add train config and metadata

conda-environment.yaml

@@ -0,0 +1,200 @@
+name: pie-document-level
+channels:
+  - pytorch
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=main
+  - _openmp_mutex=5.1=1_gnu
+  - ca-certificates=2023.05.30=h06a4308_0
+  - ld_impl_linux-64=2.38=h1181459_1
+  - libffi=3.4.4=h6a678d5_0
+  - libgcc-ng=11.2.0=h1234567_1
+  - libgomp=11.2.0=h1234567_1
+  - libstdcxx-ng=11.2.0=h1234567_1
+  - ncurses=6.4=h6a678d5_0
+  - openssl=3.0.10=h7f8727e_2
+  - pip=23.2.1=py39h06a4308_0
+  - python=3.9.17=h955ad1f_0
+  - readline=8.2=h5eee18b_0
+  - setuptools=68.0.0=py39h06a4308_0
+  - sqlite=3.41.2=h5eee18b_0
+  - tk=8.6.12=h1ccaba5_0
+  - wheel=0.38.4=py39h06a4308_0
+  - xz=5.4.2=h5eee18b_0
+  - zlib=1.2.13=h5eee18b_0
+  - pip:
+      - absl-py==1.4.0
+      - accelerate==0.22.0
+      - aiohttp==3.8.5
+      - aiosignal==1.3.1
+      - alembic==1.12.0
+      - annotated-types==0.5.0
+      - antlr4-python3-runtime==4.9.3
+      - appdirs==1.4.4
+      - asciidag==0.2.0
+      - async-timeout==4.0.3
+      - attrs==23.1.0
+      - auto-gptq==0.4.2
+      - autopage==0.5.1
+      - black==23.7.0
+      - blis==0.7.10
+      - catalogue==2.0.9
+      - certifi==2023.7.22
+      - cfgv==3.4.0
+      - charset-normalizer==3.2.0
+      - click==8.1.7
+      - cliff==4.3.0
+      - cmaes==0.10.0
+      - cmake==3.27.4.1
+      - cmd2==2.4.3
+      - coloredlogs==15.0.1
+      - colorlog==6.7.0
+      - confection==0.1.1
+      - coverage==7.3.0
+      - cymem==2.0.7
+      - datasets==2.14.4
+      - dill==0.3.7
+      - distlib==0.3.7
+      - docker-pycreds==0.4.0
+      - en-core-web-trf==3.6.1
+      - exceptiongroup==1.1.3
+      - fastjsonschema==2.18.0
+      - filelock==3.12.3
+      - flake8==6.1.0
+      - frozenlist==1.4.0
+      - fsspec==2023.6.0
+      - gitdb==4.0.10
+      - gitpython==3.1.34
+      - greenlet==2.0.2
+      - huggingface-hub==0.19.4
+      - humanfriendly==10.0
+      - hydra-colorlog==1.2.0
+      - hydra-core==1.3.2
+      - hydra-optuna-sweeper==1.2.0
+      - identify==2.5.27
+      - idna==3.4
+      - importlib-metadata==6.8.0
+      - iniconfig==2.0.0
+      - isort==5.12.0
+      - jedi==0.19.0
+      - jinja2==3.1.2
+      - joblib==1.3.2
+      - jsonschema==4.19.0
+      - jsonschema-specifications==2023.7.1
+      - jupyter-core==5.3.1
+      - langcodes==3.3.0
+      - lightning-utilities==0.9.0
+      - lit==16.0.6
+      - mako==1.2.4
+      - markdown-it-py==3.0.0
+      - markupsafe==2.1.3
+      - mccabe==0.7.0
+      - mdurl==0.1.2
+      - mpmath==1.3.0
+      - multidict==6.0.4
+      - multiprocess==0.70.15
+      - murmurhash==1.0.9
+      - mypy-extensions==1.0.0
+      - nbformat==5.9.2
+      - nbstripout==0.6.1
+      - networkx==3.1
