model update

README.md

@@ -0,0 +1,137 @@
+---
+datasets:
+- bionlp2004
+metrics:
+- f1
+- precision
+- recall
+model-index:
+- name: tner/roberta-large-bionlp2004
+  results:
+  - task:
+      name: Token Classification
+      type: token-classification
+    dataset:
+      name: bionlp2004
+      type: bionlp2004
+      args: bionlp2004
+    metrics:
+    - name: F1
+      type: f1
+      value: 0.7513434294088912
+    - name: Precision
+      type: precision
+      value: 0.7090462042823481
+    - name: Recall
+      type: recall
+      value: 0.7990071577003002
+    - name: F1 (macro)
+      type: f1_macro
+      value: 0.7165656135319811
+    - name: Precision (macro)
+      type: precision_macro
+      value: 0.6765580411075789
+    - name: Recall (macro)
+      type: recall_macro
+      value: 0.7685019796698731
+    - name: F1 (entity span)
+      type: f1_entity_span
+      value: 0.7936818107800032
+    - name: Precision (entity span)
+      type: precision_entity_span
+      value: 0.7490011269337158
+    - name: Recall (entity span)
+      type: recall_entity_span
+      value: 0.8440314015238974
+
+pipeline_tag: token-classification
+widget:
+- text: "Jacob Collier is a Grammy awarded artist from England."
+  example_title: "NER Example 1"
+---
+# tner/roberta-large-bionlp2004
+
+This model is a fine-tuned version of [roberta-large](https://huggingface.co/roberta-large) on the 
+[tner/bionlp2004](https://huggingface.co/datasets/tner/bionlp2004) dataset.
+Model fine-tuning is done via [T-NER](https://github.com/asahi417/tner)'s hyper-parameter search (see the repository
+for more detail). It achieves the following results on the test set:
+- F1 (micro): 0.7513434294088912
+- Precision (micro): 0.7090462042823481
+- Recall (micro): 0.7990071577003002
+- F1 (macro): 0.7165656135319811
+- Precision (macro): 0.6765580411075789
+- Recall (macro): 0.7685019796698731
+
+The per-entity breakdown of the F1 score on the test set are below:
+- cell_line: 0.6080273270708796
+- cell_type: 0.7536311318169361
+- dna: 0.7150259067357512
+- protein: 0.7738602374694099
+- rna: 0.7322834645669293 
+
+For F1 scores, the confidence interval is obtained by bootstrap as below:
+- F1 (micro): 
+    - 90%: [0.7433198691879565, 0.7598437899577305]
+    - 95%: [0.7420570442205622, 0.7606216680394585] 
+- F1 (macro): 
+    - 90%: [0.7433198691879565, 0.7598437899577305]
+    - 95%: [0.7420570442205622, 0.7606216680394585] 
+
+Full evaluation can be found at [metric file of NER](https://huggingface.co/tner/roberta-large-bionlp2004/raw/main/eval/metric.json) 
+and [metric file of entity span](https://huggingface.co/tner/roberta-large-bionlp2004/raw/main/eval/metric_span.json).
+
+### Usage
+This model can be used through the [tner library](https://github.com/asahi417/tner). Install the library via pip   
+```shell
+pip install tner
+```
+and activate model as below.
+```python
+from tner import TransformersNER
+model = TransformersNER("tner/roberta-large-bionlp2004")
+model.predict(["Jacob Collier is a Grammy awarded English artist from London"])
+```
+It can be used via transformers library but it is not recommended as CRF layer is not supported at the moment.
+
+### Training hyperparameters
+
+The following hyperparameters were used during training:
+ - dataset: ['tner/bionlp2004']
+ - dataset_split: train
+ - dataset_name: None
+ - local_dataset: None
+ - model: roberta-large
+ - crf: True
+ - max_length: 128
+ - epoch: 15
+ - batch_size: 64
+ - lr: 1e-05
+ - random_seed: 42
+ - gradient_accumulation_steps: 1
+ - weight_decay: 1e-07
+ - lr_warmup_step_ratio: 0.1
+ - max_grad_norm: 10.0
+
+The full configuration can be found at [fine-tuning parameter file](https://huggingface.co/tner/roberta-large-bionlp2004/raw/main/trainer_config.json).
+
+### Reference
+If you use any resource from T-NER, please consider to cite our [paper](https://aclanthology.org/2021.eacl-demos.7/).
+
+```
+
+@inproceedings{ushio-camacho-collados-2021-ner,
+    title = "{T}-{NER}: An All-Round Python Library for Transformer-based Named Entity Recognition",
+    author = "Ushio, Asahi  and
+      Camacho-Collados, Jose",
+    booktitle = "Proceedings of the 16th Conference of the European Chapter of the Association for Computational Linguistics: System Demonstrations",
+    month = apr,
+    year = "2021",
+    address = "Online",
+    publisher = "Association for Computational Linguistics",
+    url = "https://aclanthology.org/2021.eacl-demos.7",
+    doi = "10.18653/v1/2021.eacl-demos.7",
+    pages = "53--62",
+    abstract = "Language model (LM) pretraining has led to consistent improvements in many NLP downstream tasks, including named entity recognition (NER). In this paper, we present T-NER (Transformer-based Named Entity Recognition), a Python library for NER LM finetuning. In addition to its practical utility, T-NER facilitates the study and investigation of the cross-domain and cross-lingual generalization ability of LMs finetuned on NER. Our library also provides a web app where users can get model predictions interactively for arbitrary text, which facilitates qualitative model evaluation for non-expert programmers. We show the potential of the library by compiling nine public NER datasets into a unified format and evaluating the cross-domain and cross- lingual performance across the datasets. The results from our initial experiments show that in-domain performance is generally competitive across datasets. However, cross-domain generalization is challenging even with a large pretrained LM, which has nevertheless capacity to learn domain-specific features if fine- tuned on a combined dataset. To facilitate future research, we also release all our LM checkpoints via the Hugging Face model hub.",
+}
+
+```

