├── .env ├── .gitattributes ├── .gitignore ├── LICENSE ├── README.md ├── configs ├── callbacks │ ├── default.yaml │ ├── early_stopping.yaml │ ├── model_checkpoint.yaml │ ├── model_summary.yaml │ ├── none.yaml │ └── rich_progress_bar.yaml ├── datamodule │ └── multiplex.yaml ├── debug │ ├── default.yaml │ ├── fdr.yaml │ ├── limit.yaml │ ├── overfit.yaml │ └── profiler.yaml ├── eval.yaml ├── experiment │ └── example.yaml ├── extras │ └── default.yaml ├── hparams_search │ └── mnist_optuna.yaml ├── hydra │ └── default.yaml ├── local │ └── .gitkeep ├── logger │ ├── comet.yaml │ ├── csv.yaml │ ├── many_loggers.yaml │ ├── mlflow.yaml │ ├── neptune.yaml │ ├── tensorboard.yaml │ └── wandb.yaml ├── model │ ├── classifier.yaml │ ├── contrastive.yaml │ └── mnist.yaml ├── paths │ ├── default.yaml │ ├── klone.yaml │ ├── l0.yaml │ ├── l2lambda.yaml │ └── l3.yaml ├── train.yaml └── trainer │ ├── cpu.yaml │ ├── ddp.yaml │ ├── ddp_sim.yaml │ ├── deepspeed.yaml │ ├── default.yaml │ ├── dp.yaml │ ├── fsdp.yaml │ ├── fsdp_native.yaml │ ├── gpu.yaml │ └── mps.yaml ├── data ├── pubmed │ └── search_query.csv └── textbook │ └── template.config.json ├── experiments ├── .gitkeep ├── compare scale.ipynb ├── compare_manual.ipynb ├── concept_annotation.ipynb ├── data_auditing.ipynb ├── inherently_interpretable_model.ipynb └── model_auditing.ipynb ├── requirements-dev.txt ├── requirements.txt ├── scripts ├── preprocess │ ├── prepare_derm7pt.sh │ ├── prepare_ham10k.sh │ ├── prepare_isic.sh │ ├── prepare_proveai.sh │ ├── preprocess_ddi.sh │ ├── preprocess_fitzpatrick17k.sh │ ├── preprocess_fitzpatrick17k_clean.ipynb │ ├── preprocess_pdf.sh │ ├── preprocess_pubmed.sh │ ├── remove_duplicate.ipynb │ ├── remove_duplicates_fitzpatrick17k.ipynb │ └── remove_train_overlap.ipynb └── train │ ├── RN.sh │ ├── ViTB_32.sh │ ├── ViTL_14.sh │ └── classifier.sh ├── src ├── MONET │ ├── __init__.py │ ├── datamodules │ │ ├── __init__.py │ │ ├── components │ │ │ ├── __init__.py │ │ │ └── base_dataset.py │ │ ├── multiplex_datamodule.py │ │ └── setup_dataset.py │ ├── models │ │ ├── classifier_module.py │ │ ├── classifier_utils.py │ │ ├── components │ │ │ ├── image_classifier.py │ │ │ └── image_text_encoder.py │ │ └── contrastive_module.py │ ├── preprocess │ │ ├── __init__.py │ │ ├── cluster.py │ │ ├── deprecated │ │ │ ├── pubmed_match.py │ │ │ └── reference_similarity.py │ │ ├── divide.py │ │ ├── featurize.py │ │ ├── filter.py │ │ ├── glob_files.py │ │ ├── image_sanity_check.py │ │ ├── merge_files.py │ │ ├── pdf_extract.py │ │ ├── pdf_match.py │ │ ├── pubmed_download.py │ │ ├── pubmed_match.py │ │ ├── pubmed_search.py │ │ ├── save_as_binary.py │ │ └── save_as_path.py │ └── utils │ │ ├── __init__.py │ │ ├── io.py │ │ ├── loader.py │ │ ├── metrics.py │ │ ├── plotting.py │ │ ├── static.py │ │ └── text_processing.py ├── __init__.py ├── clip │ ├── __init__.py │ ├── bpe_simple_vocab_16e6.txt.gz │ ├── clip.py │ ├── model.py │ └── simple_tokenizer.py ├── eval.py ├── plugins │ └── __init__.py ├── train.py └── utils │ ├── __init__.py │ ├── pylogger.py │ ├── rich_utils.py │ └── utils.py └── tutorial └── automatic_concept_annotation.ipynb /.env: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/.env -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/.gitattributes -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/README.md -------------------------------------------------------------------------------- /configs/callbacks/default.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/callbacks/default.yaml -------------------------------------------------------------------------------- /configs/callbacks/early_stopping.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/callbacks/early_stopping.yaml -------------------------------------------------------------------------------- /configs/callbacks/model_checkpoint.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/callbacks/model_checkpoint.yaml -------------------------------------------------------------------------------- /configs/callbacks/model_summary.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/callbacks/model_summary.yaml -------------------------------------------------------------------------------- /configs/callbacks/none.yaml: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /configs/callbacks/rich_progress_bar.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/callbacks/rich_progress_bar.yaml -------------------------------------------------------------------------------- /configs/datamodule/multiplex.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/datamodule/multiplex.yaml -------------------------------------------------------------------------------- /configs/debug/default.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/debug/default.yaml -------------------------------------------------------------------------------- /configs/debug/fdr.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/debug/fdr.yaml -------------------------------------------------------------------------------- /configs/debug/limit.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/debug/limit.yaml -------------------------------------------------------------------------------- /configs/debug/overfit.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/debug/overfit.yaml -------------------------------------------------------------------------------- /configs/debug/profiler.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/debug/profiler.yaml -------------------------------------------------------------------------------- /configs/eval.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/eval.yaml -------------------------------------------------------------------------------- /configs/experiment/example.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/experiment/example.yaml -------------------------------------------------------------------------------- /configs/extras/default.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/extras/default.yaml -------------------------------------------------------------------------------- /configs/hparams_search/mnist_optuna.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/hparams_search/mnist_optuna.yaml -------------------------------------------------------------------------------- /configs/hydra/default.