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run-pubmed-csv-screening

Screen PubMed CSV rows via remote LM Studio and output an augmented CSV.

Updated Apr 30, 2025
Search Tags:#nlp#csv#screening#pubmed#data-processing#lm-studio
One-click install
npx skills add https://github.com/ZBZFirst/HyperCube --skill run-pubmed-csv-screening
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: run-pubmed-csv-screening
Source: https://github.com/ZBZFirst/HyperCube/tree/main/codex-skills/run-pubmed-csv-screening
Command: npx skills add https://github.com/ZBZFirst/HyperCube --skill run-pubmed-csv-screening

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Batch screening PubMed-style CSV rows by routing each row through a remote LM Studio model and aggregating the results into an augmented output CSV, enabling rapid triage of literature data.

Core Features & Use Cases

  • Batch processing of structured CSVs (e.g., pubmed_data.csv) by sending each row to a remote LM Studio instance and collecting LLM-applied fields.
  • Generates an augmented CSV with predicted classifications, fit flags, and error annotations for review.
  • Works with a HyperCube-style workflow, supports auditing the process, and facilitates quick validation of results against the source CSV.

Quick Start

Navigate to the HyperCube project directory and run the screening script with the input and output paths to produce the augmented CSV.

Frequently Asked Questions about run-pubmed-csv-screening

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I batch-screen PubMed CSV data for literature reviews?▼

Batch-screen PubMed CSV data by broadcasting each row to a remote LM Studio endpoint and aggregating the results into an augmented output CSV with predicted classifications and fit flags.

Do I need a specific CSV format for PubMed screening with LM Studio?▼

Yes, PubMed screening requires a correctly formatted CSV containing ResearchQuestion, Title, and Abstract fields for the script to process and route each row to the model.

Can I use LM Studio to automate NLP classification on exported PubMed search results?▼

You can automate NLP classification on PubMed exports by routing each CSV row to a remote LM Studio model, which applies classifications and generates an augmented CSV for rapid triage.

How does the script handle errors during PubMed CSV batch processing?▼

The script handles errors during PubMed CSV batch processing by annotating the augmented output CSV with error fields, allowing you to audit the process and validate results against the source data.

What's the best way to triage large volumes of PubMed abstracts locally?▼

Triage large volumes of PubMed abstracts by running the screenPubMedCsv.mjs script within the local HyperCube-main project, sending data to your LM Studio instance for end-to-end screening.

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