958 lines
37 KiB
Python
958 lines
37 KiB
Python
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"""
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DiscoveryAgent V1 - CellVoyager风格的科学发现Agent
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功能:
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1. 分析执行结果，识别异常/新模式
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2. 生成科学假设
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3. 设计验证实验
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4. 迭代优化分析计划
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基于CellVoyager论文的REPLAN机制
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"""
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from typing import Dict, List, Optional, Any
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from dataclasses import dataclass, field, asdict, is_dataclass
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from enum import Enum
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import json
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import asyncio
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from .base import AgentMessage, AgentState, BaseAgent
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from gfa_core.mas.llm import LLMManager
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from gfa_core.mas.dual_kb_qa import query_dual_kb_qa
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class DiscoveryType(Enum):
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"""发现类型"""
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ANOMALY = "anomaly" # 异常检测
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PATTERN = "pattern" # 新模式
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CORRELATION = "correlation" # 相关性
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HYPOTHESIS = "hypothesis" # 新假设
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@dataclass
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class AnomalyDetection:
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"""异常检测结果"""
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detected: bool
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description: str
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severity: str # low, medium, high
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affected_genes: List[str] = field(default_factory=list)
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expected_value: Any = None
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actual_value: Any = None
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@dataclass
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class GeneratedHypothesis:
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"""生成的假设"""
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hypothesis: str
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rationale: str
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confidence: float
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testable: bool
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suggested_experiments: List[str] = field(default_factory=list)
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required_data: List[str] = field(default_factory=list)
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@dataclass
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class DiscoveryResult:
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"""发现结果"""
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discovery_type: DiscoveryType
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description: str
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confidence: float
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hypothesis: Optional[GeneratedHypothesis] = None
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anomalies: List[AnomalyDetection] = field(default_factory=list)
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updated_plan: Optional[Dict] = None
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should_continue: bool = False
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class DiscoveryAgent(BaseAgent):
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"""
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科学发现Agent - CellVoyager风格
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核心流程:
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1. INSPECT - 检查结果
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2. ANALYZE - 分析异常/模式
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3. HYPOTHESIZE - 生成假设
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4. DESIGN - 设计验证
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5. REPLAN - 更新计划
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"""
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name = "discovery"
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role = "Scientific Discovery Assistant"
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def __init__(self, llm_manager: LLMManager):
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super().__init__(llm_manager)
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self.discovery_history: List[DiscoveryResult] = []
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self.max_iterations = 3
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async def execute(self, state: AgentState, message: AgentMessage) -> AgentState:
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"""
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执行发现流程（科研模式：存储解读结果，支持按需生成深度报告）
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Args:
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state: 当前状态，包含执行结果
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message: 消息，可能包含特定发现指令
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- mode: "quick" (快速模式，只存储结果)
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"deep" (深度模式，立即生成解读)
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"generate_report" (生成综合报告)
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Returns:
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更新后的状态，包含发现结果
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"""
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mode = message.payload.get("mode", "quick") # 默认快速模式
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print(f"[DiscoveryAgent] 开始科学发现流程 (模式: {mode})...")
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# 特殊模式：生成综合深度报告
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if mode == "generate_report":
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return await self._generate_comprehensive_report(state, message)
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# 1. 获取当前结果（支持多种数据格式）
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execution_results = self._normalize_execution_results(state)
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current_plan = state.results.get("plan", state.results.get("task_plan", {}))
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past_discoveries = state.results.get("discoveries", [])
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# 提取基因家族名称
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gene_family = self._extract_gene_family_from_state(state)
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print(f"[DiscoveryAgent] 分析基因家族: {gene_family}")
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# 2. 检查异常（使用RAG获取文献基准）
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anomalies = await self._detect_anomalies(execution_results, gene_family)
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print(f"[DiscoveryAgent] 检测到 {len(anomalies)} 个异常")
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# 3. 分析模式
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patterns = await self._analyze_patterns(execution_results)
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print(f"[DiscoveryAgent] 识别到 {len(patterns)} 个模式")
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# 4. 生成假设（只要有可用执行摘要即调用 LLM，避免「无异常就无话」）
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hypothesis = None
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if execution_results:
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hypothesis = await self._generate_hypothesis(
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anomalies, patterns, execution_results
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)
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if hypothesis:
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print(f"[DiscoveryAgent] 生成假设: {hypothesis.hypothesis[:80]}...")
