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Panacea: A foundation model for clinical trial design, recruitment, search, and summarization

This repository is the official implementation of Panacea: A foundation model for clinical trial design, recruitment, search, and summarization. Model can be downloaded here.

Requirements and Installation

See requirements.txt.

Get Started

Here we reproduced all eight tasks across different settings in our code base, including trial design, patient-trial matching, trial search, and trial summarization.

Data Download

• TrialAlign
• TrialInstruct
• TrialPanorama

Alignment Step

We first use collected TrialAlign dataset to adapt Panacea to the vocabulary commonly used in clinical trials. Run the following

bash scripts/pretrain/run_pretrain_full.sh

Instruction-tuning Step

Then, we conduct instruction-tuning step to enable Panacea to comprehend the user explanation of the task definition and the output requirement. Run

bash scripts/sft/sft.sh

Evaluation

Take patient-trial matching as an example, just run

bash scripts/eval/matching/patient2trial/panacea-7b.sh

To calculate the metrics, run

bash scripts/eval/matching/patient2trial/metrics/cls.sh 

Evaluation of the other tasks is in the same way.

Contact

Please feel free to submit a Github issue if you have any questions or find any bugs. We do not guarantee any support, but will do our best if we can help.