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/hydra/default.yaml -------------------------------------------------------------------------------- /configs/local/.gitkeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /configs/logger/comet.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/logger/comet.yaml -------------------------------------------------------------------------------- /configs/logger/csv.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/logger/csv.yaml -------------------------------------------------------------------------------- /configs/logger/many_loggers.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/logger/many_loggers.yaml -------------------------------------------------------------------------------- /configs/logger/mlflow.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/logger/mlflow.yaml -------------------------------------------------------------------------------- /configs/logger/neptune.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/logger/neptune.yaml -------------------------------------------------------------------------------- /configs/logger/tensorboard.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/logger/tensorboard.yaml -------------------------------------------------------------------------------- /configs/logger/wandb.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/logger/wandb.yaml -------------------------------------------------------------------------------- /configs/model/classifier.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/model/classifier.yaml -------------------------------------------------------------------------------- /configs/model/contrastive.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/model/contrastive.yaml -------------------------------------------------------------------------------- /configs/model/mnist.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/model/mnist.yaml -------------------------------------------------------------------------------- /configs/paths/default.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/paths/default.yaml -------------------------------------------------------------------------------- /configs/paths/klone.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/paths/klone.yaml -------------------------------------------------------------------------------- /configs/paths/l0.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/paths/l0.yaml -------------------------------------------------------------------------------- /configs/paths/l2lambda.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/paths/l2lambda.yaml -------------------------------------------------------------------------------- /configs/paths/l3.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/paths/l3.yaml -------------------------------------------------------------------------------- /configs/train.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/train.yaml -------------------------------------------------------------------------------- /configs/trainer/cpu.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/trainer/cpu.yaml -------------------------------------------------------------------------------- /configs/trainer/ddp.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/trainer/ddp.yaml -------------------------------------------------------------------------------- /configs/trainer/ddp_sim.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/trainer/ddp_sim.yaml -------------------------------------------------------------------------------- /configs/trainer/deepspeed.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/trainer/deepspeed.yaml -------------------------------------------------------------------------------- /configs/trainer/default.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/trainer/default.yaml -------------------------------------------------------------------------------- /configs/trainer/dp.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/trainer/dp.yaml -------------------------------------------------------------------------------- /configs/trainer/fsdp.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/trainer/fsdp.yaml -------------------------------------------------------------------------------- /configs/trainer/fsdp_native.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/trainer/fsdp_native.yaml -------------------------------------------------------------------------------- /configs/trainer/gpu.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/trainer/gpu.yaml -------------------------------------------------------------------------------- /configs/trainer/mps.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/configs/trainer/mps.yaml -------------------------------------------------------------------------------- /data/pubmed/search_query.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/data/pubmed/search_query.csv -------------------------------------------------------------------------------- /data/textbook/template.config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/data/textbook/template.config.json -------------------------------------------------------------------------------- /experiments/.gitkeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /experiments/compare scale.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/experiments/compare scale.ipynb -------------------------------------------------------------------------------- /experiments/compare_manual.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/experiments/compare_manual.ipynb -------------------------------------------------------------------------------- /experiments/concept_annotation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/experiments/concept_annotation.ipynb -------------------------------------------------------------------------------- /experiments/data_auditing.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/experiments/data_auditing.ipynb -------------------------------------------------------------------------------- /experiments/inherently_interpretable_model.