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Model: google/txgemma-2b-predict Source: Original Platform
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README.md
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---
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license: other
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license_name: health-ai-developer-foundations
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license_link: https://developers.google.com/health-ai-developer-foundations/terms
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language:
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- en
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pipeline_tag: text-generation
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library_name: transformers
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tags:
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- therapeutics
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- drug-development
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extra_gated_heading: Access TxGemma on Hugging Face
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extra_gated_prompt: >-
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To access TxGemma on Hugging Face, you're required to review and
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||||
agree to [Health AI Developer Foundation's terms of use](https://developers.google.com/health-ai-developer-foundations/terms).
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To do this, please ensure you're logged in to Hugging Face and click below.
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Requests are processed immediately.
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extra_gated_button_content: Acknowledge license
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---
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# TxGemma model card
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**Model documentation:** [TxGemma](https://developers.google.com/health-ai-developer-foundations/txgemma)
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**Resources:**
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* Model on Google Cloud Model Garden: [TxGemma](https://console.cloud.google.com/vertex-ai/publishers/google/model-garden/txgemma)
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* Model on Hugging Face: [TxGemma](https://huggingface.co/collections/google/txgemma-release-67dd92e931c857d15e4d1e87)
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* GitHub repository (supporting code, Colab notebooks, discussions, and
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issues):
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[TxGemma](https://github.com/google-gemini/gemma-cookbook/tree/main/TxGemma)
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* Quick start notebook: [notebooks/quick\_start](https://github.com/google-gemini/gemma-cookbook/blob/main/TxGemma/%5BTxGemma%5DQuickstart_with_Hugging_Face.ipynb)
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* Support: See
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[Contact](https://developers.google.com/health-ai-developer-foundations/txgemma/get-started.md#contact).
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|
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Terms of use: [Health AI Developer Foundations terms of
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||||
use](https://developers.google.com/health-ai-developer-foundations/terms)
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**Author:** Google
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## Model information
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This section describes the TxGemma model and how to use it.
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### Description
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TxGemma is a collection of lightweight, state-of-the-art, open language models
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built upon Gemma 2, fine-tuned for therapeutic development. It comes in 3 sizes,
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2B, 9B, and 27B.
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TxGemma models are designed to process and understand information related to
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various therapeutic modalities and targets, including small molecules, proteins,
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nucleic acids, diseases, and cell lines. TxGemma excels at tasks such as
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property prediction, and can serve as a foundation for further fine-tuning or as
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an interactive, conversational agent for drug discovery. The model is fine-tuned
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from Gemma 2 using a diverse set of instruction-tuning datasets, curated from
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the [Therapeutics Data Commons (TDC)](https://tdcommons.ai/).
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TxGemma is offered as both a prediction model that expects a narrow form of
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prompting and for the 9B and 27B version, conversational models that are more
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flexible and can be used in multi-turn interactions, including to explain its
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rationale behind a prediction. This conversational model comes at the expense of
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some raw prediction performance. See our [manuscript](https://arxiv.org/abs/2504.06196)
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for more information.
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**Key Features**
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* Versatility: Exhibits strong performance across a wide range of therapeutic
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tasks, outperforming or matching best-in-class performance on a significant
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number of benchmarks.
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* Data Efficiency: Shows competitive performance even with limited data
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compared to larger models, offering improvements over its predecessors.
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* Conversational Capability (TxGemma-Chat): Includes conversational variants
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that can engage in natural language dialogue and explain the reasoning
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behind their predictions.
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* Foundation for Fine-tuning: Can be used as a pre-trained foundation for
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specialized use cases.
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**Potential Applications**
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TxGemma can be a valuable tool for researchers in the
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following areas:
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* Accelerated Drug Discovery: Streamline the therapeutic development process
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by predicting properties of therapeutics and targets for a wide variety of
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tasks including target identification, drug-target interaction prediction,
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and clinical trial approval prediction.
