Upload BioForge Stage 4 model

README.md

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+---
+language:
+- en
+license: mit
+tags:
+- sentence-transformers
+- biomedical
+- medical
+- healthcare
+- information-retrieval
+- semantic-search
+library_name: sentence-transformers
+pipeline_tag: sentence-similarity
+---
+
+# BioForge 4: Mixed
+
+Part of the **BioForge Progressive Training Pipeline** - Stage 4: Mixed Foundational Model - Unified biomedical encoder (RECOMMENDED)
+
+## Model Overview
+
+This is **Stage 4** in the BioForge progressive training curriculum.
+
+### Training Details
+
+- **Training Data**: 2.35M mixed pairs (OWL + PubMed + CTG + UMLS)
+- **Epochs**: 2
+- **Batch Size**: 1024
+- **Architecture**: bioformer-8L (BERT-based, 8 layers)
+- **Embedding Dimension**: 384
+- **Max Sequence Length**: 1024 tokens
+
+## Usage
+
+```python
+from sentence_transformers import SentenceTransformer
+
+# Load this model
+model = SentenceTransformer("pankajrajdeo/bioforge-stage4-mixed")
+
+# Encode medical text
+sentences = [
+    "Type 2 diabetes mellitus",
+    "Myocardial infarction"
+]
+
+embeddings = model.encode(sentences)
+print(embeddings.shape)  # (2, 384)
+```
+
+## BioForge Training Pipeline
+
+The complete BioForge pipeline consists of:
+
+1. **Stage 1a**: PubMed Foundation → [`pankajrajdeo/bioforge-stage1a-pubmed`](https://huggingface.co/pankajrajdeo/bioforge-stage1a-pubmed)
+2. **Stage 1b**: Clinical Trials → [`pankajrajdeo/bioforge-stage1b-clinical-trials`](https://huggingface.co/pankajrajdeo/bioforge-stage1b-clinical-trials)
+3. **Stage 1c**: UMLS Ontology → [`pankajrajdeo/bioforge-stage1c-umls`](https://huggingface.co/pankajrajdeo/bioforge-stage1c-umls)
+4. **Stage 3b**: OWL Ontology (NameDropper) → [`pankajrajdeo/bioforge-namedropper-owl`](https://huggingface.co/pankajrajdeo/bioforge-namedropper-owl)
+5. **Stage 4**: Mixed Foundation ⭐ **RECOMMENDED** → [`pankajrajdeo/bioforge-stage4-mixed`](https://huggingface.co/pankajrajdeo/bioforge-stage4-mixed)
+
+## Recommended Model
+
+For most use cases, we recommend **Stage 4 Mixed Model** which combines all training data for the best overall performance.
+
+## Citation
+
+```bibtex
+@software{bioforge2025,
+  author = {Pankaj Rajdeo},
+  title = {BioForge: Progressive Biomedical Sentence Embeddings},
+  year = {2025},
+  publisher = {Hugging Face},
+  url = {https://huggingface.co/pankajrajdeo/bioforge-stage4-mixed},
+  note = {Stage 4}
+}
+```
+
+## License
+
+MIT License
+
+## Contact
+
+- **Author**: Pankaj Rajdeo
+- **Institution**: Cincinnati Children's Hospital Medical Center
+- **Hugging Face**: [@pankajrajdeo](https://huggingface.co/pankajrajdeo)

config.json

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+{
+  "architectures": [
+    "BertModel"
+  ],
+  "attention_probs_dropout_prob": 0.1,
+  "classifier_dropout": null,
+  "hidden_act": "gelu",
+  "hidden_dropout_prob": 0.1,
+  "hidden_size": 384,
+  "initializer_range": 0.02,
+  "intermediate_size": 1536,
+  "layer_norm_eps": 1e-12,
+  "max_position_embeddings": 1024,
+  "model_type": "bert",
+  "num_attention_heads": 6,
+  "num_hidden_layers": 16,
+  "pad_token_id": 0,
+  "position_embedding_type": "absolute",
+  "torch_dtype": "float32",
+  "transformers_version": "4.53.2",
+  "type_vocab_size": 2,
+  "use_cache": true,
+  "vocab_size": 32768
+}

config_sentence_transformers.json

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+{
+  "__version__": {
+    "sentence_transformers": "3.4.1",
+    "transformers": "4.53.2",
+    "pytorch": "2.6.0+cu124"
+  },
+  "prompts": {},
+  "default_prompt_name": null,
+  "similarity_fn_name": "cosine"
+}

model.safetensors

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+version https://git-lfs.github.com/spec/v1
+oid sha256:8580e70c3bd8f18a96f6ea13989b1300d9221020a19873d5e555d9751efe04b7
+size 166097144

modules.json

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+[
+  {
+    "idx": 0,
+    "name": "0",
+    "path": "",
+    "type": "sentence_transformers.models.Transformer"
+  },
+  {
+    "idx": 1,
+    "name": "1",
+    "path": "1_Pooling",
+    "type": "sentence_transformers.models.Pooling"
+  }
+]

sentence_bert_config.json

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+{
+  "max_seq_length": 1024,
+  "do_lower_case": false
+}

special_tokens_map.json

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+{
+  "cls_token": {
+    "content": "[CLS]",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
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+    "lstrip": false,
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+    "rstrip": false,
+    "single_word": false
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+    "single_word": false
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+    "content": "[UNK]",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  }
+}

tokenizer_config.json

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+{
+  "added_tokens_decoder": {
+    "0": {
+      "content": "[PAD]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
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+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
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+      "lstrip": false,
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+      "rstrip": false,
+      "single_word": false,
+      "special": true
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+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
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+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
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+  "clean_up_tokenization_spaces": true,
+  "cls_token": "[CLS]",
+  "do_basic_tokenize": true,
+  "do_lower_case": false,
+  "extra_special_tokens": {},
+  "mask_token": "[MASK]",
+  "max_length": 1024,
+  "model_max_length": 1024,
+  "never_split": null,
+  "pad_to_multiple_of": null,
+  "pad_token": "[PAD]",
+  "pad_token_type_id": 0,
+  "padding_side": "right",
+  "sep_token": "[SEP]",
+  "stride": 0,
+  "strip_accents": null,
+  "tokenize_chinese_chars": true,
+  "tokenizer_class": "BertTokenizer",
+  "truncation_side": "right",
+  "truncation_strategy": "longest_first",
+  "unk_token": "[UNK]"
+}