ai2-scholarqa-lib

Repo housing the open sourced code for the ai2 scholar qa app and also the corresponding library

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Ai2 Scholar QA is a system for answering scientific queries and literature review by gathering evidence from multiple documents across a corpus and synthesizing an organized report with evidence for each claim. It consists of a retrieval component and a three-step generator pipeline. The retrieval component fetches relevant evidence passages using the Semantic Scholar public API and reranks them. The generator pipeline includes quote extraction, planning and clustering, and summary generation. The system is powered by the ScholarQA class, which includes components like PaperFinder and MultiStepQAPipeline. It requires environment variables for Semantic Scholar API and LLMs, and can be run as local docker containers or embedded into another application as a Python package.

README:

Ai2 Scholar QA

This repo houses the code for the live demo and can be run as local docker containers or embedded into another application as a python package.

Ai2 Scholar QA
Overview

Ai2 Scholar QA is a system for answering scientific queries and literature review by gathering evidence from multiple documents across our corpus and synthesizing an organized report with evidence for each claim. As a RAG based architecture, Ai2 Scholar QA has a retrieval component and a three step generator pipeline.

Retrieval:

The retrieval component consists of two sub-components:

i. Retriever - Based on the user query, relevant evidence passages are fetched using the Semantic Scholar public api's snippet/search end point which looks up an index of open source papers. Further, we also use the api's keyword search to suppliement the results from the index with paper abstracts. The user query is preprocessed to extract entities for filtering the papers and re-writing the query as needed. Prompt

ii. Reranker - The results from the retriever are then reranked with mixedbread-ai/mxbai-rerank-large-v1 and top k results are retained and aggregated at the paper-level to combine all the passages from a single paper.

These components are encapsulated in the PaperFinder class.

Multi-step Generation:

The generation pipeline comprises of three steps:

i. Quote Extraction - The user query along with the aggregated passages from the retrieval component are sent to an LLM (Claude Sonnet 3.5 default) to extract exact quotes relevant to answer the query. Prompt

ii. Planning and Clustering - The llm is then prompted to generate an organization of the output report with sections headings and format of the section. The quotes from step (i) are clustered and assigned to each heading. Prompt

iii. Summary Generation - Each section is generated based on the quotes assigned to that section and all the prior text generated in the report. Prompt

These steps are encapsulated in the MultiStepQAPipeline class. For some sections, we also generate literature review tables that compare and contrast all papers referenced in that section. We generate these tables using the pipeline proposed by the ArxivDIGESTables paper, which is available here.

Both the PaperFinder and MultiStepQAPipeline are in turn members of ScholarQA, which is the main class powering our system.

For more info please refer to our blogpost.

Setup

Environment Variables

Environment Variables Ai2 Scholar QA requires Semantic Scholar api and LLMs for its core functionality of retrieval and generation. So please ensure to create a .env file in the root directory with the following environment variables:

export S2_API_KEY=  
export ANTHROPIC_API_KEY=
export OPENAI_API_KEY=

S2_API_KEY : Used to retrieve the relevant paper passages , keyword search results and associated metadata via the Semantic Scholar public api.

ANTHROPIC_API_KEY : Ai2 Scholar QA uses Anthropic's Claude 3.5 Sonnet as the primary LLM for generation, but any model served by litellm should work. Please configure the corresponding api key here.

OPENAI_API_KEY: OpenAI's GPT 4o is configured as the fallback llm.

Note: We also use OpenAI's text moderation api to validate and filter harmful queries. If you don't have access to an OpenAI api key, this feature will be disabled.

If you use Modal to serve your models, please configure MODAL_TOKEN and MODAL_TOKEN_SECRET here as well.

Application Configuration

Please refer to default.json for the default runtime config.

