# PaperQA2

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PaperQA2 is a package for doing high-accuracy retrieval augmented generation (RAG) on PDFs or text files,
with a focus on the scientific literature.
See our [recent 2024 paper](https://paper.wikicrow.ai) to see examples of PaperQA2's superhuman performance in scientific tasks like
question answering, summarization, and contradiction detection.

<!--TOC-->

- [Quickstart](#quickstart)
  - [Example Output](#example-output)
- [What is PaperQA2](#what-is-paperqa2)
  - [PaperQA2 vs PaperQA](#paperqa2-vs-paperqa)
  - [What's New in Version 5 (aka PaperQA2)?](#whats-new-in-version-5-aka-paperqa2)
  - [PaperQA2 Algorithm](#paperqa2-algorithm)
- [Installation](#installation)
- [CLI Usage](#cli-usage)
  - [Bundled Settings](#bundled-settings)
  - [Rate Limits](#rate-limits)
- [Library Usage](#library-usage)
  - [Agentic Adding/Querying Documents](#agentic-addingquerying-documents)
  - [Manual (No Agent) Adding/Querying Documents](#manual-no-agent-addingquerying-documents)
  - [Async](#async)
  - [Choosing Model](#choosing-model)
    - [Locally Hosted](#locally-hosted)
  - [Embedding Model](#embedding-model)
    - [Specifying the Embedding Model](#specifying-the-embedding-model)
    - [Local Embedding Models (Sentence Transformers)](#local-embedding-models-sentence-transformers)
  - [Adjusting number of sources](#adjusting-number-of-sources)
  - [Using Code or HTML](#using-code-or-html)
  - [Using External DB/Vector DB and Caching](#using-external-dbvector-db-and-caching)
  - [Creating Index](#creating-index)
    - [Manifest Files](#manifest-files)
  - [Reusing Index](#reusing-index)
  - [Using Clients Directly](#using-clients-directly)
- [Settings Cheatsheet](#settings-cheatsheet)
- [Where do I get papers?](#where-do-i-get-papers)
- [Callbacks](#callbacks)
  - [Caching Embeddings](#caching-embeddings)
- [Customizing Prompts](#customizing-prompts)
  - [Pre and Post Prompts](#pre-and-post-prompts)
- [FAQ](#faq)
  - [How come I get different results than your papers?](#how-come-i-get-different-results-than-your-papers)
  - [How is this different from LlamaIndex or LangChain?](#how-is-this-different-from-llamaindex-or-langchain)
  - [Can I save or load?](#can-i-save-or-load)
- [Reproduction](#reproduction)
- [Citation](#citation)

<!--TOC-->

## Quickstart

In this example we take a folder of research paper PDFs,
magically get their metadata - including citation counts with a retraction check,
then parse and cache PDFs into a full-text search index,
and finally answer the user question with an LLM agent.

```bash
pip install paper-qa
cd my_papers
pqa ask 'How can carbon nanotubes be manufactured at a large scale?'
```

### Example Output

Question: Has anyone designed neural networks that compute with proteins or DNA?

> The claim that neural networks have been designed to compute with DNA is supported by multiple sources. The work by Qian, Winfree, and Bruck demonstrates the use of DNA strand displacement cascades to construct neural network components, such as artificial neurons and associative memories, using a DNA-based system (Qian2011Neural pages 1-2, Qian2011Neural pages 15-16, Qian2011Neural pages 54-56). This research includes the implementation of a 3-bit XOR gate and a four-neuron Hopfield associative memory, showcasing the potential of DNA for neural network computation. Additionally, the application of deep learning techniques to genomics, which involves computing with DNA sequences, is well-documented. Studies have applied convolutional neural networks (CNNs) to predict genomic features such as transcription factor binding and DNA accessibility (Eraslan2019Deep pages 4-5, Eraslan2019Deep pages 5-6). These models leverage DNA sequences as input data, effectively using neural networks to compute with DNA. While the provided excerpts do not explicitly mention protein-based neural network computation, they do highlight the use of neural networks in tasks related to protein sequences, such as predicting DNA-protein binding (Zeng2016Convolutional pages 1-2). However, the primary focus remains on DNA-based computation.

## What is PaperQA2

PaperQA2 is engineered to be the best agentic RAG model for working with scientific papers.
Here are some features:

- A simple interface to get good answers with grounded responses containing in-text citations.
- State-of-the-art implementation including document metadata-awareness
  in embeddings and LLM-based re-ranking and contextual summarization (RCS).
- Support for agentic RAG, where a language agent can iteratively refine queries and answers.
- Automatic redundant fetching of paper metadata,
  including citation and journal quality data from multiple providers.
- A usable full-text search engine for a local repository of PDF/text files.
- A robust interface for customization, with default support for all [LiteLLM][LiteLLM providers] models.

[LiteLLM providers]: https://docs.litellm.ai/docs/providers
[LiteLLM general docs]: https://docs.litellm.ai/docs/

By default, it uses [OpenAI embeddings](https://platform.openai.com/docs/guides/embeddings) and [models](https://platform.openai.com/docs/models) with a Numpy vector DB to embed and search documents. However, you can easily use other closed-source, open-source models or embeddings (see details below).