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# 5. 决定是否继续迭代
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should_continue = self._should_continue_iteration(
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anomalies, patterns, hypothesis, len(past_discoveries)
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)
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# 6. 更新计划（如需要）
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updated_plan = None
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if should_continue and hypothesis:
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updated_plan = await self._update_plan(current_plan, hypothesis)
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print(f"[DiscoveryAgent] 更新分析计划")
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# 7. 构建发现结果
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discovery_result = DiscoveryResult(
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discovery_type=self._determine_discovery_type(anomalies, patterns),
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description=self._build_description(anomalies, patterns, hypothesis),
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confidence=hypothesis.confidence if hypothesis else 0.5,
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hypothesis=hypothesis,
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anomalies=anomalies,
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updated_plan=updated_plan,
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should_continue=should_continue
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)
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# 8. 构建完整发现结果（包含原始数据，供后续深度解读使用）
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discovery_data = {
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"type": discovery_result.discovery_type.value,
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"description": discovery_result.description,
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"confidence": discovery_result.confidence,
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"hypothesis": {
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"text": hypothesis.hypothesis if hypothesis else None,
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"rationale": hypothesis.rationale if hypothesis else None,
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"confidence": hypothesis.confidence if hypothesis else None,
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"suggested_experiments": hypothesis.suggested_experiments if hypothesis else []
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},
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"anomalies": [
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{
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"description": a.description,
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"severity": a.severity,
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"affected_genes": a.affected_genes
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}
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for a in anomalies
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],
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"should_continue": should_continue,
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# 新增：存储原始数据，供深度解读使用
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"raw_data": {
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"execution_results": execution_results,
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"patterns": [p for p in patterns],
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"analysis_timestamp": self._get_timestamp()
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}
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}
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# 深度模式：立即生成详细解读
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if mode == "deep":
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deep_interpretation = await self._generate_deep_interpretation(discovery_data)
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discovery_data["deep_interpretation"] = deep_interpretation
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print(f"[DiscoveryAgent] 已生成深度解读")
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state.results["discovery_result"] = discovery_data
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stage_hint = message.payload.get("stage") or ""
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if not stage_hint:
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pr = message.payload.get("parse_result") or state.results.get("parsed_report") or {}
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if isinstance(pr, dict):
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stage_hint = pr.get("stage", "unknown")
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history_entry = {**discovery_data, "stage": stage_hint}
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self.discovery_history.append(discovery_result)
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past_discoveries.append(history_entry)
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state.results["discoveries"] = past_discoveries
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# 添加消息
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state.messages.append({
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"role": "discovery",
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"content": discovery_result.description,
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"metadata": {
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"confidence": discovery_result.confidence,
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"should_continue": should_continue
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}
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})
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print(f"[DiscoveryAgent] 发现流程完成，置信度: {discovery_result.confidence:.2f}")
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return state
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def _normalize_execution_results(self, state: AgentState) -> Dict:
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"""
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标准化执行结果格式
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支持多种输入格式:
