update model

https://wandb.ai/arne/dataset-sciarg-task-ner_re-v0.3-training/runs/prik91di

conda-environment.yaml

@@ -36,6 +36,7 @@ dependencies:
       - attrs==23.1.0
       - auto-gptq==0.4.2
       - autopage==0.5.1
+      - beartype==0.17.2
       - black==23.7.0
       - blis==0.7.10
       - catalogue==2.0.9
@@ -56,6 +57,7 @@ dependencies:
       - dill==0.3.7
       - distlib==0.3.7
       - docker-pycreds==0.4.0
+      - ema-pytorch==0.4.2
       - en-core-web-trf==3.6.1
       - exceptiongroup==1.1.3
       - fastjsonschema==2.18.0
@@ -66,7 +68,7 @@ dependencies:
       - gitdb==4.0.10
       - gitpython==3.1.34
       - greenlet==2.0.2
-      - huggingface-hub==0.19.4
+      - huggingface-hub==0.23.2
       - humanfriendly==10.0
       - hydra-colorlog==1.2.0
       - hydra-core==1.3.2
@@ -102,16 +104,28 @@ dependencies:
       - nodeenv==1.8.0
       - numpy==1.25.2
       - nvidia-cublas-cu11==11.10.3.66
+      - nvidia-cublas-cu12==12.1.3.1
       - nvidia-cuda-cupti-cu11==11.7.101
+      - nvidia-cuda-cupti-cu12==12.1.105
       - nvidia-cuda-nvrtc-cu11==11.7.99
+      - nvidia-cuda-nvrtc-cu12==12.1.105
       - nvidia-cuda-runtime-cu11==11.7.99
+      - nvidia-cuda-runtime-cu12==12.1.105
       - nvidia-cudnn-cu11==8.5.0.96
+      - nvidia-cudnn-cu12==8.9.2.26
       - nvidia-cufft-cu11==10.9.0.58
+      - nvidia-cufft-cu12==11.0.2.54
       - nvidia-curand-cu11==10.2.10.91
+      - nvidia-curand-cu12==10.3.2.106
       - nvidia-cusolver-cu11==11.4.0.1
+      - nvidia-cusolver-cu12==11.4.5.107
       - nvidia-cusparse-cu11==11.7.4.91
+      - nvidia-cusparse-cu12==12.1.0.106
       - nvidia-nccl-cu11==2.14.3
+      - nvidia-nccl-cu12==2.20.5
+      - nvidia-nvjitlink-cu12==12.5.40
       - nvidia-nvtx-cu11==11.7.91
+      - nvidia-nvtx-cu12==12.1.105
       - omegaconf==2.3.0
       - optimum==1.12.0
       - optuna==2.10.1
@@ -123,9 +137,8 @@ dependencies:
       - 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
+      - pie-datasets==0.10.0
+      - pie-modules==0.11.4
       - platformdirs==3.10.0
       - plotext==5.2.8
       - pluggy==1.3.0
@@ -148,7 +161,7 @@ dependencies:
       - python-dateutil==2.8.2
       - python-dotenv==1.0.0
       - pytorch-crf==0.7.2
-      - pytorch-ie==0.29.8
+      - pytorch-ie==0.31.0
       - pytorch-lightning==2.1.2
       - pytz==2023.3.post1
       - pyyaml==6.0.1
@@ -158,7 +171,7 @@ dependencies:
       - rich==13.5.2
       - rouge==1.0.1
       - rpds-py==0.10.2
-      - safetensors==0.3.3
+      - safetensors==0.4.3
       - scipy==1.11.2
       - sentencepiece==0.1.99
       - sentry-sdk==1.30.0
@@ -176,16 +189,16 @@ dependencies:
       - sympy==1.12
       - tabulate==0.9.0
       - thinc==8.1.12
-      - tokenizers==0.15.0
+      - tokenizers==0.15.2
       - tomli==2.0.1
-      - torch==2.0.0
+      - torch==2.3.0
       - torchmetrics==1.1.1
       - tqdm==4.66.1
       - traitlets==5.9.0
-      - transformers==4.36.0
-      - triton==2.0.0
+      - transformers==4.39.3
+      - triton==2.3.0
       - typer==0.9.0
-      - typing-extensions==4.7.1
+      - typing-extensions==4.12.0
       - tzdata==2023.3
       - urllib3==2.0.4
       - urwid==2.1.2

