Upload 8 files

README.md

@@ -1,3 +1,42 @@
----
-license: apache-2.0
----
+# T5-Small Fine-tuned for Clinical Summarization of FHIR Document Reference Clinical Notes
+
+This model is a fine-tuned version of the `t5-small` model from Hugging Face, specifically tailored for the clinical summarization of FHIR Document Reference Clinical Notes.
+
+## Model Details
+
+- **Original Model**: [T5-Small](https://huggingface.co/t5-small)
+- **Fine-tuned Model**: [dlyog/t5-small-finetuned](https://huggingface.co/dlyog/t5-small-finetuned/)
+- **License**: Apache-2.0 (same as the original T5 license)
+
+## Fine-tuning Process
+
+The model was fine-tuned using a synthetic dataset created with tools like [Synthea](https://synthetichealth.github.io/synthea/). This dataset was used to simulate real-world clinical notes, ensuring the model understands the nuances and intricacies of medical terminology and context.
+
+Only the last two layers of the `t5-small` model were fine-tuned to retain most of the pre-trained knowledge while adapting it for better clinical summarization.
+
+## Usage
+
+Using the model is straightforward with the Hugging Face Transformers library:
+
+```python
+from transformers import T5ForConditionalGeneration, T5Tokenizer
+
+model = T5ForConditionalGeneration.from_pretrained("dlyog/t5-small-finetuned")
+tokenizer = T5Tokenizer.from_pretrained("dlyog/t5-small-finetuned")
+
+def summarize(text):
+    input_text = "summarize: " + text
+    input_ids = tokenizer.encode(input_text, return_tensors="pt")
+    summary_ids = model.generate(input_ids)
+    summary = tokenizer.decode(summary_ids[0])
+    return summary
+
+# Example
+text = "Your clinical note here..."
+print(summarize(text))
+
+# Acknowledgements
+A big thanks to the creators of the original t5-small model and the Hugging Face community. Also, gratitude to tools like Synthea that enabled the creation of high-quality synthetic datasets for fine-tuning purposes.
+
+# License
+This model is licensed under the Apache-2.0 License, the same as the original T5 model.

config.json

@@ -0,0 +1,60 @@
+{
+  "_name_or_path": "t5-small",
+  "architectures": [
+    "T5ForConditionalGeneration"
+  ],
+  "d_ff": 2048,
+  "d_kv": 64,
+  "d_model": 512,
+  "decoder_start_token_id": 0,
+  "dense_act_fn": "relu",
+  "dropout_rate": 0.1,
+  "eos_token_id": 1,
+  "feed_forward_proj": "relu",
+  "initializer_factor": 1.0,
+  "is_encoder_decoder": true,
+  "is_gated_act": false,
+  "layer_norm_epsilon": 1e-06,
+  "model_type": "t5",
+  "n_positions": 512,
+  "num_decoder_layers": 6,
+  "num_heads": 8,
+  "num_layers": 6,
+  "output_past": true,
+  "pad_token_id": 0,
+  "relative_attention_max_distance": 128,
+  "relative_attention_num_buckets": 32,
+  "task_specific_params": {
+    "summarization": {
+      "early_stopping": true,
+      "length_penalty": 2.0,
+      "max_length": 200,
+      "min_length": 30,
+      "no_repeat_ngram_size": 3,
+      "num_beams": 4,
+      "prefix": "summarize: "
+    },
+    "translation_en_to_de": {
+      "early_stopping": true,
+      "max_length": 300,
+      "num_beams": 4,
+      "prefix": "translate English to German: "
+    },
+    "translation_en_to_fr": {
+      "early_stopping": true,
+      "max_length": 300,
+      "num_beams": 4,
+      "prefix": "translate English to French: "
+    },
+    "translation_en_to_ro": {
+      "early_stopping": true,
+      "max_length": 300,
+      "num_beams": 4,
+      "prefix": "translate English to Romanian: "
+    }
+  },
+  "torch_dtype": "float32",
+  "transformers_version": "4.31.0",
+  "use_cache": true,
+  "vocab_size": 32128
+}

