INPUT_SHAPE, num_classes=NUM_CLASSES) tuner = RandomSearch( hypermodel, objective='val_accuracy', max_trials=24, executions_per_trial=1, directory='./random_search', project_name='MNIST' ) tuner.search_space_summary()
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PATH_SCALER_GRADBOOST = ".. /input/scaler-and-gradboost" scaler_resnest0 = pickle.load(open(f"{PATH_SCALER_GRADBOOST}/scaler_resnest0.pkl", 'rb')) scaler_resnest1 = pickle.load(open(f"{PATH_SCALER_GRADBOOST}/scaler_resnest1.pkl", 'rb')) scaler_effnet0 = pickle.load(open(f"{PATH_SCALER_GRADBOOST}/scaler_effnet0.pkl", 'r...
X_train_val, X_test, y_train_val, y_test = train_test_split(X, y, test_size=1/7 )
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class Classifier_EffNet(nn.Module, ABC_Model): def __init__(self, backbone, num_classes=19): super(Classifier_EffNet, self ).__init__() self.enet = EfficientNet.from_name(backbone, num_classes=num_classes, in_channels=3, include_top=False) dict_sizes = { 'efficientnet-b0' : 1280, 'efficientnet-b1' : 1280, 'efficientne...
search_results = tuner.search(X_train_val, y_train_val, epochs=10, validation_split=1/6, batch_size=100 )
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def get_separate_labels(ims, model, model_for_labels_state, ims_per_batch, verbose=False): bs = ims_per_batch model.load_state_dict(model_for_labels_state["model_state_dict"]) with torch.no_grad() : image_batch = copy.deepcopy(ims) image_batch = image_batch.float() image_batch_augs_fl2 = image_batch.flip(2) image_ba...
best_model = tuner.get_best_models(num_models=1)[0] best_model.summary() print(best_model.evaluate(X_test, y_test))
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sys.path.append(".. /input/faustomorales-vitkeras/vit_keras/") CONFIG_B = { "dropout": 0.1, "mlp_dim": 3072, "num_heads": 12, "num_layers": 12, "hidden_size": 768, } class TransformerBlock(tf.keras.layers.Layer): def __init__(self, *args, num_heads=12, mlp_dim=3072, dropout=0.1, **kwargs): super().__init__(*args, **...
def schedule(epoch, lr): return 10**(-(epoch//10)-3) lr_schedule = tf.keras.callbacks.LearningRateScheduler(schedule, verbose=1) cb_checkpointer_val = ModelCheckpoint(filepath = '.. /working/best_val.hdf5', monitor = 'val_accuracy', save_best_only = True, mode = 'auto' )
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if CFG.resnest: model_resnest = Classifier(CFG.model_name_resnest, CFG.classes, mode="normal") if CFG.color_mode == "rgby": weight = model_resnest.model.conv1[0].weight.clone() model_resnest.model.conv1[0] = nn.Conv2d(4, 64, kernel_size=(3, 3), stride=(2, 2), padding=(1, 1), bias=False) with torch.no_grad() : model_r...
X_train, X_val, y_train, y_val = train_test_split(X_train_val, y_train_val, test_size=1/6 )
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def inference_one_batch(batch_cam, batch_ids_cam, batch_seg, ims_per_batch, batch_eff_tf=None, batch_rn_tf_600=None, batch_vit_tf_384=None, show_image=True, show_seg=True, verbose=True): batch_ids_seg = tuple(batch_seg["ID"]) print(batch_ids_cam) print(batch_ids_seg) assert batch_ids_cam == batch_ids_seg, "IDS OF SE...
fit_history = best_model.fit(X_train, y_train, epochs=40, batch_size=100, validation_data=(X_val, y_val), callbacks = [lr_schedule, cb_checkpointer_val] )
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libc = ctypes.CDLL("libc.so.6") libc.malloc_trim(0) gc.collect() gc.collect() gc.collect() torch.cuda.empty_cache() torch.cuda.empty_cache() torch.cuda.empty_cache() torch.cuda.empty_cache()<define_variables>
best_model.load_weights('./best_val.hdf5') best_model.evaluate(X_test, y_test )
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if CFG.is_demo: index = 0 batch0, ids0 = next(itertools.islice(dl_test, index, None)) if CFG.extra_model_is_tf: batch_tf_green = next(itertools.islice(dtest_tf_green_600, index, None)) batch_tf_rgb_600 = next(itertools.islice(dtest_tf_rgb_600, index, None)) batch_tf_rgb_384 = next(itertools.islice(dtest_tf_ggg_384, ind...
