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b2da1c08a8
* [Dataset] Add SmolInstruct, Update Chembench * Add dataset metadata * update * update * update
427 lines
14 KiB
Python
427 lines
14 KiB
Python
# flake8: noqa: W605
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import re
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from collections import defaultdict
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import numpy as np
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from datasets import Dataset, DatasetDict, load_dataset
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from opencompass.openicl.icl_evaluator.icl_base_evaluator import BaseEvaluator
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from opencompass.registry import (ICL_EVALUATORS, LOAD_DATASET,
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TEXT_POSTPROCESSORS)
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from .base import BaseDataset
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@LOAD_DATASET.register_module()
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class SmolInstructDataset(BaseDataset):
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@staticmethod
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def load(path: str, name: str):
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dataset = DatasetDict()
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raw_dataset = load_dataset(path)
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for split in ['validation', 'test']:
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raw_data = []
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for data in raw_dataset[split]:
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if data['task'] == name:
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raw_data.append(data)
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dataset[split] = Dataset.from_list(raw_data)
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return dataset
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def extract_chemical_data(text):
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pattern = re.compile(r'<(MOLFORMULA|SMILES|IUPAC)>(.*?)</\1>', re.DOTALL)
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matches = pattern.findall(text)
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if not matches:
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return []
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return [match[1].strip() for match in matches]
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def parse_molecule(molecular_formula):
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valid = re.match('([A-Za-z]\d*)+([\+\-]\d*)*$', molecular_formula)
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if valid is None:
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raise ValueError("Molecular formula \"%s\" is not valid." %
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molecular_formula)
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stack = [defaultdict(int)]
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def _parse_formula(formula, _stack):
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# Set remainder equal to 'None'
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r = None
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# Regular expression matching for each of the three cases:
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atom = re.match(r'([A-Z][a-z]?)(\d+)?', formula)
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opening = re.match(r'[\(\[\{]', formula)
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closing = re.match(r'[\)\]\}](\d+)?', formula)
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# If atom is identified:
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if atom:
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r = formula[len(atom.group()):]
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_stack[-1][atom.group(1)] += int(atom.group(2) or 1)
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# If opening brackets encountered:
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elif opening:
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r = formula[len(
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opening.group()
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):] # this sets the remainder equal to everything after the opening brackets
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_stack.append(defaultdict(int))
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# If closing brackets encountered:
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elif closing:
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r = formula[len(
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closing.group()
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):] # this sets the remainder equal to everything after the closing brackets
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for k, v in _stack.pop().items():
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_stack[-1][k] += v * int(
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closing.group(1)
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or 1) # v times amount of molecule k, depending on nesting
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# If anything remains, process remainders recursively as nested formulas:
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if r:
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_parse_formula(r, _stack)
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return dict(_stack[0])
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result = _parse_formula(molecular_formula, stack)
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charge = re.search('[\+\-]\d*', molecular_formula)
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if charge is not None:
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charge_str = charge.group()
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charge_type = charge_str[0]
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if len(charge_str) == 1:
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charge_num = 1
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else:
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charge_num = int(charge_str[1:])
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result[charge_type] = charge_num
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return result
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def calculate_single_element_match_for_list(predictions, references):
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# 抽取SMILES里的化学式
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predictions = [
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extract_chemical_data(prediction) for prediction in predictions
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]
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references = [extract_chemical_data(reference) for reference in references]
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ele_match_labels = []
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ele_invalid_labels = []
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details = []
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for pred_formula, gold_formula in zip(predictions, references):
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gold_formula = gold_formula[0]
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if pred_formula:
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pred_formula = pred_formula[0]
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detail = {'pred': [pred_formula], 'answer': gold_formula}
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if not pred_formula or not pred_formula:
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ele_invalid_labels.append(False)
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ele_match_labels.append(False)
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detail['score'] = [False]
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details.append(detail)
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continue
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try:
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pred_ele = parse_molecule(pred_formula)
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except KeyboardInterrupt:
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raise
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except:
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# print(pred_formula)
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# print('=====')
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ele_invalid_labels.append(True)
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ele_match_labels.append(False)
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detail['score'] = [False]
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details.append(detail)
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continue
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ele_invalid_labels.append(False)
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ele_match = False
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gold_ele = parse_molecule(gold_formula)
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if pred_ele == gold_ele:
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ele_match = True
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ele_match_labels.append(ele_match)
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detail['score'] = [ele_match]
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details.append(detail)
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score = sum(ele_match_labels) / len(predictions) * 100
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valid_score = 100 - sum(ele_invalid_labels) / len(predictions) * 100
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return {'score': score, 'valid_score': valid_score, 'details': details}
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def calculate_single_element_match(predictions, references):
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# 抽取SMILES里的化学式
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predictions = [
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extract_chemical_data(prediction) for prediction in predictions
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]
