Smart grid initialization reduces the computational complexity of multi-objective image registration based on a dual-dynamic transformation model to account for large anatomical differences

We recently demonstrated the strong potential of using dual-dynamic transformation models when tackling deformable image registration problems involving large anatomical differences. Dual-dynamic transformation models employ two moving grids instead of the common single moving grid for the target image (and single fixed grid for the source image). We previously employed powerful optimization algorithms to make use of the additional flexibility offered by a dual-dynamic transformation model with good results, directly obtaining insight into the trade-off between important registration objectives as a result of taking a multi-objective approach to optimization. However, optimization has so far been initialized using two regular grids, which still leaves a great potential of dual-dynamic transformation models untapped: a-priori grid alignment with image structures/areas that are expected to deform more. This allows (far) less grid points to be used, compared to using a sufficiently refined regular grid, leading to (far) more efficient optimization, or, equivalently, more accurate results using the same number of grid points. We study the implications of exploiting this potential by experimenting with two new smart grid initialization procedures: one manual expert-based and one automated image-feature-based. We consider a CT test case with large differences in bladder volume with and without a multi-resolution scheme and find a substantial benefit of using smart grid initialization

A novel model-based evolutionary algorithm for multi-objective deformable image registration with content mismatch and large deformations: Benchmarking efficiency and quality

Taking a multi-objective optimization approach to deformable image registration has recently gained attention, because such an approach removes the requirement of manually tuning the weights of all the involved objectives. Especially for problems that require large complex deformations, this is a non-trivial task. From the resulting Pareto set of solutions one can then much more insightfully select a registration outcome that is most suitable for the problem at hand. To serve as an internal optimization engine, currently used multi-objective algorithms are competent, but rather inefficient. In this paper we largely improve upon this by introducing a multi-objective real-valued adaptation of the recently introduced Gene-pool Optimal Mixing Evolutionary Algorithm (GOMEA) for discrete optimization. In this work, GOMEA is tailored specifically to the problem of deformable image registration to obtain substantially improved efficiency. This improvement is achieved by exploiting a key strength of GOMEA: iteratively improving small parts of solutions, allowing to faster exploit the impact of such updates on the objectives at hand through partial evaluations. We performed experiments on three registration problems. In particular, an artificial problem containing a disappearing structure, a pair of pre- and post-operative breast CT scans, and a pair of breast MRI scans acquired in prone and supine position were considered. Results show that compared to the previously used evolutionary algorithm, GOMEA obtains a speed-up of up to a factor of ∼1600 on the tested registration problems while achieving registration outcomes of similar quality

Getting the most out of additional guidance information in deformable image registration by leveraging multi-objective optimization

Incorporating additional guidance information, e.g., landmark/contour correspondence, in deformable image registration is often desirable and is typically done by adding constraints or cost terms to the optimization function. Commonly, deciding between a “hard” constraint and a “soft” additional cost term as well as the weighting of cost terms in the optimization function is done on a trial-and-error basis. The aim of this study is to investigate the advantages of exploiting guidance information by taking a multi-objective optimization perspective. Hereto, next to objectives related to match quality and amount of deformation, we define a third objective related to guidance information. Multi-objective optimization eliminates the need to a-priori tune a weighting of objectives in a single optimization function or the strict requirement of fulfilling hard guidance constraints. Instead, Pareto-efficient trade-offs between all objectives are found, effectively making the introduction of guidance information straightforward, independent of its type or scale. Further, since complete Pareto fronts also contain less interesting parts (i.e., solutions with near-zero deformation effort), we study how adaptive steering mechanisms can be incorporated to automatically focus more on solutions of interest. We performed experiments on artificial and real clinical data with large differences, including disappearing structures. Results show the substantial benefit of using additional guidance information. Moreover, compared to the 2-objective case, additional computational cost is negligible. Finally, with the same computational budget, use of the adaptive steering mechanism provides superior solutions in the area of interest

