Upload 9 files

README.md

@@ -0,0 +1,207 @@
+---
+language: en
+license: cc-by-sa-4.0
+library_name: span-marker
+tags:
+- span-marker
+- token-classification
+- ner
+- named-entity-recognition
+- generated_from_span_marker_trainer
+metrics:
+- precision
+- recall
+- f1
+widget:
+- text: Altitude measurements based on near - IR imaging in H and Hcont filters showed
+    that the deeper BS2 clouds were located near the methane condensation level (
+    ≈1.2bars ) , while BS1 was generally ∼500 mb above that level ( at lower pressures
+    ) .
+- text: However , our model predicts different performance for large enough memory
+    - access latency and validates the intuition that the dynamic programming algorithm
+    performs better on these machines .
+- text: We established a P fertilizer need map based on integrating results from the
+    two systems .
+- text: Here , we have addressed this limitation for the endodermal lineage by developing
+    a defined culture system to expand and differentiate human foregut stem cells
+    ( hFSCs ) derived from hPSCs . hFSCs can self - renew while maintaining their
+    capacity to differentiate into pancreatic and hepatic cells .
+- text: The accumulated percentage gain from selection amounted to 51%/1 % lower Striga
+    infestation ( measured by area under Striga number progress curve , ASNPC ) ,
+    46%/62 % lower downy mildew incidence , and 49%/31 % higher panicle yield of the
+    C5 - FS compared to the mean of the genepool parents at Sadoré / Cinzana , respectively
+    .
+pipeline_tag: token-classification
+base_model: allenai/specter2_base
+model-index:
+- name: SpanMarker with allenai/specter2_base on my-data
+  results:
+  - task:
+      type: token-classification
+      name: Named Entity Recognition
+    dataset:
+      name: my-data
+      type: unknown
+      split: test
+    metrics:
+    - type: f1
+      value: 0.6906354515050167
+      name: F1
+    - type: precision
+      value: 0.7108433734939759
+      name: Precision
+    - type: recall
+      value: 0.6715447154471544
+      name: Recall
+---
+
+# SpanMarker with allenai/specter2_base on my-data
+
+This is a [SpanMarker](https://github.com/tomaarsen/SpanMarkerNER) model that can be used for Named Entity Recognition. This SpanMarker model uses [allenai/specter2_base](https://huggingface.co/allenai/specter2_base) as the underlying encoder.
+
+## Model Details
+
+### Model Description
+- **Model Type:** SpanMarker
+- **Encoder:** [allenai/specter2_base](https://huggingface.co/allenai/specter2_base)
+- **Maximum Sequence Length:** 256 tokens
+- **Maximum Entity Length:** 8 words
+<!-- - **Training Dataset:** [Unknown](https://huggingface.co/datasets/unknown) -->
+- **Language:** en
+- **License:** cc-by-sa-4.0
+
+### Model Sources
+
+- **Repository:** [SpanMarker on GitHub](https://github.com/tomaarsen/SpanMarkerNER)
+- **Thesis:** [SpanMarker For Named Entity Recognition](https://raw.githubusercontent.com/tomaarsen/SpanMarkerNER/main/thesis.pdf)
+
+### Model Labels
+| Label    | Examples                                                                                                |
+|:---------|:--------------------------------------------------------------------------------------------------------|
+| Data     | "Depth time - series", "defect", "an overall mitochondrial"                                             |
+| Material | "cross - shore measurement locations", "the subject 's fibroblasts", "COXI , COXII and COXIII subunits" |