cb_checkpointer = ModelCheckpoint(filepath = '.. /working/best.hdf5', monitor = 'accuracy', save_best_only = True, mode = 'auto' )
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df = pd.DataFrame(columns=["image_id", "pred"]) i = 0 start_time = time.time() ims_done = 0 for i,(( batch_cam, batch_ids_cam),(batch_tf_green_600),(batch_tf_rgb_600),(batch_tf_ggg_384)) in enumerate(zip(dl_test, dtest_tf_green_600, dtest_tf_rgb_600, dtest_tf_ggg_384)) : ims_per_batch = len(batch_ids_cam) batch_seg =...
final_fit_history = best_model.fit(X, y, epochs=40, batch_size=100, callbacks = [lr_schedule, cb_checkpointer] )
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sub = pd.merge( data_df, df, how="left", left_on='ID', right_on='image_id', ) def isNaN(num): return num != num for i, row in sub.iterrows() : if isNaN(row['pred']): continue sub.PredictionString.loc[i] = row['pred'] <save_to_csv>
best_model.load_weights('./best.hdf5' )
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if all(df_from_files == data_df_sample_submission): sub.to_csv("submission.csv",index=False) <install_modules>
best_model.evaluate(X, y )
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!pip install.. /input/kerasapplications/keras-team-keras-applications-3b180cb -f./ --no-index -q !pip install.. /input/efficientnet/efficientnet-1.1.0/ -f./ --no-index -q<feature_engineering>
pred = pd.DataFrame({'ImageId' : np.arange(test.shape[0])+ 1, 'Label': best_model.predict(test ).argmax(axis=-1)}) pred.to_csv('pred.csv', index=False) pred
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os.environ['SM_FRAMEWORK'] = 'tf.keras' <load_pretrained>
pip install livelossplot
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MODEL_PATH = '.. /input/train-fpn-segmentation-model-no-43/' with open(MODEL_PATH+'hparams.json')as json_file: hparams = json.load(json_file) hparams<normalization>
%matplotlib inline
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IMG_SIZE = hparams['IMG_SIZE'] SCALE_FACTOR = hparams['SCALE_FACTOR'] K_SPLITS = hparams['K_SPLITS'] def read_tif_file(fname): img = io.imread(fname) img = np.squeeze(img) if img.shape[0] == 3: img = img.swapaxes(0,1) img = img.swapaxes(1,2) return img def map_img2file(fname): img = read_tif_file(fname) dims = np....
train_set = pd.read_csv('/kaggle/input/digit-recognizer/train.csv') test_set = pd.read_csv('/kaggle/input/digit-recognizer/test.csv') img_col = 28 img_row = 28
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def rle_encode_less_memory(img): pixels = img.T.flatten() pixels[0] = 0 pixels[-1] = 0 runs = np.where(pixels[1:] != pixels[:-1])[0] + 2 runs[1::2] -= runs[::2] return ' '.join(str(x)for x in runs )<feature_engineering>
X_train_df = train_set.drop(['label'],axis = 1) y_train_df = train_set['label'] X_test_df = test_set X_tr = np.asarray(X_train_df)/255 y_tr = np.asarray(y_train_df) X_te = np.asarray(X_test_df)/255 print(type(X_tr)) print(X_tr.shape) print(X_te.shape)
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def create_TTA_batch(img): if len(img.shape)< 4: img = np.expand_dims(img, 0) batch=np.zeros(( img.shape[0]*8,img.shape[1],img.shape[2],img.shape[3]), dtype=np.float32) for i in range(img.shape[0]): orig = tf.keras.preprocessing.image.img_to_array(img[i,:,:,:])/255. batch[i*8,:,:,:] = orig batch[i*8+1,:,:,:] = np.ro...
train_set['label'].value_counts().sort_index()
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MEANING_OF_LIFE = 42 MEANING_OF_LIFE_REV = int(str(MEANING_OF_LIFE)[::-1]) PATH = '.. /input/hubmap-kidney-segmentation/test/' filelist = glob.glob(PATH+'*.tiff') if len(filelist)== 5: filelist = filelist[:1] SUB_FILE = './submission.csv' with open(SUB_FILE, 'w')as f: f.write("id,predicted ") MODELS = [MODEL_PATH+'F...
