robotreviewer
Automatic synthesis of RCTs
File Explorer
Download Latest Version (.zip)- Dockerfile
- rabbitmq.conf
- __init__.py
- robotreviewer_api.yml
- bias_doc_level.npz
- bias_sent_level.npz
- bias_ab.npz
- bias_prob_clf.pck
- domain_clf.pck
- overall_clf.pck
- drugbank.pck
- human_models.pck
- .gitattributes
- AC.hdf5
- AC.json
- BOA.hdf5
- BOA.json
- BPP.hdf5
- BPP.json
- rationale.h5
- RSG.hdf5
- RSG.json
- .gitattributes
- AC.pickle
- BOA.pickle
- BPP.pickle
- rationale.p
- RSG.pickle
- cui_subtrees.pck
- cui_to_mh.pck
- cui_to_mh_supp.pck
- cui_to_str.pck
- cui_to_str_supp.pck
- ignorelist.txt
- prepositions_conjunctions.txt
- str_to_cui.pck
- str_to_cui_supp.pck
- subtrees.pck
- architecture.json
- intervention-PCA.pickle
- weights.h5
- architecture.json
- outcomes-PCA.pickle
- weights.h5
- architecture.json
- population-PCA.pickle
- weights.h5
- abstracts.p
- I_idf.npz
- I_model.npz
- O_idf.npz
- O_model.npz
- P_idf.npz
- P_model.npz
- .data-00000-of-00001
- .index
- .meta
- checkpoint
- chars.txt
- embeddings.200d.trimmed.npz
- tags.txt
- words.txt
- pubmed_index_2016_07_24.npz
- pubmed_rcts_2016_07_24.sqlite
- pubmed_title_hash_2016_07_24.npz
- inference.weights.best.hdf5
- inference_model.json
- punchline.weights.best.hdf5
- punchline_model.json
- cnn0.h5
- cnn1.h5
- cnn2.h5
- cnn3.h5
- cnn4.h5
- cnn5.h5
- cnn6.h5
- cnn7.h5
- cnn8.h5
- cnn9.h5
- cnn_vocab_map.pck
- pubmed_expected.json
- pubmed_test.txt
- rct_model_calibration.json
- rct_model_calibration.txt
- rct_svm_weights.npz
- svm_cnn_calibration.pck
- svm_cnn_ptyp_calibration.pck
- preprocessor.pickle
- sample_size_model_architecture.json
- sample_size_weights.hdf5
- .gitkeep
- uploaded_pdfs.sqlite
- __init__.py
- drugbank.py
- __init__.py
- classifier.py
- index_numbers.py
- ner_base_model.py
- ner_config.py
- ner_data_utils.py
- ner_general_utils.py
- ner_model.py
- punchline_extractor.py
- rationale_CNN.py
- sample_size_NN.py
- vectorizer.py
- __init__.py
- ris.py
- __init__.py
- bias_ab_robot.py
- bias_robot.py
- human_robot.py
- inference_robot.py
- mendeley_robot.py
- mesh_robot.py
- pico_robot.py
- pico_span_robot.py
- pico_viz_robot.py
- pubmed_robot.py
- punchlines_robot.py
- rationale_robot.py
- rct_robot.py
- sample_size_robot.py
- main.css
- report.css
- example.pdf
- .gitkeep
- infinity.gif
- infinity.svg
- logo.svg
- breadcrumbs.jsx
- breadcrumbs.js
- foundation.css
- main.css
- normalize.css
- style.css
- .gitkeep
- loading-spin.svg
- annotate.jsx
- document.jsx
- editable.jsx
- marginalia.jsx
- minimap.jsx
- page.jsx
- fileUtil.js
- textLayerBuilder.js
- textUtil.js
- annotation.js
- document.js
- marginalia.js
- COPYING
- diff_match_patch_uncompressed.js
- README.md
- README.upstream.txt
- fuzzytext.js
- text_match_engines.js
- text_searcher.js
- 78-EUC-H.bcmap
- 78-EUC-V.bcmap
- 78-H.bcmap
- 78-RKSJ-H.bcmap
- 78-RKSJ-V.bcmap
- 78-V.bcmap
- 78ms-RKSJ-H.bcmap
- 78ms-RKSJ-V.bcmap
- 83pv-RKSJ-H.bcmap
- 90ms-RKSJ-H.bcmap
- 90ms-RKSJ-V.bcmap
- 90msp-RKSJ-H.bcmap
- 90msp-RKSJ-V.bcmap
- 90pv-RKSJ-H.bcmap
- 90pv-RKSJ-V.bcmap
- Add-H.bcmap
- Add-RKSJ-H.bcmap
- Add-RKSJ-V.bcmap
- Add-V.bcmap
- Adobe-CNS1-0.bcmap
- Adobe-CNS1-1.bcmap
- Adobe-CNS1-2.bcmap
- Adobe-CNS1-3.bcmap
- Adobe-CNS1-4.bcmap
- Adobe-CNS1-5.bcmap
- Adobe-CNS1-6.bcmap
