Spatial Transcriptomics Inferred from Pathology Whole-Slide Images Links Tumor Heterogeneity to Survival in Breast and Lung Cancer

This project contains the source code used in: "Spatial Transcriptomics Inferred from Pathology Whole-Slide Images Links Tumor Heterogeneity to Survival in Breast and Lung Cancer" by Levy-Jurgenson et al.

Note: If you are looking to compute a sample's spatial heterogeneity score or create its heterogeneity maps (e.g. after obtaining predictions using PathoMCH, or using other spatial transcriptomics data such as 10x Visium), we recommend using our HTA python package (see our HTA github page), also described in our HTA paper.

Prerequisites

• Python 3.6

• Tensorflow 1.14.0 (pip3 install tensorflow==1.14.0 or on gpu: pip3 install tensorflow-gpu==1.14.0). Make sure to uninstall other Tensorflow versions first (use uninstall instead of install).

• OpenSlide Python:

  Use installations here: https://openslide.org/download/ or use below example for Ubuntu:

  apt-get install python3-openslide

  and then:

  pip3 install openslide-python

On Google Cloud platform, we specifically used the following settings (adapted to tensorflow 1.14.0):

• For training on GPUs:

  • Operating system: "Deep Learning on Linux"
  • Version: "Deep Learning Image: TensorFlow 1.15.0 m42" (uninstall 1.15 and install 1.14 instead, see prerequisites)
  • Number of K80 GPUs per vm: 8

• For preprocessing (tiling WSIs and creating tfrecords) we used the same settings above with no GPUs, but with 60 CPUs. Less CPUs can be used by changing NUM_CPU in conf.py but this will slow down preprocessing significantly.

Obtaining our pre-trained models / output predictions

We will gladly share pre-trained weights and/or predictions for reasonable requests. Please e-mail us from your institution's e-mail address stating the intended use (levyalona at gmail dot com).
You can easily load them by using your Conf object's LOAD_WEIGHTS_PATH (replace None with the directory that contains only the weights you wish to load, e.g.: ../out/<model_name>/auc/

Training and evaluating models

This section covers the code you will likely need to adapt to your needs. We recommend that you first clone this repository, then try to run it on your PC using the "Training on mock data" section (below) and then start to read through this section so that you can identify, 'hands-on', the different parts of the code that you might need to adapt.

Note that the files under src are in a flattened hierarchy to keep things simple when transitioning between a local environment and linux servers.

There are 5 main files required for training and evaluating a model:

1. conf.py: a useful configuration class where you can create your own Conf object to set parameters for preprocessing and training. We've left our preset Confs for BRCA and LUAD TCGA cohorts as examples. Some parameters you will likely have to adapt to your needs are:

   • CLINICAL_FILEPATH - path to csv that includes a sample ID column and a label column with the name matching CLINICAL_LABEL_COLS
   • CLINICAL_LABEL_COLS - name of column used for labeling. All samples that have labels under this column will be included in model development by default (you can create other label columns to store ground truth for all samples).
   • CLINICAL_LABELS - list of labels to be used out of those under CLINICAL_LABEL_COLS e.g. ['lo','hi']
   • SVS_SLIDES_PATH - path to slides. Default is data->slides->diagnostic.
   • NUM_CPU - number of CPUs available for tiling the slides and generating tfrecords
   • NAME - the prefix name of your models. Use a unique name per trait if you don't want results to get run over between traits.
   • TCGA_COHORT_NAME - controls your out subfolder name. Useful if you're going to be using more than one dataset so results don't get run over.
   • LOAD_WEIGHTS_PATH - should be None unless you are: (a) training from a pre-trained model or (b) obtaining predictions post-training. In these cases None should be replaced with the path to the directory in which your weights reside (e.g. ../out/<model_name>/auc/).

2. preprocess.py: tiles slides (if tile_slides = True) and generates sharded tfrecords of two types:

   (1) Sharded tfrecords for training and validation - this is using your Conf object. These end with '.tfrec' and don't have any specific sample ID in their name.