+| Method   | "an approximation", "EFSA", "in vitro"                                                                  |
+| Process  | "intake", "a significant reduction of synthesis", "translation"                                         |
+
+## Evaluation
+
+### Metrics
+| Label    | Precision | Recall | F1     |
+|:---------|:----------|:-------|:-------|
+| **all**  | 0.7108    | 0.6715 | 0.6906 |
+| Data     | 0.6591    | 0.6138 | 0.6356 |
+| Material | 0.795     | 0.7910 | 0.7930 |
+| Method   | 0.5       | 0.45   | 0.4737 |
+| Process  | 0.6898    | 0.6293 | 0.6582 |
+
+## Uses
+
+### Direct Use for Inference
+
+```python
+from span_marker import SpanMarkerModel
+
+# Download from the 🤗 Hub
+model = SpanMarkerModel.from_pretrained("span-marker-allenai/specter2_base-me")
+# Run inference
+entities = model.predict("We established a P fertilizer need map based on integrating results from the two systems .")
+```
+
+### Downstream Use
+You can finetune this model on your own dataset.
+
+<details><summary>Click to expand</summary>
+
+```python
+from span_marker import SpanMarkerModel, Trainer
+
+# Download from the 🤗 Hub
+model = SpanMarkerModel.from_pretrained("span-marker-allenai/specter2_base-me")
+
+# Specify a Dataset with "tokens" and "ner_tag" columns
+dataset = load_dataset("conll2003") # For example CoNLL2003
+
+# Initialize a Trainer using the pretrained model & dataset
+trainer = Trainer(
+    model=model,
+    train_dataset=dataset["train"],
+    eval_dataset=dataset["validation"],
+)
+trainer.train()
+trainer.save_model("span-marker-allenai/specter2_base-me-finetuned")
+```
+</details>
+
+<!--
+### Out-of-Scope Use
+
+*List how the model may foreseeably be misused and address what users ought not to do with the model.*
+-->
+
+<!--
+## Bias, Risks and Limitations
+
+*What are the known or foreseeable issues stemming from this model? You could also flag here known failure cases or weaknesses of the model.*
+-->
+
+<!--
+### Recommendations
+
+*What are recommendations with respect to the foreseeable issues? For example, filtering explicit content.*
+-->
+
+## Training Details
+
+### Training Set Metrics
+| Training set          | Min | Median  | Max |
+|:----------------------|:----|:--------|:----|
+| Sentence length       | 3   | 25.6049 | 106 |
+| Entities per sentence | 0   | 5.2439  | 22  |
+
+### Training Hyperparameters
+- learning_rate: 5e-05
+- train_batch_size: 8
+- eval_batch_size: 8
+- seed: 42
+- optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
+- lr_scheduler_type: linear
+- lr_scheduler_warmup_ratio: 0.1
+- num_epochs: 10
+
+### Framework Versions
+- Python: 3.10.12
+- SpanMarker: 1.5.0
+- Transformers: 4.36.2
+- PyTorch: 2.0.1+cu118
+- Datasets: 2.16.1
+- Tokenizers: 0.15.0
+
+## Citation
+
+### BibTeX
+```
+@software{Aarsen_SpanMarker,
+    author = {Aarsen, Tom},
+    license = {Apache-2.0},
+    title = {{SpanMarker for Named Entity Recognition}},
+    url = {https://github.com/tomaarsen/SpanMarkerNER}
+}
+```
+
+<!--
+## Glossary
+
+*Clearly define terms in order to be accessible across audiences.*
+-->
+
+<!--
+## Model Card Authors
+
+*Lists the people who create the model card, providing recognition and accountability for the detailed work that goes into its construction.*
+-->
+
+<!--
+## Model Card Contact
+
+*Provides a way for people who have updates to the Model Card, suggestions, or questions, to contact the Model Card authors.*
+-->