X_train_f = X_tr.reshape(42000,img_col,img_row,1) X_test_f= X_te.reshape(28000,img_col,img_row,1) y_train_f = to_categorical(y_tr) y_train_f.shape[1]
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%rm -f *.dat<import_modules>
model = Sequential() model.add(Conv2D(64,(4,4),padding = 'valid', input_shape=(28,28,1))) model.add(BatchNormalization()) model.add(Activation('relu')) model.add(MaxPooling2D(pool_size=(2, 2))) model.add(Conv2D(128,(2,2),padding = 'same')) model.add(BatchNormalization()) model.add(Activation('relu')) model.add(MaxP...
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<save_to_csv>
init_lr = 1e-2 decay_steps = 150 alpha = 1e-5 beta = 1e-8 num_periods=4 lin_cos_dec1 = tf.keras.experimental.LinearCosineDecay(init_lr, decay_steps, num_periods=num_periods, alpha=alpha, beta=beta, name='LinCosDec 1' )
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submit_file = '.. /input/hubmaplocal/FrogUnetR34_ASPP_AttDecode_final_thr0.4.csv' submission = pd.read_csv(submit_file, index_col='id') sample_sub = pd.read_csv('.. /input/hubmap-kidney-segmentation/sample_submission.csv', index_col='id') pub_ids = submission.index.values predictions = submission.values sample_sub.lo...
opt = Adam(lr=0.00005) model.compile(optimizer=opt, loss='categorical_crossentropy', metrics=['accuracy']) model.summary()
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!pip install.. /input/packages/pretrainedmodels-0.7.4-py3-none-any.whl !pip install.. /input/segmentationmodelspytorch/segmentation_models/timm-0.1.20-py3-none-any.whl !pip install.. /input/packages/efficientnet_pytorch-0.6.3-py2.py3-none-any.whl !pip install.. /input/segmentationmodelspytorch/segmentation_models/segme...
epochs = 150 batch_size = 64 X_train, X_val, y_train, y_val = train_test_split(X_train_f, y_train_f, test_size=0.3 , random_state = 5) image_gen = ImageDataGenerator(rotation_range = 25 ,shear_range = 0.25,zoom_range = [1.25,0.75],width_shift_range= 0.1,height_shift_range=0.1) image_gen2 = ImageDataGenerator() train_...
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!pip install git+https://github.com/qubvel/segmentation_models.pytorch<load_from_csv>
steps_per_epoch = train_batches.n//train_batches.batch_size validation_steps = val_batches.n//val_batches.batch_size reduce_lr = ReduceLROnPlateau(monitor='val_loss', factor=0.75,patience=3, min_lr=0.00001, mode='auto',verbose=1) callbacks = [PlotLossesKerasTF() , reduce_lr]
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sample_submission = pd.read_csv('.. /input/hubmap-kidney-segmentation/sample_submission.csv') sample_submission = sample_submission.set_index('id') seed = 1015 np.random.seed(seed) torch.manual_seed(seed) torch.cuda.manual_seed(seed) device = torch.device('cuda' if torch.cuda.is_available() else 'cpu') def rle_en...
history=model.fit_generator(generator=train_batches, steps_per_epoch = steps_per_epoch, epochs=epochs, validation_data=val_batches, validation_steps=validation_steps , callbacks=callbacks )
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<choose_model_class><EOS>
predictions = model.predict_classes(X_test_f, verbose=0) submissions=pd.DataFrame({"ImageId": list(range(1,len(predictions)+1)) , "Label": predictions}) submissions.to_csv("mysub5.csv", index=False, header=True )
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<SOS> metric: categorizationaccuracy Kaggle data source: digit-recognizer<load_pretrained>
activations, regularizers, Sequential , utils, callbacks, optimizers ) Flatten, Dense, BatchNormalization , Activation, Dropout, Conv2D, MaxPool2D )
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PATH = ".. /input/hubmap-models2/" model_names = [ "1_unet-timm-effb7_0.9509_epoch_28.pth", "2_unet-timm-effb7_0.9488_epoch_28.pth", "3_unet-timm-effb7_0.9503_epoch_29.pth", "4_unet-timm-effb7_0.9500_epoch_28.pth", "5_unet-timm-effb7_0.9518_epoch_27.pth", ] models = [] for model_name in model_names: models.append(torch...
