A comprehensive full-stack solution has been developed for the creation of a large-scale search engine tailored for scientific papers. This system incorporates natural language processing capabilities, facilitating tasks such as citation recommendations, document summarization, and generation of citation sentences.
LIVE DEMO: https://scilit.vercel.app/
PAPER: https://aclanthology.org/2023.acl-demo.22.pdf
This step is NOT needed if Docker engine has already been installed.
sudo apt-get update
sudo apt-get install ca-certificates curl gnupg
sudo install -m 0755 -d /etc/apt/keyrings
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /etc/apt/keyrings/docker.gpg
sudo chmod a+r /etc/apt/keyrings/docker.gpg
echo \
"deb [arch="$(dpkg --print-architecture)" signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/ubuntu \
"$(. /etc/os-release && echo "$VERSION_CODENAME")" stable" | \
sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
sudo apt-get update
sudo apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
sudo docker run hello-worldSee detailed installation instruction on Docker Engine Installation (Ubuntu)
sudo apt-get update
sudo apt-get install ca-certificates curl gnupg
sudo install -m 0755 -d /etc/apt/keyrings
curl -fsSL https://download.docker.com/linux/debian/gpg | sudo gpg --dearmor -o /etc/apt/keyrings/docker.gpg
sudo chmod a+r /etc/apt/keyrings/docker.gpg
echo \
"deb [arch="$(dpkg --print-architecture)" signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/debian \
"$(. /etc/os-release && echo "$VERSION_CODENAME")" stable" | \
sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
sudo apt-get update
sudo apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
sudo docker run hello-worldPlease see detailed installation instruction on Docker Engine Installation (Debian)
sudo groupadd docker
sudo usermod -aG docker $USER
newgrp docker
sudo setfacl -m user:$USER:rw /var/run/docker.sock
## test if it works
docker run hello-worldBy default docker save its cache files and logs to /var/lib/docker. Sometimes this can be problematic due to the limited space of /var/lib. In this case, we need to change this default folder to a custom folder with a large space. Please refer https://www.ibm.com/docs/en/z-logdata-analytics/5.1.0?topic=compose-relocating-docker-root-directory for how to change the root directory of docker.
distribution=$(. /etc/os-release;echo $ID$VERSION_ID) \
&& curl -fsSL https://nvidia.github.io/libnvidia-container/gpgkey | sudo gpg --dearmor -o /usr/share/keyrings/nvidia-container-toolkit-keyring.gpg \
&& curl -s -L https://nvidia.github.io/libnvidia-container/$distribution/libnvidia-container.list | \
sed 's#deb https://#deb [signed-by=/usr/share/keyrings/nvidia-container-toolkit-keyring.gpg] https://#g' | \
sudo tee /etc/apt/sources.list.d/nvidia-container-toolkit.listThen resolve the package conflicting error before running "apt-get update": E: Conflicting values set for option Signed-By regarding source ... (See https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/troubleshooting.html#conflicting-values-set-for-option-signed-by-error-when-running-apt-update for the details.)
sudo rm $(grep -l "nvidia.github.io" /etc/apt/sources.list.d/* | grep -vE "/nvidia-container-toolkit.list\$")
Then install nvidia-container-toolkit and restart docker
sudo apt-get update
sudo apt-get install -y nvidia-container-toolkit
sudo nvidia-ctk runtime configure --runtime=docker
sudo systemctl restart dockerTest if GPU can be detected within docker containers
docker run --rm --runtime=nvidia --gpus all nvidia/cuda:11.6.2-base-ubuntu20.04 nvidia-smiSee https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/install-guide.html#setting-up-docker for more details.
pip install docker-composesudo apt update
## make sure the node version is 20.x
curl -sL https://deb.nodesource.com/setup_20.x | sudo -E bash -
sudo apt install nodejscheck node version
node -vHere we demonstrated building the search engine on papers from S2ORC, PubMed Open Access (PMCOA) and arXiv.