+      - nltk==3.8.1
+      - nodeenv==1.8.0
+      - numpy==1.25.2
+      - nvidia-cublas-cu11==11.10.3.66
+      - nvidia-cuda-cupti-cu11==11.7.101
+      - nvidia-cuda-nvrtc-cu11==11.7.99
+      - nvidia-cuda-runtime-cu11==11.7.99
+      - nvidia-cudnn-cu11==8.5.0.96
+      - nvidia-cufft-cu11==10.9.0.58
+      - nvidia-curand-cu11==10.2.10.91
+      - nvidia-cusolver-cu11==11.4.0.1
+      - nvidia-cusparse-cu11==11.7.4.91
+      - nvidia-nccl-cu11==2.14.3
+      - nvidia-nvtx-cu11==11.7.91
+      - omegaconf==2.3.0
+      - optimum==1.12.0
+      - optuna==2.10.1
+      - packaging==23.1
+      - pandas==2.1.0
+      - parso==0.8.3
+      - pathspec==0.11.2
+      - pathtools==0.1.2
+      - pathy==0.10.2
+      - pbr==5.11.1
+      - peft==0.5.0
+      - pie-datasets==0.8.1
+      - pie-models==0.3.0
+      - pie-modules==0.10.6
+      - platformdirs==3.10.0
+      - plotext==5.2.8
+      - pluggy==1.3.0
+      - pre-commit==3.4.0
+      - preshed==3.0.8
+      - prettytable==3.8.0
+      - protobuf==4.24.2
+      - psutil==5.9.5
+      - pudb==2022.1.3
+      - pyarrow==13.0.0
+      - pycodestyle==2.11.0
+      - pydantic==2.3.0
+      - pydantic-core==2.6.3
+      - pyflakes==3.1.0
+      - pygments==2.16.1
+      - pyperclip==1.8.2
+      - pyrootutils==1.0.4
+      - pytest==7.4.1
+      - pytest-cov==4.1.0
+      - python-dateutil==2.8.2
+      - python-dotenv==1.0.0
+      - pytorch-crf==0.7.2
+      - pytorch-ie==0.29.8
+      - pytorch-lightning==2.1.2
+      - pytz==2023.3.post1
+      - pyyaml==6.0.1
+      - referencing==0.30.2
+      - regex==2023.8.8
+      - requests==2.31.0
+      - rich==13.5.2
+      - rouge==1.0.1
+      - rpds-py==0.10.2
+      - safetensors==0.3.3
+      - scipy==1.11.2
+      - sentencepiece==0.1.99
+      - sentry-sdk==1.30.0
+      - setproctitle==1.3.2
+      - sh==2.0.6
+      - six==1.16.0
+      - smart-open==6.3.0
+      - smmap==5.0.0
+      - spacy-alignments==0.9.0
+      - spacy-legacy==3.0.12
+      - spacy-loggers==1.0.4
+      - sqlalchemy==2.0.20
+      - srsly==2.4.7
+      - stevedore==5.1.0
+      - sympy==1.12
+      - tabulate==0.9.0
+      - thinc==8.1.12
+      - tokenizers==0.15.0
+      - tomli==2.0.1
+      - torch==2.0.0
+      - torchmetrics==1.1.1
+      - tqdm==4.66.1
+      - traitlets==5.9.0
+      - transformers==4.36.0
+      - triton==2.0.0
+      - typer==0.9.0
+      - typing-extensions==4.7.1
+      - tzdata==2023.3
+      - urllib3==2.0.4
+      - urwid==2.1.2
+      - urwid-readline==0.13
+      - virtualenv==20.24.4
+      - wandb==0.15.9
+      - wasabi==1.1.2
+      - wcwidth==0.2.6
+      - xxhash==3.3.0
+      - yarl==1.9.2
+      - zipp==3.16.2
+prefix: /home/arne/miniconda3/envs/pie-document-level

