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PETRIC: PET Rapid Image reconstruction Challenge

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Reconstruction Methods - Educated Warm Start

Giving reconstruction algorithms a warm start can speed up reconstruction time by starting closer to the minimiser. To this end, we employ a neural network to learn a suitable warm start image. The network is a (small) 3D convolutional neural network. All layers in the network have no bias and use ReLU activation functions. This results in a 1-homogeneous network. In this way, the network should be independent of the intensity of the image. Although many different architectures and inputs were tested, the final network only takes the provided OSEM image as input. We tested a version, which also took in the gradient of the likelihood and the likelihood of the regulariser as extra inputs. This network performed slightly better. However, computing the gradients comes with a high cost, which in our opinion was better spent in the iterations of the classical iterative algorithm following the network. The network weights are available in the folder checkpoint/.

We employ three different iterative algortihms.

1) EM-preconditioner, DOwG step size rule, SAGA gradient estimation with Katyusha momentum (in branch: main)

Update rule: We use ideas from the Katyusha paper to accelerate SAGA. In particular we choose $\theta_1 = \theta_2 = 0.5$, such that the update rules becomes

$$ x_{k+1} = 0.5 z_k + 0.5 \tilde{x} \ \tilde{\nabla} = \nabla f(\tilde{x}) + \nabla f_i(x_{k+1}) - \nabla f_i(\tilde{x}) \ z_{k+1} = z_k - \alpha \tilde{\nabla}$$

We access subsets according to a Herman Meyer order. We choose $\tilde{x}$ as the last precition of the previous epoch.

Step-size rule: All iterations use DoWG (Distance over Weighted Gradients) for the step size calculation.

Preconditioner: EM-preconditioner the same as used in the BSREM example.

2) EM-preconditioner, DOwG step size rule, SGD (in branch: ews_sgd)

Update rule: SGD-like for all iterations, after 10 iterations 4 subset gradients are accumulated per iteration.

Step-size rule: All iterations use DoWG (Distance over Weighted Gradients) for the step size calculation.

Preconditioner: For the precondtioner, the ratio between the norm of RDP gradient vs. the norm of the full objective gradient is used to gauge the dominance of the RDP component of the objective function. If this fraction is larger than 0.5 (i.e. RDP is dominating) a preconditioner utilising an approximation of the Hessian of RDP is used. The preconditioner used is similar to Tsai et al. (2018), however, the Hessian row sum of the likelihood term is not updated each iteration. Additionally, we found that the Hessian row sum of the RDP prior was instable, so instead we only used the diagonal approximation of the Hessian evaluated at each iterate. This defines a kind of strange preconditioner, where only the RDP component of the preconditioner is updated per iteration. For the case when the fraction was lower than 0.5, the EM-preconditioner was used. This was observed to provided better performance when the likelihood component is more dominant, also this avoid the costly computation of the diagonal of the RDP Hessian.

3) Adaptive preconditioner, full gradient descent, Barzilai-Borwein step size rule (in branch: full_gd)

The characteristics of the datasets varied a lot, i.e., we had low count data, different scanner setups, TOF data, and so on. We tried a lot of different algorithms and approaches, both classical and deep learning based, but it was hard to design a method, which works consistently for all these different settings. Based on this experience, we submit a full gradient descent algorithm with a Barzilai-Borwein step size rule. Using the full gradient goes against almost all empirical results, which show that the convergence can be speed by using subsets. However, most work look at a speed up with respect to number of iterations and do not take into account parameter tuning specific to each algorithm. With respect to raw computation time, we sometimes saw only a minor different between full gradient descent and gradient descent using subsets. Further, often a subset-based algorithm that worked well for one dataset performed extremely poorly on another requiring adjustment of the hyper-parameters.

For the precondtioner, the ratio between the norm of RDP gradient vs. the norm of the full objective gradient is used to gauge the dominance of the RDP component of the objective function. If this fraction is larger than 0.5 (i.e. RDP is dominating) a preconditioner utilising an approximation of the Hessian of RDP is used. The preconditioner used is similar to Tsai et al. (2018), however, the Hessian row sum of the likelihood term is not updated each iteration. Additionally, we found that the Hessian row sum of the RDP prior was instable, so instead we only used the diagonal approximation of the Hessian evaluated at each iterate. This defines a kind of strange preconditioner, where only the RDP component of the preconditioner is updated per iteration. For the case when the fraction was lower than 0.5, the EM-preconditioner was used. This was observed to provided better performance when the likelihood component is more dominant, also this avoid the costly computation of the diagonal of the RDP Hessian.

Note, for TOF data, we do not use the full gradient, but instead a small number of subsets.

Update rule: GD for all iterations.

Step-size rule: Barzilai-Borwein long step size rule.

Preconditioner: Diagonal RDP Hessian + Row-sum of likelihood hessian, or EM-precondition based on a dominance of RDP component of the objective function.

Number of subset choice

To compute the number of subsets we use the functions in utils/number_of_subsets.py. This is a set of heuristic rules: 1) number of subsets has to be divisible by the number of views, 2) the number of subsets should have many prime factors (this results in a good Herman Meyer order), 3) I want at least 8 views in each subset and 4) I want at least 5 subsets. The function in utils/number_of_subsets.py is probably not really efficient.

For TOF flight data, we do not use rule 3) and 4). If several number of subsets have the same number of prime factors, we take the larger number of subsets.

All in all, this results in: 50 views (TOF) -> 25 subsets, 128 views -> 16 subsets and 252 views -> 28 views.

Challenge information

Layout

The organisers will import your submitted algorithm from main.py and then run & evaluate it. Please create this file! See the example main_*.py files for inspiration.

SIRF, CIL, and CUDA are already installed (using synerbi/sirf). Additional dependencies may be specified via apt.txt, environment.yml, and/or requirements.txt.

  • (required) main.py: must define a class Submission(cil.optimisation.algorithms.Algorithm) and a list of submission_callbacks
  • apt.txt: passed to apt install
  • environment.yml: passed to conda install
  • requirements.txt: passed to pip install

You can also find some example notebooks here which should help you with your development:

Organiser setup

The organisers will execute (after downloading https://petric.tomography.stfc.ac.uk/data/ to /path/to/data):

docker run --rm -it -v /path/to/data:/mnt/share/petric:ro -v .:/workdir -w /workdir --gpus all synerbi/sirf:edge-gpu /bin/bash
# ... or ideally synerbi/sirf:latest-gpu after the next SIRF release!
pip install git+https://github.com/TomographicImaging/Hackathon-000-Stochastic-QualityMetrics
# ... conda/pip/apt install environment.yml/requirements.txt/apt.txt
python petric.py

Tip

petric.py will effectively execute:

from main import Submission, submission_callbacks  # your submission
from petric import data, metrics  # our data & evaluation
assert issubclass(Submission, cil.optimisation.algorithms.Algorithm)
Submission(data).run(numpy.inf, callbacks=metrics + submission_callbacks)

Warning

To avoid timing out (5 min runtime), please disable any debugging/plotting code before submitting! This includes removing any progress/logging from submission_callbacks.

  • data to test/train your Algorithms is available at https://petric.tomography.stfc.ac.uk/data/ and is likely to grow (more info to follow soon)
    • fewer datasets will be used by the organisers to provide a temporary leaderboard
  • metrics are calculated by class QualityMetrics within petric.py

Any modifications to petric.py are ignored.

Team

We thank Zeljko Kereta for valuable discussion.

  • Imraj Singh and Alexander Denker (University College London)