This is a pan-cancer platform for mutation prediction from routine histology by the Kather lab (http://kather.ai). It is implemented in MATLAB and requires version R2019a+ (for some types of visualization, R2019b+; the code is tested up to R2020b). The following Matlab toolboxes are required: Image processing toolbox, Deep learning toolbox, Parallel processing toolbox; also, shufflenet model from the Matlab Add-On manager.
Briefly, to use these scripts, you should
- prepare your data according to the Aachen protocol as described here: https://zenodo.org/record/3694994
- prepare an "experiment file" which specifies the name of the project, the location of the tiles and the targets to be predicted
- run autoDeepLearn('experiment','') to run a cross-validated experiment
- visualize the results with autoVisualize('experiment','')
An example for a possible data structure (project TCGA-CRC-DX) is:
- experiment file 'tcga-crc-generated' is located in './experiments'
- CLINI table 'TCGA-CRC-DX_CLINI.xlsx' is located in './cliniData' and has a column called PATIENT
- SLIDE table 'TCGA-CRC-DX_SLIDE.csv' is located in './cliniData' and has a column called PATIENT and a column called FILENAME
- image tiles were generated with QuPath, are named according to the Aachen protocol and are located at 'E:/TCGA-CRC-DX/BLOCKS/'
This project is constantly evolving and is being updated regularly. To reproduce our previous research findings, you can use "frozen" releases of the code.
- v0.2 was used for the project "Pan-cancer image-based detection of clinically actionable genetic alterations"
more info: https://github.com/jnkather/DeepHistology/releases
This is the main function for training networks and to evaluate networks via cross-validation.
| Argument | Default Value | Description |
|---|---|---|
| experiment | '' | which experiment to load |
| gpuDev | 1 | GPU Device (1 or greater) |
| maxBlockNum | 1000 | number of blocks (tiles) per whole slide image, upper limit for computational efficiency, applies in any mode (xval, deploy, train-test, ...) |
| trainFull | false | train on full dataset after xval |
| modelTemplate | shufflenet512 | which pretrained model, possible options are defined in getAndModifyNet() |
| backwards | false | for each experiment, work backwards in the list of targets |
| binarizeQuantile | [] | split high/low at this quantile, possible options: floating point number between 0 and 0.5 or empty (use mean) |
| foldxval | 3 | if cross validation is used, this is the fold, possible option: any positive integer. If this is 0, no cross validation will be done. |
| aggregateMode | majority | how to pool block predictions per patient, possible otions: 'majority', 'ignoreClass' (variant of majority, see below), 'mean' or 'max' |
| tableModeClini | XLSX | file format of clinical table, XLSX or CSV |
| hyper | default | set of hyperparameters as defined in getDeepHyperparameters(), possible options: default, lowresource or verylowresource |
| valSet | [] | validation set proportion of training set to stop training early |
| filterBlocks | can be 'normalized' or 'stroma' or 'tumor' for specific training tasks. Default: empty. | |
| subsetTargetsBy | [] | subset the patients by a variable |
| subsetTargetsLevel | [] | subset the patients by this level in the variable |
| skipExistingTargets | false | skip target prediction if result file exists |
| forgiveError | false | ignore errors during training and go on to the next task |
| maxBlocksPerClass | 1e9 | hard limit on the number of tiles per class, with default this will never be reached; if you set this to lower values this will enforce additional random undersampling (in xval mode only!) |
| nBootstrapAUC | 10 | bootstrap number to calculate AUROC confidence intervals |
| whichIgnoreClass | '' | ignore this class for score calculation (e.g. this is a neutral class such as "no_tumor".) This will NOT be used as a negative class for all the other classes. Only works if aggregateMode == ignoreClass |
This function will use a trained network and allows to deploy it on a different patient cohort.
| Argument | Default Value | Description |
|---|---|---|
| trainedModelID | [] | use a previously trained model for deployment |
| trainedModelFolder | [] | path to previously trained model for deployment |
This function will load results from the 'DUMP' folder and create plots.
| Argument | Default Value | Description |
|---|---|---|
| doPlot | false | show the ROC curve on screen |
| doPrint | false | save the ROC to PDF and Imgs to PNG |
| plotThreshold | false | plot the operating threshold on top |
| exportBlockPred | false | save CSV file for maps |
| exportTopTiles | 0 | save top tiles |
| topPatients | 3 | showcase tiles from these patients |
| plotFontSize | 12 | font size for plots |
| saveFormat | v6 | version of results file (debug only) |
| plotAUCthreshold | 0.75 | detailed visualization only for high performance targets |
| onlyExplicitTargets | true | visualize only targets specified in experiment file |
| debugMode | false | debug mode |
This function will normalize tile images with the Macenko method. Caution: This function relies on third party subroutines in "./subroutines_normalization" - please observe the third party license in that sub-folder.
| Argument | Default Value | Description |
|---|---|---|
| experiment | '' | name of the experiment file |
| numParWorkers | 1 | number of parallel CPUs (requires Parallel Processing Toolbox) |
See separate License file which applies to all files within this repository unless noted otherwise. Please note that some functions in the subroutine folder are from third party sources and have their own license included in the file.
Get in touch at https://jnkather.github.io/contact/
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