- Adobe-CNS1-UCS2.bcmap
- Adobe-GB1-0.bcmap
- Adobe-GB1-1.bcmap
- Adobe-GB1-2.bcmap
- Adobe-GB1-3.bcmap
- Adobe-GB1-4.bcmap
- Adobe-GB1-5.bcmap
- Adobe-GB1-UCS2.bcmap
- Adobe-Japan1-0.bcmap
- Adobe-Japan1-1.bcmap
- Adobe-Japan1-2.bcmap
- Adobe-Japan1-3.bcmap
- Adobe-Japan1-4.bcmap
- Adobe-Japan1-5.bcmap
- Adobe-Japan1-6.bcmap
- Adobe-Japan1-UCS2.bcmap
- Adobe-Korea1-0.bcmap
- Adobe-Korea1-1.bcmap
- Adobe-Korea1-2.bcmap
- Adobe-Korea1-UCS2.bcmap
- B5-H.bcmap
- B5-V.bcmap
- B5pc-H.bcmap
- B5pc-V.bcmap
- CNS-EUC-H.bcmap
- CNS-EUC-V.bcmap
- CNS1-H.bcmap
- CNS1-V.bcmap
- CNS2-H.bcmap
- CNS2-V.bcmap
- ETen-B5-H.bcmap
- ETen-B5-V.bcmap
- ETenms-B5-H.bcmap
- ETenms-B5-V.bcmap
- ETHK-B5-H.bcmap
- ETHK-B5-V.bcmap
- EUC-H.bcmap
- EUC-V.bcmap
- Ext-H.bcmap
- Ext-RKSJ-H.bcmap
- Ext-RKSJ-V.bcmap
- Ext-V.bcmap
- GB-EUC-H.bcmap
- GB-EUC-V.bcmap
- GB-H.bcmap
- GB-V.bcmap
- GBK-EUC-H.bcmap
- GBK-EUC-V.bcmap
- GBK2K-H.bcmap
- GBK2K-V.bcmap
- GBKp-EUC-H.bcmap
- GBKp-EUC-V.bcmap
- GBpc-EUC-H.bcmap
- GBpc-EUC-V.bcmap
- GBT-EUC-H.bcmap
- GBT-EUC-V.bcmap
- GBT-H.bcmap
- GBT-V.bcmap
- GBTpc-EUC-H.bcmap
- GBTpc-EUC-V.bcmap
- H.bcmap
- Hankaku.bcmap
- Hiragana.bcmap
- HKdla-B5-H.bcmap
- HKdla-B5-V.bcmap
- HKdlb-B5-H.bcmap
- HKdlb-B5-V.bcmap
- HKgccs-B5-H.bcmap
- HKgccs-B5-V.bcmap
- HKm314-B5-H.bcmap
- HKm314-B5-V.bcmap
- HKm471-B5-H.bcmap
- HKm471-B5-V.bcmap
- HKscs-B5-H.bcmap
- HKscs-B5-V.bcmap
- Katakana.bcmap
- KSC-EUC-H.bcmap
- KSC-EUC-V.bcmap
- KSC-H.bcmap
- KSC-Johab-H.bcmap
- KSC-Johab-V.bcmap
- KSC-V.bcmap
- KSCms-UHC-H.bcmap
- KSCms-UHC-HW-H.bcmap
- KSCms-UHC-HW-V.bcmap
- KSCms-UHC-V.bcmap
- KSCpc-EUC-H.bcmap
- KSCpc-EUC-V.bcmap
- LICENSE
- NWP-H.bcmap
- NWP-V.bcmap
- RKSJ-H.bcmap
- RKSJ-V.bcmap
- Roman.bcmap
- UniCNS-UCS2-H.bcmap
- UniCNS-UCS2-V.bcmap
- UniCNS-UTF16-H.bcmap
- UniCNS-UTF16-V.bcmap
- UniCNS-UTF32-H.bcmap
- UniCNS-UTF32-V.bcmap
- UniCNS-UTF8-H.bcmap
- UniCNS-UTF8-V.bcmap
- UniGB-UCS2-H.bcmap
- UniGB-UCS2-V.bcmap
- UniGB-UTF16-H.bcmap
- UniGB-UTF16-V.bcmap
- UniGB-UTF32-H.bcmap
- UniGB-UTF32-V.bcmap
- UniGB-UTF8-H.bcmap
- UniGB-UTF8-V.bcmap
- UniJIS-UCS2-H.bcmap
- UniJIS-UCS2-HW-H.bcmap
- UniJIS-UCS2-HW-V.bcmap
- UniJIS-UCS2-V.bcmap
- UniJIS-UTF16-H.bcmap
- UniJIS-UTF16-V.bcmap
- UniJIS-UTF32-H.bcmap
- UniJIS-UTF32-V.bcmap
- UniJIS-UTF8-H.bcmap
- UniJIS-UTF8-V.bcmap
- UniJIS2004-UTF16-H.bcmap
- UniJIS2004-UTF16-V.bcmap
- UniJIS2004-UTF32-H.bcmap
- UniJIS2004-UTF32-V.bcmap
- UniJIS2004-UTF8-H.bcmap
- UniJIS2004-UTF8-V.bcmap
- UniJISPro-UCS2-HW-V.bcmap
- UniJISPro-UCS2-V.bcmap
- UniJISPro-UTF8-V.bcmap
- UniJISX0213-UTF32-H.bcmap
- UniJISX0213-UTF32-V.bcmap
- UniJISX02132004-UTF32-H.bcmap
- UniJISX02132004-UTF32-V.bcmap
- UniKS-UCS2-H.bcmap
- UniKS-UCS2-V.bcmap
- UniKS-UTF16-H.bcmap
- UniKS-UTF16-V.bcmap
- UniKS-UTF32-H.bcmap
- UniKS-UTF32-V.bcmap
- UniKS-UTF8-H.bcmap
- UniKS-UTF8-V.bcmap
- V.bcmap
- WP-Symbol.bcmap
- pdf.js
- pdf.worker.js
- backbone.js
- compatibility.js
- fastclick.js
- foundation.js
- immutable.js
- jquery.js
- JSXTransformer.js
- marked.js
- q.js
- react-dev.js
- react-dom.js
- react-dropzone.js
- react-prod.js
- underscore.js
- .gitignore
- LICENSE
- README.org
- document.jsx
- report.jsx
- upload.jsx
- app.js
- jsx.js
- main.js
- modernizr.js
- require.js
- text.js
- build.js
- index.html
- report_elements.html
