Medical-research-skills hypogenic

Source: https://github.com/aipoch/medical-research-skills

When to Use

• Exploratory analysis on a new dataset where you want the model to propose multiple testable hypotheses from observed patterns (e.g., AI-generated text detection).
• Benchmarking competing explanations by generating a hypothesis bank and evaluating them consistently on validation/test splits.
• Literature-informed research where you want to extract claims from papers and refine them against real data (e.g., deception cues in reviews).
• High-coverage hypothesis discovery when you need both theory-driven and data-driven hypotheses, then merge/deduplicate them (Union workflows).
• Hypothesis-driven classification/regression pipelines for domains like fraud detection, content moderation, mental health indicators, or other empirical studies using tabular/JSON datasets.

Key Features

• Automated hypothesis generation (HypoGeniC): iteratively proposes and improves hypotheses using dataset feedback.
• Literature + data integration (HypoRefine): extracts literature insights from PDFs and refines hypotheses jointly with empirical signals.
• Union method: mechanically merges literature-only hypotheses with HypoGeniC/HypoRefine outputs to maximize coverage and reduce redundancy.
• Config-driven prompting: YAML templates with variable injection (e.g.,

  ${text_features_1}

  ,

  ${num_hypotheses}

  ) for generation and inference.
• Scalable experimentation: optional Redis caching, parallelism, and adaptive selection focusing on hard examples.

Dependencies

• hypogenic

  (install via PyPI; version depends on your environment)
• Optional (recommended for cost/performance):

  • redis

    (server; used for caching repeated LLM calls)
• Optional (required for literature/PDF workflows such as HypoRefine):

  • GROBID

    (service; used for PDF preprocessing)

  • s2orc-doc2json

    (PDF-to-structured conversion used in literature pipelines)

Install:

uv pip install hypogenic

Example Usage

The following example is a minimal end-to-end workflow (dataset + config + CLI + Python). Adjust paths and prompts for your task.

1) Prepare a dataset (HuggingFace-style JSON)

Create three files:

• ./data/my_task_train.json

• ./data/my_task_val.json

• ./data/my_task_test.json

Example schema (feature keys can be renamed, but must match your config placeholders):

{
  "text_features_1": ["Text A1", "Text A2"],
  "text_features_2": ["Text B1", "Text B2"],
  "label": ["Class1", "Class2"]
}

2) Create

./data/my_task/config.yaml

task_name: my_task

train_data_path: ./data/my_task_train.json
val_data_path: ./data/my_task_val.json
test_data_path: ./data/my_task_test.json

prompt_templates:
  observations: |
    Feature 1: ${text_features_1}
    Feature 2: ${text_features_2}
    Label: ${label}

  batched_generation:
    system: |
      You are a scientific assistant. Propose testable, falsifiable hypotheses that map features to labels.
    user: |
      Given examples and labels, generate ${num_hypotheses} distinct hypotheses.
      Return a JSON list of hypotheses, each with a short name and a testable statement.

  inference:
    system: |
      You are a careful classifier. Use the provided hypothesis to predict the label.
    user: |
      Hypothesis: ${hypothesis}
      Feature 1: ${text_features_1}
      Feature 2: ${text_features_2}
      Output the final answer as: "final answer: <LABEL>"

3) Run generation + inference (CLI)

# Generate hypotheses (HypoGeniC)
hypogenic_generation \
  --config ./data/my_task/config.yaml \
  --method hypogenic \
  --num_hypotheses 20

# Evaluate generated hypotheses
hypogenic_inference \
  --config ./data/my_task/config.yaml \
  --hypotheses ./output/hypotheses.json

4) Run the same workflow (Python API)

from hypogenic import BaseTask
import re

def extract_label(llm_output: str) -> str:
    m = re.search(r"final answer:\s*(.*)", llm_output, re.IGNORECASE)
    return m.group(1).strip() if m else llm_output.strip()

task = BaseTask(
    config_path="./data/my_task/config.yaml",
    extract_label=extract_label,
)

task.generate_hypotheses(
    method="hypogenic",
    num_hypotheses=20,
    output_path="./output/hypotheses.json",
)

results = task.inference(
    hypothesis_bank="./output/hypotheses.json",
    test_data="./data/my_task_test.json",
)

print(results)

Implementation Details

Methods

• HypoGeniC (data-driven)

  • Initializes hypotheses from a subset of training data.
  • Iteratively evaluates hypotheses on validation data and replaces underperforming ones.
  • Often uses hard/challenging samples to prompt improved hypotheses.

• HypoRefine (literature + data)

  • Preprocesses PDFs into structured text (commonly via GROBID + conversion tooling).
  • Generates a literature-derived hypothesis bank and a data-derived hypothesis bank.
  • Refines both banks iteratively using performance feedback and relevance checks.

• Union

  • Produces combined banks such as:

    • Literature ∪ HypoGeniC

    • Literature ∪ HypoRefine

  • Focuses on coverage and deduplication rather than deeper joint optimization.

Configuration and Prompt Parameters

• Variable injection: prompt templates can reference dataset fields and runtime parameters:

  • ${text_features_1}

    ,

    ${text_features_2}

    , … (from dataset JSON)

  • ${label}

    (ground truth label, typically used in observation templates)

  • ${num_hypotheses}

    (generation-time control)

  • ${hypothesis}

    (inference-time hypothesis text)
• Label parsing (

  extract_label

  ):
  • Accuracy depends on extracting a label string that exactly matches the dataset’s

    label

    values.
  • Default patterns often look for

    final answer: ...

    ; customize for your output format.

Performance/Cost Controls (Optional)

• Redis caching: reduces repeated LLM calls during iterative generation and evaluation.
• Parallelism: speeds up hypothesis testing on large datasets.
• Adaptive selection: prioritizes difficult examples to improve hypothesis quality over iterations.