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Inference & Evaluation Instructions

Main Pipeline

Run inference_pipeline.sh to execute the inference-evaluation pipeline.

The script first calls inference.py for inference. We use vLLM as the inference engine for generation. Model outputs are saved into the benchmarks/generations folder. Next the script calls evaluate.py to evaluate the model outputs against gold outputs.

Run inference_pipeline.sh with parameters

./inference_pipeline.sh
    -c <model_name> or <checkpoint_name>
    -b <benchmark name>
    -s <num_shots> (in-context learning shots number, default is zero)
    -r 0 (cot prompting; 0: disabled, 1: enabled)
    -e vllm (inference backend, currently support vllm only)
    -m 0 (in-context learning with multiple seeds; 0: disabled, 1: enabled)
    -t 0 (self-consistency cot prompting; 0: disabled, 1: enabled)
    -d 32 (setting batch_size 32 for inference per gpu

Example for in-context learning (5-shot, multiple-seeds) with pubmedqa and meditron-70b:

bash inference_pipeline.sh \
    -b pubmedqa
    -c meditron-70b \
    -s 5
    -m 1

Example for self-consistency cot prompting with medqa and meditron-70b-cotmedqa:

bash inference_pipeline.sh \
    -b medqa
    -c meditron-70b-cotmedqa \
    -r 1
    -t 1

Benchmarks

Add benchmarks to benchmark.py following an existing benchmark class. Currently require the benchmark is registered in the Huggingface dataset hub.

Example benchmark class:

class MyBenchmark(Benchmark):
    '''
    MyBenchmark is <Your Description>

    Huggingface card: https://huggingface.co/datasets/<MyBenchmark>
    '''
    def __init__(self, name='pubmedqa') -> None:
        super().__init__(name)
        self.hub_name = "<MyBenchmark>"
        self.dir_name = '<Directory for MyBenchmark>'
        self.path = os.path.join(ROOT_DIR, 'benchmarks', 'datasets', self.dir_name)
        self.splits = ['train', 'validation', 'test']
        self.subsets = ['<If subset exist, specify here>']

    @staticmethod
    def custom_preprocessing(row):
        '''Add your custom preprocessing code here'''
        return row

Models

Add models with associated local path or Huggingface repo name to checkpoints in inference_pipeline.sh.

For example:

["med42"]="m42-health/med42-70b" # Huggingface repo name
["meditron-70b"]="$meditron-70b/hf_checkpoints/raw/iter_23000/ # local path

Checkpoints from Megatron-LLM needs to be converted to Huggingface format in order to continue the inference & evaluation steps. To convert the checkpoints, please use the script provided by Megatron-LLM.

Here is an example for running the converstion script: Specify proper parameters:

NUM_IN_SHARDS=8 # number of input model shards
NUM_OUT_SHARDS=8 # number of output model shards
INPUT_DIR=<path to your Megatron checkpoint>
OUTPUT_DIR=<path to save your HF model weights>
UNSHARDED_DIR=<path for stroing unsharded Megatron checkpoint, temporary>

Execute the scripts

./megatron2hf.sh