S2ORC can be accessed via semantic scholar api. Here we only download a tiny subset to demonstrate the pipeline.
mkdir -p backend/1_document_prefetch/data/S2ORC/raw/metadata
mkdir -p backend/1_document_prefetch/data/S2ORC/raw/pdf_parses
wget -P backend/1_document_prefetch/data/S2ORC/raw/metadata https://huggingface.co/scieditor/example_data_S2ORC/raw/main/metadata/metadata_0.jsonl
wget -P backend/1_document_prefetch/data/S2ORC/raw/metadata https://huggingface.co/scieditor/example_data_S2ORC/raw/main/metadata/metadata_1.jsonl
wget -P backend/1_document_prefetch/data/S2ORC/raw/pdf_parses https://huggingface.co/scieditor/example_data_S2ORC/resolve/main/pdf_parses/pdf_parses_0.jsonl
wget -P backend/1_document_prefetch/data/S2ORC/raw/pdf_parses https://huggingface.co/scieditor/example_data_S2ORC/resolve/main/pdf_parses/pdf_parses_1.jsonl
This is how the files are organized:
backend/1_document_prefetch/data/S2ORC/
└── raw
├── metadata
│ ├── metadata_0.jsonl
│ └── metadata_1.jsonl
└── pdf_parses
├── pdf_parses_0.jsonl
└── pdf_parses_1.jsonl
We can download the .tar.gz files from the official FTP service https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk/oa_comm/xml/, and put the files into the folder:
backend/1_document_prefetch/data/PMCOA/raw/tar_gz/
Here we only download one .tar.gz file oa_comm_xml.incr.2023-07-06.tar.gz as an example:
## create the folder if not exist
mkdir -p backend/1_document_prefetch/data/PMCOA/raw/tar_gz/
## download the tar.gz file
wget -P backend/1_document_prefetch/data/PMCOA/raw/tar_gz https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk/oa_comm/xml/oa_comm_xml.incr.2023-07-06.tar.gz
This is how the files are organized:
backend/1_document_prefetch/data/
└── PMCOA
└── raw
└── tar_gz
└── oa_comm_xml.incr.2023-07-06.tar.gz
First we need to install "gsutil" to to able to bulk download arXiv PDFs. For detail, please refer to https://cloud.google.com/storage/docs/gsutil_install#sdk-install
After gsutil has been installed and initiated, we can bulk download arXiv PDFs from google cloud storage. See https://www.kaggle.com/datasets/Cornell-University/arxiv for official instructions.
Here we only download a small percentage of the PDF published within July 2023.
mkdir -p backend/1_document_prefetch/data/arXiv/raw/pdf/2307
gsutil -m cp -r gs://arxiv-dataset/arxiv/arxiv/pdf/2307/2307.00* backend/1_document_prefetch/data/arXiv/raw/pdf/2307/
This is how the files are organized:
backend/1_document_prefetch/data/arXiv/
└── raw
└── pdf
└── 2307
Convert the corpus from the original format (tar.gz for PMCOA and PDF for arXiv) to a unified SQLite paper database, in which each record represents a paper and follows the same JSON schema. This is used for search engine for existing collections.
BASE_DIR=$PWD
cd backend/1_document_prefetch/ && bash script_build_all_databases.sh
cd $BASE_DIRRunning this script automatically builds the databases for PMCOA and arXiv. The dockerized code base for building databases for these two collections is available at backend/1_document_prefetch/src/build_database/
If the host machine does not have GPUs, before running the following commands, first comment out the line "runtime: nvidia" (by adding a "#" before "runtime") in the following docker-compose.yaml files:
backend/1_document_prefetch/docker-compose-document-prefetch.yaml#L38
backend/3_citation_generation/docker-compose.yaml#L9
backend/3_document_reranking/docker-compose.yaml#L9
backend/3_extractive_summarization/docker-compose.yaml#L9
Note: Running the SciBERT-based document reranking on CPU can be slow, please consider skipping reranking in this case by setting "requires_reranking" to False in line: backend/4_document_search_overall/service.py#L267
Once "runtime: nvidia" is commented out, the environment "USE_GPU" is deactivated automatically, so there is no need to change the environment variables.