config.json

@@ -5,6 +5,7 @@
     "pretrained_model_name_or_path": "facebook/bart-base",
     "use_encoder_mlp": true,
     "use_constraints_encoder_mlp": true,
+    "decoder_position_id_mode": "pattern",
     "decoder_position_id_pattern": [
       0,
       0,
@@ -14,6 +15,13 @@
       1,
       1
     ],
+    "decoder_position_id_mapping": {
+      "default": 2,
+      "vocab": 3,
+      "bos": 0,
+      "eos": 1,
+      "pad": 1
+    },
     "encoder_layer_norm_decay": 0.005,
     "lr": 6e-05,
     "num_beams": 4,
@@ -25,49 +33,49 @@
     "target_token_ids": [
       0,
       2,
-      50267,
-      50265,
-      50268,
-      50270,
       50271,
-      50269,
+      50266,
       50272,
-      50266
+      50269,
+      50268,
+      50267,
+      50265,
+      50270
     ],
     "embedding_weight_mapping": {
-      "50267": [
+      "50271": [
         4146
       ],
-      "50265": [
+      "50266": [
         3618,
         1215,
         31628
       ],
-      "50268": [
+      "50272": [
         414
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-      "50270": [
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         308,
         1215,
         31628
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-      "50271": [
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         37820
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-      "50269": [
+      "50267": [
         1667,
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         1116,
         1215,
         41690
       ],
-      "50272": [
+      "50265": [
         9031,
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         1215,
         41690
       ],
-      "50266": [
+      "50270": [
         4548
       ]
     }
@@ -90,7 +98,6 @@
     "tokenizer_name_or_path": "facebook/bart-base",
     "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",

pytorch_model.bin

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:1ba1c6af701ccda91275955a32da3eb8b9968017e0ecf2b701d9571ea7e7f2ce
-size 567262209
+oid sha256:03c4ad1f1ed0f5cad71e7ebbe689f626ad3fd933f93d90caf8857d7588244338
+size 567262654

requirements.txt

@@ -0,0 +1,190 @@
+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
+beartype==0.17.2
+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
+ema-pytorch==0.4.2
+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==0.23.2
+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-specifications==2023.7.1
+jsonschema==4.19.0
+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-cublas-cu12==12.1.3.1
+nvidia-cuda-cupti-cu11==11.7.101
+nvidia-cuda-cupti-cu12==12.1.105
+nvidia-cuda-nvrtc-cu11==11.7.99
+nvidia-cuda-nvrtc-cu12==12.1.105
+nvidia-cuda-runtime-cu11==11.7.99
+nvidia-cuda-runtime-cu12==12.1.105
+nvidia-cudnn-cu11==8.5.0.96
+nvidia-cudnn-cu12==8.9.2.26
+nvidia-cufft-cu11==10.9.0.58
+nvidia-cufft-cu12==11.0.2.54
+nvidia-curand-cu11==10.2.10.91
+nvidia-curand-cu12==10.3.2.106
+nvidia-cusolver-cu11==11.4.0.1
+nvidia-cusolver-cu12==11.4.5.107
+nvidia-cusparse-cu11==11.7.4.91
+nvidia-cusparse-cu12==12.1.0.106
+nvidia-nccl-cu11==2.14.3
+nvidia-nccl-cu12==2.20.5
+nvidia-nvjitlink-cu12==12.5.40
+nvidia-nvtx-cu11==11.7.91
+nvidia-nvtx-cu12==12.1.105
+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==0.10.0
+pie-modules==0.11.4
+pip==23.2.1
+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-core==2.6.3
+pydantic==2.3.0
+pyflakes==3.1.0
+pygments==2.16.1
+pyperclip==1.8.2
+pyrootutils==1.0.4
+pytest-cov==4.1.0
+pytest==7.4.1
+python-dateutil==2.8.2
+python-dotenv==1.0.0
+pytorch-crf==0.7.2
+pytorch-ie==0.31.0
+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==0.4.3
+scipy==1.11.2
+sentencepiece==0.1.99
+sentry-sdk==1.30.0
+setproctitle==1.3.2
+setuptools==68.0.0
+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==0.15.2
+tomli==2.0.1
+torch==2.3.0
+torchmetrics==1.1.1
+tqdm==4.66.1
+traitlets==5.9.0
+transformers==4.39.3
+triton==2.3.0
+typer==0.9.0
+typing-extensions==4.12.0
+tzdata==2023.3
+urllib3==2.0.4
+urwid-readline==0.13
+urwid==2.1.2
+virtualenv==20.24.4
+wandb==0.15.9
+wasabi==1.1.2
+wcwidth==0.2.6
+wheel==0.38.4
+xxhash==3.3.0
+yarl==1.9.2
+zipp==3.16.2

