kormilitzin
commited on
Commit
•
aa0e64c
1
Parent(s):
c097d43
Update spaCy pipeline
Browse files- .gitattributes +1 -0
- README.md +12 -12
- config.cfg +24 -14
- en_core_med7_trf-any-py3-none-any.whl +2 -2
- meta.json +37 -37
- ner/model +2 -2
- ner/moves +1 -1
- tokenizer +0 -0
- vocab/key2row +3 -1
- vocab/lookups.bin +2 -2
- vocab/strings.json +2 -2
- vocab/vectors +2 -2
- vocab/vectors.cfg +3 -0
.gitattributes
CHANGED
@@ -30,3 +30,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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*strings.json filter=lfs diff=lfs merge=lfs -text
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vectors filter=lfs diff=lfs merge=lfs -text
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model filter=lfs diff=lfs merge=lfs -text
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*strings.json filter=lfs diff=lfs merge=lfs -text
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vectors filter=lfs diff=lfs merge=lfs -text
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model filter=lfs diff=lfs merge=lfs -text
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+
vocab/key2row filter=lfs diff=lfs merge=lfs -text
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README.md
CHANGED
@@ -14,25 +14,25 @@ model-index:
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metrics:
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- name: NER Precision
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type: precision
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-
value: 0.
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- name: NER Recall
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type: recall
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-
value: 0.
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- name: NER F Score
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type: f_score
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-
value: 0.
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---
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| Feature | Description |
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| --- | --- |
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| **Name** | `en_core_med7_trf` |
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-
| **Version** | `3.
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-
| **spaCy** | `>=3.
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| **Default Pipeline** | `transformer`, `ner` |
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| **Components** | `transformer`, `ner` |
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-
| **Vectors** |
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| **Sources** | n/a |
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| **License** | `MIT` |
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-
| **Author** | [Andrey Kormilitzin](kormilitzin.com) |
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### Label Scheme
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@@ -50,8 +50,8 @@ model-index:
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| Type | Score |
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| --- | --- |
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-
| `ENTS_F` |
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-
| `ENTS_P` |
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-
| `ENTS_R` |
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-
| `TRANSFORMER_LOSS` |
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-
| `NER_LOSS` |
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metrics:
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- name: NER Precision
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type: precision
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+
value: 0.8822157434
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18 |
- name: NER Recall
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type: recall
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+
value: 0.925382263
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- name: NER F Score
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type: f_score
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+
value: 0.9032835821
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---
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| Feature | Description |
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| --- | --- |
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| **Name** | `en_core_med7_trf` |
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+
| **Version** | `3.4.2.1` |
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+
| **spaCy** | `>=3.4.2,<3.5.0` |
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| **Default Pipeline** | `transformer`, `ner` |
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| **Components** | `transformer`, `ner` |
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+
| **Vectors** | 514157 keys, 514157 unique vectors (300 dimensions) |
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| **Sources** | n/a |
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| **License** | `MIT` |
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+
| **Author** | [Andrey Kormilitzin](https://www.kormilitzin.com/) |
|
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### Label Scheme
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| Type | Score |
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| --- | --- |
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| `ENTS_F` | 90.33 |
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+
| `ENTS_P` | 88.22 |
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+
| `ENTS_R` | 92.54 |
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+
| `TRANSFORMER_LOSS` | 2502627.06 |
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+
| `NER_LOSS` | 114576.77 |
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config.cfg
CHANGED
@@ -1,8 +1,8 @@
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[paths]
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-
train = "./data/spacy_format/
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-
dev = "./data/spacy_format/
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-
vectors =
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-
init_tok2vec =
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[system]
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gpu_allocator = "pytorch"
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@@ -11,7 +11,7 @@ seed = 0
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[nlp]
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lang = "en"
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pipeline = ["transformer","ner"]
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-
batch_size =
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disabled = []
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before_creation = null
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after_creation = null
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@@ -24,13 +24,14 @@ tokenizer = {"@tokenizers":"spacy.Tokenizer.v1"}
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factory = "ner"
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incorrect_spans_key = null
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moves = null
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update_with_oracle_cut_size = 100
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[components.ner.model]
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@architectures = "spacy.TransitionBasedParser.v2"
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state_type = "ner"
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extra_state_tokens = false
|
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-
hidden_width =
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maxout_pieces = 2
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use_upper = false
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nO = null
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@@ -47,17 +48,22 @@ max_batch_items = 4096
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set_extra_annotations = {"@annotation_setters":"spacy-transformers.null_annotation_setter.v1"}
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[components.transformer.model]
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-
@architectures = "spacy-transformers.TransformerModel.