PaperQA2 depends on some awesome libraries/APIs that make our repo possible.
Here are some in no particular order:

1. [Semantic Scholar](https://www.semanticscholar.org/)
2. [Crossref](https://www.crossref.org/)
3. [Unpaywall](https://unpaywall.org/)
4. [Pydantic](https://docs.pydantic.dev/latest/)
5. [tantivy](https://github.com/quickwit-oss/tantivy)
6. [LiteLLM][LiteLLM general docs]
7. [pybtex](https://pybtex.org/)
8. [PyMuPDF](https://pymupdf.readthedocs.io/en/latest/)

### PaperQA2 vs PaperQA

We've been working on hard on fundamental upgrades for a while and mostly followed [SemVer](https://semver.org/).
meaning we've incremented the major version number on each breaking change.
This brings us to the current major version number v5.
So why call is the repo now called PaperQA2?
We wanted to remark on the fact though that we've exceeded human performance on [many important metrics](https://paper.wikicrow.ai).
So we arbitrarily call version 5 and onward PaperQA2,
and versions before it as PaperQA1 to denote the significant change in performance.
We recognize that we are challenged at naming and counting at FutureHouse,
so we reserve the right at any time to arbitrarily change the name to PaperCrow.

### What's New in Version 5 (aka PaperQA2)?

Version 5 added:

- A CLI `pqa`
- Agentic workflows invoking tools for
  paper search, gathering evidence, and generating an answer
- Removed much of the statefulness from the `Docs` object
- A migration to LiteLLM for compatibility with many LLM providers
  as well as centralized rate limits and cost tracking
- A bundled set of configurations (read [here](#bundled-settings)))
  containing known-good hyperparameters

Note that `Docs` objects pickled from prior versions of `PaperQA` are incompatible with version 5,
and will need to be rebuilt.
Also, our minimum Python version was increased to Python 3.11.

### PaperQA2 Algorithm

To understand PaperQA2, let's start with the pieces of the underlying algorithm.
The default workflow of PaperQA2 is as follows:

| Phase                  | PaperQA2 Actions                                                          |
| ---------------------- | ------------------------------------------------------------------------- |
| **1. Paper Search**    | - Get candidate papers from LLM-generated keyword query                   |
|                        | - Chunk, embed, and add candidate papers to state                         |
| **2. Gather Evidence** | - Embed query into vector                                                 |
|                        | - Rank top _k_ document chunks in current state                           |
|                        | - Create scored summary of each chunk in the context of the current query |
|                        | - Use LLM to re-score and select most relevant summaries                  |
| **3. Generate Answer** | - Put best summaries into prompt with context                             |
|                        | - Generate answer with prompt                                             |

The tools can be invoked in any order by a language agent.
For example, an LLM agent might do a narrow and broad search,
or using different phrasing for the gather evidence step from the generate answer step.

## Installation

For a non-development setup,
install PaperQA2 (aka version 5) from [PyPI](https://pypi.org/project/paper-qa/).
Note version 5 requires Python 3.11+.

```bash
pip install paper-qa>=5
```

For development setup,
please refer to the [CONTRIBUTING.md](CONTRIBUTING.md) file.

PaperQA2 uses an LLM to operate,
so you'll need to either set an appropriate [API key environment variable][LiteLLM providers] (i.e. `export OPENAI_API_KEY=sk-...`)
or set up an open source LLM server (i.e. using [llamafile](https://github.com/Mozilla-Ocho/llamafile).
Any LiteLLM compatible model can be configured to use with PaperQA2.

If you need to index a large set of papers (100+),
you will likely want an API key for both [Crossref](https://www.crossref.org/documentation/metadata-plus/metadata-plus-keys/) and [Semantic Scholar](https://www.semanticscholar.org/product/api#api-key),
which will allow you to avoid hitting public rate limits using these metadata services.
Those can be exported as `CROSSREF_API_KEY` and `SEMANTIC_SCHOLAR_API_KEY` variables.

## CLI Usage

The fastest way to test PaperQA2 is via the CLI. First navigate to a directory with some papers and use the `pqa` cli:

```bash
$ pqa ask 'What manufacturing challenges are unique to bispecific antibodies?'
```

You will see PaperQA2 index your local PDF files, gathering the necessary metadata for each of them (using [Crossref](https://www.crossref.org/) and [Semantic Scholar](https://www.semanticscholar.org/)),
search over that index, then break the files into chunked evidence contexts, rank them, and ultimately generate an answer. The next time this directory is queried, your index will already be built (save for any differences detected, like new added papers), so it will skip the indexing and chunking steps.