{
  "logs": {
    "log_dir": "logs",
    "llm_cache_dir": "llm_cache",
    "event_trace_loc": "scholarqa_traces",
    "tracing_mode": "local"
  },
  "run_config": {
    "retrieval_service": "public_api",
    "retriever_args": {
      "n_retrieval": 256,
      "n_keyword_srch": 20
    },
    "reranker_service": "modal",
    "reranker_args": {
      "app_name": "ai2-scholar-qa",
      "api_name": "inference_api",
      "batch_size": 256,
      "gen_options": {}
    },
    "paper_finder_args": {
      "n_rerank": 50,
      "context_threshold": 0.5
    },
    "pipeline_args": {
      "validate": true,
      "llm": "anthropic/claude-3-5-sonnet-20241022",
      "decomposer_llm": "anthropic/claude-3-5-sonnet-20241022"
    }
  }
}

The config is used to populate the AppConfig instance:

Logging

class LogsConfig(BaseModel):
    log_dir: str = Field(default="logs", description="Directory to store logs, event traces and litellm cache")
    llm_cache_dir: str = Field(default="llm_cache", description="Sub directory to cache llm calls")
    event_trace_loc: str = Field(default="scholarqa_traces", description="Sub directory to store event traces"
                                                                         "OR the GCS bucket name")
    tracing_mode: Literal["local", "gcs"] = Field(default="local",
                                                  description="Mode to store event traces (local or gcs)")

Note:

i. Event Traces are json documents containing a trace of the entire pipeline i.e. the results of retrieval, reranking, each step of the qa pipeline and associated costs, if any.

ii. llm_cache_dir is used to initialize the local disk cache for caching llm calls via litellm.

iii. The traces are stored locally in {log_dir}/{event_trace_loc} by default. They can also be persisted in a Google Cloud Storage (GCS) bucket. Please set the tracing_mode="gcs" and event_trace_loc=<GCS bucket name> here and the export GOOGLE_APPLICATION_CREDENTIALS=<Service Account Key json file path> in .env.

iv. By default, the working directory is ./api , so the log_dir will be created inside it as a sub-directory unless the config is modified.

You can also activate Langsmith based log traces if you have an api key configured. Please add the following environment variables:

LANGCHAIN_API_KEY
LANGCHAIN_TRACING_V2
LANGCHAIN_ENDPOINT
LANGCHAIN_PROJECT

Pipeline

class RunConfig(BaseModel):  
    retrieval_service: str = Field(default="public_api", description="Service to use for paper retrieval")
    retriever_args: dict = Field(default=None, description="Arguments for the retrieval service")
    reranker_service: str = Field(default="modal", description="Service to use for paper reranking")
    reranker_args: dict = Field(default=None, description="Arguments for the reranker service")
    paper_finder_args: dict = Field(default=None, description="Arguments for the paper finder service")
    pipeline_args: dict = Field(default=None, description="Arguments for the Scholar QA pipeline service")

Note:

i. *(retrieval, reranker)_service can be used to indicate the type of retrieval/reranker you want to instantiate. Ai2 Scholar QA uses the FullTextRetriever and ModalReranker respectively, which are chosen based on the default public_api and modal keywords. To choose a SentenceTransformers reranker, replace modal with cross_encoder or biencoder or define your own types.

ii. *(retriever, reranker, paper_finder, pipeline)_args are used to initialize the corresponding instances of the pipeline components. eg. retriever = FullTextRetriever(**run_config.retriever_args). You can initialize multiple runs and customize your pipeline.

iii. If the reranker_args are not defined, the app resorts to using only the retrieval service.

docker-compose.yaml

The web app initializes 4 docker containers - one each for the API, GUI, nginx proxy and sonar with their own Dockerfile. The api container config can also be used to declare environment variables -

api:  
build: ./api  
volumes:  
- ./api:/api  
- ./secret:/secret  
environment:  
# This ensures that errors are printed as they occur, which  
# makes debugging easier.  
- PYTHONUNBUFFERED=1  
- LOG_LEVEL=INFO
- CONFIG_PATH=run_configs/default.json  
ports:  
- 8000:8000  
env_file:  
- .env

environment.CONFIG_PATH indicates the path of the application configuration json file. env_file indicates the path of the file with environment variables.