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-
name = "
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[components.transformer.model.get_spans]
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@span_getters = "spacy-transformers.strided_spans.v1"
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-
window =
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stride = 96
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[components.transformer.model.tokenizer_config]
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use_fast = true
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[corpora]
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[corpora.dev]
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@@ -83,9 +89,9 @@ train_corpus = "corpora.train"
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seed = ${system.seed}
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gpu_allocator = ${system.gpu_allocator}
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dropout = 0.1
|
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-
patience =
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max_epochs = 0
|
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-
max_steps =
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eval_frequency = 200
|
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frozen_components = []
|
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annotating_components = []
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@@ -94,13 +100,13 @@ before_to_disk = null
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[training.batcher]
|
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@batchers = "spacy.batch_by_padded.v1"
|
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discard_oversize = true
|
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-
size =
|
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buffer = 256
|
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get_length = null
|
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|
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[training.logger]
|
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@loggers = "spacy.ConsoleLogger.v1"
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-
progress_bar =
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104 |
|
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[training.optimizer]
|
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@optimizers = "Adam.v1"
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@@ -130,10 +136,14 @@ ents_per_type = null
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vectors = ${paths.vectors}
|
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init_tok2vec = ${paths.init_tok2vec}
|
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vocab_data = null
|
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-
lookups = null
|
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before_init = null
|
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after_init = null
|
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|
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[initialize.components]
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[initialize.tokenizer]
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[paths]
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+
train = "./data/spacy_format/train_med7_v34.spacy"
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+
dev = "./data/spacy_format/dev_med7_v34.spacy"
|
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+
vectors = "en_core_web_lg"
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+
init_tok2vec = "/mnt/sdf/andrey/projects/med7_v3/output_pretrain_lg/model169.bin"
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[system]
|
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gpu_allocator = "pytorch"
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|
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[nlp]
|
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lang = "en"
|
13 |
pipeline = ["transformer","ner"]
|
14 |
+
batch_size = 64
|
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disabled = []
|
16 |
before_creation = null
|
17 |
after_creation = null
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|
|
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factory = "ner"
|
25 |
incorrect_spans_key = null
|
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moves = null
|
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+
scorer = {"@scorers":"spacy.ner_scorer.v1"}
|
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update_with_oracle_cut_size = 100
|
29 |
|
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[components.ner.model]
|
31 |
@architectures = "spacy.TransitionBasedParser.v2"
|
32 |
state_type = "ner"
|
33 |
extra_state_tokens = false
|
34 |
+
hidden_width = 128
|
35 |
maxout_pieces = 2
|
36 |
use_upper = false
|
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nO = null
|
|
|
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set_extra_annotations = {"@annotation_setters":"spacy-transformers.null_annotation_setter.v1"}
|
49 |
|
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[components.transformer.model]
|
51 |
+
@architectures = "spacy-transformers.TransformerModel.v3"
|
52 |
+
name = "/mnt/sdf/andrey/projects/med7_v3/RoBERTa-base-PM-M3-hf"
|
53 |
+
mixed_precision = false
|
54 |
|
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[components.transformer.model.get_spans]
|
56 |
@span_getters = "spacy-transformers.strided_spans.v1"
|
57 |
+
window = 256
|
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stride = 96
|
59 |
|
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+
[components.transformer.model.grad_scaler_config]
|
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+
|
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[components.transformer.model.tokenizer_config]
|
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use_fast = true
|
64 |
|
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+
[components.transformer.model.transformer_config]
|
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+
|
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[corpora]
|
68 |
|
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[corpora.dev]
|
|
|
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seed = ${system.seed}