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### How to use
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Below are some example code snippets to help you quickly get started running the
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model locally on GPU. If you want to use the model to run inference on a large
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number of inputs, we recommend that you create a production version using [Model
|
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Garden](https://console.cloud.google.com/vertex-ai/publishers/google/model-garden/txgemma).
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#### Formatting prompts for therapeutic tasks
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```python
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import json
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from huggingface_hub import hf_hub_download
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# Load prompt template for tasks from TDC
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tdc_prompts_filepath = hf_hub_download(
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repo_id="google/txgemma-2b-predict",
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filename="tdc_prompts.json",
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)
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with open(tdc_prompts_filepath, "r") as f:
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tdc_prompts_json = json.load(f)
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# Set example TDC task and input
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task_name = "BBB_Martins"
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input_type = "{Drug SMILES}"
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drug_smiles = "CN1C(=O)CN=C(C2=CCCCC2)c2cc(Cl)ccc21"
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# Construct prompt using template and input drug SMILES string
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TDC_PROMPT = tdc_prompts_json[task_name].replace(input_type, drug_smiles)
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print(TDC_PROMPT)
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```
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The resulting prompt is in the format expected by the model:
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```none
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Instructions: Answer the following question about drug properties.
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Context: As a membrane separating circulating blood and brain extracellular fluid, the blood-brain barrier (BBB) is the protection layer that blocks most foreign drugs. Thus the ability of a drug to penetrate the barrier to deliver to the site of action forms a crucial challenge in development of drugs for central nervous system.
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Question: Given a drug SMILES string, predict whether it
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(A) does not cross the BBB (B) crosses the BBB
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Drug SMILES: CN1C(=O)CN=C(C2=CCCCC2)c2cc(Cl)ccc21
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Answer:
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```
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#### Running the model on predictive tasks
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```python
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# pip install accelerate transformers
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from transformers import AutoTokenizer, AutoModelForCausalLM
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# Load model directly from Hugging Face Hub
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tokenizer = AutoTokenizer.from_pretrained("google/txgemma-2b-predict")
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model = AutoModelForCausalLM.from_pretrained(
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"google/txgemma-2b-predict",
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device_map="auto",
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)
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# Formatted TDC prompt (see "Formatting prompts for therapeutic tasks" section above)
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prompt = TDC_PROMPT
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# Prepare tokenized inputs
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input_ids = tokenizer(prompt, return_tensors="pt").to("cuda")
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# Generate response
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outputs = model.generate(**input_ids, max_new_tokens=8)
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print(tokenizer.decode(outputs[0], skip_special_tokens=True))
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```
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Alternatively, you can use the `pipeline` API, which provides a simple way to
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run inference while abstracting away complex details of loading and using the
|
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model and tokenizer:
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```python
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# pip install transformers
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from transformers import pipeline
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# Instantiate a text generation pipeline using the model
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pipe = pipeline(
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"text-generation",
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model="google/txgemma-2b-predict",
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device="cuda",
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)
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# Formatted TDC prompt (see "Formatting prompts for therapeutic tasks" section above)
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prompt = TDC_PROMPT
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# Generate response
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outputs = pipe(prompt, max_new_tokens=8)
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response = outputs[0]["generated_text"]
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print(response)
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```
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### Examples
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See the following Colab notebooks for examples of how to use TxGemma:
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|
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* To give the model a quick try, running it locally with weights from Hugging
|
||||
Face, see [Quick start notebook in
|
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Colab](https://colab.research.google.com/github/google-gemini/gemma-cookbook/blob/main/TxGemma/%5BTxGemma%5DQuickstart_with_Hugging_Face.ipynb),
|
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which includes some example eval tasks from TDC.
|
||||
* For a demo of how to fine-tune TxGemma in Hugging Face, see our [Fine-tuning notebook in Colab](https://colab.research.google.com/github/google-gemini/gemma-cookbook/blob/main/TxGemma/%5BTxGemma%5DFinetune_with_Hugging_Face.ipynb).