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1. Dict格式: {"identify": {...}, "phylogeny": {...}}
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2. List格式: [{"stage": "identify", ...}, {"stage": "phylogeny", ...}]
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3. 从parsed_report提取
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"""
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results = {}
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# 尝试从execution_results获取（可能是list或dict）
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execution_results = state.results.get("execution_results", {})
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if isinstance(execution_results, dict):
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results = execution_results
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elif isinstance(execution_results, list):
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# 转换为dict格式
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for item in execution_results:
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if isinstance(item, dict):
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stage = item.get("stage", "unknown")
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results[stage] = item
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# 尝试从parsed_report获取更详细的数据
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parsed_report = state.results.get("parsed_report", {})
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if parsed_report:
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stage = parsed_report.get("stage", "unknown")
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if stage not in results:
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results[stage] = {}
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# 合并parsed数据
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results[stage].update({
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"metrics": parsed_report.get("metrics", {}),
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"parsed_data": parsed_report.get("parsed_data", {}),
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"status": parsed_report.get("status", "unknown")
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})
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# 尝试从单个execution_result获取（最新执行结果）
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execution_result = state.results.get("execution_result", {})
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if execution_result:
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manifest = execution_result.get("manifest", {})
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stage = manifest.get("stage", "unknown")
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if stage not in results:
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results[stage] = {}
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results[stage].update({
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"metrics": manifest.get("metrics", {}),
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"status": execution_result.get("status", "unknown"),
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"manifest": manifest
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})
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return results
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def _bucket_metrics(self, bucket: Any) -> Dict[str, Any]:
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if not isinstance(bucket, dict):
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return {}
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m = bucket.get("metrics")
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if isinstance(m, dict) and m:
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return m
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manifest = bucket.get("manifest") or {}
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if isinstance(manifest, dict):
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mm = manifest.get("metrics")
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if isinstance(mm, dict):
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return mm
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return {}
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def _discovery_record_as_dict(self, discovery: Any) -> Dict[str, Any]:
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"""兼容历史中的 DiscoveryResult dataclass 与 dict。"""
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if isinstance(discovery, dict):
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return discovery
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if isinstance(discovery, DiscoveryResult):
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hyp = discovery.hypothesis
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hyp_dict = {}
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if hyp is not None:
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hyp_dict = {
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"text": hyp.hypothesis,
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"rationale": hyp.rationale,
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"confidence": hyp.confidence,
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"suggested_experiments": hyp.suggested_experiments or [],
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}
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return {
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"type": discovery.discovery_type.value,
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"description": discovery.description,
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"confidence": discovery.confidence,
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"should_continue": discovery.should_continue,
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"stage": getattr(discovery, "stage", None),
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"hypothesis": hyp_dict,
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"anomalies": [
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asdict(a) if is_dataclass(a) else a for a in (discovery.anomalies or [])
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],
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}
