From 36720c72046133706957e6f7db5397b0de189258 Mon Sep 17 00:00:00 2001
From: PNRIA - Julien <julien.rabault@irit.fr>
Date: Tue, 17 May 2022 10:59:06 +0200
Subject: [PATCH] Add README.md
---
.gitignore | 10 +-
Configuration/Configuration.py | 17 ---
Configuration/config.ini | 18 ---
Datasets/index_to_pos1.pkl | Bin 0 -> 1632 bytes
Datasets/index_to_super.pkl | Bin 0 -> 168867 bytes
.../{m2_dataset_V2.csv => m2_dataset.csv} | 0
README.md | 76 +++++++++++-
SuperTagger/SuperTagger.py | 113 +++++++++++++-----
SuperTagger/Utils/SentencesTokenizer.py | 24 ----
SuperTagger/Utils/utils.py | 11 +-
bash_GPU.sh | 13 --
requirements.txt | Bin 99 -> 476 bytes
train.py | 12 +-
13 files changed, 170 insertions(+), 124 deletions(-)
delete mode 100644 Configuration/Configuration.py
delete mode 100644 Configuration/config.ini
create mode 100644 Datasets/index_to_pos1.pkl
create mode 100644 Datasets/index_to_super.pkl
rename Datasets/{m2_dataset_V2.csv => m2_dataset.csv} (100%)
delete mode 100644 bash_GPU.sh
diff --git a/.gitignore b/.gitignore
index 371503a..f57c436 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,17 +1,11 @@
.idea
-tests
venv
*.pyc
.DS_Store
-.env
-./bash_GPU.sh
-push pull texte
-logs
-Output
.data
TensorBoard
models
-*.pkl
-good_models/model_check.pt
+good_models
main.py
*.pt
+Datasets/Utils
diff --git a/Configuration/Configuration.py b/Configuration/Configuration.py
deleted file mode 100644
index 3d94c9b..0000000
--- a/Configuration/Configuration.py
+++ /dev/null
@@ -1,17 +0,0 @@
-import os
-from configparser import ConfigParser
-
-# Read configuration file
-path_current_directory = os.path.dirname(__file__)
-path_config_file = os.path.join(path_current_directory, 'config.ini')
-config = ConfigParser()
-config.read(path_config_file)
-
-# region Get section
-
-version = config["VERSION"]
-
-modelDecoderConfig = config["MODEL_DECODER"]
-modelTrainingConfig = config["MODEL_TRAINING"]
-
-# endregion Get section
diff --git a/Configuration/config.ini b/Configuration/config.ini
deleted file mode 100644
index 3fb0157..0000000
--- a/Configuration/config.ini
+++ /dev/null
@@ -1,18 +0,0 @@
-[VERSION]
-transformers = 4.16.2
-[MODEL_DECODER]
-dim_encoder = 768
-dim_decoder = 128
-num_rnn_layers=1
-dropout=0.1
-teacher_forcing=0.05
-[MODEL_TRAINING]
-batch_size=16
-epoch=10
-seed_val=42
-learning_rate=0.005
-use_checkpoint_SAVE=1
-output_path=Output
-use_checkpoint_LOAD=1
-input_path=models_save
-model_to_load=model_check.pt
\ No newline at end of file
diff --git a/Datasets/index_to_pos1.pkl b/Datasets/index_to_pos1.pkl
new file mode 100644
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diff --git a/Datasets/m2_dataset_V2.csv b/Datasets/m2_dataset.csv
similarity index 100%
rename from Datasets/m2_dataset_V2.csv
rename to Datasets/m2_dataset.csv
diff --git a/README.md b/README.md
index 5994f14..5ece8c3 100644
--- a/README.md
+++ b/README.md
@@ -1,15 +1,87 @@
# DeepGrail
+This repository contains a Python implementation of BertForTokenClassification using TLGbank data to develop
+part-of-speech taggers and supertaggers.
