From 56a55b84893aaa0379eaf15f49cdfa7b44d11cd8 Mon Sep 17 00:00:00 2001 From: ModelHub XC Date: Mon, 10 Aug 2026 21:49:24 +0800 Subject: [PATCH] =?UTF-8?q?=E5=88=9D=E5=A7=8B=E5=8C=96=E9=A1=B9=E7=9B=AE?= =?UTF-8?q?=EF=BC=8C=E7=94=B1ModelHub=20XC=E7=A4=BE=E5=8C=BA=E6=8F=90?= =?UTF-8?q?=E4=BE=9B=E6=A8=A1=E5=9E=8B?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Model: BSVGK/gemma-1.1-2b-it-drugbank-kg2text-merged-v2 Source: Original Platform --- .gitattributes | 36 +++++++++++ README.md | 137 +++++++++++++++++++++++++++++++++++++++++ chat_template.jinja | 4 ++ config.json | 32 ++++++++++ generation_config.json | 7 +++ model.safetensors | 3 + tokenizer.json | 3 + tokenizer_config.json | 19 ++++++ 8 files changed, 241 insertions(+) create mode 100644 .gitattributes create mode 100644 README.md create mode 100644 chat_template.jinja create mode 100644 config.json create mode 100644 generation_config.json create mode 100644 model.safetensors create mode 100644 tokenizer.json create mode 100644 tokenizer_config.json diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..52373fe --- /dev/null +++ b/.gitattributes @@ -0,0 +1,36 @@ +*.7z filter=lfs diff=lfs merge=lfs -text +*.arrow filter=lfs diff=lfs merge=lfs -text +*.bin filter=lfs diff=lfs merge=lfs -text +*.bz2 filter=lfs diff=lfs merge=lfs -text +*.ckpt filter=lfs diff=lfs merge=lfs -text +*.ftz filter=lfs diff=lfs merge=lfs -text +*.gz filter=lfs diff=lfs merge=lfs -text +*.h5 filter=lfs diff=lfs merge=lfs -text +*.joblib filter=lfs diff=lfs merge=lfs -text +*.lfs.* filter=lfs diff=lfs merge=lfs -text +*.mlmodel filter=lfs diff=lfs merge=lfs -text +*.model filter=lfs diff=lfs merge=lfs -text +*.msgpack filter=lfs diff=lfs merge=lfs -text +*.npy filter=lfs diff=lfs merge=lfs -text +*.npz filter=lfs diff=lfs merge=lfs -text +*.onnx filter=lfs diff=lfs merge=lfs -text +*.ot filter=lfs diff=lfs merge=lfs -text +*.parquet filter=lfs diff=lfs merge=lfs -text +*.pb filter=lfs diff=lfs merge=lfs -text +*.pickle filter=lfs diff=lfs merge=lfs -text +*.pkl filter=lfs diff=lfs merge=lfs -text +*.pt filter=lfs diff=lfs merge=lfs -text +*.pth filter=lfs diff=lfs merge=lfs -text +*.rar filter=lfs diff=lfs merge=lfs -text +*.safetensors filter=lfs diff=lfs merge=lfs -text +saved_model/**/* filter=lfs diff=lfs merge=lfs -text +*.tar.* filter=lfs diff=lfs merge=lfs -text +*.tar filter=lfs diff=lfs merge=lfs -text +*.tflite filter=lfs diff=lfs merge=lfs -text +*.tgz filter=lfs diff=lfs merge=lfs -text +*.wasm filter=lfs diff=lfs merge=lfs -text +*.xz filter=lfs diff=lfs merge=lfs -text +*.zip filter=lfs diff=lfs merge=lfs -text +*.zst filter=lfs diff=lfs merge=lfs -text +*tfevents* filter=lfs diff=lfs merge=lfs -text +tokenizer.json filter=lfs diff=lfs merge=lfs -text diff --git a/README.md b/README.md new file mode 100644 index 0000000..eac30ba --- /dev/null +++ b/README.md @@ -0,0 +1,137 @@ +--- +language: +- en +license: mit +base_model: google/gemma-1.1-2b-it +tags: +- text-generation +- knowledge-graph +- kg-to-text +- pharmaceutical +- drugbank +- natural-language-generation +- nlp +- trustworthy-ai +- hallucination-detection +- lora +- fine-tuned +- merged +datasets: +- BSVGK/drugbank_dataset +metrics: +- bleu +- bertscore +pipeline_tag: text-generation +--- + +# Gemma 1.1 2B IT β€” Merged Model v2 (DrugBank KG-to-Text) + +## Model Summary + +This is the **full merged model** of Gemma 1.1 2B IT fine-tuned with LoRA to generate fluent, hallucination-free