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return {"description": str(discovery), "type": "unknown"}
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async def _detect_anomalies(self, results: Dict, gene_family: str = "SPL") -> List[AnomalyDetection]:
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"""
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检测异常
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检查执行结果中的异常情况:
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- 基因数量异常（过多/过少）- 基于RAG文献数据
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- 表达模式异常
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- 进化关系异常
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"""
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anomalies = []
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# 检查鉴定结果 - 支持多种数据路径
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identify_data = results.get("identify", {})
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# 尝试多种路径获取基因数量
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gene_count = 0
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if "parsed_data" in identify_data:
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gene_count = identify_data["parsed_data"].get("gene_count", 0)
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if gene_count == 0 and "metrics" in identify_data:
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gene_count = identify_data["metrics"].get("final_members", 0)
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if gene_count == 0 and "manifest" in identify_data:
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gene_count = identify_data["manifest"].get("metrics", {}).get("final_members", 0)
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# 基因数量异常检测 - 使用RAG获取文献基准
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if gene_count > 0:
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# 查询RAG获取该基因家族的典型规模
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expected_range = await self._get_gene_family_size_from_rag(gene_family)
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min_expected = expected_range.get("min", 5)
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max_expected = expected_range.get("max", 200)
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median_expected = expected_range.get("median", (min_expected + max_expected) // 2)
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# 动态阈值：低于最小值50%或高于最大值200%视为异常
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|
|
# 例如：文献报道10-30个，低于5个或高于60个视为异常
|
|||
|
|
lower_threshold = max(3, int(min_expected * 0.5)) # 至少低于3个才触发
|
|||
|
|
upper_threshold = int(max_expected * 2.0)
|
|||
|
|
|
|||
|
|
if gene_count < lower_threshold:
|
|||
|
|
anomalies.append(AnomalyDetection(
|
|||
|
|
detected=True,
|
|||
|
|
description=f"鉴定到的基因数量过少 ({gene_count}个)，远低于文献报道的{min_expected}-{max_expected}个",
|
|||
|
|
severity="high",
|
|||
|
|
affected_genes=[],
|
|||
|
|
expected_value=f"{min_expected}-{max_expected} (中位数: {median_expected})",
|
|||
|
|
actual_value=gene_count
|
|||
|
|
))
|
|||
|
|
elif gene_count > upper_threshold:
|
|||
|
|
anomalies.append(AnomalyDetection(
|
|||
|
|
detected=True,
|
|||
|
|
description=f"鉴定到的基因数量过多 ({gene_count}个)，远高于文献报道的{min_expected}-{max_expected}个",
|
|||
|
|
severity="medium",
|
|||
|
|
affected_genes=[],
|
|||
|
|
expected_value=f"{min_expected}-{max_expected} (中位数: {median_expected})",
|
|||
|
|
actual_value=gene_count
|
|||
|
|
))
|
|||
|
|
|
|||
|
|
# 检查表达分析结果
|
|||
|
|
if "expression" in results:
|
|||
|
|
expr_data = results["expression"]
|
|||
|
|
# 检测异常表达模式
|
|||
|
|
# TODO: 实现具体检测逻辑
|
|||
|
|
|
|||
|
|
return anomalies
|
|||
|
|
|
|||
|
|
async def _get_gene_family_size_from_rag(self, gene_family: str) -> Dict:
|
|||
|
|
"""
|
|||
|
|
从RAG查询基因家族的典型规模
|
|||
|
|
|
|||
|
|
查询几个模式物种的数据，返回统计范围
|
|||
|
|
"""
|
|||
|
|
try:
|
|||
|
|
import aiohttp
|
|||
|
|
import os
|
|||
|
|
|
|||
|
|
api_url = os.environ.get("LEGACY_RAG_API_URL", "").rstrip("/")
|
|||
|
|
if api_url:
|
|||
|
|
async with aiohttp.ClientSession() as session:
|
|||
|
|
async with session.get(
|
|||
|
|
f"{api_url}/api/v1/rag/family/baseline",
|
|||
|
|
params={"family": gene_family}
|
|||
|
|
) as response:
|
|||
|
|
if response.status == 200:
|
|||
|
|
data = await response.json()
|
|||
|
|
baseline = data.get("baseline") or {}
|
|||
|
|
if baseline.get("count", 0) and baseline.get("min") is not None and baseline.get("max") is not None:
|
|||
|
|
return {
|
|||
|
|
"min": int(baseline.get("min")),
|
|||
|
|
"max": int(baseline.get("max")),
|
|||
|
|
"median": baseline.get("median"),
|
|||
|
|
"count": int(baseline.get("count") or 0),
|
|||
|
|
"by_species": baseline.get("by_species") or [],
|
|||
|
|
"source": "rag_family_baseline"
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
# 查询RAG获取基因家族规模信息
|
|||
|
|
query = f"{gene_family} gene family member count size Arabidopsis rice"
|
|||
|
|
|
|||
|
|
data = await asyncio.to_thread(query_dual_kb_qa, query, top_k=5, use_llm=False)
|
|||
|
|
sources = data.get("sources", [])
|
|||
|
|
|
|||
|
|
# 从文献中提取基因数量
|
|||
|
|
sizes = []
|
|||
|
|
for source in sources:
|
|||
|
|
content = str(source.get("content") or source.get("evidence") or "")
|
|||
|
|
# 尝试提取数字（如 "16 members", "about 20 genes"）
|
|||
|
|
import re
|
|||
|
|
# 匹配模式：数字 + members/genes/family
|
|||
|
|
matches = re.findall(r'(\d+)\s+(?:members?|genes?|family)', content, re.IGNORECASE)
|
|||
|
|
for match in matches:
|
|||
|
|
try:
|
|||
|
|
size = int(match)
|
|||
|
|
if 1 <= size <= 1000: # 合理范围
|
|||
|
|
sizes.append(size)
|
|||
|
|
except:
|
|||
|
|
pass
|
|||
|
|
|
|||
|
|
if sizes:
|
|||
|
|
sizes.sort()
|
|||
|
|
return {
|
|||
|
|
"min": min(sizes),
|
|||
|
|
"max": max(sizes),
|
|||
|
|
"median": sizes[len(sizes)//2],
|
|||
|
|
"count": len(sizes),
|
|||
|
|
"source": "dual_kb_qa"
|
|||
|
|
}
|
|||
|
|
except Exception as e:
|
|||
|
|
print(f"[Discovery] RAG查询失败: {e}")
|
|||
|
|
|
|||
|
|
# 回退到默认阈值（更严格的默认值）
|
|||
|
|
return {"min": 10, "max": 100, "median": 30, "source": "default"}
|
|||
|
|
|
|||
|
|
def _extract_gene_family_from_state(self, state: AgentState) -> str:
|
|||
|
|
"""从状态中提取基因家族名称"""
|
|||
|
|
# 尝试从多个来源提取
|
|||
|
|
intent = state.results.get("results", {}).get("intent", {}) or state.results.get("intent", {})
|
|||
|
|
if intent and "gene_family" in intent:
|
|||
|
|
return intent["gene_family"]
|
|||
|
|
|
|||
|
|
# 从user_input提取
|
|||
|
|
user_input = state.results.get("user_input", {})
