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Attention Tripnet: Exploiting attention mechanisms for the recognition of surgical action triplets in endoscopic videos

<i>C.I. Nwoye and N. Padoy</i>

This repo contains an ablation model of Rendezvous network, known as Attention Tripnet. <br />

Introduction

Recognising action as a triplet of subject, verb, and object provides truly fine-grained and comprehensive information on surgical activities. In the natural vision, it model as <subject, verb, object> representing the Human Object Interaction (HOI). In Surgical Computer Vision, the information is presented as <instrument, verb, target>. Triplet recognition involves simultaneous recognition of all three triplet components and correctly establishing the data association between them.

A lot of efforts has been made to recognize surgical triplets directly from videos. The predominant ones include Tripnet and Rendezvous models leveraging class activations and attention mechanisms.

Fig 1: Architecture of Attention Tripnet.

The first effort at exploiting attention mechanisms in this Rendezvous led to the development of a Class Activation Guided Attention Mechanism (CAGAM) to better detect the verb and target components of the triplet, which are instrument-centric. CAGAM is a form of spatial attention mechanism that propagates attention from a known to an unknown context features thereby enhancing the unknown context for relevant pattern discovery. Usually the known context feature is a class activation map (CAM). In this work, CAGAM explicitly uses tool type and location information to highlight discriminative features for verbs and targets respectively. Integrating CAGAM in the state-of-the-art Tripnet model results in a new model that is now known as Attention Tripnet with improved performance.

Fig 2: Overview of CAGAM.

Model Overview

The Attention-Tripnet model is composed of:

• Feature Extraction layer: extract high and low level features from input image from a video
• Encoder: for triplet components encoding
  • Weakly-Supervised Localization (WSL) Layer: for localizing the instruments
  • Class Activation Guided Attention Mechanism (CAGAM): for detecting the verbs and targets leveraging attention resulting from instrument activations. (channel anad position spatial attentions are used here)
• Decoder: for triplet assocaition due to multi-instances
  • 3D interaction space (3Dis): for learning to associate instrument-verb-target using a learning projection and for final triplet classification.

We hope this repo will help researches/engineers in the development of surgical action recognition systems. For algorithm development, we provide training data, baseline models and evaluation methods to make a level playground. For application usage, we also provide a small video demo that takes raw videos as input without any bells and whistles.

Performance

Results Table

Video Demo

Usefulness of CAGAM is demonstrated at the second phase of the video:

<a href="https://www.youtube.com/watch?v=d_yHdJtCa98&t=61s"><img src="https://github.com/CAMMA-public/rendezvous/raw/main/files/vid.png" width="20.2%" ></a>

Available on Youtube.

Installation

Requirements

The model depends on the following libraries:

1. sklearn
2. PIL
3. Python >= 3.5
4. ivtmetrics
5. Developer's framework:
   1. For Tensorflow version 1:
      • TF >= 1.10
   2. For Tensorflow version 2:
      • TF >= 2.1
   3. For PyTorch version:
      • Pyorch >= 1.10.1
      • TorchVision >= 0.11

System Requirements:

The code has been test on Linux operating system. It runs on both CPU and GPU. Equivalence of basic OS commands such as unzip, cd, wget, etc. will be needed to run in Windows or Mac OS.

Quick Start

• clone the git repository: git clone https://github.com/CAMMA-public/attention-tripnet.git
• install all the required libraries according to chosen your framework.
• download the dataset
• download model's weights
• train
• evaluate

Dataset Zoo

• CholecT45
• CholecT50
• Dataset splits

Data Preparation

• All frames are resized to 256 x 448 during training and evaluation.
• Image data are mean normalized.
• The dataset variants are tagged in this code as follows:
  • cholect50 = CholecT50 with split used in the original paper.
  • cholect50-challenge = CholecT50 with split used in the CholecTriplet challenge.
  • cholect45-crossval = CholecT45 with official cross-val split (currently public released).
  • cholect50-crossval = CholecT50 with official cross-val split.

Evaluation Metrics

The ivtmetrics computes AP for triplet recognition. It also support the evaluation of the recognition of the triplet components.

pip install ivtmetrics

or

conda install -c nwoye ivtmetrics

Usage guide is found on pypi.org.