- reportview.doc
- reportview.html
- after.npy
- before.npy
- kv_transform.npy
- pdf_as_list.txt
- pdffile.json
- pico.json
- pico_viz.json
- pubmedtest.json
- query.json
- rationale_robot_data.json
- rct.json
- run_grobid.txt
- vec_builder.npz
- vector_si.json
- vector_tests.json
- X_data.npz
- __init__.py
- test_app.py
- test_ml.py
- test_robots.py
- test_textprocessing.py
- __init__.py
- minimap.py
- pdfreader.py
- schwartz_hearst.py
- tokenizer.py
- __init__.py
- __main__.py
- app.py
- cnxapp.py
- config.json.example
- config.py
- data_structures.py
- formatting.py
- ml_worker.py
- ris.py
- testing out human tagger code.ipynb
- util.py
- README.md
- sql.sh
- vocab generation.ipynb
- .dockerignore
- .envTemplate
- .gitattributes
- .gitignore
- apt-requirements.txt
- clean_uploaded_pdfs.py
- crontab
- deploy-beta.sh
- deploy-gpu.sh
- deploy.sh
- docker-compose.dev.yml
- docker-compose.gpu.yml
- docker-compose.yml
- Dockerfile
- entrypoint.sh
- LICENSE.txt
- README.md
- robotreviewer_env.yml
- rr.png
- run
- server.py
- server_api.py
- setup.py
- setup.sh
- start-api-gpu.sh
- start-api.sh
- start-beta.sh
- start-gpu.sh
- start.sh
# Installation Guide
1. Get the code
git clone https://github.com/ijmarshall/robotreviewer
Downloads the entire project code from GitHub to your computer.
cd robotreviewer
Moves into the project folder you just downloaded.
2. Official Install Script
Easy RecommendedPrerequisites
- Python 3 Python is required to use pip.
pip install tensorflow==1.12.0 # OR
Installs the package published on PyPI directly β no need to clone the source.
pip install tensorflow-gpu==1.12.0
Installs the package published on PyPI directly β no need to clone the source.
After installing, open a new terminal and run the program's version command (e.g. --version) to confirm it worked.
Pulled directly from this repo's README.
3. Docker
EasyPrerequisites
- Git Needed to download the project code from GitHub.
- Docker Desktop Needed to build and run containers. Install it and keep it running in the background.
docker-compose build
Runs the command against the services defined in the compose file.
docker-compose up -d
Runs the command against the services defined in the compose file.
docker-compose down --remove-orphans
Runs the command against the services defined in the compose file.
docker run -it --rm --gpus all ubuntu nvidia-smi
Runs the built image as an actual container.
docker-compose -f docker-compose.gpu.yml build
Runs the command against the services defined in the compose file.
Run docker compose ps to check the containers are Up. If the README mentions a port, open http://localhost:PORT in your browser.
Pulled directly from this repo's README.
4. Python
EasyPrerequisites
python -m spacy download en
Runs the Python script (or module).
python -m nltk.downloader punkt stopwords
Runs the Python script (or module).
pip install tensorflow==1.12.0 # OR
Installs the package published on PyPI directly β no need to clone the source.
pip install tensorflow-gpu==1.12.0
Installs the package published on PyPI directly β no need to clone the source.
If it runs without errors and prints output in the terminal, it worked.
Pulled directly from this repo's README.
// repository documentation
Was this content helpful?
(0 ratings)