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* For a demo of how TxGemma can be used as a tool as part of a larger agentic
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workflow powered by Gemini 2 see the [Agentic workflow notebook in Colab](https://colab.research.google.com/github/google-gemini/gemma-cookbook/blob/main/TxGemma/%5BTxGemma%5DAgentic_Demo_with_Hugging_Face.ipynb).
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### Model architecture overview
|
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* TxGemma is based on the Gemma 2 family of lightweight, state-of-the-art open
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LLMs. It utilizes a decoder-only transformer architecture.
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* Base Model: Gemma 2 (2B, 9B, and 27B parameter versions).
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* Fine-tuning Data: Therapeutics Data Commons, a collection of
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instruction-tuning datasets covering diverse therapeutic modalities and
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targets.
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* Training Approach: Instruction fine-tuning using a mixture of therapeutic
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data (TxT) and, for conversational variants, general instruction-tuning
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data.
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* Conversational Variants: TxGemma-Chat models (9B and 27B) are trained with a
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mixture of therapeutic and general instruction-tuning data to maintain
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conversational abilities.
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### Technical Specifications
|
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* Model type: Decoder-only Transformer (based on Gemma 2)
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* Key publication: [TxGemma: Efficient and Agentic LLMs for Therapeutics](https://arxiv.org/abs/2504.06196)
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* Model created: 2025-03-18 (From the TxGemma Variant Proposal)
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* Model Version: 1.0.0
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### Performance & Validation
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TxGemma's performance has been validated on a comprehensive
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[benchmark](https://tdcommons.ai/) of 66 therapeutic tasks derived from TDC.
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### Key performance metrics
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* Aggregated Improvement: Improves over the original [Tx-LLM
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paper](https://arxiv.org/abs/2406.06316) on 45 out of 66 therapeutic tasks.
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* Best-in-Class Performance: Surpasses or matches best-in-class performance on
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50 out of 66 tasks, exceeding specialist models on 26 tasks. See [Table A.11](https://arxiv.org/abs/2504.06196)
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of the TxGemma paper for the full breakdown.
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### Inputs and outputs
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* **Input:** Text. For best performance, text prompts should be formatted
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according to the TDC structure, including
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instructions, context, question, and, optionally, few-shot examples. Inputs
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can include SMILES strings, amino acid sequences, nucleotide sequences, and
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natural language text.
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* **Output:** Text.
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## Dataset details
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### Training dataset
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**Therapeutics Data Commons**: A curated collection of instruction-tuning
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datasets covering 66 tasks spanning the discovery and development of safe and
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effective medicine. This includes over 15 million data points across different
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biomedical entities. Released TxGemma models are only trained on datasets with
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commercial licenses, whereas models in our publication are also trained on
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datasets with non-commercial licenses.
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**General Instruction-Tuning Data**: Used for TxGemma-Chat in combination with
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TDC.
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### Evaluation dataset
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**Therapeutics Data Commons**: The same 66 tasks used for training are used
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for evaluation, following TDC's recommended methodologies for data splits
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(random, scaffold, cold-start, combination, and temporal).
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## License
|
||||
|
||||
The use of TxGemma is governed by the [Health AI Developer Foundations terms of
|
||||
use](https://developers.google.com/health-ai-developer-foundations/terms).
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## Implementation information
|
||||
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This section contains details about the model internals.
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### Software
|
||||
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Training was done using [JAX](https://github.com/jax-ml/jax).
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JAX allows researchers to take advantage of the latest generation of hardware,
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including TPUs, for faster and more efficient training of large models.
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## Use and limitations
|
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|
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### Intended use
|
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* Research and development of therapeutics.
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|
||||
### Benefits
|
||||
|
||||
TxGemma provides a versatile and powerful tool for accelerating therapeutic
|
||||
development. It offers:
|
||||
|
||||
* Strong performance across a wide range of tasks.
|
||||
* Data efficiency compared to larger models.
|
||||
* A foundation for further fine-tuning from private data.
|
||||
* Integration into agentic workflows.
|
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|
||||
### Limitations
|
||||
|
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* Trained on public data from TDC.