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references = [extract_chemical_data(reference) for reference in references]
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ele_match_labels = []
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ele_invalid_labels = []
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details = []
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for pred_formula, gold_formula in zip(predictions, references):
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gold_formula = gold_formula[0]
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if pred_formula:
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pred_formula = pred_formula[0]
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detail = {'pred': pred_formula, 'answer': gold_formula}
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if not pred_formula or not pred_formula:
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ele_invalid_labels.append(False)
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ele_match_labels.append(False)
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detail['score'] = False
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details.append(detail)
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continue
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try:
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pred_ele = parse_molecule(pred_formula)
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except KeyboardInterrupt:
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raise
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except:
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# print(pred_formula)
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# print('=====')
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ele_invalid_labels.append(True)
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ele_match_labels.append(False)
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detail['score'] = False
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details.append(detail)
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continue
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ele_invalid_labels.append(False)
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ele_match = False
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gold_ele = parse_molecule(gold_formula)
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if pred_ele == gold_ele:
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ele_match = True
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ele_match_labels.append(ele_match)
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detail['score'] = ele_match
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details.append(detail)
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score = sum(ele_match_labels) / len(predictions) * 100
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valid_score = 100 - sum(ele_invalid_labels) / len(predictions) * 100
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return {'score': score, 'valid_score': valid_score, 'details': details}
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@ICL_EVALUATORS.register_module()
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class NCElementMatchEvaluator(BaseEvaluator):
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"""Element match evaluator for name conversion."""
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def __init__(self) -> None:
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super().__init__()
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def score(self, predictions, references):
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print('len(predictions):', len(predictions))
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print('len(references):', len(references))
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if len(predictions) != len(references):
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return {
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'error': 'predictions and references have different '
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'length'
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}
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# topk的prediction，要拆开
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if isinstance(predictions[0], str):
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return calculate_single_element_match(predictions, references)
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else:
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num_k = len(predictions[0])
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scores = []
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for i in range(num_k):
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pred = [prediction[i] for prediction in predictions]
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ref = references
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score = calculate_single_element_match_for_list(pred, ref)
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scores.append(score)
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# 按照instance合并成一个完整的dict
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final_details = scores[0]['details']
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final_scores = [scores[0]['score']]
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final_valid_scores = [scores[0]['valid_score']]
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for _k in scores[1:]:
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for i, _d in enumerate(_k['details']):
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# print(_d)
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final_details[i]['pred'].extend(_d['pred'])
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final_details[i]['score'].extend(_d['score'])
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final_scores.append(_k['score'])
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final_valid_scores.append(_k['valid_score'])
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avg_score = []
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for _d in final_details:
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if True in _d['score']:
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avg_score.append(1)
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else:
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avg_score.append(0)
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max_score = sum(avg_score) / len(avg_score) * 100
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return {
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'score': max_score,
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'all_score': final_scores,
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'valid_score': final_valid_scores,
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'details': final_details,
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}
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@ICL_EVALUATORS.register_module()
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class NCExactMatchEvaluator(BaseEvaluator):
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"""Exact match evaluator for name conversion."""
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def __init__(self) -> None:
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super().__init__()
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def score(self, predictions, references):
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if len(predictions) != len(references):
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return {
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'error': 'predictions and references have different '
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'length'
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}
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predictions = [
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extract_chemical_data(prediction) for prediction in predictions
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]
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references = [
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extract_chemical_data(reference) for reference in references
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]
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cnt = 0
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valid_cnt = 0
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details = []
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for pred, ans in zip(predictions, references):
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ans = ans[0]
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if pred:
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pred = pred[0]
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valid_cnt += 1
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detail = {'pred': pred, 'answer': ans}
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if pred and pred.strip() == ans.strip():
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cnt += 1
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detail['correct'] = True
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else:
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detail['correct'] = False
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details.append(detail)
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score = cnt / len(predictions) * 100
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valid_score = valid_cnt / len(predictions) * 100
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return {'score': score, 'valid_score': valid_score, 'details': details}
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def extract_number(text):
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pattern = re.compile(r'<NUMBER>\s*(-?\d*\.?\d+)\s*</NUMBER>')
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matches = pattern.findall(text)
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return [float(match) for match in matches]
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@ICL_EVALUATORS.register_module()
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class RMSEEvaluator(BaseEvaluator):
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"""Exact match evaluator for name conversion."""