config.yaml

@@ -0,0 +1,837 @@
+wandb_version: 1
+
+_wandb:
+  desc: null
+  value:
+    python_version: 3.9.17
+    cli_version: 0.15.9
+    framework: huggingface
+    huggingface_version: 4.36.0
+    is_jupyter_run: false
+    is_kaggle_kernel: false
+    start_time: 1709313942.075548
+    t:
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+      4: 3.9.17
+      5: 0.15.9
+      6: 4.36.0
+      8:
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+_config:
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+  value:
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+    name: dataset-sciarg/task-ner_re/v0.3
+    tags:
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+    - model=pointer_network
+    train: true
+    validate: true
+    test: true
+    monitor_metric: metric/binary_relations/micro/f1/val
+    monitor_mode: max
+    seed: 1
+    ckpt_path: null
+    push_to_hub: false
+    model_save_dir: /home/arne/projects/pie-document-level/models/dataset-sciarg/task-ner_re/v0.3/2024-03-01_18-25-32
+    dataset:
+      _target_: src.utils.execute_pipeline
+      input:
+        _target_: pie_datasets.DatasetDict.load_dataset
+        path: pie/sciarg
+        revision: 982d5682ba414ee13cf92cb93ec18fc8e78e2b81
+      select_n:
+        _processor_: pie_datasets.DatasetDict.select
+        split: train
+        stop: null
+      select_n_test:
+        _processor_: pie_datasets.DatasetDict.select
+        split: test
+        stop: null
+      select_n_validation:
+        _processor_: pie_datasets.DatasetDict.select
+        split: validation
+        stop: null
+      create_test_split:
+        _processor_: pie_datasets.DatasetDict.move_to_new_split
+        source_split: train
+        target_split: test
+        ids:
+        - A32
+        - A33
+        - A34
+        - A35
+        - A36
+        - A37
+        - A38
+        - A39
+        - A40
+      create_validation_split:
+        _processor_: pie_datasets.DatasetDict.add_test_split
+        test_size: 0.1
+        seed: 1
+        source_split: train
+        target_split: validation
+    datamodule:
+      _target_: src.datamodules.PieDataModule
+      batch_size: 2
+      num_workers: 0
+      pin_memory: false
+      show_progress_for_encode: true
+      train_split: train
+      val_split: validation
+      test_split: test
+    taskmodule:
+      _target_: pie_modules.taskmodules.PointerNetworkTaskModuleForEnd2EndRE
+      tokenizer_init_kwargs:
+        add_prefix_space: true
+      tokenizer_name_or_path: facebook/bart-base
+      tokenizer_kwargs:
+        truncation: true
+        return_overflowing_tokens: true
+        stride: 128
+        strict_span_conversion: false
+      create_constraints: true
+      constrained_generation: true
+      partition_layer_name: labeled_partitions
+    model:
+      _target_: pie_modules.models.SimpleGenerativeModel
+      base_model_type: pie_modules.models.base_models.BartAsPointerNetwork
+      base_model_config:
+        pretrained_model_name_or_path: facebook/bart-base
+        use_encoder_mlp: true
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+        max_length: 768
+        decoder_layer_norm_decay: 0.05
+      metric_stages:
+      - val
+      - test
+      - train
+      metric_call_predict:
+      - val
+      - test
+      warmup_proportion: 0.01
+    callbacks:
+      model_checkpoint:
+        _target_: pytorch_lightning.callbacks.ModelCheckpoint
+        dirpath: /home/arne/projects/pie-document-level/logs/training/multiruns/dataset-sciarg/task-ner_re/v0.3/2024-03-01_18-25-31/0/checkpoints
+        filename: epoch_{epoch:03d}
+        monitor: metric/binary_relations/micro/f1/val
+        verbose: false
+        save_last: true
+        save_top_k: 1
+        mode: max
+        auto_insert_metric_name: false
+        save_weights_only: false
+        every_n_train_steps: null
+        train_time_interval: null
+        every_n_epochs: null
+        save_on_train_epoch_end: null
+      early_stopping:
+        _target_: pytorch_lightning.callbacks.EarlyStopping
+        monitor: metric/binary_relations/micro/f1/val
+        min_delta: 0.0
+        patience: 100
+        verbose: false
+        mode: max
+        strict: true
+        check_finite: true
+        stopping_threshold: null
+        divergence_threshold: null
+        check_on_train_epoch_end: null
+      model_summary:
+        _target_: pytorch_lightning.callbacks.RichModelSummary
+        max_depth: -1
+      rich_progress_bar:
+        _target_: pytorch_lightning.callbacks.RichProgressBar
+    logger:
+      wandb:
+        _target_: pytorch_lightning.loggers.wandb.WandbLogger
+        save_dir: /home/arne/projects/pie-document-level/logs/training/multiruns/dataset-sciarg/task-ner_re/v0.3/2024-03-01_18-25-31/0
+        offline: false
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+        anonymous: null
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+        log_model: false
+        prefix: ''
+        group: ''
+        tags:
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+        - model=pointer_network
+        job_type: ''
+    trainer:
+      _target_: pytorch_lightning.Trainer
+      default_root_dir: /home/arne/projects/pie-document-level/logs/training/multiruns/dataset-sciarg/task-ner_re/v0.3/2024-03-01_18-25-31/0
+      min_epochs: 150
+      max_epochs: 150
+      accelerator: gpu
+      devices: 1
+      check_val_every_n_epoch: 1
+      deterministic: false
+      gradient_clip_val: 5
+      gradient_clip_algorithm: value
+    paths:
+      root_dir: /home/arne/projects/pie-document-level
+      data_dir: /home/arne/projects/pie-document-level/data/
+      log_dir: /home/arne/projects/pie-document-level/logs/
+      output_dir: /home/arne/projects/pie-document-level/logs/training/multiruns/dataset-sciarg/task-ner_re/v0.3/2024-03-01_18-25-31/0
+      save_dir: /home/arne/projects/pie-document-level
+      work_dir: /home/arne/projects/pie-document-level
+    extras:
+      ignore_warnings: false
+      enforce_tags: true
+      print_config: true
+    base_model: facebook/bart-base
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+  value: pie_modules.models.base_models.BartAsPointerNetwork
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+  value:
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+    document_type: pytorch_ie.documents.TextDocumentWithLabeledSpansBinaryRelationsAndLabeledPartitions
+    tokenized_document_type: pie_modules.documents.TokenDocumentWithLabeledSpansBinaryRelationsAndLabeledPartitions
+    span_layer_name: labeled_spans
+    relation_layer_name: binary_relations
+    none_label: none
+    loop_dummy_relation_name: loop
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+    label_tokens: null
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wandb-metadata.json

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