generation_config.json

@@ -0,0 +1,6 @@
+{
+  "decoder_start_token_id": 0,
+  "eos_token_id": 1,
+  "pad_token_id": 0,
+  "transformers_version": "4.31.0"
+}

pytorch_model.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ff27084bcb3db59d409150110a20a0f790b1adc30a2950fbfde6f863b9cac77d
+size 242071641

special_tokens_map.json

@@ -0,0 +1,107 @@
+{
+  "additional_special_tokens": [
+    "<extra_id_0>",
+    "<extra_id_1>",
+    "<extra_id_2>",
+    "<extra_id_3>",
+    "<extra_id_4>",
+    "<extra_id_5>",
+    "<extra_id_6>",
+    "<extra_id_7>",
+    "<extra_id_8>",
+    "<extra_id_9>",
+    "<extra_id_10>",
+    "<extra_id_11>",
+    "<extra_id_12>",
+    "<extra_id_13>",
+    "<extra_id_14>",
+    "<extra_id_15>",
+    "<extra_id_16>",
+    "<extra_id_17>",
+    "<extra_id_18>",
+    "<extra_id_19>",
+    "<extra_id_20>",
+    "<extra_id_21>",
+    "<extra_id_22>",
+    "<extra_id_23>",
+    "<extra_id_24>",
+    "<extra_id_25>",
+    "<extra_id_26>",
+    "<extra_id_27>",
+    "<extra_id_28>",
+    "<extra_id_29>",
+    "<extra_id_30>",
+    "<extra_id_31>",
+    "<extra_id_32>",
+    "<extra_id_33>",
+    "<extra_id_34>",
+    "<extra_id_35>",
+    "<extra_id_36>",
+    "<extra_id_37>",
+    "<extra_id_38>",
+    "<extra_id_39>",
+    "<extra_id_40>",
+    "<extra_id_41>",
+    "<extra_id_42>",
+    "<extra_id_43>",
+    "<extra_id_44>",
+    "<extra_id_45>",
+    "<extra_id_46>",
+    "<extra_id_47>",
+    "<extra_id_48>",
+    "<extra_id_49>",
+    "<extra_id_50>",
+    "<extra_id_51>",
+    "<extra_id_52>",
+    "<extra_id_53>",
+    "<extra_id_54>",
+    "<extra_id_55>",
+    "<extra_id_56>",
+    "<extra_id_57>",
+    "<extra_id_58>",
+    "<extra_id_59>",
+    "<extra_id_60>",
+    "<extra_id_61>",
+    "<extra_id_62>",
+    "<extra_id_63>",
+    "<extra_id_64>",
+    "<extra_id_65>",
+    "<extra_id_66>",
+    "<extra_id_67>",
+    "<extra_id_68>",
+    "<extra_id_69>",
+    "<extra_id_70>",
+    "<extra_id_71>",
+    "<extra_id_72>",
+    "<extra_id_73>",
+    "<extra_id_74>",
+    "<extra_id_75>",
+    "<extra_id_76>",
+    "<extra_id_77>",
+    "<extra_id_78>",
+    "<extra_id_79>",
+    "<extra_id_80>",
+    "<extra_id_81>",
+    "<extra_id_82>",
+    "<extra_id_83>",
+    "<extra_id_84>",
+    "<extra_id_85>",
+    "<extra_id_86>",
+    "<extra_id_87>",
+    "<extra_id_88>",
+    "<extra_id_89>",
+    "<extra_id_90>",
+    "<extra_id_91>",
+    "<extra_id_92>",
+    "<extra_id_93>",
+    "<extra_id_94>",
+    "<extra_id_95>",
+    "<extra_id_96>",
+    "<extra_id_97>",
+    "<extra_id_98>",
+    "<extra_id_99>"
+  ],
+  "eos_token": "</s>",
+  "pad_token": "<pad>",
+  "unk_token": "<unk>"
+}

