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AUCMEDI: a framework for Automated Classification of Medical Images

Authors: Müller, Dominik; Mayer, Simone; Hartmann, Dennis; Meyer, Philip; Schneider, Pia; Soto-Rey, Iñaki; Kramer, Frank;

AUCMEDI: a framework for Automated Classification of Medical Images

Abstract

:sparkles: New Features 21323b5 - Ensemble: Implemented Composite (cross-validation based stacking) (commit by @muellerdo) 20f61f4 - AutoML: Implemented function block - training (commit by @muellerdo) 099e105 - AutoML: Added multilabel support for function block training (commit by @muellerdo) 74fcfbd - AutoML: added metadata storing in training block (commit by @muellerdo) 5fab10a - AutoML: Implemented function block prediction (commit by @muellerdo) 2a2e9e9 - AutoML: Implemented XAI option in code block inference (commit by @muellerdo) 5b4c095 - Evaluation: added support for transfer learning in fitting evaluation (commit by @muellerdo) 47aff85 - AutoML: added evaluation plot generation in block function training (commit by @muellerdo) fad6f2d - AutoML: implemented block function evaluation (commit by @muellerdo) f7ccf82 - AutoML: Added CLI parser for Training (commit by @muellerdo) c521785 - AutoML: added CLI interface for YAML (commit by @muellerdo) 0b52a90 - AutoML: added CLI interface for prediction (commit by @muellerdo) 6a54157 - AutoML: added CLI interface for evaluation (commit by @muellerdo) 2f90edd - AutoML: added more sanity checks to evaluation function block (commit by @muellerdo) 7f66f48 - performance: add display option for charts (commit by @SherlockMones) 87ae17a - io_interfaces: add file extension to index_list (commit by @SherlockMones) 2d563b0 - AutoML: added binary packaging via entry script (commit by @muellerdo) 2c5ac70 - data_processing: Improve documentation (commit by @SherlockMones) 3566791 - AutoML: reworked AutoML CLI arguments - closes #151 (commit by @muellerdo) 96c8d44 - AutoML: dockerized AUCMEDI AutoML - closes #150 (commit by @muellerdo) c53819f - evaluation: display fitting progress (commit by @SherlockMones) 4711894 - Evaluation: added full transfer learning support for fitting evaluation - closes #157 (commit by @muellerdo) cbc2510 - Stacking: added automated standardize and resize parameter estimation for DataGenerator (commit by @muellerdo) :bug: Bug Fixes ea04aad - Ensemble: Added missing library import in Stacking & Bagging (commit by @muellerdo) cc53a57 - AutoML: changed incorrect grayscale parameter of DataGenerator in training function block (commit by @muellerdo) 8b973d2 - AutoML: some hotfixes for AutoML XAI support (commit by @muellerdo) 7c78357 - AutoML: incorrect output path as directory creation (commit by @muellerdo) 4a23572 - AutoML: added more config parsing for CLI (3D shape, input and output path) (commit by @muellerdo) c31355d - Evaluation: catch no-possible AUROC computation (commit by @muellerdo) f4b165c - AutoML: fixed multiple architecture passing for advanced training (commit by @muellerdo) 6729798 - Evaluation: fixed unequal length of training epochs by multi model pipelines (commit by @muellerdo) c5f9712 - AutoML: forget to exluce yaml parser function in main runner (commit by @muellerdo) 05169cf - XAI: added missing inverse of occlusion sensitivity heatmap (commit by @muellerdo) 87e3f9d - evaluation: fix evaluate training charts (commit by @SherlockMones) e474282 - Evaluation: added support for only transfer learning epochs in evaluate_fitting() (commit by @muellerdo) :zap: Performance Improvements c79110f - Ensemble: Replaced python built-in multiprocessing to pathos multiprocessing (commit by @muellerdo) 816fea3 - Ensemble: Re-initialize NeuralNetworks in processes to allow custom loss functions (commit by @muellerdo) ab6c0bc - Ensemble: allow dumping of ensemble output into already existing directories (commit by @muellerdo) d3988a5 - AutoML: Various improvements of the function block training (commit by @muellerdo) e5b8ae2 - AutoML: added sanity checks for multi_label supported metalearners (commit by @muellerdo) 2b9b355 - Evaluation: call explicit categorical parsing of class names for omnious class names (numbers) (commit by @muellerdo) 834799e - AutoML: switched csvlogger to append mode (commit by @muellerdo) 850a6a1 - AutoML: adjusted training hyperparameters of early stopping & dynamicLR (commit by @muellerdo) e3fe4ff - AutoML: increased batch size from 12 to 24 (commit by @muellerdo) 3db0252 - AutoML: increased sensitivity for help page hook (commit by @muellerdo) 2dea1e1 - NeuralNetwork: increased default number of transfer learning epochs to 10 (commit by @muellerdo) :recycle: Refactors dfea756 - AutoML: Changed analysis name from composite to advanced (commit by @muellerdo) 43ccaa1 - AutoML: Removed data augmentation option from config (commit by @muellerdo) cca63ad - AutoML: renamed attribute 'two_dim' to 'three_dim' (commit by @muellerdo) b400348 - AutoML: Introduced new AutoML submodule structure (commit by @muellerdo) e228403 - AutoML: refactored AutoML script structure (commit by @muellerdo) 4a22ed0 - AutoML: added empty script file for yaml parser (commit by @muellerdo) 97adf14 - AutoML: separated main method and runner of AutoML main (commit by @muellerdo) :white_check_mark: Tests c9eae04 - Ensemble: Added unittesting for Composite (commit by @muellerdo) d9b7e58 - Ensemble: removed remaining debugging prints (commit by @muellerdo) 3657ac5 - AutoML: added unittesting for AutoML function block training (commit by @muellerdo) 173d235 - AutoML: Updated some class names and docs (commit by @muellerdo) 6f00ca2 - AutoML: Added unittesting for function block prediction (commit by @muellerdo) 2024f9a - AutoML: Added tests for XAI (commit by @muellerdo) d350858 - AutoML: added unittesting for block function evaluation (commit by @muellerdo) 7733e34 - AutoML: added unittesting for CLI (commit by @muellerdo) a44bf25 - AutoML: removed no argument testing (commit by @muellerdo) 9e75baf - Evaluation: added unittesting for only transfer learning fitting_evaluate() (commit by @muellerdo) 0f068aa - AutoML: test CLI only for build Action (commit by @muellerdo) :construction_worker: Build System 018aed8 - Added pathos as dependency (commit by @muellerdo) 1a76950 - AutoML: fixed a typo in docker release (commit by @muellerdo) f0128d4 - Security: updated Pillow & Tensorflow version (commit by @muellerdo) 4e5da31 - CodeQuality: changed codecov coverage from requirements to setup build (commit by @muellerdo) d0504ac - Updated to version 0.7.0 (commit by

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
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influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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