config.json

@@ -1,5 +1,5 @@
 {
-  "_name_or_path": "tner_ckpt/bionlp2004_roberta_large/best_model",
+  "_name_or_path": "tner_ckpt/bionlp2004_roberta_large/model_nhosiz/epoch_5",
   "architectures": [
     "RobertaForTokenClassification"
   ],

eval/metric.json

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+{"micro/f1": 0.7513434294088912, "micro/f1_ci": {"90": [0.7433198691879565, 0.7598437899577305], "95": [0.7420570442205622, 0.7606216680394585]}, "micro/recall": 0.7990071577003002, "micro/precision": 0.7090462042823481, "macro/f1": 0.7165656135319811, "macro/f1_ci": {"90": [0.7002937185557381, 0.7321969535350632], "95": [0.6972270983192475, 0.7346600395389665]}, "macro/recall": 0.7685019796698731, "macro/precision": 0.6765580411075789, "per_entity_metric": {"cell_line": {"f1": 0.6080273270708796, "f1_ci": {"90": [0.5711689355062354, 0.6439245116433064], "95": [0.5646332431360657, 0.6512838392124692]}, "precision": 0.5305514157973175, "recall": 0.712}, "cell_type": {"f1": 0.7536311318169361, "f1_ci": {"90": [0.7377440562233388, 0.7696953060664288], "95": [0.734812150861425, 0.7715685683137088]}, "precision": 0.7957175925925926, "recall": 0.7157730348776679}, "dna": {"f1": 0.7150259067357512, "f1_ci": {"90": [0.6943567374473204, 0.735043845043845], "95": [0.6908566375260775, 0.7386313612968293]}, "precision": 0.6571428571428571, "recall": 0.7840909090909091}, "protein": {"f1": 0.7738602374694099, "f1_ci": {"90": [0.7639543086904872, 0.7835213383443399], "95": [0.7612824390243694, 0.7853303273853405]}, "precision": 0.7155548105933623, "recall": 0.84251036116045}, "rna": {"f1": 0.7322834645669293, "f1_ci": {"90": [0.6693211406343131, 0.7923219373219372], "95": [0.6514665889665888, 0.8032804033198435]}, "precision": 0.6838235294117647, "recall": 0.788135593220339}}}

eval/metric_span.json

@@ -0,0 +1 @@
+{"micro/f1": 0.7936818107800032, "micro/f1_ci": {"90": [0.7864966635201485, 0.8008673786899809], "95": [0.7850648957246626, 0.8018852848485037]}, "micro/recall": 0.8440314015238974, "micro/precision": 0.7490011269337158, "macro/f1": 0.7936818107800032, "macro/f1_ci": {"90": [0.7864966635201485, 0.8008673786899809], "95": [0.7850648957246626, 0.8018852848485037]}, "macro/recall": 0.8440314015238974, "macro/precision": 0.7490011269337158}

pytorch_model.bin

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-size 1417416753
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+size 1417422193

tokenizer_config.json

@@ -6,7 +6,7 @@
   "errors": "replace",
   "mask_token": "<mask>",
   "model_max_length": 512,
-  "name_or_path": "tner_ckpt/bionlp2004_roberta_large/best_model",
+  "name_or_path": "tner_ckpt/bionlp2004_roberta_large/model_nhosiz/epoch_5",
   "pad_token": "<pad>",
   "sep_token": "</s>",
   "special_tokens_map_file": "tner_ckpt/bionlp2004_roberta_large/model_nhosiz/epoch_5/special_tokens_map.json",

trainer_config.json

@@ -0,0 +1 @@
+{"dataset": ["tner/bionlp2004"], "dataset_split": "train", "dataset_name": null, "local_dataset": null, "model": "roberta-large", "crf": true, "max_length": 128, "epoch": 15, "batch_size": 64, "lr": 1e-05, "random_seed": 42, "gradient_accumulation_steps": 1, "weight_decay": 1e-07, "lr_warmup_step_ratio": 0.1, "max_grad_norm": 10.0}