All prior answers will be indexed and stored, you can view them by querying via the `search` subcommand, or access them yourself in your `PQA_HOME` directory, which defaults to `~/.pqa/`.

```bash
$ pqa search -i 'answers' 'antibodies'
```

PaperQA2 is highly configurable, when running from the command line, `pqa --help` shows all options and short descriptions. For example to run with a higher temperature:

```bash
$ pqa --temperature 0.5 ask 'What manufacturing challenges are unique to bispecific antibodies?'
```

You can view all settings with `pqa view`. Another useful thing is to change to other templated settings - for example `fast` is a setting that answers more quickly and you can see it with `pqa -s fast view`

Maybe you have some new settings you want to save? You can do that with

```bash
pqa -s my_new_settings --temperature 0.5 --llm foo-bar-5 save
```

and then you can use it with

```bash
pqa -s my_new_settings ask 'What manufacturing challenges are unique to bispecific antibodies?'
```

If you run `pqa` with a command which requires a new indexing, say if you change the default chunk_size, a new index will automatically be created for you.

```bash
pqa --parsing.chunk_size 5000 ask 'What manufacturing challenges are unique to bispecific antibodies?'
```

You can also use `pqa` to do full-text search with use of LLMs view the search command. For example, let's save the index from a directory and give it a name:

```bash
pqa -i nanomaterials index
```

Now I can search for papers about thermoelectrics:

```bash
pqa -i nanomaterials search thermoelectrics
```

or I can use the normal ask

```bash
pqa -i nanomaterials ask 'Are there nm scale features in thermoelectric materials?'
```

Both the CLI and module have pre-configured settings based on prior performance and our publications, they can be invoked as follows:

```bash
pqa --settings <setting name> ask 'Are there nm scale features in thermoelectric materials?'
```

### Bundled Settings

Inside [`paperqa/configs`](paperqa/configs) we bundle known useful settings:

| Setting Name | Description                                                                                                                  |
| ------------ | ---------------------------------------------------------------------------------------------------------------------------- |
| high_quality | Highly performant, relatively expensive (due to having `evidence_k` = 15) query using a `ToolSelector` agent.                |
| fast         | Setting to get answers cheaply and quickly.                                                                                  |
| wikicrow     | Setting to emulate the Wikipedia article writing used in our WikiCrow publication.                                           |
| contracrow   | Setting to find contradictions in papers, your query should be a claim that needs to be flagged as a contradiction (or not). |
| debug        | Setting useful solely for debugging, but not in any actual application beyond debugging.                                     |
| tier1_limits | Settings that match OpenAI rate limits for each tier, you can use `tier<1-5>_limits` to specify the tier.                    |

### Rate Limits

If you are hitting rate limits, say with the OpenAI Tier 1 plan, you can add them into PaperQA2.
For each OpenAI tier, a pre-built setting exists to limit usage.

```bash
pqa --settings 'tier1_limits' ask 'Are there nm scale features in thermoelectric materials?'
```

This will limit your system to use the [tier1_limits](paperqa/configs/tier1_limits.json),
and slow down your queries to accommodate.

You can also specify them manually with any rate limit string that matches the specification in the [limits](https://limits.readthedocs.io/en/stable/quickstart.html#rate-limit-string-notation) module:

```bash
pqa --summary_llm_config '{"rate_limit": {"gpt-4o-2024-11-20": "30000 per 1 minute"}}' ask 'Are there nm scale features in thermoelectric materials?'
```

Or by adding into a `Settings` object, if calling imperatively:

```python
from paperqa import Settings, ask

answer_response = ask(
    "What manufacturing challenges are unique to bispecific antibodies?",
    settings=Settings(
        llm_config={"rate_limit": {"gpt-4o-2024-11-20": "30000 per 1 minute"}},
        summary_llm_config={"rate_limit": {"gpt-4o-2024-11-20": "30000 per 1 minute"}},
    ),
)
```

## Library Usage

PaperQA2's full workflow can be accessed via Python directly:

```python
from paperqa import Settings, ask

answer_response = ask(
    "What manufacturing challenges are unique to bispecific antibodies?",
    settings=Settings(temperature=0.5, paper_directory="my_papers"),
)
```

Please see our [installation docs](#installation) for how to install the package from PyPI.

### Agentic Adding/Querying Documents

The answer object has the following attributes: `formatted_answer`, `answer` (answer alone), `question` , and `context` (the summaries of passages found for answer).
`ask` will use the `SearchPapers` tool, which will query a local index of files, you can specify this location via the `Settings` object:

```python
from paperqa import Settings, ask

answer_response = ask(
    "What manufacturing challenges are unique to bispecific antibodies?",
    settings=Settings(temperature=0.5, paper_directory="my_papers"),
)
```

`ask` is just a convenience wrapper around the real entrypoint, which can be accessed if you'd like to run concurrent asynchronous workloads:

```python
from paperqa import Settings, agent_query

answer_response = await agent_query(
    query="What manufacturing challenges are unique to bispecific antibodies?",
    settings=Settings(temperature=0.5, paper_directory="my_papers"),
)
```

The default agent will use an LLM based agent,
but you can also specify a `"fake"` agent to use a hard coded call path of search -> gather evidence -> answer to reduce token usage.

### Manual (No Agent) Adding/Querying Documents

Normally via agent execution, the agent invokes the search tool,
which adds documents to the `Docs` object for you behind the scenes.
However, if you prefer fine-grained control,
you can directly interact with the `Docs` object.