|
|||
|
|
if user_input and "gene_family" in user_input:
|
|||
|
|
return user_input["gene_family"]
|
|||
|
|
|
|||
|
|
# 从prefix提取（如 "Ft.SPL" -> "SPL"）
|
|||
|
|
prefix = state.results.get("prefix", "")
|
|||
|
|
if prefix and "." in prefix:
|
|||
|
|
return prefix.split(".")[-1]
|
|||
|
|
|
|||
|
|
return "SPL" # 默认
|
|||
|
|
|
|||
|
|
async def _analyze_patterns(self, results: Dict) -> List[Dict]:
|
|||
|
|
"""
|
|||
|
|
基于 manifest 常见 metrics 做轻量模式提炼（给假设生成结构化抓手）。
|
|||
|
|
"""
|
|||
|
|
patterns: List[Dict] = []
|
|||
|
|
|
|||
|
|
id_b = results.get("identify") or {}
|
|||
|
|
mid = self._bucket_metrics(id_b)
|
|||
|
|
gcount = mid.get("final_members") or id_b.get("parsed_data", {}).get("gene_count")
|
|||
|
|
if gcount:
|
|||
|
|
patterns.append({
|
|||
|
|
"type": "gene_family_size_observed",
|
|||
|
|
"label": "鉴定规模",
|
|||
|
|
"detail": f"当前鉴定成员数(final_members/gene_count)={gcount}",
|
|||
|
|
})
|
|||
|
|
|
|||
|
|
de_b = results.get("rnaseq_de") or {}
|
|||
|
|
mde = self._bucket_metrics(de_b)
|
|||
|
|
if mde.get("de_genes_total") is not None:
|
|||
|
|
tot = int(mde.get("de_genes_total") or 0)
|
|||
|
|
fam = mde.get("family_analysis") or {}
|
|||
|
|
dfg = fam.get("de_family_genes")
|
|||
|
|
tfg = fam.get("total_family_genes")
|
|||
|
|
patterns.append({
|
|||
|
|
"type": "rnaseq_de_overview",
|
|||
|
|
"label": "差异表达规模",
|
|||
|
|
"detail": (
|
|||
|
|
f"全局 DE 基因 {tot}（上/下={mde.get('de_genes_up')}/{mde.get('de_genes_down')}）；"
|
|||
|
|
f"家族内 DE {dfg}/{tfg}"
|
|||
|
|
),
|
|||
|
|
})
|
|||
|
|
if tot >= 80 and dfg == 0:
|
|||
|
|
patterns.append({
|
|||
|
|
"type": "global_de_decoupled_from_family",
|
|||
|
|
"label": "家族与全局差异脱节",
|
|||
|
|
"detail": "全局大量差异基因但家族层面计数为 0，提示胁迫响应可能主要在非家族基因或其它家族",
|
|||
|
|
})
|
|||
|
|
|
|||
|
|
for st in ("rnaseq_kegg_enrich", "rnaseq_go_enrich"):
|
|||
|
|
eb = results.get(st) or {}
|
|||
|
|
me = self._bucket_metrics(eb)
|
|||
|
|
kp = me.get("kegg_enriched_pathways")
|
|||
|
|
gt = me.get("go_enriched_terms")
|
|||
|
|
if kp is not None or gt is not None:
|
|||
|
|
patterns.append({
|
|||
|
|
"type": "enrichment_yield",
|
|||
|
|
"label": f"{st} 产出",
|
|||
|
|
"detail": f"KEGG pathways={kp}, GO terms={gt}, DE_input={me.get('de_genes_input')}",
|
|||
|
|
})
|
|||
|
|
|
|||
|
|
phy_b = results.get("phylogeny") or {}
|
|||
|
|
mp = self._bucket_metrics(phy_b)
|
|||
|
|
if mp.get("tips") or mp.get("taxa_count"):
|
|||
|
|
patterns.append({
|
|||
|
|
"type": "phylogeny_resolution",
|
|||
|
|
"label": "系统发育规模",
|
|||
|
|
"detail": f"tips/taxa≈{mp.get('tips') or mp.get('taxa_count')}",
|
|||
|
|
})
|
|||
|
|
|
|||
|
|
return patterns
|
|||
|
|
|
|||
|
|
async def _generate_hypothesis(
|
|||
|
|
self,
|
|||
|
|
anomalies: List[AnomalyDetection],
|
|||
|
|
patterns: List[Dict],
|
|||
|
|
results: Dict
|
|||
|
|
) -> GeneratedHypothesis:
|
|||
|
|
"""
|
|||
|
|
基于异常和模式生成科学假设
|
|||
|
|
|
|||
|
|
使用LLM生成可验证的假设
|
|||
|
|
"""
|
|||
|
|
# 构建上下文
|
|||
|
|
context = {
|
|||
|
|
"anomalies": [
|
|||
|
|
{"description": a.description, "severity": a.severity}
|
|||
|
|
for a in anomalies
|
|||
|
|
],
|
|||
|
|
"patterns": patterns,
|
|||
|
|
"results_summary": self._summarize_results(results)
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
prompt = f"""基于以下基因家族分析结果（可包含空的 anomalies/patterns），生成科学假设。
|
|||
|
|
若未发现异常，请根据定量指标提出可检验的下一步科学问题，避免泛泛而谈。
|
|||
|
|
|
|||
|
|
分析结果摘要:
|
|||
|
|
{json.dumps(context, ensure_ascii=False, indent=2)}
|
|||
|
|
|
|||
|
|
请生成:
|
|||
|
|
1. 一个具体的、可验证的科学假设
|
|||
|
|
2. 假设的生物学依据
|
|||
|
|
3. 建议的验证实验
|
|||
|
|
4. 需要的额外数据
|
|||
|
|
5. 置信度评估 (0.0-1.0)
|
|||
|
|
|
|||
|
|
以JSON格式返回:
|
|||
|
|
{{
|
|||
|
|
"hypothesis": "假设描述",
|
|||
|
|
"rationale": "依据",
|
|||
|
|
"confidence": 0.8,
|
|||
|
|
"testable": true,
|
|||
|
|
"suggested_experiments": ["实验1", "实验2"],
|
|||
|
|
"required_data": ["数据1", "数据2"]
|
|||
|
|
}}"""
|
|||
|
|
|
|||
|
|
try:
|
|||
|
|
response = await self._acall_llm(prompt, temperature=0.7)
|
|||
|
|
content = response.content
|
|||
|
|
|
|||
|
|
# 解析JSON
|
|||
|
|
if "```json" in content:
|
|||
|
|
content = content.split("```json")[1].split("```")[0]
|
|||
|
|
elif "```" in content:
|
|||
|
|
content = content.split("```")[1].split("```")[0]
|
|||
|
|
|
|||
|
|
data = json.loads(content.strip())
|
|||
|
|
|
|||
|
|
return GeneratedHypothesis(
|
|||
|
|
hypothesis=data.get("hypothesis", "无法生成假设"),
|
|||
|
|
rationale=data.get("rationale", ""),
|
|||
|
|
confidence=data.get("confidence", 0.5),
|
|||
|
|
testable=data.get("testable", False),
|
|||
|
|
suggested_experiments=data.get("suggested_experiments", []),
|
|||
|
|
required_data=data.get("required_data", [])
|
|||
|
|
)
|
|||
|
|
except Exception as e:
|
|||
|
|
print(f"[DiscoveryAgent] 生成假设失败: {e}")
|
|||
|
|
return GeneratedHypothesis(
|
|||
|
|
hypothesis="基于当前结果无法生成明确假设",
|
|||
|
|
rationale="数据不足或分析结果不明确",
|
|||
|
|
confidence=0.3,
|
|||
|
|
testable=False
|
|||
|
|
)
|
|||
|
|
|
|||
|
|
def _should_continue_iteration(
|
|||
|
|
self,
|
|||
|
|
anomalies: List[AnomalyDetection],
|
|||
|
|
patterns: List[Dict],
|
|||
|
|
hypothesis: Optional[GeneratedHypothesis],
|
|||
|
|
iteration_count: int
|
|||
|
|
) -> bool:
|
|||
|
|
"""
|
|||
|
|
决定是否继续迭代
|
|||
|
|
|
|||
|
|
条件:
|
|||
|
|
1. 检测到重要异常（high或medium严重性）
|
|||
|
|
2. 生成了高置信度假设
|
|||
|
|
3. 未达到最大迭代次数
|
|||
|
|
"""
|
|||
|
|
if iteration_count >= self.max_iterations:
|
|||
|
|
return False
|
|||
|
|
|
|||
|
|
# 有高严重性异常（必须修复）
|
|||
|
|
high_severity = any(a.severity == "high" for a in anomalies)
|
|||
|
|
|
|||
|
|
# 有中等严重性异常且没有高置信度假设时也需要迭代
|
|||
|
|
medium_severity = any(a.severity == "medium" for a in anomalies)
|
|||
|
|
|
|||
|
|
# 有高置信度假设
|
|||
|
|
high_confidence = hypothesis and hypothesis.confidence > 0.7
|
|||
|
|
|
|||
|
|
# 有值得关注的异常模式（非normal模式）
|
|||
|
|
significant_patterns = any(
|
|||
|
|
p.get("type") not in ["normal_gene_family_size"] for p in patterns
|
|||
|
|
)
|
|||
|
|
|
|||
|
|
return high_severity or (medium_severity and not high_confidence) or significant_patterns
|
|||
|
|
|
|||
|
|
async def _update_plan(
|
|||
|
|
self,
|
|||
|
|
current_plan: Dict,
|
|||
|
|
hypothesis: GeneratedHypothesis,
|
|||
|
|
learning_agent=None # 传入Learning Agent获取参数建议
|
|||
|
|
) -> Dict:
|
|||
|
|
"""
|
|||
|
|
基于假设更新分析计划
|
|||
|
|
|
|||
|
|
根据异常类型和假设，返回可执行的分析阶段
|
|||
|
|
|
|||
|
|
返回格式必须与 PlanningAgentV2 一致:
|
|||
|
|
{
|
|||
|
|
"stages": [{"id": "identify", "params": {...}}, ...],
|
|||
|
|
"job_id": "...",
|
|||
|
|
"prefix": "...",
|
|||
|
|
"workspace": "..."
