lmagp

Repository of the paper "Language models are good pathologists: using attention-based sequence reduction and text-pretrained transformers for efficient WSI classification"

Set up

Required packages:

• The models' implementation only require pytorch. We use language models from the transformers library.
• The packages required for training are pytorch-lightning, hydra-zen, torchmetrics.
• conda env create -f env.yaml will create a conda environment lmagp-env with the required dependencies

Methods

The methods proposed in the paper are available in src/models/adapted_transformers.py . A frozen pre-trained RoBERTa-base with a SeqShort layer can be instantiated in the following way:

import torch
from transformers import AutoModelForSequenceClassification
from src.models.adapted_transformers import AdaptedModel, MHASequenceShortenerWithLN, freeze_model

lm_classifier = freeze_model(AutoModelForSequenceClassification.from_pretrained('roberta-base', num_labels=2)) # will freeze the encoder parameters except for the layer norm layers.
seq_shortener = MHASequenceShortenerWithLN(target_len=256, embed_dim=768, kdim=1280, vdim=1280, num_heads=4, batch_first=True) # kdim, vdim: hidden dim of efficientnet v2 l
adapted_lm = AdaptedModel(model=lm_classifier, seq_shortener=seq_shortener, embed_dim=768)

x = torch.rand([1,5000,1280]) # [batch_size, num_tiles, feature_extractor_hidden_dim]
y = adapted_lm(x) # y['attentions'][0] will have the attention matrix of the SeqShort layer

The models should be easily plugged to an existing Multiple Instance Learning pipeline.

Training:

Data

We require the WSIs to be preprocessed previously. Our implementation relies on each sample being a dict (saved as a .pickle file) with a features key, whose value is a torch.Tensor of shape [num_tiles, feature_extractor_hidden_dim]. For example for a WSI comprising 100 tiles whose features were obtained with EfficientNetV2-L, the features field should be a tensor of shape [100, 1280].

The csvs directory contain the TCGA-BRCA splits that were used in our study.

Running

We use Hydra and PyTorch-Lightning for training, and every hyperparameter is configurable from .yaml config files. We provide an example config, where it is only needed to specify the correct path to the 10-fold .csvs root, and the fold number for which we want to train, validate and test.

# conda env create -f env.yaml
conda activate lmagp-env
python3 train_classifier.py -cp configs -cn seq-short-roberta-base.yaml ++csvs_root=/path/to/the/csvs ++fold=0