Auto-Research 1.0

Description:

AutoResearch 1.0

Auto-Research
A no-code utility to generate a detailed well-cited survey with topic clustered sections (draft paper format) and other interesting artifacts from a single research query.
Requires:

python 3.7 or above
poppler-utils
list of requirements in requirements.txt
8GB disk space
13GB CUDA(GPU) memory - for a survey of 100 searched papers(max_search) and 25 selected papers(num_papers)

Steps to run (pip coming soon):
apt install -y poppler-utils libpoppler-cpp-dev
git clone https://github.com/sidphbot/Auto-Research.git

cd Auto-Research/
pip install -r requirements.txt
python Surveyor.py [options] <your_research_query>

Artifacts generated (zipped):

Detailed survey draft paper as txt file
A curated list of top 25+ papers as pdfs and txts
Images extracted from above papers as jpegs, bmps etc
Heading/Section wise highlights extracted from above papers as a re-usable pure python joblib dump
Tables extracted from papers(optional)
Corpus of metadata highlights/text of top 100 papers as a re-usable pure python joblib dump

Example run #1 - python utility
python src/Surveyor.py 'multi-task representation learning'

Example run #2 - python class
from Surveyor import Surveyor
mysurveyor = Surveyor()
mysurveyor.survey('quantum entanglement')

Access/Modify defaults:

inside code

from Surveyor import DEFAULTS
from pprint import pprint

pprint(DEFAULTS)

or,

Modify static config file - defaults.py

or,

At runtime (utility)

python src/Surveyor.py --help

usage: Surveyor.py [-h] [--max_search max_metadata_papers]
[--num_papers max_num_papers] [--pdf_dir pdf_dir]
[--txt_dir txt_dir] [--img_dir img_dir] [--tab_dir tab_dir]
[--dump_dir dump_dir] [--models_dir save_models_dir]
[--title_model_name title_model_name]
[--ex_summ_model_name extractive_summ_model_name]
[--ledmodel_name ledmodel_name]
[--embedder_name sentence_embedder_name]
[--nlp_name spacy_model_name]
[--similarity_nlp_name similarity_nlp_name]
[--kw_model_name kw_model_name]
[--refresh_models refresh_models] [--high_gpu high_gpu]
query_string

Generate a survey just from a query !!

positional arguments:
query_string your research query/keywords

optional arguments:
-h, --help show this help message and exit
--max_search max_metadata_papers
maximium number of papers to gaze at - defaults to 100
--num_papers max_num_papers
maximium number of papers to download and analyse -
defaults to 25
--pdf_dir pdf_dir pdf paper storage directory - defaults to
arxiv_data/tarpdfs/
--txt_dir txt_dir text-converted paper storage directory - defaults to
arxiv_data/fulltext/
--img_dir img_dir image storage directory - defaults to
arxiv_data/images/
--tab_dir tab_dir tables storage directory - defaults to
arxiv_data/tables/
--dump_dir dump_dir all_output_dir - defaults to arxiv_dumps/
--models_dir save_models_dir
directory to save models (> 5GB) - defaults to
saved_models/
--title_model_name title_model_name
title model name/tag in hugging-face, defaults to
'Callidior/bert2bert-base-arxiv-titlegen'
--ex_summ_model_name extractive_summ_model_name
extractive summary model name/tag in hugging-face,
defaults to 'allenai/scibert_scivocab_uncased'
--ledmodel_name ledmodel_name
led model(for abstractive summary) name/tag in
hugging-face, defaults to 'allenai/led-
large-16384-arxiv'
--embedder_name sentence_embedder_name
sentence embedder name/tag in hugging-face, defaults
to 'paraphrase-MiniLM-L6-v2'
--nlp_name spacy_model_name
spacy model name/tag in hugging-face (if changed -
needs to be spacy-installed prior), defaults to
'en_core_sci_scibert'
--similarity_nlp_name similarity_nlp_name
spacy downstream model(for similarity) name/tag in
hugging-face (if changed - needs to be spacy-installed
prior), defaults to 'en_core_sci_lg'
--kw_model_name kw_model_name
keyword extraction model name/tag in hugging-face,
defaults to 'distilbert-base-nli-mean-tokens'
--refresh_models refresh_models
Refresh model downloads with given names (needs
atleast one model name param above), defaults to False
--high_gpu high_gpu High GPU usage permitted, defaults to False




At runtime (code)

during surveyor object initialization with surveyor_obj = Surveyor()


pdf_dir: String, pdf paper storage directory - defaults to arxiv_data/tarpdfs/
txt_dir: String, text-converted paper storage directory - defaults to arxiv_data/fulltext/
img_dir: String, image image storage directory - defaults to arxiv_data/images/
tab_dir: String, tables storage directory - defaults to arxiv_data/tables/
dump_dir: String, all_output_dir - defaults to arxiv_dumps/
models_dir: String, directory to save to huge models, defaults to saved_models/
title_model_name: String, title model name/tag in hugging-face, defaults to Callidior/bert2bert-base-arxiv-titlegen
ex_summ_model_name: String, extractive summary model name/tag in hugging-face, defaults to allenai/scibert_scivocab_uncased
ledmodel_name: String, led model(for abstractive summary) name/tag in hugging-face, defaults to allenai/led-large-16384-arxiv
embedder_name: String, sentence embedder name/tag in hugging-face, defaults to paraphrase-MiniLM-L6-v2
nlp_name: String, spacy model name/tag in hugging-face (if changed - needs to be spacy-installed prior), defaults to en_core_sci_scibert
similarity_nlp_name: String, spacy downstream trained model(for similarity) name/tag in hugging-face (if changed - needs to be spacy-installed prior), defaults to en_core_sci_lg
kw_model_name: String, keyword extraction model name/tag in hugging-face, defaults to distilbert-base-nli-mean-tokens
high_gpu: Bool, High GPU usage permitted, defaults to False
refresh_models: Bool, Refresh model downloads with given names (needs atleast one model name param above), defaults to False


during survey generation with surveyor_obj.survey(query="my_research_query")


max_search: int maximium number of papers to gaze at - defaults to 100
num_papers: int maximium number of papers to download and analyse - defaults to 25