Publishing Papers

This guide covers the full workflow from experiment results to a published paper on arXiv. Hubify Labs handles drafting, review, compilation, and submission packaging.

Overview

Experiments → Claims Table → Outline → Draft → Review → Revise → Compile → Submit

The paper pipeline is agent-assisted at every step, but you maintain full editorial control.

Step 1: Create a Paper

Web UI
CLI

Go to Papers in the sidebar
Click New Paper
Enter title, select template (prd for Physical Review D)
The Paper Lead generates an initial outline based on your lab’s completed experiments

hubify paper create \
  --title "Observational Constraints on Bounce Cosmology" \
  --template prd

Step 2: Build the Claims Table

The claims table is the backbone of your paper. Every scientific assertion must be backed by evidence.

# View the claims table
hubify paper claims paper-1

#	Claim	Evidence	Confidence	Status
1	”Matter bounce predicts f_NL = -4.375”	EXP-031, Branch V	High	Verified
2	”NANOGrav signal consistent with bounce”	EXP-042, gamma=3.0	Medium	Verified
3	”Quintom-B favored at 2.3 sigma”	EXP-048, w0-wa MCMC	Medium	Under review

# Add a claim
hubify paper claim add paper-1 \
  --claim "SPHEREx can detect bounce f_NL at 4.7-12 sigma" \
  --evidence EXP-055 \
  --confidence high

Step 3: Draft Sections

Agents draft sections in parallel. You can direct which experiments feed into which sections:

# Have agents draft the full paper
hubify paper draft paper-1

# Or draft a specific section
hubify paper draft paper-1 --section results

# Review a section draft
hubify paper show paper-1 --section introduction

Step 4: Cross-Model Peer Review

Run a structured peer review using multiple AI models:

hubify paper review paper-1

The review checks:

Accuracy, Are claims consistent with the data?
Completeness, Are there missing analyses or citations?
Clarity, Is the writing clear and well-structured?
Overclaiming, Are conclusions justified by the evidence?
Novelty, Does the paper clearly state what is new?

Review results appear as structured feedback with specific suggestions per section.

Step 5: Revise

Apply review feedback:

# Auto-apply review suggestions
hubify paper revise paper-1

# Apply specific suggestions
hubify paper revise paper-1 --apply "suggestion-3,suggestion-7"

# View revision history
hubify paper history paper-1

Each revision round is logged with a diff showing what changed and the rationale.

Step 6: Compile to PDF

LaTeX compilation requires texlive-publishers (for revtex4-2). This runs on a GPU pod, not locally.

# Compile
hubify paper compile paper-1

# View the PDF
hubify paper open paper-1

# Check for issues
hubify paper compile paper-1 --check

The compiler verifies:

Zero undefined references
All figures embedded (PDF size should be 15-25 MB for a paper with 10+ figures)
Correct page count
Bibliography completeness

Step 7: Package and Submit

# Create arXiv submission package
hubify paper package paper-1 --output submission.tar.gz

The package includes:

Compiled PDF
LaTeX source (.tex)
Figures (all PNGs)
Bibliography (.bib)
Supplementary data (if any)

Upload the package to arxiv.org following their submission guidelines.

Tracking Readiness

Monitor paper progress in the readiness dashboard:

hubify paper status paper-1 --verbose

Paper: Observational Constraints on Bounce Cosmology
Status: In Review (Round 3)

Content:    ████████░░  80%  (6/7 sections drafted)
Figures:    ██████████  100% (11/11 placed)
Bibliography: █████████░  90%  (57/63 resolved)
Claims:     ██████████  100% (12/12 verified)
Compilation: ██████████  100% (0 errors)
Review:     ██████░░░░  60%  (3/5 rounds)

Overall Readiness: 88%

Best Practices

Lock claims before drafting, do not write sections around unverified claims
Run reviews after every major revision, not just at the end
Compile frequently to catch LaTeX issues early
Use revtex4-2, not aastex631
Keep figures in the same directory as the .tex file

Getting Started

Core Concepts

Features

Guides

Integrations

Resources

Publishing Papers

Publishing Papers

Overview

Step 1: Create a Paper

Step 2: Build the Claims Table

Step 3: Draft Sections

Step 4: Cross-Model Peer Review

Step 5: Revise

Step 6: Compile to PDF

Step 7: Package and Submit

Tracking Readiness

Best Practices

​Publishing Papers

​Overview

​Step 1: Create a Paper

​Step 2: Build the Claims Table

​Step 3: Draft Sections

​Step 4: Cross-Model Peer Review

​Step 5: Revise

​Step 6: Compile to PDF

​Step 7: Package and Submit

​Tracking Readiness

​Best Practices

Publishing Papers

Overview

Step 1: Create a Paper

Step 2: Build the Claims Table

Step 3: Draft Sections

Step 4: Cross-Model Peer Review

Step 5: Revise

Step 6: Compile to PDF

Step 7: Package and Submit

Tracking Readiness

Best Practices