taskmodule_config.json

@@ -3,7 +3,6 @@
   "tokenizer_name_or_path": "facebook/bart-base",
   "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",

wandb-metadata.json

@@ -1,8 +1,8 @@
 {
     "os": "Linux-5.15.0-86-generic-x86_64-with-glibc2.35",
     "python": "3.9.17",
-    "heartbeatAt": "2024-03-01T17:25:43.088987",
-    "startedAt": "2024-03-01T17:25:42.069556",
+    "heartbeatAt": "2024-05-28T21:33:56.005050",
+    "startedAt": "2024-05-28T21:33:54.883067",
     "docker": null,
     "cuda": null,
     "args": [
@@ -23,7 +23,7 @@
     "codePath": "src/train.py",
     "git": {
         "remote": "[email protected]:ArneBinder/pie-document-level.git",
-        "commit": "6deb3a264efba32f48f10addd87ccea04d4f8b5e"
+        "commit": "98092aa0b288a843bfaa5e07ff06cfe3cd882b32"
     },
     "email": "[email protected]",
     "root": "/home/arne/projects/pie-document-level",
@@ -33,7 +33,7 @@
     "cpu_count": 6,
     "cpu_count_logical": 12,
     "cpu_freq": {
-        "current": 2199.99725,
+        "current": 2304.1169999999997,
         "min": 2200.0,
         "max": 3600.0
     },
@@ -84,7 +84,7 @@
             "max": 3600.0
         },
         {
-            "current": 2200.0,
+            "current": 2049.404,
             "min": 2200.0,
             "max": 3600.0
         },
@@ -94,14 +94,14 @@
             "max": 3600.0
         },
         {
-            "current": 2199.967,
+            "current": 3600.0,
             "min": 2200.0,
             "max": 3600.0
         }
     ],
     "disk": {
         "total": 878.620922088623,
-        "used": 658.1419486999512
+        "used": 661.2135887145996
     },
     "gpu": "NVIDIA GeForce RTX 2080 Ti",
     "gpu_count": 1,

wandb-summary.json

@@ -1 +1 @@
-{"loss/train_step": 0.01761285401880741, "epoch": 150, "trainer/global_step": 39450, "_timestamp": 1709331727.5671468, "_runtime": 17785.49159884453, "_step": 1090, "loss/val": 2.5551652908325195, "metric/exact_encoding_matches/val": 0.3253012001514435, "metric/decoding_errors/all/val": 0.0, "metric/labeled_spans/micro/f1/val": 0.4795539081096649, "metric/labeled_spans/micro/recall/val": 0.4955185651779175, "metric/labeled_spans/micro/precision/val": 0.4645858407020569, "metric/labeled_spans/background_claim/f1/val": 0.5347467660903931, "metric/labeled_spans/background_claim/recall/val": 0.5159090757369995, "metric/labeled_spans/background_claim/precision/val": 0.5550122261047363, "metric/labeled_spans/data/f1/val": 0.5673912763595581, "metric/labeled_spans/data/recall/val": 0.5661605000495911, "metric/labeled_spans/data/precision/val": 0.5686274766921997, "metric/labeled_spans/own_claim/f1/val": 0.3920493423938751, "metric/labeled_spans/own_claim/recall/val": 0.4326777756214142, "metric/labeled_spans/own_claim/precision/val": 0.3583959937095642, "metric/labeled_spans/macro/f1/val": 0.49806246161460876, "metric/labeled_spans/macro/recall/val": 0.5049158334732056, "metric/labeled_spans/macro/precision/val": 0.49401187896728516, "metric/binary_relations/micro/f1/val": 0.2759901285171509, "metric/binary_relations/micro/recall/val": 0.2657926082611084, "metric/binary_relations/micro/precision/val": 0.28700128197669983, "metric/binary_relations/parts_of_same/f1/val": 0.2459016591310501, "metric/binary_relations/parts_of_same/recall/val": 0.23999999463558197, "metric/binary_relations/parts_of_same/precision/val": 0.2521008551120758, "metric/binary_relations/supports/f1/val": 0.2857142686843872, "metric/binary_relations/supports/recall/val": 0.27953410148620605, "metric/binary_relations/supports/precision/val": 0.29217392206192017, "metric/binary_relations/contradicts/f1/val": 0.26455026865005493, "metric/binary_relations/contradicts/recall/val": 0.23364485800266266, 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