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Research Scripts

Overview

This folder is the canonical home for exploratory generation, large-batch screening, dataset expansion, and restoration scripts that support research campaigns rather than stable operator workflows.

Key Components

  • generate_expert_1000.py
  • generate_denovo_novel_amps.py
  • generate_100_novel_amps.py
  • generate_1000_novel_amps.py
  • screen_1000_candidates.py
  • restore_master_csv.py
  • build_amp_library.py
  • expand_hemolysis_benchmark.py
  • expand_scrambled_decoys.py
  • generate_phase3_batch.py

Diagrams (Mermaid)

  • Flowchart
flowchart TD
  Generate["Candidate generation"] --> Screen["Screening and restoration"]
  Screen --> Expand["Benchmark / reference expansion"]
  Expand --> Review["Research outputs for later workflow lanes"]
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  • Component Diagram
flowchart LR
  ResearchScripts["scripts/research"] --> Outputs["outputs/*research*"]
  ResearchScripts --> Examples["examples/*"]
  ResearchScripts --> Data["data/novelty_db"]
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  • Sequence Diagram
sequenceDiagram
  participant Researcher
  participant Generate
  participant Screen
  participant Expand
  Researcher->>Generate: produce candidate set
  Generate->>Screen: prioritize and filter
  Screen->>Expand: reuse expanded reference sets
  Expand-->>Researcher: refined research artifacts
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