Niksa Praljak
commited on
Commit
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d85f01b
1
Parent(s):
26a45a2
Add section on model weight installation
Browse files
README.md
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@@ -32,11 +32,32 @@ Create and activate a conda environment and install the required packages:
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```bash
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conda create -p /env_path/BioM3_env python=3.10 # /env_path/ is the location that contains the conda env
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conda activate /env_path/BioM3_env
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cd /path/BioM3 # /path/ is the location that contains the huggingface repo for BioM3
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sh torch_requirements.sh # install torch software
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pip install -r requirements.txt # install remaining packages
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```
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## Stage 1: PenCL Inference
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### Overview
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### Running the Model
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1.
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```bash
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cd BioM3_PenCL
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```
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2. Run inference:
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### Running the Facilitator Model
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1.
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```bash
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git clone https://huggingface.co/your_username/BioM3_Facilitator
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cd BioM3_Facilitator
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```
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2. Run inference:
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```bash
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python run_Facilitator_sample.py \
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--json_path "stage2_facilitator_config.json" \
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```bash
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conda create -p /env_path/BioM3_env python=3.10 # /env_path/ is the location that contains the conda env
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conda activate /env_path/BioM3_env
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git clone https://huggingface.co/niksapraljak1/BioM3 /path/
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cd /path/BioM3 # /path/ is the location that contains the huggingface repo for BioM3
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sh torch_requirements.sh # install torch software
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pip install -r requirements.txt # install remaining packages
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```
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## Model Weights Installation
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Before running models, change directory to `BioM3/weights` folder, follow instructions, and download pretrained weights for the desired BioM3 configuration:
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```bash
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cd /path/BioM3/weights
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# after changing directory, follow instructions of README.md to install weights for each model component
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```
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Note: choose the desired BioM3 configuration/checkpoint, then install weights for each folder:
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- `/path/BioM3/weights/PenCL`
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- `/path/BioM3/weights/Facilitator`
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- `/path/BioM3/weights/ProteoScribe`
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Each folder contains a `README.md` detailing the different model weight configurations. For benchmarking, the optimal configuration is:
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- `BioM3_PenCL_epoch20.bin`
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- `BioM3_Facilitator_epoch20.bin`
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- `BioM3_ProteoScribe_epoch20.bin`
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## Stage 1: PenCL Inference
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### Overview
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### Running the Model
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1. Change directory to BioM3 repo:
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```bash
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cd /path/BioM3 # /path/ where is the location to the cloned BioM3 repo
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```
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2. Run inference:
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### Running the Facilitator Model
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1. Run sampling:
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```bash
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python run_Facilitator_sample.py \
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--json_path "stage2_facilitator_config.json" \
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