--- title: Researcher emoji: 🤓 colorFrom: gray colorTo: pink sdk: streamlit sdk_version: 1.2.0 app_file: app.py pinned: false --- # Auto-Research ![Auto-Research][logo] [logo]: https://github.com/sidphbot/Auto-Research/blob/main/logo.png 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. Data Provider: [arXiv](https://arxiv.org/) Open Archive Initiative OAI Requirements: - python 3.7 or above - poppler-utils - `sudo apt-get install build-essential libpoppler-cpp-dev pkg-config python-dev` - list of requirements in requirements.txt - `cat requirements.txt | xargs pip install` - 8GB disk space - 13GB CUDA(GPU) memory - for a survey of 100 searched papers(max_search) and 25 selected papers(num_papers) #### Demo : Video Demo : https://drive.google.com/file/d/1-77J2L10lsW-bFDOGdTaPzSr_utY743g/view?usp=sharing Kaggle Re-usable Demo : https://www.kaggle.com/sidharthpal/auto-research-generate-survey-from-query (`[TIP]` click 'edit and run' to run the demo for your custom queries on a free GPU) #### Installation: ``` sudo apt-get install build-essential poppler-utils libpoppler-cpp-dev pkg-config python-dev pip install git+https://github.com/sidphbot/Auto-Research.git ``` #### Run Survey (cli): ``` python survey.py [options] ``` #### Run Survey (Streamlit web-interface - new): ``` streamlit run app.py ``` #### Run Survey (Python API): ``` from survey import Surveyor mysurveyor = Surveyor() mysurveyor.survey('quantum entanglement') ``` ### Research tools: These are independent tools for your research or document text handling needs. ``` *[Tip]* :(models can be changed in defaults or passed on during init along with `refresh-models=True`) ``` - `abstractive_summary` - takes a long text document (`string`) and returns a 1-paragraph abstract or “abstractive” summary (`string`) Input: `longtext` : string Returns: `summary` : string - `extractive_summary` - takes a long text document (`string`) and returns a 1-paragraph of extracted highlights or “extractive” summary (`string`) Input: `longtext` : string Returns: `summary` : string - `generate_title` - takes a long text document (`string`) and returns a generated title (`string`) Input: `longtext` : string Returns: `title` : string - `extractive_highlights` - takes a long text document (`string`) and returns a list of extracted highlights (`[string]`), a list of keywords (`[string]`) and key phrases (`[string]`) Input: `longtext` : string Returns: `highlights` : [string] `keywords` : [string] `keyphrases` : [string] - `extract_images_from_file` - takes a pdf file name (`string`) and returns a list of image filenames (`[string]`). Input: `pdf_file` : string Returns: `images_files` : [string] - `extract_tables_from_file` - takes a pdf file name (`string`) and returns a list of csv filenames (`[string]`). Input: `pdf_file` : string Returns: `images_files` : [string] - `cluster_lines` - takes a list of lines (`string`) and returns the topic-clustered sections (`dict(generated_title: [cluster_abstract])`) and clustered lines (`dict(cluster_id: [cluster_lines])`) Input: `lines` : [string] Returns: `sections` : dict(generated_title: [cluster_abstract]) `clusters` : dict(cluster_id: [cluster_lines]) - `extract_headings` - *[for scientific texts - Assumes an ‘abstract’ heading present]* takes a text file name (`string`) and returns a list of headings (`[string]`) and refined lines (`[string]`). `[Tip 1]` : Use `extract_sections` as a wrapper (e.g. `extract_sections(extract_headings(“/path/to/textfile”)`) to get heading-wise sectioned text with refined lines instead (`dict( heading: text)`) `[Tip 2]` : write the word ‘abstract’ at the start of the file text to get an extraction for non-scientific texts as well !! Input: `text_file` : string Returns: `refined` : [string], `headings` : [string] `sectioned_doc` : dict( heading: text) (Optional - Wrapper case) ## Access/Modify defaults: - inside code ``` from survey.Surveyor import DEFAULTS from pprint import pprint pprint(DEFAULTS) ``` or, - Modify static config file - `defaults.py` or, - At runtime (utility) ``` python survey.py --help ``` ``` usage: survey.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` #### 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 Please cite this repo if it helped you :)