212 lines
5.4 KiB
Markdown
212 lines
5.4 KiB
Markdown
# BC2GM
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## 概述
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BC2GM（BioCreative II Gene Mention）数据集是一个广泛使用的基因提及识别语料库，包含来自MEDLINE摘要的20,000个句子，其中的基因和蛋白质名称均由领域专家手动标注。
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## 任务描述
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- **任务类型**：生物医学命名实体识别（NER）
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- **输入**：来自MEDLINE摘要的生物医学文本
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- **输出**：识别出的基因和蛋白质名称片段
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- **领域**：分子生物学、遗传学
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## 主要特点
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- 包含20,000个来自MEDLINE摘要的句子
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- 由专家标注的基因和蛋白质提及
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- 源自BioCreative II挑战赛的基准数据集
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- 广泛用于生物医学NER评估
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- 高质量的人工标注
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## 评估说明
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- 默认配置使用 **5-shot** 评估
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- 评估指标：精确率（Precision）、召回率（Recall）、F1分数（F1-Score）、准确率（Accuracy）
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- 实体类型：GENE（基因和蛋白质名称）
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## 属性
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| 属性 | 值 |
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|----------|-------|
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| **基准测试名称** | `bc2gm` |
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| **数据集ID** | [extraordinarylab/bc2gm](https://modelscope.cn/datasets/extraordinarylab/bc2gm/summary) |
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| **论文** | N/A |
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| **标签** | `Knowledge`, `NER` |
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| **指标** | `precision`, `recall`, `f1_score`, `accuracy` |
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| **默认示例数** | 5-shot |
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| **评估划分** | `test` |
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| **训练划分** | `train` |
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## 数据统计
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| 指标 | 值 |
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|--------|-------|
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| 总样本数 | 5,000 |
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| 提示词长度（平均） | 2228.52 字符 |
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| 提示词长度（最小/最大） | 2073 / 3129 字符 |
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## 样例示例
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**子集**: `default`
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```json
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{
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"input": [
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{
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"id": "06f75061",
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"content": "Here are some examples of named entity recognition:\n\nInput:\nComparison with alkaline phosphatases and 5 - nucleotidase\n\nOutput:\n<response>Comparison with <gene>alkaline phosphatases</gene> and 5 - nucleotidase</response>\n\nInput:\nPharmacologic ... [TRUNCATED] ... most specific entity type.\n7. Ensure every opening tag has a matching closing tag.\n\nText to process:\nPhenotypic analysis demonstrates that trio and Abl cooperate in regulating axon outgrowth in the embryonic central nervous system ( CNS ) .\n"
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}
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],
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"target": "<response>Phenotypic analysis demonstrates that <gene>trio</gene> and <gene>Abl</gene> cooperate in regulating axon outgrowth in the embryonic central nervous system ( CNS ) .</response>",
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"id": 0,
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"group_id": 0,
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"metadata": {
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"tokens": [
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"Phenotypic",
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"analysis",
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"demonstrates",
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"that",
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"trio",
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"and",
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"Abl",
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"cooperate",
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"in",
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"regulating",
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"axon",
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"outgrowth",
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"in",
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"the",
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"embryonic",
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"central",
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"nervous",
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"system",
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"(",
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"CNS",
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")",
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"."
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],
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"ner_tags": [
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"O",
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"O",
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"O",
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"O",
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"B-GENE",
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"O",
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"B-GENE",
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"O",
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"O",
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"O",
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"O",
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"O",
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"O",
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"O",
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"O",
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"O",
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"O",
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"O",
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"O",
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"O",
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"O",
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"O"
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]
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}
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}
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```
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*注：部分内容为显示目的已截断。*
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## 提示模板
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**提示模板：**
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```text
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You are a named entity recognition system that identifies the following entity types:
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{entities}
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Process the provided text and mark all named entities with XML-style tags.
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For example:
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<person>John Smith</person> works at <organization>Google</organization> in <location>Mountain View</location>.
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Available entity tags: {entity_list}
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INSTRUCTIONS:
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1. Wrap your entire response in <response>...</response> tags.
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2. Inside these tags, include the original text with entity tags inserted.
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3. Do not change the original text in any way (preserve spacing, punctuation, case, etc.).
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4. Tag ALL entities you can identify using the exact tag names provided.
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5. Do not include explanations, just the tagged text.
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6. If entity spans overlap, choose the most specific entity type.
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7. Ensure every opening tag has a matching closing tag.
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Text to process:
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{text}
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```
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<details>
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<summary>少样本提示模板</summary>
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```text
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Here are some examples of named entity recognition:
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{fewshot}
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You are a named entity recognition system that identifies the following entity types:
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{entities}
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Process the provided text and mark all named entities with XML-style tags.
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For example:
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<person>John Smith</person> works at <organization>Google</organization> in <location>Mountain View</location>.
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Available entity tags: {entity_list}
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INSTRUCTIONS:
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1. Wrap your entire response in <response>...</response> tags.
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2. Inside these tags, include the original text with entity tags inserted.
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3. Do not change the original text in any way (preserve spacing, punctuation, case, etc.).
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4. Tag ALL entities you can identify using the exact tag names provided.
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5. Do not include explanations, just the tagged text.
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6. If entity spans overlap, choose the most specific entity type.
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7. Ensure every opening tag has a matching closing tag.
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Text to process:
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{text}
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```
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</details>
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## 使用方法
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### 使用命令行接口（CLI）
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```bash
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evalscope eval \
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--model YOUR_MODEL \
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--api-url OPENAI_API_COMPAT_URL \
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--api-key EMPTY_TOKEN \
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--datasets bc2gm \
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--limit 10 # 正式评估时请删除此行
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```
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### 使用Python
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```python
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from evalscope import run_task
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from evalscope.config import TaskConfig
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task_cfg = TaskConfig(
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model='YOUR_MODEL',
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api_url='OPENAI_API_COMPAT_URL',
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api_key='EMPTY_TOKEN',
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datasets=['bc2gm'],
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limit=10, # 正式评估时请删除此行
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)
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run_task(task_cfg=task_cfg)
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``` |