added_tokens.json

@@ -0,0 +1,4 @@
+{
+  "<end>": 31091,
+  "<start>": 31090
+}

config.json

@@ -0,0 +1,110 @@
+{
+  "architectures": [
+    "SpanMarkerModel"
+  ],
+  "encoder": {
+    "_name_or_path": "allenai/specter2_base",
+    "adapters": {
+      "adapters": {},
+      "config_map": {},
+      "fusion_config_map": {},
+      "fusions": {}
+    },
+    "add_cross_attention": false,
+    "architectures": [
+      "BertModel"
+    ],
+    "attention_probs_dropout_prob": 0.1,
+    "bad_words_ids": null,
+    "begin_suppress_tokens": null,
+    "bos_token_id": null,
+    "chunk_size_feed_forward": 0,
+    "classifier_dropout": null,
+    "cross_attention_hidden_size": null,
+    "decoder_start_token_id": null,
+    "diversity_penalty": 0.0,
+    "do_sample": false,
+    "early_stopping": false,
+    "encoder_no_repeat_ngram_size": 0,
+    "eos_token_id": null,
+    "exponential_decay_length_penalty": null,
+    "finetuning_task": null,
+    "forced_bos_token_id": null,
+    "forced_eos_token_id": null,
+    "hidden_act": "gelu",
+    "hidden_dropout_prob": 0.1,
+    "hidden_size": 768,
+    "id2label": {
+      "0": "O",
+      "1": "Data",
+      "2": "Material",
+      "3": "Method",
+      "4": "Process"
+    },
+    "initializer_range": 0.02,
+    "intermediate_size": 3072,
+    "is_decoder": false,
+    "is_encoder_decoder": false,
+    "label2id": {
+      "Data": 1,
+      "Material": 2,
+      "Method": 3,
+      "O": 0,
+      "Process": 4
+    },
+    "layer_norm_eps": 1e-12,
+    "length_penalty": 1.0,
+    "max_length": 20,
+    "max_position_embeddings": 512,
+    "min_length": 0,
+    "model_type": "bert",
+    "no_repeat_ngram_size": 0,
+    "num_attention_heads": 12,
+    "num_beam_groups": 1,
+    "num_beams": 1,
+    "num_hidden_layers": 12,
+    "num_return_sequences": 1,
+    "output_attentions": false,
+    "output_hidden_states": false,
+    "output_scores": false,
+    "pad_token_id": 0,
+    "position_embedding_type": "absolute",
+    "prefix": null,
+    "problem_type": null,
+    "pruned_heads": {},
+    "remove_invalid_values": false,
+    "repetition_penalty": 1.0,
+    "return_dict": true,
+    "return_dict_in_generate": false,
+    "sep_token_id": null,
+    "suppress_tokens": null,
+    "task_specific_params": null,
+    "temperature": 1.0,
+    "tf_legacy_loss": false,
+    "tie_encoder_decoder": false,
+    "tie_word_embeddings": true,
+    "tokenizer_class": null,
+    "top_k": 50,
+    "top_p": 1.0,
+    "torch_dtype": "float32",
+    "torchscript": false,
+    "transformers_version": "4.36.2",
+    "type_vocab_size": 2,
+    "typical_p": 1.0,
+    "use_bfloat16": false,
+    "use_cache": true,
+    "vocab_size": 31096
+  },
+  "entity_max_length": 8,
+  "marker_max_length": 128,
+  "max_next_context": null,
+  "max_prev_context": null,
+  "model_max_length": 256,
+  "model_max_length_default": 512,
+  "model_type": "span-marker",
+  "span_marker_version": "1.5.0",
+  "torch_dtype": "float32",
+  "trained_with_document_context": false,
+  "transformers_version": "4.36.2",
+  "vocab_size": 31096
+}

model.safetensors

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9e0c789490988f2ce89f0dcd35e0b268b6e9696ae97ead87da0132205272843d
+size 439747140

special_tokens_map.json

@@ -0,0 +1,37 @@
+{
+  "cls_token": {
+    "content": "[CLS]",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "mask_token": {
+    "content": "[MASK]",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "pad_token": {
+    "content": "[PAD]",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "sep_token": {
+    "content": "[SEP]",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "unk_token": {
+    "content": "[UNK]",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  }
+}

tokenizer_config.json

@@ -0,0 +1,76 @@
+{
+  "add_prefix_space": true,
+  "added_tokens_decoder": {
+    "0": {
+      "content": "[PAD]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "101": {
+      "content": "[UNK]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "102": {
+      "content": "[CLS]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "103": {
+      "content": "[SEP]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "104": {
+      "content": "[MASK]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "31090": {
+      "content": "<start>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "31091": {
+      "content": "<end>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    }
+  },
+  "clean_up_tokenization_spaces": true,
+  "cls_token": "[CLS]",
+  "do_basic_tokenize": true,
+  "do_lower_case": true,
+  "entity_max_length": 8,
+  "marker_max_length": 128,
+  "mask_token": "[MASK]",
+  "model_max_length": 256,
+  "never_split": null,
+  "pad_token": "[PAD]",
+  "sep_token": "[SEP]",
+  "strip_accents": null,
+  "tokenize_chinese_chars": true,
+  "tokenizer_class": "BertTokenizer",
+  "unk_token": "[UNK]"
+}

training_args.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3402aba2424bc17fea8b4d9e1f63674ae9cb4d510b83ff618718c43c2571700f
+size 4283