Note that manually adding and querying `Docs` does not impact performance.
It just removes the automation associated with an agent picking the documents to add.

```python
from paperqa import Docs, Settings

# valid extensions include .pdf, .txt, .md, and .html
doc_paths = ("myfile.pdf", "myotherfile.pdf")

# Prepare the Docs object by adding a bunch of documents
docs = Docs()
for doc_path in doc_paths:
    docs.add(doc_path)

# Set up how we want to query the Docs object
settings = Settings()
settings.llm = "claude-3-5-sonnet-20240620"
settings.answer.answer_max_sources = 3

# Query the Docs object to get an answer
session = docs.query(
    "What manufacturing challenges are unique to bispecific antibodies?",
    settings=settings,
)
print(session)
```

### Async

PaperQA2 is written to be used asynchronously.
The synchronous API is just a wrapper around the async.
Here are the methods and their `async` equivalents:

| Sync                | Async                |
| ------------------- | -------------------- |
| `Docs.add`          | `Docs.aadd`          |
| `Docs.add_file`     | `Docs.aadd_file`     |
| `Docs.add_url`      | `Docs.aadd_url`      |
| `Docs.get_evidence` | `Docs.aget_evidence` |
| `Docs.query`        | `Docs.aquery`        |

The synchronous version just calls the async version in a loop.
Most modern python environments support `async` natively (including Jupyter notebooks!).
So you can do this in a Jupyter Notebook:

```python
import asyncio
from paperqa import Docs


async def main() -> None:
    docs = Docs()
    # valid extensions include .pdf, .txt, .md, and .html
    for doc in ("myfile.pdf", "myotherfile.pdf"):
        await docs.aadd(doc)

    session = await docs.aquery(
        "What manufacturing challenges are unique to bispecific antibodies?"
    )
    print(session)


asyncio.run(main())
```

### Choosing Model

By default, PaperQA2 uses OpenAI's `gpt-4o-2024-11-20` model for the
`summary_llm`, `llm`, and `agent_llm`.
Please see the [Settings Cheatsheet](#settings-cheatsheet)
for more information on these settings.

We use the [`lmi`](https://github.com/Future-House/ldp/tree/main/packages/lmi) package for our LLM interface,
which in turn uses `litellm` to support many LLM providers.
You can adjust this easily to use any model supported by `litellm`:

```python
from paperqa import Settings, ask

answer_response = ask(
    "What manufacturing challenges are unique to bispecific antibodies?",
    settings=Settings(
        llm="gpt-4o-mini", summary_llm="gpt-4o-mini", paper_directory="my_papers"
    ),
)
```

To use Claude, make sure you set the `ANTHROPIC_API_KEY`

```python
from paperqa import Settings, ask
from paperqa.settings import AgentSettings

answer_response = ask(
    "What manufacturing challenges are unique to bispecific antibodies?",
    settings=Settings(
        llm="claude-3-5-sonnet-20240620",
        summary_llm="claude-3-5-sonnet-20240620",
        agent=AgentSettings(agent_llm="claude-3-5-sonnet-20240620"),
    ),
)
```

Or Gemini, by setting the `GEMINI_API_KEY` from Google AI Studio

```python
from paperqa import Settings, ask

answer_response = ask(
    "What manufacturing challenges are unique to bispecific antibodies?",
    settings=Settings(
        llm="gemini-1.5-pro",
        summary_llm="gemini-1.5-pro",
        agent=AgentSettings(agent_llm="gemini-1.5-pro"),
    ),
)
```

#### Locally Hosted

You can use llama.cpp to be the LLM. Note that you should be using relatively large models, because PaperQA2 requires following a lot of instructions. You won't get good performance with 7B models.

The easiest way to get set-up is to download a [llama file](https://github.com/Mozilla-Ocho/llamafile) and execute it with `-cb -np 4 -a my-llm-model --embedding` which will enable continuous batching and embeddings.

```python
from paperqa import Settings, ask

local_llm_config = dict(
    model_list=[
        dict(
            model_name="my_llm_model",
            litellm_params=dict(
                model="my-llm-model",
                api_base="http://localhost:8080/v1",
                api_key="sk-no-key-required",
                temperature=0.1,
                frequency_penalty=1.5,
                max_tokens=512,
            ),
        )
    ]
)

answer_response = ask(
    "What manufacturing challenges are unique to bispecific antibodies?",
    settings=Settings(
        llm="my-llm-model",
        llm_config=local_llm_config,
        summary_llm="my-llm-model",
        summary_llm_config=local_llm_config,
    ),
)
```

Models hosted with `ollama` are also supported.
To run the example below make sure you have downloaded llama3.2 and mxbai-embed-large via ollama.

```python
from paperqa import Settings, ask

local_llm_config = {
    "model_list": [
        {
            "model_name": "ollama/llama3.2",
            "litellm_params": {
                "model": "ollama/llama3.2",
                "api_base": "http://localhost:11434",
            },
        }
    ]
}

answer_response = ask(
    "What manufacturing challenges are unique to bispecific antibodies?",
    settings=Settings(
        llm="ollama/llama3.2",
        llm_config=local_llm_config,
        summary_llm="ollama/llama3.2",
        summary_llm_config=local_llm_config,
        embedding="ollama/mxbai-embed-large",
    ),
)
```

### Embedding Model

Embeddings are used to retrieve k texts (where k is specified via `Settings.answer.evidence_k`)
for re-ranking and contextual summarization.
If you don't want to use embeddings, but instead just fetch all chunks,
disable "evidence retrieval" via the `Settings.answer.evidence_retrieval` setting.

PaperQA2 defaults to using OpenAI (`text-embedding-3-small`) embeddings,
but has flexible options for both vector stores and embedding choices.