natural language drug descriptions from **pharmaceutical RDF knowledge graph triples** sourced from DrugBank. It was developed as part of a UEL–Depixen industrial placement research project focused on building **trustworthy, domain-specific SLMs**. + +This is the recommended model for inference β€” no additional adapter loading required. + +> For the LoRA adapter only, use: +> πŸ‘‰ [BSVGK/gemma-1.1-2b-it-drugbank-kg2text-lora-v2](https://huggingface.co/BSVGK/gemma-1.1-2b-it-drugbank-kg2text-lora-v2) + +## Key Results + +| Metric | Score | +|--------|-------| +| BLEU Score | **0.9737** | +| BERTScore F1 | **0.9896** | +| Fact F1 | **0.9966** | +| Hallucination Rate | **0.54%** | +| Test Samples | 254 unseen DrugBank entries | + +## Model Details + +- **Base Model:** google/gemma-1.1-2b-it +- **Fine-tuning Method:** LoRA (Low-Rank Adaptation) +- **Task:** KG-to-Text β€” RDF triples β†’ fluent drug descriptions +- **Domain:** Pharmaceutical β€” DrugBank +- **Training Dataset:** 2,537 verified DrugBank RDF triples +- **Hardware:** NVIDIA A100 +- **Framework:** PyTorch, Hugging Face PEFT, TRL, SFTTrainer + +## Usage + +from transformers import AutoTokenizer, AutoModelForCausalLM + +# Load merged model directly β€” no adapter needed +tokenizer = AutoTokenizer.from_pretrained( + "BSVGK/gemma-1.1-2b-it-drugbank-kg2text-merged-v2" +) +model = AutoModelForCausalLM.from_pretrained( + "BSVGK/gemma-1.1-2b-it-drugbank-kg2text-merged-v2" +) + +prompt = """Generate a natural language description from the following RDF triples: + +Triples: +- DrugA hasIndication Condition_X +- DrugA hasMechanism Mechanism_Y +- DrugA hasInteraction DrugB + +Description:""" + +inputs = tokenizer(prompt, return_tensors="pt") +outputs = model.generate(**inputs, max_new_tokens=256) +print(tokenizer.decode(outputs[0], skip_special_tokens=True)) + +## Dataset + +- **Dataset:** [BSVGK/drugbank_dataset](https://huggingface.co/datasets/BSVGK/drugbank_dataset) +- **Size:** 2,537 training + 254 test samples +- **Source:** DrugBank pharmaceutical database +- **Format:** RDF Triples β†’ Natural Language Drug Description + +## Comparison with LoRA Adapter + +| | Merged Model v2 | LoRA Adapter v2 | +|--|--|--| +| Inference | βœ… Direct β€” no base model needed | ❌ Requires base model + PEFT | +| Storage | Larger (full model) | Smaller (adapter only) | +| Speed | Faster to load | Slower to load | +| Recommended for | Production inference | Research & experimentation | + +## Intended Use + +- Pharmaceutical knowledge graph verbalisation +- Drug information summarisation and description generation +- Research in trustworthy and hallucination-free biomedical NLP +- Natural language generation from biomedical knowledge graphs + +## Out of Scope + +- Non-pharmaceutical domains +- Clinical diagnosis or medical advice +- General purpose text generation + +## Important Notice + +This model is intended for **research purposes only**. It should not be used for clinical decision-making or medical advice. Always consult a qualified healthcare professional. + +## Citation + +@misc{bubathula2026drugbank_merged, + author = {Sai Venkata Gopala Krishna Bubathula}, + title = {Gemma 1.1 2B IT Merged Model v2: KG-to-Text Generation + for DrugBank Pharmaceutical Data}, + year = {2026}, + publisher = {HuggingFace}, + url = {https://huggingface.co/BSVGK/gemma-1.1-2b-it-drugbank-kg2text-merged-v2}, + institution = {University of East London & Depixen} +} + +## Developer + +**Sai Venkata Gopala Krishna Bubathula** +- πŸŽ“ MSc Big Data Technologies, University of East London +- 🏒 AI Engineer β€” UEL–Depixen Industrial Placement +- πŸ”— [GitHub](https://github.com/BSVGK1919) +- πŸ”— [LoRA Adapter](https://huggingface.co/BSVGK/gemma-1.1-2b-it-drugbank-kg2text-lora-v2) +- πŸ”— [LinkedIn](https://www.linkedin.com/in/sai-venkata-gopala-krishna-bubathula-a05a26283/) + + diff --git a/chat_template.jinja b/chat_template.jinja new file mode 100644 index 0000000..923ec25 --- /dev/null +++ b/chat_template.jinja @@ -0,0 +1,4 @@ +{{ bos_token }}{% if messages[0]['role'] == 'system' %}{{ raise_exception('System role not supported') }}{% endif %}{% for message in messages %}{% if (message['role'] == 'user') != (loop.index0 % 2 == 0) %}{{ raise_exception('Conversation roles must alternate user/assistant/user/assistant/...') }}{% endif %}{% if (message['role'] == 'assistant') %}{% set role = 'model' %}{% else %}{% set role = message['role'] %}{% endif %}{{ '' + role + ' +' + message['content'] | trim + ' +' }}{% endfor %}{% if add_generation_prompt %}{{'model +'}}{% endif %} \ No newline at end of file diff --git a/config.json b/config.json new file mode 100644 index 0000000..815f1a3 --- /dev/null +++ b/config.json @@ -0,0 +1,32 @@ +{ + "architectures": [ + "GemmaForCausalLM" + ], + "attention_bias": false, + "attention_dropout": 0.0, + "bos_token_id": 2, + "dtype": "bfloat16", + "eos_token_id": 1, + "head_dim": 256, + "hidden_act": "gelu_pytorch_tanh", + "hidden_activation": "gelu_pytorch_tanh", + "hidden_size": 2048, + "initializer_range": 0.02, + "intermediate_size": 16384, + "max_position_embeddings": 8192, + "model_type": "gemma", + "num_attention_heads": 8, + "num_hidden_layers": 18, + "num_key_value_heads": 1, + "pad_token_id": 0, + "rms_norm_eps": 1e-06, + "rope_parameters": { + "rope_theta": 10000.0, + "rope_type": "default" + }, + "tie_word_embeddings": true, + "transformers_version": "5.5.3", + "use_bidirectional_attention": null, + "use_cache": true, + "vocab_size": 256000 +} diff --git a/generation_config.json b/generation_config.json new file mode 100644 index 0000000..6787d42 --- /dev/null +++ b/generation_config.json @@ -0,0 +1,7 @@ +{ + "_from_model_config": true, + "bos_token_id": 2, + "eos_token_id": 1, + "pad_token_id": 0, + "transformers_version": "5.5.3" +} diff --git a/model.safetensors b/model.safetensors new file mode 100644 index 0000000..d47bbf4 --- /dev/null +++ b/model.safetensors @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8c949560082a41c13a72b0c441cc87c73540c793c75a1ae6e036e54d0fb5ff3a +size 5012363856 diff --git a/tokenizer.json b/tokenizer.json new file mode 100644 index 0000000..e113393 --- /dev/null +++ b/tokenizer.json @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e70d575dcb9d112715587c310734ac9085f24b162585ec589b02389fcbe0561c +size 34349429 diff --git a/tokenizer_config.json b/tokenizer_config.json new file mode 100644 index 0000000..dd45bb5 --- /dev/null +++ b/tokenizer_config.json @@ -0,0 +1,19 @@ +{ + "backend": "tokenizers", + "bos_token": "", + "clean_up_tokenization_spaces": false, + "eos_token": "", + "extra_special_tokens": [ + "", + "" + ], + "is_local": true, + "mask_token": "", + "model_max_length": 1000000000000000019884624838656, + "pad_token": "", + "sp_model_kwargs": {}, + "spaces_between_special_tokens": false, + "tokenizer_class": "GemmaTokenizer", + "unk_token": "", + "use_default_system_prompt": false +}