# CALICO: A Human-Centered, Codebook-Aligned System for Annotation

arXiv: https://arxiv.org/abs/2609.14726 · HTML: https://mlsanity.com/paper/2609.14726/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in LLM preference optimization methods, one of 10 directions in LLM alignment / RLHF / preference optimisation.
- Builds on 16 of its 35 references that are in the map.
- First posted on arXiv 13 Sep 2026.

## Placed in

- LLM alignment / RLHF / preference optimisation / [LLM preference optimization methods](https://mlsanity.com/alignment/llm-preference-optimization-methods/)

## Builds on (most cited first, 16 of 16)

- [Judging LLM-as-a-Judge with MT-Bench and Chatbot Arena](https://mlsanity.com/paper/2306.05685/) (2023)
- [Large Language Models as Optimizers](https://mlsanity.com/paper/2309.03409/) (2023)
- [DSPy: Compiling Declarative Language Model Calls into Self-Improving Pipelines](https://mlsanity.com/paper/2310.03714/) (2023)
- [GEPA: Reflective Prompt Evolution Can Outperform Reinforcement Learning](https://mlsanity.com/paper/2507.19457/) (2025)
- [Optimizing Instructions and Demonstrations for Multi-Stage Language Model Programs](https://mlsanity.com/paper/2406.11695/) (2024)
- [Large Language Models for Data Annotation and Synthesis: A Survey](https://mlsanity.com/paper/2402.13446/) (2024)
- [Who Validates the Validators? Aligning LLM-Assisted Evaluation of LLM Outputs with Human Preferences](https://mlsanity.com/paper/2404.12272/) (2024)
- [Supporting Qualitative Analysis with Large Language Models: Combining Codebook with GPT-3 for Deductive Coding](https://mlsanity.com/paper/2304.10548/) (2023)
- [Automated Annotation with Generative AI Requires Validation](https://mlsanity.com/paper/2306.00176/) (2023)
- [MEGAnno+: A Human-LLM Collaborative Annotation System](https://mlsanity.com/paper/2402.18050/) (2024)
- [EvoAgentX: An Automated Framework for Evolving Agentic Workflows](https://mlsanity.com/paper/2507.03616/) (2025)
- [Codebook LLMs: Evaluating LLMs as Measurement Tools for Political Science Concepts](https://mlsanity.com/paper/2407.10747/) (2024)
- [Just Put a Human in the Loop? Investigating LLM-Assisted Annotation for Subjective Tasks](https://mlsanity.com/paper/2507.15821/) (2025)
- [The Promises and Pitfalls of LLM Annotations in Dataset Labeling: a Case Study on Media Bias Detection](https://mlsanity.com/paper/2411.11081/) (2024)
- [CrowdAgent: Multi-Agent Managed Multi-Source Annotation System](https://mlsanity.com/paper/2509.14030/) (2025)
- [Co-DETECT: Collaborative Discovery of Edge Cases in Text Classification](https://mlsanity.com/paper/2507.05010/) (2025)

## Abstract (arXiv)

Large language models are increasingly used to scale codebook-based annotation in scientific research, but existing workflows provide limited support for translating domain experts' codebooks into reliable, revisable, and auditable prompts. Prompts are often treated as fixed instructions and hidden from annotators, making it difficult for non-technical domain experts to diagnose and correct model behavior when outputs violate codebook guidelines. In this paper, we present CALICO, a human-centered, codebook-aligned annotation workflow that treats prompts as editable, versioned, and optimizable artifacts. CALICO integrates codebook parsing, prompt generation, result inspection, prompt versioning, natural language human feedback, and label-supervised prompt optimization through existing optimizers such as GEPA, MIPROv2, and OPRO, together with our reflection-based optimizer, ReflectAgent. Empirically, we evaluate CALICO on domain-specific AI-companion chatbot conversation codebooks. Across evaluated dimensions, CALICO improves mean held-out performance by +13.0 and +7.4 absolute points for two coders, respectively. A coder-specificity analysis further suggests that optimized prompts capture coder-specific interpretations rather than only generic codebook clarification. CALICO runs as a web application that takes users from raw codebook materials to inspectable, exportable labels; the website, codebase, and live demo are released at https://calico-annotation.github.io/ under the Apache 2.0 License.