BASEPATH = '.. /input/digit-recognizer/' def reload(df='train.csv', msg=True, path=BASEPATH): o = pd.read_csv(BASEPATH + df) print(f'{df} loaded!') return o train = reload() y_train = train.label.copy() y_train = utils.to_categorical(y_train, 10) X_train = train.drop(columns='label') def preprocess(df): df = df / 2...
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sz = 512 test_path = '.. /input/hubmap-kidney-segmentation/test/' for step, person_idx in enumerate(test_files): print(f'load {step+1}/{len(test_files)} data...') img = tiff.imread(test_path + person_idx + '.tiff' ).squeeze() if img.shape[0] == 3: img = img.transpose(1,2,0) predict_mask_l1 = np.zeros(( img.shape[0], ...
l1 = 0 l2 = 0.01 ini_lr = 0.001 val_size = 0.3 batch_size = 30 activation = 'relu' if activation == 'selu': initializer = 'lecun_normal' elif activation in ['relu', 'elu']: initializer = 'he_normal' else: initializer = 'glorot_normal' sched_lr_val_acc = True decay_rate = 0.97 X_tr, X_val, y_tr, y_val = train_test_split...
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!pip install.. /input/keras-applications/Keras_Applications-1.0.8/ -f./ --no-index !pip install.. /input/image-classifiers/image_classifiers-1.0.0/ -f./ --no-index !pip install.. /input/efficientnet-1-0-0/efficientnet-1.0.0/ -f./ --no-index !pip install.. /input/segmentation-models/segmentation_models-1.0.1/ -f./ --no-...
def get_regularizer(l1=l1, l2=l2): return regularizers.l1_l2(l1=l1, l2=l2) def get_optimizer(lr=ini_lr, beta_1=0.9, beta_2=0.999 , decay_rate=decay_rate , n_samples=n_train_samples, batch_size=batch_size): if sched_lr_val_acc == False: lr = optimizers.schedules.ExponentialDecay( lr , decay_steps = n_samples // batch_...
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%env SM_FRAMEWORK=tf.keras<set_options>
verbose = 1 model = get_model(n_samples=n_train_val_samples) print(model.summary()) epochs = 100 cb = get_callbacks() history = model.fit(tr_set, epochs = epochs , steps_per_epoch = n_train_val_samples // batch_size , validation_data = val_set , callbacks = cb , verbose = verbose )
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warnings.filterwarnings('ignore') print('tensorflow version:', tf.__version__) os.environ['CUDA_VISIBLE_DEVICES'] = '0' gpu_devices = tf.config.experimental.list_physical_devices('GPU') if gpu_devices: for gpu_device in gpu_devices: print('device available:', gpu_device) pd.set_option('display.max_columns', None )<...
y_pred = model.predict(test_set) y_pred = np.argmax(y_pred, axis=1) submission = reload('sample_submission.csv') submission['Label'] = y_pred submission.to_csv('submission.csv', index=False )
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TEST = True KAGGLE = True MDLS_FOLDS = {'v39': [0, 2, 3, 4]} if KAGGLE: DATA_PATH = '.. /input/hubmap-kidney-segmentation' MDLS_PATHS = {ver: f'.. /input/kidney-models-{ver}' for ver, _ in MDLS_FOLDS.items() } else: DATA_PATH = './data2' MDLS_PATHS = {ver: f'./models_{ver}' for ver, _ in MDLS_FOLDS.items() } THRESHOLD ...
train, test = pd.read_csv('.. /input/digit-recognizer/train.csv'), \ pd.read_csv('.. /input/digit-recognizer/test.csv') train.head()
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params_dict = {} for ver, _ in MDLS_FOLDS.items() : with open(f'{MDLS_PATHS[ver]}/params.json')as file: params_dict[ver] = json.load(file) for ver, params in params_dict.items() : print('version:', ver, '| loaded params:', params, ' ' )<categorify>
y_train = train['label'] x_train, x_test = train.iloc[:,1:], test
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def enc2mask(encs, shape): img = np.zeros(shape[0] * shape[1], dtype=np.uint8) for m, enc in enumerate(encs): if isinstance(enc, np.float)and np.isnan(enc): continue s = enc.split() for i in range(len(s)// 2): start = int(s[2 * i])- 1 length = int(s[2 * i + 1]) img[start : start + length] = 1 + m return img.reshape(s...