+
+This code was designed to work with the [DeepGrail Linker](https://gitlab.irit.fr/pnria/global-helper/deepgrail-linker)
+to provide a wide coverage syntactic and semantic parser for French. But the Tagger is independent, you can use it for your own tags.
+
## Usage
+### Structure
+
+```
+.
+├── Datasets # TLGbank data
+├── SuperTagger # Implementation of BertForTokenClassification
+│ ├── SuperTagger.py # Main class
+│ └── Tagging_bert_model.py # Bert model
+├── predict.py # Example of prediction
+└── train.py # Example of train
+```
+
### Installation
+
Python 3.9.10 **(Warning don't use Python 3.10**+**)**
Clone the project locally. In a clean python venv do `pip install -r requirements.txt`
+Download already trained models or prepare data for **your** train.
+
## How To use
-TODO ...
+**predict.py** and **train.py** show simple examples of how to use the model, feel free to look at them before using the
+SupperTagger
+
+### Utils
+
+For load **m2_dataset.csv**, you can use `SuperTagger.Utils.utils.read_csv_pgbar(...)`. This function return a pandas
+dataframe.
+
+### Prediction
+
+For predict on your data you need to load a model (save with this code).
+
+```
+df = read_csv_pgbar(file_path,20)
+texts = df['X'].tolist()
+
+tagger = SuperTagger()
+
+tagger.load_weights("your/model/path")
+
+pred_without_argmax, pred_convert, bert_hidden_state = tagger.predict(texts[7])
+
+print(pred_convert)
+#['let', 'dr(0,s,s)', 'let', 'dr(0,dr(0,s,s),np)', 'dr(0,np,n)', 'dr(0,n,n)', 'let', 'n', 'let', 'dl(0,n,n)', 'dr(0,dl(0,dl(0,n,n),dl(0,n,n)),dl(0,n,n))', 'dl(0,n,n)', 'let', 'dr(0,np,np)', 'np', 'dr(0,dl(0,np,np),np)', 'np', 'dr(0,dl(0,np,np),np)', 'np', 'dr(0,dl(0,np,s),dl(0,np,s))', 'dr(0,dl(0,np,s),np)', 'dl(1,s,s)', 'np', 'dr(0,dl(0,np,np),n)', 'n', 'dl(0,s,txt)']
+```
+
+### Training
+
+```
+df = read_csv_pgbar(file_path,1000)
+texts = df['X'].tolist()
+tags = df['Z'].tolist()
+
+#Dict for convert ID to token (The dict is save with the model for prediction)
+index_to_super = load_obj('Datasets/index_to_super')
+
+tagger = SuperTagger()
+
+bert_name = 'camembert-base'
+
+tagger.create_new_model(len(index_to_super), bert_name, index_to_super)
+# You can load your model for re-train this
+# tagger.load_weights("your/model/path")
+
+tagger.train(texts,tags, checkpoint=True)
+
+pred_without_argmax, pred_convert, bert_hidden_state = tagger.predict(texts[7])
+```
+
+In train, if you use `checkpoint=True`, the model is automatically saved in a folder: Training_XX-XX_XX-XX. It saves after each epoch.
