---
title: "Citation Configuration and Behavior in Brainfish Search Responses"
description: "Overview"
canonical_url: "https://help.brainfi.sh/articles/citation-configuration-and-behavior-in-brainfish-search-responses-RgkWt3biV0"
md_url: "https://help.brainfi.sh/articles/citation-configuration-and-behavior-in-brainfish-search-responses-RgkWt3biV0.md"
---
# Citation Configuration and Behavior in Brainfish Search Responses

## Overview

This article describes how citation functionality works in Brainfish search responses, including the three supported citation modes, how each behaves, and key implications for accuracy and user experience.

## Citation Modes

Brainfish currently supports three distinct citation configurations:


1. **Citations enabled via settings**
2. **Citations disabled via settings (top sources only)**
3. **Inline citations via custom instructions**

Each mode affects how sources are selected, displayed, and interpreted.


---

## 1. Citations Enabled via Settings

When citations are **turned on** in the settings:

* The response includes **proper citations** that indicate exactly **which documents were actually used** to generate the answer.
* Citations are **reliable** for tracing the origin of information in the response.

### Behavior

* The model generates an answer based on retrieved documents.
* The system then attaches citations specifically for the documents that directly contributed to the final answer.
* Users can trust that a cited document was used in the reasoning process, not just retrieved.

### When to Use

Enable this mode when:

* You need **auditable, trustworthy answers**.
* You want users to be able to quickly confirm information in the original source documents.
* Compliance, governance, or quality review requires **traceable sources**.


---

## 2. Citations Disabled via Settings (Top 4 Search Sources)

When citations are **turned off** in the settings:

* The system **does not** show true answer-level citations.
* Instead, it returns the **top 4 search sources** based purely on **embedding similarity** to the user’s query.
* These sources **may or may not** have been used to generate the final answer.

### Behavior

* The model still uses retrieved documents to form an answer.
* However, the list of sources shown is simply the **top 4 documents most similar to the user query embedding**.
* The relevance score displayed reflects **query-to-document similarity**, **not** the document’s actual role in producing the answer.

### Important Caveats

* **Not guaranteed used in the answer**: A displayed source might not have influenced the answer at all.
* **Score is not fully accurate for answer relevance**: The score only measures how close the **user query embedding** is to the document embedding.
* Do **not** treat these sources as authoritative citations; they are **search hints**, not a provenance trail.

### When to Use

Use this mode when:

* You want a **simpler, less opinionated UI** that just shows “related documents.”
* You do **not** need strict source traceability.
* You are comfortable with users seeing **likely-relevant** but not guaranteed-used documents.


---

## 3. Inline Citations via Custom Instructions

Inline citations are implemented by adding specific instructions in the **custom instructions** for the assistant.

When configured, the system automatically:

* Adds **citation numbers** (for example, `[1]`, `[2]`) within the response.
* Makes these citation numbers **clickable links** that lead to the underlying documents.
* Places citations within **step headings** and **key points** to highlight where information comes from.

### Behavior

* The inline citation style is enforced at the **prompt/instructions** level.
* The underlying citation logic can still be controlled **via settings**, meaning:
  * You can pair inline styling with **true answer-based citations**, or
  * You can adapt it alongside other citation configuration options.

### Implementation Notes

* Inline citations are supported **directly in the codebase** via a pull request that:
  * Adds inline citation formatting behavior to the assistant.
  * Allows this behavior to be **optionally controlled via settings**.
* Custom instructions determine:
  * When and how citation numbers appear.
  * Where links are embedded (e.g., headings, bullet points, or specific claims).

### When to Use

Use inline citations when you want:

* A **documentation-like experience** with numbered references.
* Users to quickly jump from a statement to the supporting document via **clickable links**.
* Citations to appear in structured parts of the answer, such as:
  * Step titles in a how-to guide
  * Key recommendations
  * Major conclusions and definitions


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## Choosing the Right Citation Mode

Consider the following when selecting a configuration:

* **Need for traceability**
  * High: Enable citations via settings; optionally add inline format via custom instructions.
  * Medium/Low: Disable citations and rely on top 4 search sources as suggestions.
* **User experience expectations**
  * Documentation-style, formal: Use **inline citations** with clickable numbered references.
  * Simple, search-like: Show **top related sources only**.
* **Accuracy requirements**
  * If users must know **exactly which sources were used**, do **not** rely solely on the “top 4 search sources” mode.


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## Key Takeaways

* There are **three distinct citation behaviors**: full citations, top-4 search sources, and inline citations via custom instructions.
* With **citations enabled**, each citation reflects a document that truly influenced the answer.
* With **citations disabled**, the displayed sources are **similar to the query** but may not be used in the answer; their scores reflect **embedding similarity only**.
* **Inline citations** provide a structured, clickable way to show sources within headings and key points and can be controlled through both custom instructions and settings.