LICENSE
README.md
pyproject.toml
deepmirt/__init__.py
deepmirt/predict.py
deepmirt.egg-info/PKG-INFO
deepmirt.egg-info/SOURCES.txt
deepmirt.egg-info/dependency_links.txt
deepmirt.egg-info/entry_points.txt
deepmirt.egg-info/requires.txt
deepmirt.egg-info/top_level.txt
deepmirt/data_module/__init__.py
deepmirt/data_module/datamodule.py
deepmirt/data_module/dataset.py
deepmirt/data_module/preprocessing.py
deepmirt/evaluation/__init__.py
deepmirt/evaluation/bias_analysis.py
deepmirt/evaluation/calibration.py
deepmirt/evaluation/comparison.py
deepmirt/evaluation/error_analysis.py
deepmirt/evaluation/metrics.py
deepmirt/evaluation/predict.py
deepmirt/evaluation/run_full_evaluation.py
deepmirt/evaluation/stratified_eval.py
deepmirt/evaluation/visualization.py
deepmirt/model/__init__.py
deepmirt/model/classifier.py
deepmirt/model/cross_attention.py
deepmirt/model/mirna_target_model.py
deepmirt/model/rnafm_encoder.py
deepmirt/pipeline/__init__.py
deepmirt/pipeline/build_curriculum_splits.py
deepmirt/pipeline/build_training_pairs.py
deepmirt/pipeline/dedup_training_splits.py
deepmirt/pipeline/download_3utr_sequences.py
deepmirt/pipeline/download_cdna_sequences.py
deepmirt/pipeline/extract_clashub.py
deepmirt/pipeline/extract_mirbench.py
deepmirt/pipeline/extract_mirtarbase.py
deepmirt/pipeline/extract_mirtarclash.py
deepmirt/pipeline/extract_tarbase.py
deepmirt/pipeline/extract_targetscan.py
deepmirt/pipeline/finalize_dataset.py
deepmirt/pipeline/merge_all_sources.py
deepmirt/pipeline/site_utils.py
deepmirt/pipeline/test_download_cdna.py
deepmirt/pipeline/test_n_padding_fix.py
deepmirt/pipeline/literature/01_search_pubmed.py
deepmirt/pipeline/literature/02_screen_abstracts.py
deepmirt/pipeline/literature/03_download_fulltext.py
deepmirt/pipeline/literature/04_pdf_to_text.py
deepmirt/pipeline/literature/05_llm_extract.py
deepmirt/pipeline/literature/06_normalize_and_output.py
deepmirt/pipeline/literature/__init__.py
deepmirt/pipeline/literature/llm_client.py
deepmirt/pipeline/literature/prompts.py
deepmirt/scanning/__init__.py
deepmirt/scanning/_utils.py
deepmirt/scanning/output_formatter.py
deepmirt/scanning/scanner.py
deepmirt/scanning/site_finder.py
deepmirt/tests/__init__.py
deepmirt/tests/test_literature_download.py
deepmirt/tests/test_literature_extract.py
deepmirt/tests/test_literature_llm_client.py
deepmirt/tests/test_literature_normalize.py
deepmirt/tests/test_literature_pdf_parse.py
deepmirt/tests/test_literature_screen.py
deepmirt/tests/test_literature_search.py
deepmirt/tests/test_smoke.py
deepmirt/tests/test_split_leakage.py
deepmirt/tests/test_unit.py
deepmirt/training/__init__.py
deepmirt/training/callbacks.py
deepmirt/training/lightning_module.py
deepmirt/training/train.py