+Use `tensorboard=True` for log in same folder. (`tensorboard --logdir=logs` for see logs)
-tensorboard --logdir=logs
+## Authors
+[Rabault Julien](https://www.linkedin.com/in/julienrabault), de Pourtales Caroline
\ No newline at end of file
diff --git a/SuperTagger/SuperTagger.py b/SuperTagger/SuperTagger.py
index 70c1592..95b3d59 100644
--- a/SuperTagger/SuperTagger.py
+++ b/SuperTagger/SuperTagger.py
@@ -1,26 +1,45 @@
+import datetime
import os
import sys
-
import time
-import datetime
-from tkinter import Variable
import torch
import transformers
-from torch import nn
+from torch import nn, Tensor
from torch.optim import Adam
+from torch.utils.data import Dataset, TensorDataset, random_split, DataLoader
from torch.utils.tensorboard import SummaryWriter
from tqdm import tqdm
from transformers import AutoTokenizer
-
-from torch.utils.data import Dataset, TensorDataset, random_split
+from transformers import logging
from SuperTagger.Utils.SentencesTokenizer import SentencesTokenizer
from SuperTagger.Utils.SymbolTokenizer import SymbolTokenizer
from SuperTagger.Utils.Tagging_bert_model import Tagging_bert_model
+logging.set_verbosity(logging.ERROR)
+
+
+def output_create_dir():
+ """
+
+ @return:
+ """
+ from datetime import datetime
+ outpout_path = 'TensorBoard'
+ training_dir = os.path.join(outpout_path, 'Tranning_' + datetime.today().strftime('%d-%m_%H-%M'))
+ logs_dir = os.path.join(training_dir, 'logs')
+ writer = SummaryWriter(log_dir=logs_dir)
+ return training_dir, writer
+
-def categorical_accuracy(preds, truth):
+def categorical_accuracy(preds: list[list[int]], truth: list[list[int]]) -> float:
+ """
+
+ @param preds:
+ @param truth:
+ @return:
+ """
good_label = 0
nb_label = 0
for i in range(len(truth)):
@@ -48,7 +67,9 @@ def format_time(elapsed):
class SuperTagger:
def __init__(self):
+ """
+ """
self.index_to_tags = None
self.num_label = None
self.bert_name = None
@@ -65,7 +86,11 @@ class SuperTagger:
self.trainable = False
self.model_load = False
- def load_weights(self, model_file):
+ def load_weights(self, model_file: str):
+ """
+ yo mec
+ @param model_file:
+ """
self.trainable = False
print("#" * 15)
@@ -95,8 +120,13 @@ class SuperTagger:
self.model_load = True
self.trainable = True
- def create_new_model(self, num_label, bert_name, index_to_tags: dict):
+ def create_new_model(self, num_label: int, bert_name: str, index_to_tags: dict):
+ """
+ @param num_label:
+ @param bert_name:
+ @param index_to_tags:
+ """
assert len(
index_to_tags) == num_label, f" len(index_to_tags) : {len(index_to_tags)} must be equels with num_label: {num_label}"
@@ -114,9 +144,15 @@ class SuperTagger:
self.trainable = True
self.model_load = True
- def predict(self, sentences):
+ def predict(self, sentences: list[str]) -> (list[list[list[float]]], list[list[str]], Tensor):
+ """
+ @param sentences:
+ @return:
+ """
assert self.trainable or self.model is None, "Please use the create_new_model(...) or load_weights(...) function before the predict, the model is not integrated"
+ sentences = [sentences] if type(sentences) == str else sentences
+
self.model.eval()
with torch.no_grad():
sents_tokenized_t, sents_mask_t = self.sent_tokenizer.fit_transform_tensors(sentences)
@@ -127,13 +163,23 @@ class SuperTagger:
return preds, self.tags_tokenizer.convert_ids_to_tags(preds.detach()), hidden
- def train(self, sentences, tags, validation_rate=0.1, epochs=20, batch_size=32, tensorboard=False,