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/experiments/inherently_interpretable_model.ipynb -------------------------------------------------------------------------------- /experiments/model_auditing.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/experiments/model_auditing.ipynb -------------------------------------------------------------------------------- /requirements-dev.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/requirements-dev.txt -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/requirements.txt -------------------------------------------------------------------------------- /scripts/preprocess/prepare_derm7pt.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/scripts/preprocess/prepare_derm7pt.sh -------------------------------------------------------------------------------- /scripts/preprocess/prepare_ham10k.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/scripts/preprocess/prepare_ham10k.sh -------------------------------------------------------------------------------- /scripts/preprocess/prepare_isic.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/scripts/preprocess/prepare_isic.sh -------------------------------------------------------------------------------- /scripts/preprocess/prepare_proveai.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/scripts/preprocess/prepare_proveai.sh -------------------------------------------------------------------------------- /scripts/preprocess/preprocess_ddi.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/scripts/preprocess/preprocess_ddi.sh -------------------------------------------------------------------------------- /scripts/preprocess/preprocess_fitzpatrick17k.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/scripts/preprocess/preprocess_fitzpatrick17k.sh -------------------------------------------------------------------------------- /scripts/preprocess/preprocess_fitzpatrick17k_clean.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/scripts/preprocess/preprocess_fitzpatrick17k_clean.ipynb -------------------------------------------------------------------------------- /scripts/preprocess/preprocess_pdf.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/scripts/preprocess/preprocess_pdf.sh -------------------------------------------------------------------------------- /scripts/preprocess/preprocess_pubmed.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/scripts/preprocess/preprocess_pubmed.sh -------------------------------------------------------------------------------- /scripts/preprocess/remove_duplicate.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/scripts/preprocess/remove_duplicate.ipynb -------------------------------------------------------------------------------- /scripts/preprocess/remove_duplicates_fitzpatrick17k.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/scripts/preprocess/remove_duplicates_fitzpatrick17k.ipynb -------------------------------------------------------------------------------- /scripts/preprocess/remove_train_overlap.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/scripts/preprocess/remove_train_overlap.ipynb -------------------------------------------------------------------------------- /scripts/train/RN.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/scripts/train/RN.sh -------------------------------------------------------------------------------- /scripts/train/ViTB_32.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/scripts/train/ViTB_32.sh -------------------------------------------------------------------------------- /scripts/train/ViTL_14.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/scripts/train/ViTL_14.sh -------------------------------------------------------------------------------- /scripts/train/classifier.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/scripts/train/classifier.sh -------------------------------------------------------------------------------- /src/MONET/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/MONET/datamodules/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/MONET/datamodules/components/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/MONET/datamodules/components/base_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/datamodules/components/base_dataset.py -------------------------------------------------------------------------------- /src/MONET/datamodules/multiplex_datamodule.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/datamodules/multiplex_datamodule.py -------------------------------------------------------------------------------- /src/MONET/datamodules/setup_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/datamodules/setup_dataset.py -------------------------------------------------------------------------------- /src/MONET/models/classifier_module.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/models/classifier_module.py -------------------------------------------------------------------------------- /src/MONET/models/classifier_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/models/classifier_utils.py -------------------------------------------------------------------------------- /src/MONET/models/components/image_classifier.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/models/components/image_classifier.py -------------------------------------------------------------------------------- /src/MONET/models/components/image_text_encoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/models/components/image_text_encoder.py -------------------------------------------------------------------------------- /src/MONET/models/contrastive_module.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/models/contrastive_module.py -------------------------------------------------------------------------------- /src/MONET/preprocess/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/MONET/preprocess/cluster.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/preprocess/cluster.py -------------------------------------------------------------------------------- /src/MONET/preprocess/deprecated/pubmed_match.