#### Specifying the Embedding Model

The simplest way to specify the embedding model is via `Settings.embedding`:

```python
from paperqa import Settings, ask

answer_response = ask(
    "What manufacturing challenges are unique to bispecific antibodies?",
    settings=Settings(embedding="text-embedding-3-large"),
)
```

`embedding` accepts any embedding model name supported by litellm. PaperQA2 also supports an embedding input of `"hybrid-<model_name>"` i.e. `"hybrid-text-embedding-3-small"` to use a hybrid sparse keyword (based on a token modulo embedding) and dense vector embedding, where any litellm model can be used in the dense model name. `"sparse"` can be used to use a sparse keyword embedding only.

Embedding models are used to create PaperQA2's index of the full-text embedding vectors (`texts_index` argument). The embedding model can be specified as a setting when you are adding new papers to the `Docs` object:

```python
from paperqa import Docs, Settings

docs = Docs()
for doc in ("myfile.pdf", "myotherfile.pdf"):
    docs.add(doc, settings=Settings(embedding="text-embedding-large-3"))
```

Note that PaperQA2 uses Numpy as a dense vector store.
Its design of using a keyword search initially reduces the number of chunks needed for each answer to a relatively small number < 1k.
Therefore, `NumpyVectorStore` is a good place to start, it's a simple in-memory store, without an index.
However, if a larger-than-memory vector store is needed, you can an external vector database like [Qdrant](https://qdrant.tech/) via the `QdrantVectorStore` class.

The hybrid embeddings can be customized:

```python
from paperqa import (
    Docs,
    HybridEmbeddingModel,
    SparseEmbeddingModel,
    LiteLLMEmbeddingModel,
)


model = HybridEmbeddingModel(
    models=[LiteLLMEmbeddingModel(), SparseEmbeddingModel(ndim=1024)]
)
docs = Docs()
for doc in ("myfile.pdf", "myotherfile.pdf"):
    docs.add(doc, embedding_model=model)
```

The sparse embedding (keyword) models default to having 256 dimensions, but this can be specified via the `ndim` argument.

#### Local Embedding Models (Sentence Transformers)

You can use a `SentenceTransformerEmbeddingModel` model if you install `sentence-transformers`, which is [a local embedding library](https://sbert.net/) with support for HuggingFace models and more. You can install it by adding the `local` extras.

```sh
pip install paper-qa[local]
```

and then prefix embedding model names with `st-`:

```python
from paperqa import Settings, ask

answer_response = ask(
    "What manufacturing challenges are unique to bispecific antibodies?",
    settings=Settings(embedding="st-multi-qa-MiniLM-L6-cos-v1"),
)
```

or with a hybrid model

```python
from paperqa import Settings, ask

answer_response = ask(
    "What manufacturing challenges are unique to bispecific antibodies?",
    settings=Settings(embedding="hybrid-st-multi-qa-MiniLM-L6-cos-v1"),
)
```

### Adjusting number of sources

You can adjust the numbers of sources (passages of text) to reduce token usage or add more context. `k` refers to the top k most relevant and diverse (may from different sources) passages. Each passage is sent to the LLM to summarize, or determine if it is irrelevant. After this step, a limit of `max_sources` is applied so that the final answer can fit into the LLM context window. Thus, `k` > `max_sources` and `max_sources` is the number of sources used in the final answer.

```python
from paperqa import Settings

settings = Settings()
settings.answer.answer_max_sources = 3
settings.answer.k = 5

docs.query(
    "What manufacturing challenges are unique to bispecific antibodies?",
    settings=settings,
)
```

### Using Code or HTML

You do not need to use papers -- you can use code or raw HTML. Note that this tool is focused on answering questions, so it won't do well at writing code. One note is that the tool cannot infer citations from code, so you will need to provide them yourself.

```python
import glob
import os
from paperqa import Docs

source_files = glob.glob("**/*.js")

docs = Docs()
for f in source_files:
    # this assumes the file names are unique in code
    docs.add(f, citation="File " + os.path.name(f), docname=os.path.name(f))
session = docs.query("Where is the search bar in the header defined?")
print(session)
```

### Using External DB/Vector DB and Caching

You may want to cache parsed texts and embeddings in an external database or file. You can then build a Docs object from those directly:

```python
from paperqa import Docs, Doc, Text

docs = Docs()

for ... in my_docs:
    doc = Doc(docname=..., citation=..., dockey=..., citation=...)
    texts = [Text(text=..., name=..., doc=doc) for ... in my_texts]
    docs.add_texts(texts, doc)
```

### Creating Index

Indexes will be placed in the [home directory][home dir] by default.
This can be controlled via the `PQA_HOME` environment variable.

Indexes are made by reading files in the `Settings.paper_directory`.
By default, we recursively read from subdirectories of the paper directory,
unless disabled using `Settings.index_recursively`.
The paper directory is not modified in any way, it's just read from.

[home dir]: https://docs.python.org/3/library/pathlib.html#pathlib.Path.home

#### Manifest Files

The indexing process attempts to infer paper metadata like title and DOI
using LLM-powered text processing.
You can avoid this point of uncertainty using a "manifest" file,
which is a CSV containing three columns (order doesn't matter):

- `file_location`: relative path to the paper's PDF within the index directory
- `doi`: DOI of the paper
- `title`: title of the paper

By providing this information,
we ensure queries to metadata providers like Crossref are accurate.