|
|||
|
|
}
|
|||
|
|
"""
|
|||
|
|
import copy
|
|||
|
|
|
|||
|
|
# 获取当前计划的元信息
|
|||
|
|
job_id = current_plan.get("job_id", "")
|
|||
|
|
prefix = current_plan.get("prefix", "")
|
|||
|
|
workspace = current_plan.get("workspace", "")
|
|||
|
|
|
|||
|
|
# 根据异常/假设确定需要重新执行的阶段
|
|||
|
|
# 这里是示例逻辑，实际应根据 hypothesis.content 分析
|
|||
|
|
stages_to_add = []
|
|||
|
|
|
|||
|
|
# 如果假设涉及参数调整，重新执行相关阶段
|
|||
|
|
if hypothesis and hypothesis.confidence > 0.7:
|
|||
|
|
# 解析假设中提到的建议
|
|||
|
|
suggested = hypothesis.suggested_experiments if hypothesis.suggested_experiments else []
|
|||
|
|
|
|||
|
|
# 根据建议映射到可执行的 stage_id
|
|||
|
|
# 例如: "调整鉴定参数" -> 重新执行 identify
|
|||
|
|
# 例如: "增加motif数量" -> 重新执行 motif
|
|||
|
|
stage_mapping = {
|
|||
|
|
"鉴定": "identify",
|
|||
|
|
"进化树": "phylogeny",
|
|||
|
|
"motif": "motif",
|
|||
|
|
"结构域": "domain",
|
|||
|
|
"基因结构": "structure",
|
|||
|
|
"启动子": "promoter",
|
|||
|
|
"种间共线性": "interspecies_synteny",
|
|||
|
|
"物种间共线性": "interspecies_synteny",
|
|||
|
|
"跨物种共线性": "interspecies_synteny",
|
|||
|
|
"种内共线性": "synteny",
|
|||
|
|
"共线性": "synteny",
|
|||
|
|
"表达": "expression",
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
for suggestion in suggested:
|
|||
|
|
for keyword, stage_id in stage_mapping.items():
|
|||
|
|
if keyword in suggestion:
|
|||
|
|
stages_to_add.append({
|
|||
|
|
"id": stage_id,
|
|||
|
|
"reason": f"基于假设: {hypothesis.hypothesis[:50]}",
|
|||
|
|
"params_adjustment": self._extract_param_adjustment(suggestion)
|
|||
|
|
})
|
|||
|
|
break
|
|||
|
|
|
|||
|
|
# 如果没有特定阶段，默认重新执行 identify（参数调整）
|
|||
|
|
if not stages_to_add and hypothesis:
|
|||
|
|
stages_to_add.append({
|
|||
|
|
"id": "identify",
|
|||
|
|
"reason": f"基于异常检测重新鉴定",
|
|||
|
|
"params_adjustment": {"evalue": "放宽到 0.01"}
|
|||
|
|
})
|
|||
|
|
|
|||
|
|
# 构建新计划
|
|||
|
|
updated_plan = {
|
|||
|
|
"stages": stages_to_add,
|
|||
|
|
"job_id": job_id,
|
|||
|
|
"prefix": prefix,
|
|||
|
|
"workspace": workspace,
|
|||
|
|
"triggered_by_hypothesis": hypothesis.hypothesis if hypothesis else "",
|
|||
|
|
"iteration_reason": "DiscoveryAgent 建议重新分析"
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
return updated_plan
|
|||
|
|
|
|||
|
|
def _extract_param_adjustment(self, suggestion: str) -> Dict:
|
|||
|
|
"""从建议中提取参数调整"""
|
|||
|
|
adjustments = {}
|
|||
|
|
|
|||
|
|
# 简单的关键词匹配
|
|||
|
|
if "放宽" in suggestion or "增加" in suggestion:
|
|||
|
|
adjustments["mode"] = "relaxed"
|
|||
|
|
if "严格" in suggestion or "减少" in suggestion:
|
|||
|
|
adjustments["mode"] = "strict"
|
|||
|
|
|
|||
|
|
return adjustments
|
|||
|
|
|
|||
|
|
def _determine_discovery_type(
|
|||
|
|
self,
|
|||
|
|
anomalies: List[AnomalyDetection],
|
|||
|
|
patterns: List[Dict]
|
|||
|
|
) -> DiscoveryType:
|
|||
|
|
"""确定发现类型"""
|
|||
|
|
if anomalies:
|
|||
|
|
return DiscoveryType.ANOMALY
|
|||
|
|
elif patterns:
|
|||
|
|
return DiscoveryType.PATTERN
|
|||
|
|
else:
|
|||
|
|
return DiscoveryType.HYPOTHESIS
|
|||
|
|
|
|||
|
|
def _build_description(
|
|||
|
|
self,
|
|||
|
|
anomalies: List[AnomalyDetection],
|
|||
|
|
patterns: List[Dict],
|
|||
|
|
hypothesis: Optional[GeneratedHypothesis]
|
|||
|
|
) -> str:
|
|||
|
|
"""构建发现描述"""
|
|||
|
|
parts = []
|
|||
|
|
|
|||
|
|
if anomalies:
|
|||
|
|
parts.append(f"检测到{len(anomalies)}个异常:")
|
|||
|
|
for a in anomalies:
|
|||
|
|
parts.append(f" - {a.description} (严重性: {a.severity})")
|
|||
|
|
|
|||
|
|
if patterns:
|
|||
|
|
parts.append(f"\n数据模式 ({len(patterns)}):")
|
|||
|
|
for p in patterns:
|
|||
|
|
lab = p.get("label") or p.get("type")
|
|||
|
|