x_train, x_test = x_train / 255., x_test / 255. x_train, x_test = x_train.values.reshape(-1,28,28,1),\ x_test.values.reshape(-1,28,28,1 )
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def dice_coef(y_true, y_pred, smooth=1): y_true_f = K.flatten(y_true) y_pred_f = K.flatten(y_pred) intersection = K.sum(y_true_f * y_pred_f) return(2 * intersection + smooth)/(K.sum(y_true_f)+ K.sum(y_pred_f)+ smooth) def dice_loss(y_true, y_pred, smooth=1): return(1 - dice_coef(y_true, y_pred, smooth)) def bce_dic...
y_train = to_categorical(y_train, num_classes=10 )
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def make_grid(shape, window=256, min_overlap=32): x, y = shape nx = x //(window - min_overlap)+ 1 x1 = np.linspace(0, x, num=nx, endpoint=False, dtype=np.int64) x1[-1] = x - window x2 =(x1 + window ).clip(0, x) ny = y //(window - min_overlap)+ 1 y1 = np.linspace(0, y, num=ny, endpoint=False, dtype=np.int64) y1[-1] =...
model = tf.keras.models.Sequential([ tf.keras.layers.Conv2D(filters=32, kernel_size=(5,5), \ activation='relu', input_shape=(28,28,1)) , tf.keras.layers.MaxPooling2D(pool_size=(2,2)) , tf.keras.layers.BatchNormalization() , tf.keras.layers.Conv2D(filters=64, kernel_size=(3,3), \ activation='relu', input_shape=(28,28,...
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img_files = [x for x in os.listdir(SUB_PATH)if '.tiff' in x] print('images idxs:', img_files )<create_dataframe>
num_epochs = 50 history = model.fit(x_train, y_train, epochs=num_epochs, callbacks=[ tf.keras.callbacks.EarlyStopping(monitor='loss', patience=6), tf.keras.callbacks.ReduceLROnPlateau(monitor='loss', patience=4) ], validation_split=0.2, verbose=0 )
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df_sub = pd.DataFrame(subm ).T df_sub<save_to_csv>
scores = model.evaluate(x_train, y_train, batch_size=32) print(f'Loss: {scores[0]} Accuracy: {scores[1]}' )
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df_sub.to_csv('submission.csv', index=False )<set_options>
y_predicted = model.predict(x_test) y_test_labels = np.argmax(y_predicted, axis=1 )
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color = sns.color_palette() %matplotlib inline warnings.filterwarnings("ignore") pd.set_option('display.max_columns', 500) pd.set_option('display.max_rows', 50 )<load_from_csv>
x_test_ids = [(i + 1)for i in range(x_test.shape[0])]
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<feature_engineering><EOS>
results = pd.DataFrame({ 'ImageId': x_test_ids, 'Label': y_test_labels }) results.to_csv('submission.csv', index=False )
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<SOS> metric: categorizationaccuracy Kaggle data source: digit-recognizer<filter>
DEVICE = "TPU" SEED = 8080 FOLDS = 5 FOLD_WEIGHTS = [1./FOLDS]*FOLDS BATCH_SIZE = 256 EPOCHS = 5000 MONITOR = "val_loss" MONITOR_MODE = "min" ES_PATIENCE = 5 LR_PATIENCE = 0 LR_FACTOR = 0.5 EFF_NET = 3 EFF_NET_WEIGHTS = 'noisy-student' LABEL_SMOOTHING = 0.1 VERBOSE = 1
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df_train[(df_train['floor'])== 33]<drop_column>
!pip install -q efficientnet >> /dev/null
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df_train.drop(df_train.index[7457], inplace=True )<data_type_conversions>
import numpy as np import pandas as pd from tqdm import tqdm import matplotlib.pyplot as plt import tensorflow as tf import tensorflow.keras.backend as K import efficientnet.tfkeras as efn from sklearn.model_selection import KFold from keras.preprocessing.image import ImageDataGenerator
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df_train['year'] = df_train['timestamp'].apply(lambda x: x[:4] ).astype(int) df_train['month'] = df_train['timestamp'].apply(lambda x: x[5:7] ).astype(int) df_test['year'] = df_test['timestamp'].apply(lambda x: x[:4] ).astype(int) df_test['month'] = df_test['timestamp'].apply(lambda x: x[5:7] ).astype(int )<sort_val...
if DEVICE == "TPU": print("connecting to TPU...") try: tpu = tf.distribute.cluster_resolver.TPUClusterResolver() print('Running on TPU ', tpu.master()) except ValueError: print("Could not connect to TPU") tpu = None if tpu: try: print("initializing TPU...") tf.config.experimental_connect_to_cluster(tpu) tf.tpu.exp...