### Reusing Index

The local search indexes are built based on a hash of the current `Settings` object.
So make sure you properly specify the `paper_directory` to your `Settings` object.
In general, it's advisable to:

1. Pre-build an index given a folder of papers (can take several minutes)
2. Reuse the index to perform many queries

```python
import os

from paperqa import Settings
from paperqa.agents.main import agent_query
from paperqa.agents.search import get_directory_index


async def amain(folder_of_papers: str | os.PathLike) -> None:
    settings = Settings(paper_directory=folder_of_papers)

    # 1. Build the index. Note an index name is autogenerated when unspecified
    built_index = await get_directory_index(settings=settings)
    print(settings.get_index_name())  # Display the autogenerated index name
    print(await built_index.index_files)  # Display the index contents

    # 2. Use the settings as many times as you want with ask
    answer_response_1 = await agent_query(
        query="What is the best way to make a vaccine?",
        settings=settings,
    )
    answer_response_2 = await agent_query(
        query="What manufacturing challenges are unique to bispecific antibodies?",
        settings=settings,
    )
```

### Using Clients Directly

One of the most powerful features of PaperQA2 is its ability to combine data from multiple metadata sources. For example, [Unpaywall](https://unpaywall.org/) can provide open access status/direct links to PDFs, [Crossref](https://www.crossref.org/) can provide bibtex, and [Semantic Scholar](https://www.semanticscholar.org/) can provide citation licenses. Here's a short demo of how to do this:

```python
from paperqa.clients import DocMetadataClient, ALL_CLIENTS

client = DocMetadataClient(clients=ALL_CLIENTS)
details = await client.query(title="Augmenting language models with chemistry tools")

print(details.formatted_citation)
# Andres M. Bran, Sam Cox, Oliver Schilter, Carlo Baldassari, Andrew D. White, and Philippe Schwaller.
#  Augmenting large language models with chemistry tools. Nature Machine Intelligence,
# 6:525-535, May 2024. URL: https://doi.org/10.1038/s42256-024-00832-8,
# doi:10.1038/s42256-024-00832-8.
# This article has 243 citations and is from a domain leading peer-reviewed journal.

print(details.citation_count)
# 243

print(details.license)
# cc-by

print(details.pdf_url)
# https://www.nature.com/articles/s42256-024-00832-8.pdf
```

the `client.query` is meant to check for exact matches of title. It's a bit robust (like to casing, missing a word). There are duplicates for titles though - so you can also add authors to disambiguate. Or you can provide a doi directly `client.query(doi="10.1038/s42256-024-00832-8")`.

If you're doing this at a large scale, you may not want to use `ALL_CLIENTS` (just omit the argument) and you can specify which specific fields you want to speed up queries. For example:

```python
details = await client.query(
    title="Augmenting large language models with chemistry tools",
    authors=["Andres M. Bran", "Sam Cox"],
    fields=["title", "doi"],
)
```

will return much faster than the first query and we'll be certain the authors match.