parts.append(f" - [{lab}] {p.get('detail', '')}")
|
|||
|
|
|
|||
|
|
if hypothesis:
|
|||
|
|
parts.append(f"\n生成假设: {hypothesis.hypothesis}")
|
|||
|
|
parts.append(f"置信度: {hypothesis.confidence:.2f}")
|
|||
|
|
elif not anomalies and not patterns:
|
|||
|
|
parts.append("当前未发现显著异常或结构化模式；建议查看下游 manifest 是否齐全。")
|
|||
|
|
|
|||
|
|
return "\n".join(parts)
|
|||
|
|
|
|||
|
|
def _summarize_results(self, results: Dict) -> Dict:
|
|||
|
|
"""汇总各阶段关键 metrics，供假设生成使用"""
|
|||
|
|
summary: Dict[str, Any] = {}
|
|||
|
|
|
|||
|
|
if "identify" in results:
|
|||
|
|
mid = self._bucket_metrics(results["identify"])
|
|||
|
|
summary["identify"] = {
|
|||
|
|
"final_members": mid.get("final_members"),
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
if "phylogeny" in results:
|
|||
|
|
summary["phylogeny"] = self._bucket_metrics(results["phylogeny"])
|
|||
|
|
|
|||
|
|
if "rnaseq_de" in results:
|
|||
|
|
summary["rnaseq_de"] = self._bucket_metrics(results["rnaseq_de"])
|
|||
|
|
|
|||
|
|
for k in ("rnaseq_quant", "rnaseq_align", "annotation"):
|
|||
|
|
if k in results:
|
|||
|
|
summary[k] = self._bucket_metrics(results[k])
|
|||
|
|
|
|||
|
|
for k in ("rnaseq_go_enrich", "rnaseq_kegg_enrich"):
|
|||
|
|
if k in results:
|
|||
|
|
summary[k] = self._bucket_metrics(results[k])
|
|||
|
|
|
|||
|
|
return summary
|
|||
|
|
|
|||
|
|
async def _generate_deep_interpretation(self, discovery_data: Dict) -> Dict:
|
|||
|
|
"""生成深度解读（科研模式）"""
|
|||
|
|
stage = discovery_data.get("type", "unknown")
|
|||
|
|
hypothesis = discovery_data.get("hypothesis", {})
|
|||
|
|
anomalies = discovery_data.get("anomalies", [])
|
|||
|
|
raw_compact = json.dumps(
|
|||
|
|
discovery_data.get("raw_data") or {},
|
|||
|
|
ensure_ascii=False,
|
|||
|
|
indent=2,
|
|||
|
|
)
|
|||
|
|
if len(raw_compact) > 3200:
|
|||
|
|
raw_compact = raw_compact[:3200] + "\n…(截断)"
|
|||
|
|
|
|||
|
|
prompt = f"""你是一个基因家族分析专家。请基于以下发现结果，生成详细的科学解读。
|
|||
|
|
|
|||
|
|
发现类型: {stage}
|
|||
|
|
假设: {hypothesis.get('text', '无')}
|
|||
|
|
假设依据: {hypothesis.get('rationale', '无')}
|
|||
|
|
异常检测: {len(anomalies)} 个异常
|
|||
|
|
|
|||
|
|
原始上下文摘录（patterns + execution_results 摘要）:
|
|||
|
|
{raw_compact}
|
|||
|
|
|
|||
|
|
请生成以下内容的详细解读（JSON格式）:
|
|||
|
|
{{
|
|||
|
|
"biological_significance": "该发现的生物学意义（2-3句）",
|
|||
|
|
"mechanism_hypothesis": "可能的分子机制假设",
|
|||
|
|
"functional_implications": "对基因功能的影响",
|
|||
|
|
"evolutionary_insights": "进化层面的启示",
|
|||
|
|
"experimental_suggestions": ["建议的验证实验1", "建议的验证实验2"],
|
|||
|
|
"literature_context": "与已知研究的关联"
|
|||
|
|
}}
|
|||
|
|
|
|||
|
|
只返回JSON，不要其他内容。"""
|
|||
|
|
|
|||
|
|
try:
|
|||
|
|
response = await self._acall_llm(prompt, temperature=0.7)
|
|||
|
|
content = response.content if hasattr(response, 'content') else str(response)
|
|||
|
|
|
|||
|
|
# 提取JSON
|
|||
|
|
if "```json" in content:
|
|||
|
|
content = content.split("```json")[1].split("```")[0]
|
|||
|
|
elif "```" in content:
|
|||
|
|
content = content.split("```")[1].split("```")[0]
|
|||
|
|
|
|||
|
|
interpretation = json.loads(content.strip())
|
|||
|
|
return interpretation
|
|||
|
|
|
|||
|
|
except Exception as e:
|
|||
|
|
print(f"[DiscoveryAgent] 深度解读生成失败: {e}")
|
|||
|
|
return {
|
|||
|
|
"biological_significance": "需要进一步分析",
|
|||
|
|
"mechanism_hypothesis": "暂不明确",
|
|||
|
|
"error": str(e)
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
async def _generate_comprehensive_report(self, state: AgentState, message: AgentMessage) -> AgentState:
|
|||
|
|
"""生成综合深度报告（所有阶段完成后调用，或按需调用）"""
|
|||
|
|
print(f"[DiscoveryAgent] 生成综合深度报告...")