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missingValues = df_train.columns[df_train.isnull().any() ].tolist() pd.isnull(df_train[missingValues] ).sum().sort_values(ascending=False )<define_variables>
train = pd.read_csv("/kaggle/input/digit-recognizer/train.csv") train.describe()
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cols_fillna_mode = ['floor', 'product_type', 'num_room', 'state', 'hospital_beds_raion', 'build_count_brick', 'build_count_monolith', 'green_part_2000'] cols_fillna_mean = ['life_sq', 'metro_min_walk', 'metro_km_walk', 'railroad_station_walk_km', 'railroad_station_walk_min', 'cafe_sum_1500_min_price_avg', 'cafe_sum_150...
X = train.drop(labels=['label'], axis=1) X = X.astype('float32') X = X / 255 X = X.values.reshape(X.shape[0],28,28,1) X = np.pad(X,(( 0,0),(2,2),(2,2),(0,0)) , mode='constant') X = np.squeeze(X, axis=-1) X = stacked_img = np.stack(( X,)*3, axis=-1) X.shape
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for col in cols_fillna_mode: df_train[col].fillna(df_train[col].mode().iloc[0],inplace=True) df_test[col].fillna(df_train[col].mode().iloc[0],inplace=True) for col in cols_fillna_mean: df_train[col].fillna(df_train[col].mean() ,inplace=True) df_test[col].fillna(df_train[col].mean() ,inplace=True )<define_variables>
y = train['label'].values.astype('float32') y = tf.keras.utils.to_categorical(y, 10) y
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numerical_features = df_train.dtypes[df_train.dtypes != "object"].index categorical_features = df_train.dtypes[df_train.dtypes == "object"].index print("Кол-во количественных признаков: ", len(numerical_features)) print("Кол-во категориальных признаков: ", len(categorical_features))<sort_values>
test = pd.read_csv("/kaggle/input/digit-recognizer/test.csv") test.describe()
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df_train.isna().sum().sort_values(ascending=False )<drop_column>
X_test = test.astype('float32') X_test = X_test / 255 X_test = X_test.values.reshape(X_test.shape[0],28,28,1) X_test = np.pad(X_test,(( 0,0),(2,2),(2,2),(0,0)) , mode='constant') X_test = np.squeeze(X_test, axis=-1) X_test = stacked_img = np.stack(( X_test,)*3, axis=-1) X_test.shape
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df_train.drop(['id', 'price_doc', 'timestamp'], axis=1, inplace=True) id_test = df_test['id'] df_test.drop(['id', 'timestamp'], axis=1, inplace=True )<define_variables>
datagen = ImageDataGenerator( featurewise_center=False, samplewise_center=False, featurewise_std_normalization=False, samplewise_std_normalization=False, zca_whitening=False, rotation_range=10, zoom_range = 0.1, width_shift_range=0.1, height_shift_range=0.1, horizontal_flip=False, vertical_flip=False )
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numerical_features = df_train.dtypes[df_train.dtypes != "object"].index categorical_features = df_train.dtypes[df_train.dtypes == "object"].index print("Кол-во количественных признаков: ", len(numerical_features)) print("Кол-во категориальных признаков: ", len(categorical_features))<categorify>
eff_nets = [ efn.EfficientNetB0, efn.EfficientNetB1, efn.EfficientNetB2, efn.EfficientNetB3, efn.EfficientNetB4, efn.EfficientNetB5, efn.EfficientNetB6, efn.EfficientNetB7, efn.EfficientNetL2, ] def build_model() : inp = tf.keras.layers.Input(shape=(X.shape[1], X.shape[2], X.shape[3])) oup = eff_nets[EFF_NET]( input_s...