## Settings Cheatsheet

| Setting                                      | Default                                | Description                                                                                             |
| -------------------------------------------- | -------------------------------------- | ------------------------------------------------------------------------------------------------------- |
| `llm`                                        | `"gpt-4o-2024-11-20"`                  | Default LLM for most things, including answers. Should be 'best' LLM.                                   |
| `llm_config`                                 | `None`                                 | Optional configuration for `llm`.                                                                       |
| `summary_llm`                                | `"gpt-4o-2024-11-20"`                  | Default LLM for summaries and parsing citations.                                                        |
| `summary_llm_config`                         | `None`                                 | Optional configuration for `summary_llm`.                                                               |
| `embedding`                                  | `"text-embedding-3-small"`             | Default embedding model for texts.                                                                      |
| `embedding_config`                           | `None`                                 | Optional configuration for `embedding`.                                                                 |
| `temperature`                                | `0.0`                                  | Temperature for LLMs.                                                                                   |
| `batch_size`                                 | `1`                                    | Batch size for calling LLMs.                                                                            |
| `texts_index_mmr_lambda`                     | `1.0`                                  | Lambda for MMR in text index.                                                                           |
| `verbosity`                                  | `0`                                    | Integer verbosity level for logging (0-3). 3 = all LLM/Embeddings calls logged.                         |
| `answer.evidence_k`                          | `10`                                   | Number of evidence pieces to retrieve.                                                                  |
| `answer.evidence_detailed_citations`         | `True`                                 | Include detailed citations in summaries.                                                                |
| `answer.evidence_retrieval`                  | `True`                                 | Use retrieval vs processing all docs.                                                                   |
| `answer.evidence_summary_length`             | `"about 100 words"`                    | Length of evidence summary.                                                                             |
| `answer.evidence_skip_summary`               | `False`                                | Whether to skip summarization.                                                                          |
| `answer.answer_max_sources`                  | `5`                                    | Max number of sources for an answer.                                                                    |
| `answer.max_answer_attempts`                 | `None`                                 | Max attempts to generate an answer.                                                                     |
| `answer.answer_length`                       | `"about 200 words, but can be longer"` | Length of final answer.                                                                                 |
| `answer.max_concurrent_requests`             | `4`                                    | Max concurrent requests to LLMs.                                                                        |
| `answer.answer_filter_extra_background`      | `False`                                | Whether to cite background info from model.                                                             |
| `answer.get_evidence_if_no_contexts`         | `True`                                 | Allow lazy evidence gathering.                                                                          |
| `parsing.chunk_size`                         | `5000`                                 | Characters per chunk (0 for no chunking).                                                               |
| `parsing.page_size_limit`                    | `1,280,000`                            | Character limit per page.                                                                               |
| `parsing.use_doc_details`                    | `True`                                 | Whether to get metadata details for docs.                                                               |
| `parsing.overlap`                            | `250`                                  | Characters to overlap chunks.                                                                           |
| `parsing.defer_embedding`                    | `False`                                | Whether to defer embedding until summarization.                                                         |
| `parsing.chunking_algorithm`                 | `ChunkingOptions.SIMPLE_OVERLAP`       | Algorithm for chunking.                                                                                 |
| `parsing.doc_filters`                        | `None`                                 | Optional filters for allowed documents.                                                                 |
| `parsing.use_human_readable_clinical_trials` | `False`                                | Parse clinical trial JSONs into readable text.                                                          |
| `prompt.summary`                             | `summary_prompt`                       | Template for summarizing text, must contain variables matching `summary_prompt`.                        |
| `prompt.qa`                                  | `qa_prompt`                            | Template for QA, must contain variables matching `qa_prompt`.                                           |
| `prompt.select`                              | `select_paper_prompt`                  | Template for selecting papers, must contain variables matching `select_paper_prompt`.                   |
| `prompt.pre`                                 | `None`                                 | Optional pre-prompt templated with just the original question to append information before a qa prompt. |
| `prompt.post`                                | `None`                                 | Optional post-processing prompt that can access PQASession fields.                                      |
| `prompt.system`                              | `default_system_prompt`                | System prompt for the model.                                                                            |
| `prompt.use_json`                            | `True`                                 | Whether to use JSON formatting.                                                                         |
| `prompt.summary_json`                        | `summary_json_prompt`                  | JSON-specific summary prompt.                                                                           |
| `prompt.summary_json_system`                 | `summary_json_system_prompt`           | System prompt for JSON summaries.                                                                       |
| `prompt.context_outer`                       | `CONTEXT_OUTER_PROMPT`                 | Prompt for how to format all contexts in generate answer.                                               |
| `prompt.context_inner`                       | `CONTEXT_INNER_PROMPT`                 | Prompt for how to format a single context in generate answer. Must contain 'name' and 'text' variables. |
| `agent.agent_llm`                            | `"gpt-4o-2024-11-20"`                  | Model to use for agent making tool selections.                                                          |
| `agent.agent_llm_config`                     | `None`                                 | Optional configuration for `agent_llm`.                                                                 |
| `agent.agent_type`                           | `"ToolSelector"`                       | Type of agent to use.                                                                                   |
| `agent.agent_config`                         | `None`                                 | Optional kwarg for AGENT constructor.                                                                   |
| `agent.agent_system_prompt`                  | `env_system_prompt`                    | Optional system prompt message.                                                                         |
| `agent.agent_prompt`                         | `env_reset_prompt`                     | Agent prompt.                                                                                           |
| `agent.return_paper_metadata`                | `False`                                | Whether to include paper title/year in search tool results.                                             |
| `agent.search_count`                         | `8`                                    | Search count.                                                                                           |
| `agent.timeout`                              | `500.0`                                | Timeout on agent execution (seconds).                                                                   |
| `agent.should_pre_search`                    | `False`                                | Whether to run search tool before invoking agent.                                                       |
| `agent.tool_names`                           | `None`                                 | Optional override on tools to provide the agent.                                                        |
| `agent.max_timesteps`                        | `None`                                 | Optional upper limit on environment steps.                                                              |
| `agent.index.name`                           | `None`                                 | Optional name of the index.                                                                             |
| `agent.index.paper_directory`                | `Current working directory`            | Directory containing papers to be indexed.                                                              |
| `agent.index.manifest_file`                  | `None`                                 | Path to manifest CSV with document attributes.                                                          |
| `agent.index.index_directory`                | `pqa_directory("indexes")`             | Directory to store PQA indexes.                                                                         |
| `agent.index.use_absolute_paper_directory`   | `False`                                | Whether to use absolute paper directory path.                                                           |
| `agent.index.recurse_subdirectories`         | `True`                                 | Whether to recurse into subdirectories when indexing.                                                   |
| `agent.index.concurrency`                    | `5`                                    | Number of concurrent filesystem reads.                                                                  |
| `agent.index.sync_with_paper_directory`      | `True`                                 | Whether to sync index with paper directory on load.                                                     |

## Where do I get papers?

Well that's a really good question! It's probably best to just download PDFs of papers you think will help answer your question and start from there.

See detailed docs [about zotero, openreview and parsing](docs/tutorials/where_do_I_get_papers.md)

## Callbacks

To execute a function on each chunk of LLM completions, you need to provide a function that can be executed on each chunk. For example, to get a typewriter view of the completions, you can do:

```python
from paperqa import Docs


def typewriter(chunk: str) -> None:
    print(chunk, end="")


docs = Docs()

# add some docs...

docs.query(
    "What manufacturing challenges are unique to bispecific antibodies?",
    callbacks=[typewriter],
)
```

### Caching Embeddings

In general, embeddings are cached when you pickle a `Docs` regardless of what vector store you use. So as long as you save your underlying `Docs` object, you should be able to avoid re-embedding your documents.