spiece.model

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d60acb128cf7b7f2536e8f38a5b18a05535c9e14c7a355904270e15b0945ea86
+size 791656

tokenizer_config.json

@@ -0,0 +1,111 @@
+{
+  "additional_special_tokens": [
+    "<extra_id_0>",
+    "<extra_id_1>",
+    "<extra_id_2>",
+    "<extra_id_3>",
+    "<extra_id_4>",
+    "<extra_id_5>",
+    "<extra_id_6>",
+    "<extra_id_7>",
+    "<extra_id_8>",
+    "<extra_id_9>",
+    "<extra_id_10>",
+    "<extra_id_11>",
+    "<extra_id_12>",
+    "<extra_id_13>",
+    "<extra_id_14>",
+    "<extra_id_15>",
+    "<extra_id_16>",
+    "<extra_id_17>",
+    "<extra_id_18>",
+    "<extra_id_19>",
+    "<extra_id_20>",
+    "<extra_id_21>",
+    "<extra_id_22>",
+    "<extra_id_23>",
+    "<extra_id_24>",
+    "<extra_id_25>",
+    "<extra_id_26>",
+    "<extra_id_27>",
+    "<extra_id_28>",
+    "<extra_id_29>",
+    "<extra_id_30>",
+    "<extra_id_31>",
+    "<extra_id_32>",
+    "<extra_id_33>",
+    "<extra_id_34>",
+    "<extra_id_35>",
+    "<extra_id_36>",
+    "<extra_id_37>",
+    "<extra_id_38>",
+    "<extra_id_39>",
+    "<extra_id_40>",
+    "<extra_id_41>",
+    "<extra_id_42>",
+    "<extra_id_43>",
+    "<extra_id_44>",
+    "<extra_id_45>",
+    "<extra_id_46>",
+    "<extra_id_47>",
+    "<extra_id_48>",
+    "<extra_id_49>",
+    "<extra_id_50>",
+    "<extra_id_51>",
+    "<extra_id_52>",
+    "<extra_id_53>",
+    "<extra_id_54>",
+    "<extra_id_55>",
+    "<extra_id_56>",
+    "<extra_id_57>",
+    "<extra_id_58>",
+    "<extra_id_59>",
+    "<extra_id_60>",
+    "<extra_id_61>",
+    "<extra_id_62>",
+    "<extra_id_63>",
+    "<extra_id_64>",
+    "<extra_id_65>",
+    "<extra_id_66>",
+    "<extra_id_67>",
+    "<extra_id_68>",
+    "<extra_id_69>",
+    "<extra_id_70>",
+    "<extra_id_71>",
+    "<extra_id_72>",
+    "<extra_id_73>",
+    "<extra_id_74>",
+    "<extra_id_75>",
+    "<extra_id_76>",
+    "<extra_id_77>",
+    "<extra_id_78>",
+    "<extra_id_79>",
+    "<extra_id_80>",
+    "<extra_id_81>",
+    "<extra_id_82>",
+    "<extra_id_83>",
+    "<extra_id_84>",
+    "<extra_id_85>",
+    "<extra_id_86>",
+    "<extra_id_87>",
+    "<extra_id_88>",
+    "<extra_id_89>",
+    "<extra_id_90>",
+    "<extra_id_91>",
+    "<extra_id_92>",
+    "<extra_id_93>",
+    "<extra_id_94>",
+    "<extra_id_95>",
+    "<extra_id_96>",
+    "<extra_id_97>",
+    "<extra_id_98>",
+    "<extra_id_99>"
+  ],
+  "clean_up_tokenization_spaces": true,
+  "eos_token": "</s>",
+  "extra_ids": 100,
+  "model_max_length": 512,
+  "pad_token": "<pad>",
+  "tokenizer_class": "T5Tokenizer",
+  "unk_token": "<unk>"
+}