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encoder = OneHotEncoder(handle_unknown='error') encoder_cols_train = pd.DataFrame(encoder.fit_transform(df_train[categorical_features] ).toarray()) encoder_cols_test = pd.DataFrame(encoder.transform(df_test[categorical_features] ).toarray() )<categorify>
%%time oof = np.zeros(( X.shape[0], y.shape[1])) preds = np.zeros(( X_test.shape[0], y.shape[1])) skf = KFold(n_splits=FOLDS,shuffle=True,random_state=SEED) for fold,(idxT,idxV)in enumerate(skf.split(X)) : if DEVICE=='TPU': if tpu: tf.tpu.experimental.initialize_tpu_system(tpu) print(' print(' print(' K.clear_session...
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encoder_cols_train.columns = encoder.get_feature_names(categorical_features) encoder_cols_test.columns = encoder.get_feature_names(categorical_features) encoder_cols_train.index = df_train.index encoder_cols_test.index = df_test.index<drop_column>
final_predictions = pd.Series(np.argmax(preds, axis=1), name="Label") submission = pd.concat([pd.Series(range(1,28001),name = "ImageId"),final_predictions], axis=1) submission.to_csv("submission.csv",index=False) submission.head()
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num_df_train = df_train.drop(categorical_features, axis=1) num_df_test = df_test.drop(categorical_features, axis=1 )<categorify>
train = pd.read_csv(".. /input/digit-recognizer/train.csv") test = pd.read_csv(".. /input/digit-recognizer/test.csv" )
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df_train_encoded = pd.concat([num_df_train, encoder_cols_train], axis=1) df_test_encoded = pd.concat([num_df_test, encoder_cols_test], axis=1) print("Train dataset shape:", df_train_encoded.shape) print("Test dataset shape:", df_test_encoded.shape )<sort_values>
( x_train1, y_train1),(x_test1, y_test1)= mnist.load_data() train1 = np.concatenate([x_train1, x_test1], axis=0) y_train1 = np.concatenate([y_train1, y_test1], axis=0) Y_train1 = y_train1 X_train1 = train1.reshape(-1, 28*28 )
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df_train_encoded.median().sort_values(ascending=False )<train_model>
X_train = X_train / 255.0 test = test / 255.0 X_train1 = X_train1 / 255.0
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X = df_train_encoded.drop(['price_doc_log'], axis=1) y = df_train_encoded['price_doc_log'] print("X shape:", X.shape) print("y shape:", y.shape )<split>
X_train = np.concatenate(( X_train.values, X_train1)) Y_train = np.concatenate(( Y_train, Y_train1))
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X_train, X_val, y_train, y_val = train_test_split(X, y, test_size=0.2, random_state=2022) X_test = df_test_encoded<predict_on_test>
Y_train = to_categorical(Y_train, num_classes = 10 )
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tree = DecisionTreeRegressor(random_state=2022, max_depth=5, min_samples_split=20) tree.fit(X_train, y_train) tree_predictions_log = tree.predict(X_val) tree_predictions = np.exp(tree_predictions_log )<compute_test_metric>
random_seed = 2
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print('RMSLE:', np.sqrt(mean_squared_log_error(np.exp(y_val), tree_predictions)) )<predict_on_test>
X_train, X_val, Y_train, Y_val = train_test_split(X_train, Y_train, test_size = 0.1, random_state=random_seed )
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predict = np.exp(tree.predict(X_test)) submission = pd.DataFrame({'id': id_test, 'price_doc': predict}) submission.head()<save_to_csv>
model = Sequential() model.add(Conv2D(filters = 64, kernel_size =(5,5),padding = 'Same', activation ='relu', input_shape =(28,28,1))) model.add(BatchNormalization()) model.add(Conv2D(filters = 64, kernel_size =(5,5),padding = 'Same', activation ='relu')) model.add(BatchNormalization()) model.add(MaxPool2D(pool_siz...