## Customizing Prompts

You can customize any of the prompts using settings.

```python
from paperqa import Docs, Settings

my_qa_prompt = (
    "Answer the question '{question}'\n"
    "Use the context below if helpful. "
    "You can cite the context using the key like (Example2012). "
    "If there is insufficient context, write a poem "
    "about how you cannot answer.\n\n"
    "Context: {context}"
)

docs = Docs()
settings = Settings()
settings.prompts.qa = my_qa_prompt
docs.query("Are covid-19 vaccines effective?", settings=settings)
```

### Pre and Post Prompts

Following the syntax above, you can also include prompts that
are executed after the query and before the query. For example, you can use this to critique the answer.

## FAQ

### How come I get different results than your papers?

Internally at FutureHouse, we have a slightly different set of tools. We're trying to get some of them, like citation traversal, into this repo. However, we have APIs and licenses to access research papers that we cannot share openly. Similarly, in our research papers' results we do not start with the known relevant PDFs. Our agent has to identify them using keyword search over all papers, rather than just a subset. We're gradually aligning these two versions of PaperQA, but until there is an open-source way to freely access papers (even just open source papers) you will need to provide PDFs yourself.

### How is this different from LlamaIndex or LangChain?

[LangChain](https://github.com/langchain-ai/langchain)
and [LlamaIndex](https://github.com/run-llama/llama_index)
are both frameworks for working with LLM applications,
with abstractions made for agentic workflows and retrieval augmented generation.

Over time, the PaperQA team over time chose to become framework-agnostic,
instead outsourcing LLM drivers to [LiteLLM][LiteLLM general docs]
and no framework besides Pydantic for its tools.
PaperQA focuses on scientific papers and their metadata.

PaperQA can be reimplemented using either LlamaIndex or LangChain.
For example, our `GatherEvidence` tool can be reimplemented
as a retriever with an LLM-based re-ranking and contextual summary.
There is similar work with the tree response method in LlamaIndex.

### Can I save or load?

The `Docs` class can be pickled and unpickled. This is useful if you want to save the embeddings of the documents and then load them later.

```python
import pickle

# save
with open("my_docs.pkl", "wb") as f:
    pickle.dump(docs, f)

# load
with open("my_docs.pkl", "rb") as f:
    docs = pickle.load(f)
```

## Reproduction

Contained in [docs/2024-10-16_litqa2-splits.json5](docs/2024-10-16_litqa2-splits.json5)
are the question IDs used in train, evaluation, and test splits,
as well as paper DOIs used to build the splits' indexes.

- Train and eval splits: question IDs come from
  [LAB-Bench's LitQA2 question IDs](https://github.com/Future-House/LAB-Bench/blob/main/LitQA2/litqa-v2-public.jsonl).
- Test split: questions IDs come from
  [aviary-paper-data's LitQA2 question IDs](https://huggingface.co/datasets/futurehouse/aviary-paper-data).

There are multiple papers slowly building PaperQA, shown below in [Citation](#citation).
To reproduce:

- `skarlinski2024language`: train and eval splits are applicable.
  The test split remains held out.
- `narayanan2024aviarytraininglanguageagents`: train, eval, and test splits are applicable.

Example on how to use LitQA for evaluation can be found in
[aviary.litqa](https://github.com/Future-House/aviary/tree/main/packages/litqa#running-litqa).

## Citation

Please read and cite the following papers if you use this software:

```bibtex
@article{narayanan2024aviarytraininglanguageagents,
      title = {Aviary: training language agents on challenging scientific tasks},
      author = {
      Siddharth Narayanan and
 James D. Braza and
 Ryan-Rhys Griffiths and
 Manu Ponnapati and
 Albert Bou and
 Jon Laurent and
 Ori Kabeli and
 Geemi Wellawatte and
 Sam Cox and
 Samuel G. Rodriques and
 Andrew D. White},
      journal = {arXiv preprent arXiv:2412.21154},
      year = {2024},
      url = {https://doi.org/10.48550/arXiv.2412.21154},
}
```

```bibtex
@article{skarlinski2024language,
    title = {Language agents achieve superhuman synthesis of scientific knowledge},
    author = {
    Michael D. Skarlinski and
 Sam Cox and
 Jon M. Laurent and
 James D. Braza and
 Michaela Hinks and
 Michael J. Hammerling and
 Manvitha Ponnapati and
 Samuel G. Rodriques and
 Andrew D. White},
    journal = {arXiv preprent arXiv:2409.13740},
    year = {2024},
    url = {https://doi.org/10.48550/arXiv.2409.13740}
}
```

```bibtex
@article{lala2023paperqa,
    title = {PaperQA: Retrieval-Augmented Generative Agent for Scientific Research},
    author = {
    Jakub Lála and
 Odhran O'Donoghue and
 Aleksandar Shtedritski and
 Sam Cox and
 Samuel G. Rodriques and
 Andrew D. White},
    journal = {arXiv preprint arXiv:2312.07559},
    year = {2023},
    url = {https://doi.org/10.48550/arXiv.2312.07559}
}
```