Run Webapp

Please refer to DOCKER.md for more info on setting up the docker app.

i. Clone the repo

git clone [email protected]:allenai/ai2-scholarqa-lib.git
cd ai2-scholarqa-lib

ii. Run docker-compose

docker compose up --build

The docker compose command takes a while to run the first time to install torch and related dependencies. You can get the verbose output with the following command:

docker compose build --progress plain

Async API

The Ai2 Scholar QA UI is powered by an async api at the back end in app.py which is run from dev.sh.

i. The query_corpusqa end point is first called with the query, and a uuid as the user_id, adn it returns a task_id.

ii. Subsequently, the query_corpusqa is then polled to get the updated status of the async task until the task status is not COMPLETED

Sample response

Python Package

conda create -n scholarqa python=3.11.3
conda activate scholarqa
pip install ai2-scholar-qa

#to use sentence transformer models as re-ranker
pip install 'ai2-scholar-qa[all]'

Both the webapp and the api are powered by the same pipeline represented by the ScholarQA class. The pipeline consists of a retrieval component, the PaperFinder which consists of a retriever and maybe a reranker and a 3 step generator component MultiStepQAPipeline. Each component is extensible and can be replaced by custom instances/classes as required.

Sample usage

from scholarqa.rag.reranker.modal_engine import ModalReranker
from scholarqa.rag.retrieval import PaperFinderWithReranker
from scholarqa.rag.retriever_base import FullTextRetriever
from scholarqa import ScholarQA
from scholarqa.llms.constants import CLAUDE_35_SONNET

retriever = FullTextRetriever(n_retrieval=256, n_keyword_srch=20)
reranker = ModalReranker(app_name=<modal_app_name>, api_name=<modal_api_name>, batch_size=256, gen_options=dict())
paper_finder = PaperFinderWithReranker(retriever, reranker, n_rerank=50, context_threshold=0.5)

#For wrapper class with MultiStepQAPipeline integrated
scholar_qa = ScholarQA(paper_finder=paper_finder, llm_model=CLAUDE_35_SONNET) #llm_model can be any litellm model
print(scholar_qa.answer_query("Which is the 9th planet in our solar system?"))

#Custom MultiStepQAPipeline class/steps
from scholarqa.rag.multi_step_qa_pipeline import MultiStepQAPipeline
mqa_pipeline = MultiStepQAPipeline(llm_model=CLAUDE_35_SONNET)

per_paper_summaries, completion_results = mqa_pipeline.step_select_quotes(query, scored_df, sys_prompt)

plan_json = mqa_pipeline.step_clustering(query, per_paper_summaries, sys_prompt)

response = list(generate_iterative_summary(query, per_paper_summaries, plan_json, sys_prompt))

Custom Pipeline

API end points

The api end points in app.py can be extended with a fastapi APIRouter in another script. eg. custom_app.py

from fastapi import APIRouter, FastAPI
from scholarqa.app import create_app as create_app_base

def create_app() -> FastAPI:
  app = create_app_base()
  custom_router = APIRouter()

  @custom_router.post("/custom")
  def custom_endpt():
      pass

  app.include_router(custom_router)
  return app.py

To run custom_app.py, simply replace scholarqa.app:create_app in dev.sh with <package>.custom_app:create_app

ScholarQA class

To extend the existing ScholarQA functionality in a new class you can either create a sub class of ScholarQA or a new class altogether. Either way, lazy_load_scholarqa in app.py should be reimplemented in the new api script to ensure the correct class is initialized.
Pipeline Components

The components of the pipeline are individually extensible. We have the following abstract classes that can be extended to achieve desired customization for retrieval:
and the MultiStepQAPipeline can be extended/modified as needed for generation.
Modal deployment

If you would prefer to serve your models via modal, please refer to MODAL.md for more info and sample code that we used to deploy the reranker model in the live demo.

For Tasks:

Click tags to check more tools for each tasks

answer queries review literature extract quotes generate summaries compare papers

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ai2-scholarqa-lib

README:

Ai2 Scholar QA

Overview

Retrieval:

Multi-step Generation:

Setup

Environment Variables

Application Configuration

docker-compose.yaml

Run Webapp

Startup

UI

Backend

Async API

Python Package

Custom Pipeline

API end points

ScholarQA class

Pipeline Components

Modal deployment

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