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||||
* Task-specific validation remains an important aspect of downstream model
|
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development by the end user.
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* As with any research, developers should ensure that any downstream
|
||||
application is validated to understand performance using data that is
|
||||
appropriately representative of the intended use setting for the specific
|
||||
application (e.g., age, sex, gender, condition, scanner, etc.).
|
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|
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## Citation
|
||||
|
||||
```bibtex
|
||||
@article{wang2025txgemma,
|
||||
title={TxGemma: Efficient and Agentic LLMs for Therapeutics},
|
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author={Wang, Eric and Schmidgall, Samuel and Jaeger, Paul F. and Zhang, Fan and Pilgrim, Rory and Matias, Yossi and Barral, Joelle and Fleet, David and Azizi, Shekoofeh},
|
||||
year={2025},
|
||||
}
|
||||
```
|
||||
|
||||
Find the paper [here](https://arxiv.org/abs/2504.06196).
|
||||
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config.json
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config.json
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{
|
||||
"architectures": [
|
||||
"Gemma2ForCausalLM"
|
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],
|
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"attention_bias": false,
|
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"attention_dropout": 0.0,
|
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"attn_logit_softcapping": 50.0,
|
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"bos_token_id": 2,
|
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"cache_implementation": "hybrid",
|
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"eos_token_id": 1,
|
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"final_logit_softcapping": 30.0,
|
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"head_dim": 256,
|
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"hidden_act": "gelu_pytorch_tanh",
|
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"hidden_activation": "gelu_pytorch_tanh",
|
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"hidden_size": 2304,
|
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"initializer_range": 0.02,
|
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"intermediate_size": 9216,
|
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"max_position_embeddings": 8192,
|
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"model_type": "gemma2",
|
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"num_attention_heads": 8,
|
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"num_hidden_layers": 26,
|
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"num_key_value_heads": 4,
|
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"pad_token_id": 0,
|
||||
"query_pre_attn_scalar": 256,
|
||||
"rms_norm_eps": 1e-06,
|
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"rope_theta": 10000.0,
|
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"sliding_window": 4096,
|
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"torch_dtype": "float32",
|
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"transformers_version": "4.47.1",
|
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"use_cache": true,
|
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"vocab_size": 256000
|
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}
|
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1
configuration.json
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configuration.json
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{"framework": "pytorch", "task": "text-generation", "allow_remote": true}
|
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8
generation_config.json
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generation_config.json
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{
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"_from_model_config": true,
|
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"bos_token_id": 2,
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"cache_implementation": "hybrid",
|
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"eos_token_id": 1,
|
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"pad_token_id": 0,
|
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"transformers_version": "4.47.1"
|
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}
|
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model-00001-of-00003.safetensors
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version https://git-lfs.github.com/spec/v1
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oid sha256:445c75b48013d59b7ee078ce7d0805fa022139e6001c39285e8a3a4b132ae44d
|
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size 4992576136
|
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3
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34
special_tokens_map.json
Normal file
34
special_tokens_map.json
Normal file
@@ -0,0 +1,34 @@
|
||||
{
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||||
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||||
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1
tdc_prompts.json
Normal file
1
tdc_prompts.json
Normal file
File diff suppressed because one or more lines are too long
3
tokenizer.json
Normal file
3
tokenizer.json
Normal file
@@ -0,0 +1,3 @@
|
||||
version https://git-lfs.github.com/spec/v1
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||||
size 17525357
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3
tokenizer.model
Normal file
3
tokenizer.model
Normal file
@@ -0,0 +1,3 @@
|
||||
version https://git-lfs.github.com/spec/v1
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2012
tokenizer_config.json
Normal file
2012
tokenizer_config.json
Normal file
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user