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def __init__(self) -> None:
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super().__init__()
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def score(self, predictions, references):
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if len(predictions) != len(references):
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return {
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'error': 'predictions and references have different '
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'length'
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}
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avg_score = 0
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details = []
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for prediction, reference in zip(predictions, references):
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pred = extract_number(prediction)
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ans = extract_number(reference)
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if not pred:
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pred = 0
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else:
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pred = pred[0]
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try:
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ans = ans[0]
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except:
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raise ValueError(f'ans: {reference}')
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detail = {'pred': pred, 'answer': ans}
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rmse_score = np.sqrt(np.mean((np.array(pred) - np.array(ans))**2))
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detail['score'] = rmse_score
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avg_score += rmse_score
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details.append(detail)
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score = avg_score / len(predictions)
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return {'score': score, 'details': details}
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@ICL_EVALUATORS.register_module()
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class FTSEvaluator(BaseEvaluator):
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"""Exact match evaluator for name conversion."""
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def __init__(self) -> None:
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super().__init__()
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def score(self, predictions, references):
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if len(predictions) != len(references):
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return {
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'error': 'predictions and references have different '
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'length'
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}
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predictions = [
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extract_chemical_data(prediction) for prediction in predictions
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]
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references = [
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extract_chemical_data(reference) for reference in references
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]
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avg_score = 0
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valid_cnt = 0
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details = []
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for pred, ans in zip(predictions, references):
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ans = ans[0]
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if not pred:
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detail = {'pred': '', 'answer': ans, 'score': 0}
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details.append(detail)
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continue
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pred = pred[0]
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detail = {'pred': pred, 'answer': ans}
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# 将 SMILES 转换为 RDKit 分子对象
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from rdkit import Chem
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mol1 = Chem.MolFromSmiles(pred)
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mol2 = Chem.MolFromSmiles(ans)
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if mol1 is None or mol2 is None:
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detail['score'] = 0
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details.append(detail)
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continue
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valid_cnt += 1
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# 生成 Morgan 指纹（等同于 ECFP4）
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# fp1 = AllChem.GetMorganFingerprintAsBitVect(mol1, radius=2, nBits=2048)
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# fp2 = AllChem.GetMorganFingerprintAsBitVect(mol2, radius=2, nBits=2048)
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from rdkit.Chem.rdFingerprintGenerator import GetMorganGenerator
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generator = GetMorganGenerator(radius=2, fpSize=2048)
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fp1 = generator.GetFingerprint(mol1)
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fp2 = generator.GetFingerprint(mol2)
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from rdkit.Chem import DataStructs
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similarity = DataStructs.TanimotoSimilarity(fp1, fp2) * 100
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detail['score'] = similarity
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avg_score += similarity
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details.append(detail)
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score = avg_score / len(predictions)
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valid_score = valid_cnt / len(predictions) * 100
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return {'score': score, 'valid_score': valid_score, 'details': details}
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@ICL_EVALUATORS.register_module()
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class MeteorEvaluator(BaseEvaluator):
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"""Exact match evaluator for name conversion."""
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def __init__(self) -> None:
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super().__init__()
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def score(self, predictions, references):
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if len(predictions) != len(references):
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return {
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'error': 'predictions and references have different '
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'length'
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}
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avg_score = 0
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details = []
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for pred, ans in zip(predictions, references):
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score = meteor_score([ans.split()], pred.split())
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avg_score += score
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detail = {'pred': pred, 'answer': ans, 'score': score}
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details.append(detail)
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score = avg_score / len(predictions)
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return {'score': score, 'details': details}
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@TEXT_POSTPROCESSORS.register_module('smolinstruct-acc')
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def smolinstruct_acc_postprocess(text: str) -> str:
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if 'yes' in text.lower():
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return '<BOOLEAN> Yes </BOOLEAN>'
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elif 'no' in text.lower():
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return '<BOOLEAN> No </BOOLEAN>'
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