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submission.to_csv('DecisionTree.csv', index=False )<prepare_x_and_y>
optimizer = RMSprop(lr=0.001, rho=0.9, epsilon=1e-08, decay=0.0 )
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dmatrix_train = xgb.DMatrix(X_train, y_train) dmatrix_val = xgb.DMatrix(X_val, y_val) dmatrix_test = xgb.DMatrix(X_test )<train_model>
model.compile(optimizer = optimizer , loss = "categorical_crossentropy", metrics=["accuracy"] )
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xgb_params = { 'eta': 0.05, 'max_depth': 5, 'subsample': 1.0, 'colsample_bytree': 0.7, 'objective': 'reg:squarederror', 'eval_metric': 'rmse', 'verbosity': 0 } partial_model = xgb.train(xgb_params, dmatrix_train, num_boost_round=1000, evals=[(dmatrix_val, 'val')], early_stopping_rounds=20, verbose_eval=20) num_boost_r...
learning_rate_reduction = ReduceLROnPlateau(monitor='val_acc', patience=3, verbose=1, factor=0.5, min_lr=0.00001 )
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model = xgb.train(dict(xgb_params, verbose=1), dmatrix_train, num_boost_round=num_boost_round )<predict_on_test>
epochs = 50 batch_size = 32
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predict = np.exp(model.predict(dmatrix_val)) print('RMSLE:', np.sqrt(mean_squared_log_error(np.exp(y_val), predict)) )<predict_on_test>
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ylog_pred = model.predict(dmatrix_test) y_pred = np.exp(ylog_pred) submission = pd.DataFrame({'id': id_test, 'price_doc': y_pred}) submission.head()<save_to_csv>
datagen = ImageDataGenerator( featurewise_center=False, samplewise_center=False, featurewise_std_normalization=False, samplewise_std_normalization=False, zca_whitening=False, rotation_range=10, zoom_range = 0.1, width_shift_range=0.1, height_shift_range=0.1, horizontal_flip=False, vertical_flip=False) datagen.fit(X_t...
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submission.to_csv("XGB_new_clear_submission.csv", index=False )<prepare_x_and_y>
history = model.fit_generator(datagen.flow(X_train,Y_train, batch_size=batch_size), epochs = epochs, validation_data =(X_val,Y_val), verbose = 2, steps_per_epoch=X_train.shape[0] // batch_size , callbacks=[learning_rate_reduction] )
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dmatrix_train = xgb.DMatrix(X_train, y_train) dmatrix_test = xgb.DMatrix(X_test )<init_hyperparams>
results = model.predict(test) results = np.argmax(results,axis = 1) results = pd.Series(results,name="Label" )
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xgb_params = { 'eta': 0.05, 'max_depth': 5, 'subsample': 0.7, 'colsample_bytree': 0.7, 'objective': 'reg:squarederror', 'eval_metric': 'rmse', 'verbosity': 0 }<compute_train_metric>
submission = pd.concat([pd.Series(range(1,28001),name = "ImageId"),results],axis = 1) submission.to_csv("cnn_mnist_submission.csv",index=False )
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cv_output = xgb.cv(xgb_params, dmatrix_train, num_boost_round=1000, early_stopping_rounds=20, verbose_eval=50, show_stdv=False) num_boost_rounds = len(cv_output )<train_model>
import matplotlib.pyplot as plt
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model = xgb.train(dict(xgb_params, verbose=1), dmatrix_train, num_boost_round=num_boost_rounds )<predict_on_test>
train = pd.read_csv(".. /input/digit-recognizer/train.csv") test = pd.read_csv(".. /input/digit-recognizer/test.csv" )
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predict = np.exp(model.predict(dmatrix_test)) submission = pd.DataFrame({'id': id_test, 'price_doc': predict}) submission.head()<save_to_csv>
sample_submission = pd.read_csv('.. /input/digit-recognizer/sample_submission.csv' )
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submission.to_csv('XGB_CV.csv', index=False )<split>
X_train = train.drop(['label'], axis = 1) y_train = train['label'] X_test = test X_train = X_train / 255.0 X_test = X_test / 255.0
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X_train, X_val, y_train, y_val = train_test_split(X, y, test_size=0.2, random_state=2022) X_test = df_test_encoded<categorify>
X_train=X_train.values X_test=X_test.values test=test.values X_train=X_train.reshape(X_train.shape[0], 28, 28, 1) X_test=X_test.reshape(X_test.shape[0], 28, 28, 1) test=test.reshape(test.shape[0] , 28 , 28 , 1 )
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pca = PCA(n_components=20 ).fit(X_train) X_train_pca=pca.transform(X_train) X_val_pca=pca.transform(X_val )<prepare_x_and_y>
import tensorflow as tf from tensorflow.keras.layers import Dense, Flatten, Conv2D, MaxPool2D, Dropout from tensorflow.keras.models import Sequential from tensorflow.keras.callbacks import EarlyStopping
Digit Recognizer