|
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gpu_allocator = ${system.gpu_allocator}
|
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dropout = 0.1
|
92 |
+
patience = 3600
|
93 |
max_epochs = 0
|
94 |
+
max_steps = 20000
|
95 |
eval_frequency = 200
|
96 |
frozen_components = []
|
97 |
annotating_components = []
|
|
|
100 |
[training.batcher]
|
101 |
@batchers = "spacy.batch_by_padded.v1"
|
102 |
discard_oversize = true
|
103 |
+
size = 1000
|
104 |
buffer = 256
|
105 |
get_length = null
|
106 |
|
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[training.logger]
|
108 |
@loggers = "spacy.ConsoleLogger.v1"
|
109 |
+
progress_bar = true
|
110 |
|
111 |
[training.optimizer]
|
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@optimizers = "Adam.v1"
|
|
|
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vectors = ${paths.vectors}
|
137 |
init_tok2vec = ${paths.init_tok2vec}
|
138 |
vocab_data = null
|
|
|
139 |
before_init = null
|
140 |
after_init = null
|
141 |
|
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[initialize.components]
|
143 |
|
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+
[initialize.lookups]
|
145 |
+
@misc = "spacy.LookupsDataLoader.v1"
|
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+
lang = ${nlp.lang}
|
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+
tables = ["lexeme_norm"]
|
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+
|
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[initialize.tokenizer]
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en_core_med7_trf-any-py3-none-any.whl
CHANGED
@@ -1,3 +1,3 @@
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meta.json
CHANGED
@@ -1,19 +1,19 @@
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{
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"lang":"en",
|
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"name":"core_med7_trf",
|
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-
"version":"3.
|
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"description":"",
|
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"author":"Andrey Kormilitzin",
|
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"email":"kormilitzin@gmail.com",
|
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"url":"kormilitzin.com",
|
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"license":"MIT",
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"spacy_version":">=3.
|
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"vectors":{
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"labels":{
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"transformer":[
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@@ -41,50 +41,50 @@
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"transformer_loss":
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"ner_loss":
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"requirements":[
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-
"spacy-transformers>=1.1.
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}
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{
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"lang":"en",
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"name":"core_med7_trf",
|
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"version":"3.4.2.1",
|
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"description":"",
|
6 |
"author":"Andrey Kormilitzin",
|
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"email":"kormilitzin@gmail.com",
|
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"url":"https://www.kormilitzin.com/",
|
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"license":"MIT",
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"spacy_version":">=3.4.2,<3.5.0",
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"spacy_git_version":"Unknown",
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"vectors":{
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"width":300,
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"vectors":514157,
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"keys":514157,
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"name":"en_vectors"
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"labels":{
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"transformer":[
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"performance":{
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"ents_r":0.925382263,
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"ents_per_type":{
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"DRUG":{
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"r":0.9349206349,
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"ROUTE":{
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"requirements":[
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}
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ner/model
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ner/moves
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��moves��{"0":{},"1":{"DRUG":27417,"STRENGTH":21625,"DOSAGE":18350,"FREQUENCY":16642,"FORM":14267,"ROUTE":8996,"DURATION":2140},"2":{"DRUG":27417,"STRENGTH":21625,"DOSAGE":18350,"FREQUENCY":16642,"FORM":14267,"ROUTE":8996,"DURATION":2140},"3":{"DRUG":27417,"STRENGTH":21625,"DOSAGE":18350,"FREQUENCY":16642,"FORM":14267,"ROUTE":8996,"DURATION":2140},"4":{"DRUG":27417,"STRENGTH":21625,"DOSAGE":18350,"FREQUENCY":16642,"FORM":14267,"ROUTE":8996,"DURATION":2140,"":1},"5":{"":1}}�cfg��neg_key�
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tokenizer
CHANGED
The diff for this file is too large to render.
See raw diff
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vocab/key2row
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vocab/lookups.bin
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vocab/strings.json
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oid sha256:0b1693baa4ec8d99e20fa93b38ecafa6b4f49f244472d455f35e7605f20345e0
|
3 |
+
size 10856674
|
vocab/vectors
CHANGED
@@ -1,3 +1,3 @@
|
|
1 |
version https://git-lfs.github.com/spec/v1
|
2 |
-
oid sha256:
|
3 |
-
size
|
|
|
1 |
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:234dcf234bfdf01775ae6182715d55eaacfcde8555b189f25440b56d3c39fd5d
|
3 |
+
size 616988528
|
vocab/vectors.cfg
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"mode":"default"
|
3 |
+
}
|