   (2) Per-sample tfrecords used for per-sample predictions. These are generated using a new configuration, e.g.: c = Conf_BRCA_DUMMY_LABEL() (make sure to have a 'dummy' column in you clinical file which will hold ALL samples' labels). These will end with '.tfrecords' - there will be one per sample in the data. These are used only during inference (when you set training=False in model.py).

   After generating tfrecords, you will have to move the resulting tfrec and tfrecords to your desired location (we used google cloud storage (GCS)), which means you will need to adapt the following paths in conf.py: GCS_PATTERN and GCS_PATTERN_PER_SAMPLE. IMPORTANT: Make sure to save the .pkl files named ..patient_ids..pkl and ..img_paths..pkl as they are used during evaluation.

   • If you intend to train on more than one trait for the same cohort, make sure that, after preprocessing for your first trait, you set remove_patient_ids_master_split = False so that all traits see the same patient split.

3. model.py

   • The only necessary parts to modify are under # General settings -- TO BE MODIFIED BY YOU ---, some described here:
   • While debugging locally (not yet training the 'real' model), leave c.set_local() in model.py. When ready to fully train on GPUs, comment this out.
   • If training = True trains Inception-v3 using the training and validation tfrecords under GCS_PATTERN. It will use all available GPUs on the machine (or only CPU if no GPUs are detected).
   • If training = False it will load the latest checkpoint found under LOAD_WEIGHTS_PATH (in conf) and will begin producing predictions for each sample using the per-sample tfrecords files under GCS_PATTERN_PER_SAMPLE (note that if LOAD_WEIGHTS_PATH = None when train = False it will throw an exception). This part will utilize only one GPU, so there's no need to set GPUs to 8 as we did for training.

4. conf_postprocess.py - settings used for evaluation/cartography/heterogeneity. The current format is derived from settings in your Conf object, so you can tell where the files are expected to be from your conf settings:

   • For pickles generated by preprocessor, the default is: ../res/postprocess/<c.TCGA_COHORT_NAME>/data_splits/<c.NAME>/' (c is a Conf object from conf.py). Under this folder you need three subfolders - 'train','val','test'. Simply place the pickles under these folders according to their name.
   • For predictions, the default is: ../res/postprocess/<c.TCGA_COHORT_NAME>/preds/<c.NAME>/' (c is a Conf object from conf.py). Under this folder you need to place the exact folder produced during inference (i.e. ../out/<c.TCGA_COHORT_NAME>/predict/). Simply copy these folders from your server to this postprocess path. If you want to change these formats, simply modify: Conf_Postprocess().DATA_SPLIT_DIR) and Conf_Postprocess().MODEL_PREDS_DIR_WITH_RESAMPLE_ROUND.

5. evaluate.py - evaluates the model predictions and produces log files under '../out/' describing results. Expects to have the aforementioned pickles (for data_split and predictions) under ../res/postprocess/.. (see previous point).

Training on mock data

We have included under the res folder pre-generated train and validation mock tfrec files. You may use these to check that the training pipeline works properly by running model.py with the default settings (currently set to training = True). Note that for this data, the model is not expected to converge, nor can this data be used to train a clinically meaningful model. For this purpose, original whole-slide images need to be placed under data->slides folder as explained above (see conf.py). Slides may be obtained from the GDC website, as discussed in the Methods section. The manifest files that list the slides used in this research are provided under the 'data' folder.

Generating molecular cartographies and computing heterogeneity scores

To generate molecular cartogrpahies and heterogeneity maps simply use cartography.py and heterogeneity.py with the same configuration settings (Conf and Conf_Postprocess) as used in evaluation. The output will be generated under ../out/<c.TCGA_COHORT_NAME>/ under cartography and heterogeneity. HTI appears in the name of each image under heterogeneity (e.g. for heterogeneity map ending with: '..._0.64.png', HTI is 0.64).

We have created a new python package, hta, which can be used to compute a sample's spatial heterogeneity score using its molecular cartographies. For more details see our HTA github page and our HTA paper.