+ def train(self, sentences: list[str], tags: list[list[str]], validation_rate=0.1, epochs=20, batch_size=32,
+ tensorboard=False,
checkpoint=False):
-
+ """
+
+ @param sentences:
+ @param tags:
+ @param validation_rate:
+ @param epochs:
+ @param batch_size:
+ @param tensorboard:
+ @param checkpoint:
+ """
assert self.trainable or self.model is None, "Please use the create_new_model(...) or load_weights(...) function before the train, the model is not integrated"
if checkpoint or tensorboard:
- checkpoint_dir, writer = self.__output_create()
+ checkpoint_dir, writer = output_create_dir()
training_dataloader, validation_dataloader = self.__preprocess_data(batch_size, sentences, tags,
1 - validation_rate)
@@ -171,8 +217,16 @@ class SuperTagger:
if checkpoint:
self.__checkpoint_save(path=os.path.join(checkpoint_dir, 'model_check.pt'))
- def __preprocess_data(self, batch_size, sentences, tags, validation_rate):
+ def __preprocess_data(self, batch_size: int, sentences: list[str], tags: list[list[str]],
+ validation_rate: float) -> (DataLoader, DataLoader):
+ """
+ @param batch_size:
+ @param sentences:
+ @param tags:
+ @param validation_rate:
+ @return:
+ """
validation_dataloader = None
sents_tokenized_t, sents_mask_t = self.sent_tokenizer.fit_transform_tensors(sentences)
@@ -191,15 +245,12 @@ class SuperTagger:
training_dataloader = torch.utils.data.DataLoader(train_dataset, batch_size=batch_size, shuffle=True)
return training_dataloader, validation_dataloader
- def __output_create(self):
- from datetime import datetime
- outpout_path = 'TensorBoard'
- training_dir = os.path.join(outpout_path, 'Tranning_' + datetime.today().strftime('%d-%m_%H-%M'))
- logs_dir = os.path.join(training_dir, 'logs')
- writer = SummaryWriter(log_dir=logs_dir)
- return training_dir, writer
+ def __train_epoch(self, training_dataloader: DataLoader) -> (float, float, str):
+ """
- def __train_epoch(self, training_dataloader):
+ @param training_dataloader:
+ @return:
+ """
self.model.train()
epoch_loss = 0
epoch_acc = 0
@@ -217,8 +268,6 @@ class SuperTagger:
predictions = torch.argmax(logit, dim=2).detach().cpu().numpy()
label_ids = targets.cpu().numpy()
- # torch.nn.functional.one_hot(targets).long()
- # torch.argmax(logit)
acc = categorical_accuracy(predictions, label_ids)
@@ -238,11 +287,17 @@ class SuperTagger:
return epoch_acc, epoch_loss, training_time
- def foward(self,b_sents_tokenized, b_sents_mask):
+ def foward(self, b_sents_tokenized: Tensor, b_sents_mask: Tensor) -> (Tensor, Tensor):
+ """
+
+ @param b_sents_tokenized:
+ @param b_sents_mask:
+ @return:
+ """
_, logit, hidden = self.model((b_sents_tokenized, b_sents_mask))
return logit, hidden
- def __eval_epoch(self, validation_dataloader):
+ def __eval_epoch(self, validation_dataloader: DataLoader) -> (float, float, int):
self.model.eval()
eval_loss = 0
eval_accuracy = 0
@@ -270,6 +325,10 @@ class SuperTagger:
return eval_accuracy, eval_loss, nb_eval_steps
def __checkpoint_save(self, path='/model_check.pt'):
+ """
+
+ @param path:
+ """
self.model.cpu()
# print('save model parameters to [%s]' % path, file=sys.stderr)
@@ -279,5 +338,3 @@ class SuperTagger:
'optimizer': self.optimizer,
}, path)
self.model.to(self.device)
-
-
diff --git a/SuperTagger/Utils/SentencesTokenizer.py b/SuperTagger/Utils/SentencesTokenizer.py
index f1fbea5..ee72006 100644
--- a/SuperTagger/Utils/SentencesTokenizer.py
+++ b/SuperTagger/Utils/SentencesTokenizer.py