Running the Model

The code can be run in a trianing mode (-t) or testing mode (-e) or both (-t -e) if you want to evaluate at the end of training :

Training on CholecT45/CholecT50 Dataset

Simple training on CholecT50 dataset:

python run.py -t  --data_dir="/path/to/dataset" --dataset_variant=cholect50 --version=1

You can include more details such as epoch, batch size, cross-validation and evaluation fold, weight initialization, learning rates for all subtasks, etc.:

python3 run.py -t -e  --data_dir="/path/to/dataset" --dataset_variant=cholect45-crossval --kfold=1 --epochs=180 --batch=64 --version=2 -l 1e-2 1e-3 1e-4 --pretrain_dir='path/to/imagenet/weights'

All the flags can been seen in the run.py file. The experimental setup of the published model is contained in the paper.

Testing

python3 run.py -e --data_dir="/path/to/dataset" --dataset_variant=cholect45-crossval --kfold 3 --batch 32 --version=1 --test_ckpt="/path/to/model-k3/weights"

Training on Custom Dataset

Adding custom datasets is quite simple, what you need to do are:

• organize your annotation files in the same format as in CholecT45 dataset.
• final model layers can be modified to suit your task by changing the class-size (num_tool_classes, num_verb_classes, num_target_classes, num_triplet_classes) in the argparse.

Model Zoo

• N.B. Download links to models' weights will not be provided until after the CholecTriplet2022 challenge.

PyTorch

TensorFlow v1

TensorFlow v2

Model weights are released periodically because some training are in progress.

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License

This code, models, and datasets are available for non-commercial scientific research purposes provided by CC BY-NC-SA 4.0 LICENSE attached as LICENSE file. By downloading and using this code you agree to the terms in the LICENSE. Third-party codes are subject to their respective licenses.

Related Resources

• CholecT45 / CholecT50 Datasets
• Offical Dataset Splits
• Tripnet
• Rendezvous
• CholecTriplet2021 Challenge
• CholecTriplet2022 Challenge

Citation

If you find this repo useful in your project or research, please consider citing the relevant publications:

• For the CholecT45/CholecT50 Dataset:

@article{nwoye2021rendezvous,
  title={Rendezvous: Attention Mechanisms for the Recognition of Surgical Action Triplets in Endoscopic Videos},
  author={Nwoye, Chinedu Innocent and Yu, Tong and Gonzalez, Cristians and Seeliger, Barbara and Mascagni, Pietro and Mutter, Didier and Marescaux, Jacques and Padoy, Nicolas},
  journal={Medical Image Analysis},
  volume={78},
  pages={102433},
  year={2022}
}

• For the CholecT45/CholecT50 Official Dataset Splits:

@article{nwoye2022data,
  title={Data Splits and Metrics for Benchmarking Methods on Surgical Action Triplet Datasets},
  author={Nwoye, Chinedu Innocent and Padoy, Nicolas},
  journal={arXiv preprint arXiv:2204.05235},
  year={2022}
}

• For the Rendezvous or Attention Tripnet Baseline Models or any snippet of code from this repo:

@article{nwoye2021rendezvous,
  title={Rendezvous: Attention Mechanisms for the Recognition of Surgical Action Triplets in Endoscopic Videos},
  author={Nwoye, Chinedu Innocent and Yu, Tong and Gonzalez, Cristians and Seeliger, Barbara and Mascagni, Pietro and Mutter, Didier and Marescaux, Jacques and Padoy, Nicolas},
  journal={Medical Image Analysis},
  volume={78},
  pages={102433},
  year={2022}
}

• For the Tripnet Baseline Model:

@inproceedings{nwoye2020recognition,
   title={Recognition of instrument-tissue interactions in endoscopic videos via action triplets},
   author={Nwoye, Chinedu Innocent and Gonzalez, Cristians and Yu, Tong and Mascagni, Pietro and Mutter, Didier and Marescaux, Jacques and Padoy, Nicolas},
   booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI)},
   pages={364--374},
   year={2020},
   organization={Springer}
}

• For the models presented @ CholecTriplet2021 Challenge:

@article{nwoye2022cholectriplet2021,
  title={CholecTriplet2021: a benchmark challenge for surgical action triplet recognition},
  author={Nwoye, Chinedu Innocent and Alapatt, Deepak and Vardazaryan, Armine ... Gonzalez, Cristians and Padoy, Nicolas},
  journal={arXiv preprint arXiv:2204.04746},
  year={2022}
}

This repo is maintained by CAMMA. Comments and suggestions on models are welcomed. Check this page for updates.