Run the following commands to start the backend services:
#### We denote BASE_DIR as the root path of this repo, where this README is located.
BASE_DIR=$PWD
#### create "common_network" if it does not exist
NETWORK_NAME="common_network"; if ! docker network ls --format "{{.Name}}" | grep -q "^${NETWORK_NAME}$"; then docker network create ${NETWORK_NAME}; fi
cd $BASE_DIR/backend/0_base_image_deep_learning && docker-compose up --build
cd $BASE_DIR/backend/1_document_prefetch && bash script_start_all_services.sh
cd $BASE_DIR/backend/1_helper_functions && docker-compose up --build -d
cd $BASE_DIR/backend/2_fast_metadata_search && docker-compose up --build -d
cd $BASE_DIR/backend/2_paper_database_service && docker-compose up --build -d
cd $BASE_DIR/backend/3_citation_formating && docker-compose up --build -d
cd $BASE_DIR/backend/3_citation_generation && docker-compose up --build -d
cd $BASE_DIR/backend/3_document_reranking && docker-compose up --build -d
cd $BASE_DIR/backend/3_extractive_summarization && docker-compose up --build -d
cd $BASE_DIR/backend/4_document_search_overall && docker-compose up --build -d
cd $BASE_DIR/backend/5_title_generic_search && docker-compose up --build -d
cd $BASE_DIR/backend/final_api_gateway && docker-compose up --build -d
cd $BASE_DIR
By default, port 8060 is used by the final API gateway to communicate with the frontend or API developers. This PORT can be changed in the docker-compose.yaml file of the api gateway.
Please refer to the API documentation for details on the usage of all backend APIs for developing a scientific document search engine enriched with NLP functions.
Here we suppose that the backend is running on the same local machine and is listening to the PORT 8060. If the backend is running on a remote server (e.g., google cloud VM), please replace "localhost" with the server's IP address.
BASE_DIR=$PWD
cd $BASE_DIR/frontend/SciLit-React
npm install
export REACT_APP_NLP_SERVER_ADDRESS=http://localhost:8060; npm start
Now the frontend service (React based) is running on PORT 3000. You can now open your browser and go to http://localhost:3000 to use SciLit!
This installation pipeline is not suitable on a host machine with proxy.
When using our code or models for your application, please cite the following paper:
@inproceedings{gu-hahnloser-2023-scilit,
title = "{S}ci{L}it: A Platform for Joint Scientific Literature Discovery, Summarization and Citation Generation",
author = "Gu, Nianlong and
Hahnloser, Richard H.R.",
booktitle = "Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 3: System Demonstrations)",
month = jul,
year = "2023",
address = "Toronto, Canada",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/2023.acl-demo.22",
pages = "235--246",
abstract = "Scientific writing involves retrieving, summarizing, and citing relevant papers, which can be time-consuming processes. Although in many workflows these processes are serially linked, there are opportunities for natural language processing (NLP) to provide end-to-end assistive tools. We propose SciLit, a pipeline that automatically recommends relevant papers, extracts highlights, and suggests a reference sentence as a citation of a paper, taking into consideration the user-provided context and keywords. SciLit efficiently recommends papers from large databases of hundreds of millions of papers using a two-stage pre-fetching and re-ranking literature search system that flexibly deals with addition and removal of a paper database. We provide a convenient user interface that displays the recommended papers as extractive summaries and that offers abstractively-generated citing sentences which are aligned with the provided context and which mention the chosen keyword(s). Our assistive tool for literature discovery and scientific writing is available at https://scilit.vercel.app",
}
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