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/preprocess/deprecated/pubmed_match.py -------------------------------------------------------------------------------- /src/MONET/preprocess/deprecated/reference_similarity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/preprocess/deprecated/reference_similarity.py -------------------------------------------------------------------------------- /src/MONET/preprocess/divide.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/preprocess/divide.py -------------------------------------------------------------------------------- /src/MONET/preprocess/featurize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/preprocess/featurize.py -------------------------------------------------------------------------------- /src/MONET/preprocess/filter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/preprocess/filter.py -------------------------------------------------------------------------------- /src/MONET/preprocess/glob_files.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/preprocess/glob_files.py -------------------------------------------------------------------------------- /src/MONET/preprocess/image_sanity_check.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/preprocess/image_sanity_check.py -------------------------------------------------------------------------------- /src/MONET/preprocess/merge_files.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/preprocess/merge_files.py -------------------------------------------------------------------------------- /src/MONET/preprocess/pdf_extract.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/preprocess/pdf_extract.py -------------------------------------------------------------------------------- /src/MONET/preprocess/pdf_match.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/preprocess/pdf_match.py -------------------------------------------------------------------------------- /src/MONET/preprocess/pubmed_download.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/preprocess/pubmed_download.py -------------------------------------------------------------------------------- /src/MONET/preprocess/pubmed_match.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/preprocess/pubmed_match.py -------------------------------------------------------------------------------- /src/MONET/preprocess/pubmed_search.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/preprocess/pubmed_search.py -------------------------------------------------------------------------------- /src/MONET/preprocess/save_as_binary.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/preprocess/save_as_binary.py -------------------------------------------------------------------------------- /src/MONET/preprocess/save_as_path.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/preprocess/save_as_path.py -------------------------------------------------------------------------------- /src/MONET/utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/MONET/utils/io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/utils/io.py -------------------------------------------------------------------------------- /src/MONET/utils/loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/utils/loader.py -------------------------------------------------------------------------------- /src/MONET/utils/metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/utils/metrics.py -------------------------------------------------------------------------------- /src/MONET/utils/plotting.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/utils/plotting.py -------------------------------------------------------------------------------- /src/MONET/utils/static.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/utils/static.py -------------------------------------------------------------------------------- /src/MONET/utils/text_processing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/MONET/utils/text_processing.py -------------------------------------------------------------------------------- /src/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/clip/__init__.py: -------------------------------------------------------------------------------- 1 | from .clip import available_models, load, tokenize 2 | -------------------------------------------------------------------------------- /src/clip/bpe_simple_vocab_16e6.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/clip/bpe_simple_vocab_16e6.txt.gz -------------------------------------------------------------------------------- /src/clip/clip.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/clip/clip.py -------------------------------------------------------------------------------- /src/clip/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/clip/model.py -------------------------------------------------------------------------------- /src/clip/simple_tokenizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/clip/simple_tokenizer.py -------------------------------------------------------------------------------- /src/eval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/eval.py -------------------------------------------------------------------------------- /src/plugins/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/plugins/__init__.py -------------------------------------------------------------------------------- /src/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/train.py -------------------------------------------------------------------------------- /src/utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/utils/__init__.py -------------------------------------------------------------------------------- /src/utils/pylogger.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/utils/pylogger.py -------------------------------------------------------------------------------- /src/utils/rich_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/utils/rich_utils.py -------------------------------------------------------------------------------- /src/utils/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/src/utils/utils.py -------------------------------------------------------------------------------- /tutorial/automatic_concept_annotation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/MONET/HEAD/tutorial/automatic_concept_annotation.ipynb --------------------------------------------------------------------------------