|
|||
|
|
|
|||
|
|
raw_discoveries = state.results.get("discoveries", [])
|
|||
|
|
all_discoveries = [self._discovery_record_as_dict(d) for d in raw_discoveries]
|
|||
|
|
execution_results = state.results.get("execution_results", {})
|
|||
|
|
|
|||
|
|
# 获取当前阶段（如果是按需解读，只解读到当前阶段）
|
|||
|
|
current_stage = message.payload.get("current_stage", None)
|
|||
|
|
|
|||
|
|
# 过滤发现结果：如果只解读到某个阶段
|
|||
|
|
if current_stage:
|
|||
|
|
filtered_discoveries = []
|
|||
|
|
for discovery in all_discoveries:
|
|||
|
|
filtered_discoveries.append(discovery)
|
|||
|
|
# 如果找到当前阶段，停止添加
|
|||
|
|
if discovery.get("stage") == current_stage:
|
|||
|
|
break
|
|||
|
|
all_discoveries = filtered_discoveries
|
|||
|
|
print(f"[DiscoveryAgent] 生成阶段性报告，包含 {len(all_discoveries)} 个阶段")
|
|||
|
|
|
|||
|
|
# 构建综合报告
|
|||
|
|
report_sections = []
|
|||
|
|
stage_names = []
|
|||
|
|
|
|||
|
|
for i, discovery in enumerate(all_discoveries, 1):
|
|||
|
|
stage = discovery.get("stage") or discovery.get("type", f"阶段{i}")
|
|||
|
|
stage_names.append(stage)
|
|||
|
|
description = discovery.get("description", "")
|
|||
|
|
|
|||
|
|
section = f"## 阶段 {i}: {stage}\n\n{description}\n"
|
|||
|
|
|
|||
|
|
# 如果有深度解读，加入报告
|
|||
|
|
if "deep_interpretation" in discovery:
|
|||
|
|
interp = discovery["deep_interpretation"]
|
|||
|
|
section += f"\n### 科学解读\n"
|
|||
|
|
section += f"- **生物学意义**: {interp.get('biological_significance', 'N/A')}\n"
|
|||
|
|
section += f"- **机制假设**: {interp.get('mechanism_hypothesis', 'N/A')}\n"
|
|||
|
|
section += f"- **功能影响**: {interp.get('functional_implications', 'N/A')}\n"
|
|||
|
|
|
|||
|
|
report_sections.append(section)
|
|||
|
|
|
|||
|
|
# 生成阶段性综合结论（强调阶段间的关联）
|
|||
|
|
conclusion_prompt = f"""你是一个基因家族分析专家。请基于以下各阶段的分析结果，生成阶段性综合结论。
|
|||
|
|
|
|||
|
|
已完成的阶段: {' → '.join(stage_names)}
|
|||
|
|
|
|||
|
|
各阶段结果:
|
|||
|
|
{chr(10).join([f"阶段 {i+1} ({d.get('stage', d.get('type', 'unknown'))}): {d.get('description', '')[:200]}" for i, d in enumerate(all_discoveries)])}
|
|||
|
|
|
|||
|
|
请重点分析：
|
|||
|
|
1. 各阶段结果的内在关联（如：鉴定到的基因数如何影响进化树构建）
|
|||
|
|
2. 阶段性科学发现（基于目前已完成的工作）
|
|||
|
|
3. 下一步分析的建议（基于当前结果）
|
|||
|
|
4. 潜在的生物学意义
|
|||
|
|
|
|||
|
|
请用中文生成专业、详细的解读。"""
|
|||
|
|
|
|||
|
|
try:
|
|||
|
|
conclusion_response = await self._acall_llm(conclusion_prompt, temperature=0.7)
|
|||
|
|
conclusion = conclusion_response.content if hasattr(conclusion_response, 'content') else str(conclusion_response)
|
|||
|
|
except Exception as e:
|
|||
|
|
conclusion = f"综合结论生成失败: {e}"
|
|||
|
|
|
|||
|
|
# 组装完整报告
|
|||
|
|
report_title = f"阶段性综合深度报告（{' → '.join(stage_names)}）" if len(stage_names) < 5 else "基因家族分析综合深度报告"
|
|||
|
|
|
|||
|
|
comprehensive_report = f"""# 🔬 {report_title}
|
|||
|
|
|
|||
|
|
**分析流程**: {' → '.join(stage_names)}
|
|||
|
|
|
|||
|
|
**报告类型**: {'阶段性综合解读' if current_stage else '完整分析报告'}
|
|||
|
|
|
|||
|
|
---
|
|||
|
|
|
|||
|
|
{chr(10).join(report_sections)}
|
|||
|
|
|
|||
|
|
## 📊 阶段性综合结论
|
|||
|
|
|
|||
|
|
{conclusion}
|
|||
|
|
|
|||
|
|
---
|
|||
|
|
*报告生成时间: {self._get_timestamp()}*
|
|||
|
|
"""
|
|||
|
|
|
|||
|
|
# 更新状态
|
|||
|
|
state.results["comprehensive_report"] = comprehensive_report
|
|||
|
|
state.results["discovery_result"] = {
|
|||
|
|
"report_generated": True,
|
|||
|
|
"sections_count": len(report_sections),
|
|||
|
|
"stages_included": stage_names,
|
|||
|
|
"mode": "comprehensive",
|
|||
|
|
"is_partial": current_stage is not None # 标记是否为阶段性报告
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
state.messages.append({
|
|||
|
|
"role": "discovery",
|
|||
|
|
"content": f"📊 阶段性综合报告已生成（包含 {len(stage_names)} 个阶段）" if current_stage else "📊 完整综合报告已生成",
|
|||
|
|
"metadata": {
|
|||
|
|
"report_length": len(comprehensive_report),
|
|||
|
|
"stages": stage_names
|
|||
|
|
}
|
|||
|
|
})
|
|||
|
|
|
|||
|
|
print(f"[DiscoveryAgent] 综合报告已生成，包含 {len(stage_names)} 个阶段，长度: {len(comprehensive_report)} 字符")
|
|||
|
|
|
|||
|
|
return state
|
|||
|
|
|
|||
|
|
def _get_timestamp(self) -> str:
|
|||
|
|
"""获取当前时间戳"""
|
|||
|
|
from datetime import datetime
|
|||
|
|
return datetime.now().isoformat()
|
|||
|
|
|
|||
|
|
|
|||
|
|
# 便捷函数
|
|||
|
|
def create_discovery_agent(llm_manager: LLMManager) -> DiscoveryAgent:
|
|||
|
|
"""创建DiscoveryAgent实例"""
|
|||
|
|
return DiscoveryAgent(llm_manager)
|