@lzhzzzzwill/cofos 1.0.1 → 1.0.4

package/runtime/config/config.yaml

@@ -0,0 +1,313 @@
+# COF-ROS-Reasoner 配置文件
+
+project_name: COF-ROS-Reasoner
+version: 1.0.0
+
+paths:
+  # 原始数据路径
+  raw_pdfs: data/raw_pdfs
+  raw_json: data/raw_json
+  raw_wos: data/raw_wos/wos_abstracts.xlsx
+
+  # 处理后数据路径
+  processed_dir: data/processed
+  sft_dir: data/sft
+  kg_dir: data/kg
+  eval_dir: data/eval
+
+  # 检索库路径
+  retrieval_store: retrieval_store/embedding
+  bm25_store: retrieval_store/bm25
+
+  # 模型和输出路径
+  checkpoints_dir: checkpoints
+  outputs_dir: outputs
+  logs_dir: outputs/logs
+
+models:
+  # fwdemo 的 QA 学生模型默认从 Hugging Face 加载：Willlzh/COFOS。
+  # 以下 teacher/student Ollama 名称只用于完整 COFOS 项目的抽取、蒸馏等离线流程；
+  # 独立 npx QA 不会调用这些内网 Ollama 模型。
+  teacher_model: qwen3.6:35b
+  student_model: qwen3.5:4b
+
+  # 如需启用 FAISS 向量检索，可改成本地 embedding 模型目录。
+  embedding_model: ""
+  reranker_model: ""
+
+# 本地/内网 LLM 调用配置。fwdemo 独立 QA 路径不使用该配置；
+# 它只保留给完整项目里的 Silver 抽取、教师蒸馏、KG-RAG 教师回答等流程。
+llm:
+  provider: ollama
+  generate_url: http://10.161.138.150:11434/api/generate
+  teacher_model: qwen3.6:35b
+  student_model: qwen3.5:4b
+  extraction_model: qwen3.6:35b
+  inference_model: qwen3.6:35b
+  student_inference_model: qwen3.5:4b
+  timeout: 120
+  stream: false
+  temperature: 0.2
+  top_p: 0.9
+
+extraction:
+  only_ros_related_chunks: true
+  resume: true
+  save_every: 10
+  progress_every: 1
+  max_chunks: null
+
+distillation:
+  input_file: data/sft/cofros_train.jsonl
+  output_file: data/sft/cofros_teacher_distill.jsonl
+  progress_file: data/sft/teacher_distillation_progress.json
+  resume: true
+  save_every: 10
+  max_samples: null
+
+rag_sft:
+  output_file: data/sft/cofros_rag_sft.jsonl
+  max_records: null
+  max_evidence_items: 5
+  skip_generic_material: true
+  include_support_status:
+    - supported
+    - partially_supported
+  include_gold: true
+
+# 训练配置
+# Linux服务器 Qwen3.5 系列优化配置
+training:
+  target_model: qwen3.5:4b
+  # QLoRA 训练需要 Transformers 格式的本地基础模型目录。
+  # 这里不要填 Ollama tag；请在服务器上改成实际模型目录，例如 /models/qwen3.5-4b-instruct。
+  base_model_path: ""
+  # 主训练集仍然是教师蒸馏数据；辅助集补充 RAG 输入格式、氧化还原基础和自然问答风格。
+  train_file: data/sft/cofros_teacher_distill.jsonl
+  aux_train_files:
+    - data/sft/cofros_rag_sft.jsonl
+    - data/sft/chem_redox_sft.jsonl
+    - data/sft/style_correction_sft.jsonl
+  output_dir: checkpoints/lora_adapter_natural_redox_mix
+  max_seq_length: 4096
+  learning_rate: 2.0e-4
+  num_train_epochs: 3
+  per_device_train_batch_size: 1
+  gradient_accumulation_steps: 8
+  lora_r: 32
+  lora_alpha: 64
+  lora_dropout: 0.05
+  load_in_4bit: true
+  bf16: true
+  fp16: false  # Qwen3.5 推荐使用 bf16
+  seed: 42
+  logging_steps: 10
+  save_steps: 500
+  save_total_limit: 3
+  resume_from_checkpoint: auto
+  warmup_ratio: 0.03
+  weight_decay: 0.0
+  max_grad_norm: 0.3
+  local_files_only: true
+  trust_remote_code: true
+  gradient_checkpointing: true
+  target_modules:
+    - q_proj
+    - k_proj
+    - v_proj
+    - o_proj
+    - gate_proj
+    - up_proj
+    - down_proj
+
+  # Qwen3.5 专用配置
+  model_type: qwen3  # qwen, qwen2, qwen3
+  use_flash_attn: true  # 启用 FlashAttention 加速
+
+# 学生模型推理与部署路径。脚本参数可覆盖这些值。
+student_inference:
+  # 独立 fwdemo 默认使用 Hugging Face 模型；若本地已有 merged checkpoint，可在 CLI 中传 --model 覆盖。
+  base_model_path: ""
+  adapter_path: ""