@@ -1,6 +1,3 @@
-import numpy as np
-import torch
-
class SentencesTokenizer():
@@ -12,28 +9,7 @@ class SentencesTokenizer():
return self.tokenizer(sents, padding=True)
def fit_transform_tensors(self, sents):
- # , return_tensors = 'pt'
temp = self.tokenizer(sents, padding=True, return_tensors = 'pt')
- #
- # len_sent_max = len(temp['attention_mask'][0])
- #
- # input_ids = np.ones((len(sents),len_sent_max))
- # attention_mask = np.zeros((len(sents),len_sent_max))
- #
- # for i in range(len(temp['offset_mapping'])):
- # h = 1
- # input_ids[i][0] = self.tokenizer.cls_token_id
- # attention_mask[i][0] = 1
- # for j in range (1,len_sent_max-1):
- # if temp['offset_mapping'][i][j][1] != temp['offset_mapping'][i][j+1][0]:
- # input_ids[i][h] = temp['input_ids'][i][j]
- # attention_mask[i][h] = 1
- # h += 1
- # input_ids[i][h] = self.tokenizer.eos_token_id
- # attention_mask[i][h] = 1
- #
- # input_ids = torch.tensor(input_ids).long()
- # attention_mask = torch.tensor(attention_mask)
return temp["input_ids"], temp["attention_mask"]
diff --git a/SuperTagger/Utils/utils.py b/SuperTagger/Utils/utils.py
index 03aadfe..4c22a68 100644
--- a/SuperTagger/Utils/utils.py
+++ b/SuperTagger/Utils/utils.py
@@ -1,7 +1,4 @@
-import datetime
-
import pandas as pd
-import torch
from tqdm import tqdm
@@ -16,7 +13,8 @@ def read_csv_pgbar(csv_path, nrows=float('inf'), chunksize=100):
rows = nrows
with tqdm(total=rows, desc='Rows read: ') as bar:
- for chunk in pd.read_csv(csv_path, converters={'Y1': pd.eval,'Y2': pd.eval,'Z': pd.eval}, chunksize=chunksize, nrows=rows):
+ for chunk in pd.read_csv(csv_path, converters={'Y1': pd.eval, 'Y2': pd.eval, 'Z': pd.eval}, chunksize=chunksize,
+ nrows=rows):
chunk_list.append(chunk)
bar.update(len(chunk))
@@ -24,5 +22,10 @@ def read_csv_pgbar(csv_path, nrows=float('inf'), chunksize=100):
print("#" * 20)
return df
+def load_obj(name):
+ with open(name + '.pkl', 'rb') as f:
+ import pickle
+ return pickle.load(f)
+
diff --git a/bash_GPU.sh b/bash_GPU.sh
deleted file mode 100644
index 665f769..0000000
--- a/bash_GPU.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/bin/sh
-#SBATCH --job-name=N-tensorboard
-#SBATCH --partition=RTX6000Node
-#SBATCH --gres=gpu:1
-#SBATCH --mem=32000
-#SBATCH --gres-flags=enforce-binding
-#SBATCH --error="error_rtx1.err"
-#SBATCH --output="out_rtx1.out"
-
-module purge
-module load singularity/3.0.3
-
-srun singularity exec /logiciels/containerCollections/CUDA11/pytorch-NGC-21-03-py3.sif python "train.py"
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index c611e9b46c45eac6d06ab14c47a951c0c641796c..41ce3b5b133a0d8ce94376ac0e32283b3c9f2417 100644
GIT binary patch
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diff --git a/train.py b/train.py
index d5e66aa..ddcda4c 100644
--- a/train.py
+++ b/train.py
@@ -1,14 +1,7 @@
from SuperTagger.SuperTagger import SuperTagger
-from SuperTagger.Utils.utils import read_csv_pgbar
+from SuperTagger.Utils.utils import read_csv_pgbar, load_obj
-
-def load_obj(name):
- with open(name + '.pkl', 'rb') as f:
- import pickle
- return pickle.load(f)
-
-
-file_path = 'Datasets/m2_dataset_V2.csv'
+file_path = 'Datasets/m2_dataset.csv'
df = read_csv_pgbar(file_path,1000)
@@ -25,7 +18,6 @@ tags = tags[4:]
index_to_super = load_obj('Datasets/index_to_pos1')
-super_to_index = {v: int(k) for k, v in index_to_super.items()}
tagger = SuperTagger()
--
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