+  merged_model_path: Willlzh/COFOS
+
+# 检索配置
+retrieval:
+  enable_faiss: false
+  enable_bm25: true
+  vector_top_k: 20
+  bm25_top_k: 20
+  rerank_top_k: 5
+  # 无结果优于错误结果：低于阈值时不向模型注入 RAG 上下文。
+  min_bm25_score: 7.0
+  min_vector_score: 0.35
+  min_kg_confidence: 2.0
+  source_priority:
+    gold_silver_json: 4
+    gold_json: 4
+    silver_json: 3
+    pdf: 2
+    pdf_fulltext: 2
+    wos: 1
+    wos_abstract: 1
+
+# 生成配置
+generation:
+  temperature: 0.2
+  top_p: 0.9
+  max_new_tokens: 1024
+  do_sample: true
+  repetition_penalty: 1.08
+  num_beams: 1
+  no_repeat_ngram_size: 0
+  min_new_tokens: 0
+  history_max_turns: 4
+  refine_answers: true
+  refinement_max_new_tokens: 512
+
+# 数据处理配置
+data_processing:
+  # PDF chunk 配置
+  chunk_size: 768
+  chunk_overlap: 50
+
+  # ROS 物种标准化
+  ros_normalization:
+    "center dot OH": "·OH"
+    "OH·": "·OH"
+    "•OH": "·OH"
+    "⋅OH": "·OH"
+    "hydroxyl radical": "·OH"
+
+    "O2 center dot-": "O2·-"
+    "O2•−": "O2·-"
+    "•O2-": "O2·-"
+    "superoxide": "O2·-"
+    "superoxide radical": "O2·-"
+
+    "1O2": "1O2"
+    "¹O₂": "1O2"
+    "singlet oxygen": "1O2"
+
+    "H2O2": "H2O2"
+    "hydrogen peroxide": "H2O2"
+
+    "SO4·-": "SO4·-"
+    "SO4•−": "SO4·-"
+    "sulfate radical": "SO4·-"
+
+    "*O2": "*O2"
+    "*OOH": "*OOH"
+    "*HOOH": "*HOOH"
+
+    "OH": "·OH"
+    "O2-": "O2·-"
+    "O2*": "*O2"
+    "OOH*": "*OOH"
+    "HOOH*": "*HOOH"
+
+  # ROS 关键词（用于段落筛选）
+  ros_keywords:
+    - "ROS"
+    - "reactive oxygen species"
+    - "H2O2"
+    - "hydrogen peroxide"
+    - "2e- ORR"
+    - "oxygen reduction reaction"
+    - "superoxide"
+    - "O2·-"
+    - "singlet oxygen"
+    - "1O2"
+    - "hydroxyl radical"
+    - "·OH"
+    - "sulfate radical"
+    - "SO4·-"
+    - "PMS"
+    - "PDS"
+    - "EPR"
+    - "ESR"
+    - "DMPO"
+    - "TEMP"
+    - "TEMPO"
+    - "scavenger"
+    - "quenching"
+    - "probe"
+    - "photocatalysis"
+    - "photodynamic"
+    - "donor-acceptor"
+    - "COF"
+    - "covalent organic framework"
+
+  # 证据方法关键词
+  evidence_methods:
+    - "EPR"
+    - "ESR"
+    - "DMPO"
+    - "TEMP"
+    - "TEMPO"
+    - "scavenger"
+    - "quenching"
+    - "probe"
+    - "in situ"
+    - "DRIFTS"
+    - "DFT"
+    - "calculation"
+
+# KG 构建配置
+kg:
+  progress_every: 100
+  node_types:
+    - Material
+    - Reaction_Condition
+    - Driving_Force
+    - Oxidant_Source
+    - ROS_or_Product
+    - Intermediate
+    - Evidence_Method
+    - Application
+    - Target
+    - Paper
+  relation_types:
+    - dominantly_generates
+    - secondarily_generates
+    - has_intermediate
+    - under_condition
+    - driven_by
+    - uses_oxidant
+    - evidenced_by
+    - reported_in
+    - applied_to
+    - targets
+
+# 推理配置
+inference:
+  # KG-RAG 配置
+  kg_rag:
+    top_k_facts: 10
+    top_k_evidence: 5
+    evidence_weight: 0.7
+    kg_weight: 0.3
+
+  # 幻觉检测配置
+  hallucination_detection:
+    check_ros_speices: true
+    check_evidence_methods: true
+    check_conditions: true
+    check_sources: true
+
+# 评测配置
+evaluation:
+  # 评测样本数量
+  num_samples: 100
+
+  # 幻觉类型
+  hallucination_types:
+    - fabricated_ros
+    - wrong_dominant_species
+    - h2o2_as_radical
+    - so4_for_pms_absent
+    - epr_fabricated
+    - condition_omitted
+    - abstract_as_evidence
+    - overconfident
+    - cross_cof_misattribution