On explaining machine learning models by evolving crucial and compact features

Feature construction can substantially improve the accuracy of Machine Learning (ML) algorithms. Genetic Programming (GP) has been proven to be effective at this task by evolving non-linear combinations of input features. GP additionally has the potential to improve ML explainability since explicit expressions are evolved. Yet, in most GP works the complexity of evolved features is not explicitly bound or minimized though this is arguably key for explainability. In this article, we assess to what extent GP still performs favorably at feature construction when constructing features that are (1) Of small-enough number, to enable visualization of the behavior of the ML model; (2) Of small-enough size, to enable interpretability of the features themselves; (3) Of sufficient informative power, to retain or even improve the performance of the ML algorithm. We consider a simple feature construction scheme using three different GP algorithms, as well as random search, to evolve features for five ML algorithms, including support vector machines and random forest. Our results on 21 datasets pertaining to classification and regression problems show that constructing only two compact features can be sufficient to rival the use of the entire original feature set. We further find that a modern GP algorithm, GP-GOMEA, performs best overall. These results, combined with examples that we provide of readable constructed features and of 2D visualizations of ML behavior, lead us to positively conclude that GP-based feature construction still works well when explicitly searching for compact features, making it extremely helpful to explain ML models

Multi-Objective Population Based Training

Population Based Training (PBT) is an efficient hyperparameter optimization algorithm. PBT is a single-objective algorithm, but many real-world hyperparameter optimization problems involve two or more conflicting objectives. In this work, we therefore introduce a multi-objective version of PBT, MO-PBT. Our experiments on diverse multi-objective hyperparameter optimization problems (Precision/Recall, Accuracy/Fairness, Accuracy/Adversarial Robustness) show that MO-PBT outperforms random search, single-objective PBT, and the state-of-the-art multi-objective hyperparameter optimization algorithm MO-ASHA

The Impact of Asynchrony on Parallel Model-Based EAs

In a parallel EA one can strictly adhere to the generational clock, and wait for all evaluations in a generation to be done. However, this idle time limits the throughput of the algorithm and wastes computational resources. Alternatively, an EA can be made asynchronous parallel. However, EAs using classic recombination and selection operators (GAs) are known to suffer from an evaluation time bias, which also influences the performance of the approach. Model-Based Evolutionary Algorithms (MBEAs) are more scalable than classic GAs by virtue of capturing the structure of a problem in a model. If this model is learned through linkage learning based on the population, the learned model may also capture biases. Thus, if an asynchronous parallel MBEA is also affected by an evaluation time bias, this could result in learned models to be less suited to solving the problem, reducing performance. Therefore, in this work, we study the impact and presence of evaluation time biases on MBEAs in an asynchronous parallelization setting, and compare this to the biases in GAs. We find that a modern MBEA, GOMEA, is unaffected by evaluation time biases, while the more classical MBEA, ECGA, is affected, much like GAs are.Comment: 9 pages, 3 figures, 3 tables, submitted to GECCO 202

Shrink-Perturb Improves Architecture Mixing during Population Based Training for Neural Architecture Search

In this work, we show that simultaneously training and mixing neural networks is a promising way to conduct Neural Architecture Search (NAS). For hyperparameter optimization, reusing the partially trained weights allows for efficient search, as was previously demonstrated by the Population Based Training (PBT) algorithm. We propose PBT-NAS, an adaptation of PBT to NAS where architectures are improved during training by replacing poorly-performing networks in a population with the result of mixing well-performing ones and inheriting the weights using the shrink-perturb technique. After PBT-NAS terminates, the created networks can be directly used without retraining. PBT-NAS is highly parallelizable and effective: on challenging tasks (image generation and reinforcement learning) PBT-NAS achieves superior performance compared to baselines (random search and mutation-based PBT).Comment: 10 pages, 7 figures. Accepted at ECAI 202

Less is More: A Call to Focus on Simpler Models in Genetic Programming for Interpretable Machine Learning

Interpretability can be critical for the safe and responsible use of machine learning models in high-stakes applications. So far, evolutionary computation (EC), in particular in the form of genetic programming (GP), represents a key enabler for the discovery of interpretable machine learning (IML) models. In this short paper, we argue that research in GP for IML needs to focus on searching in the space of low-complexity models, by investigating new kinds of search strategies and recombination methods. Moreover, based on our experience of bringing research into clinical practice, we believe that research should strive to design better ways of modeling and pursuing interpretability, for the obtained solutions to ultimately be most useful

Observer variation-aware medical image segmentation by combining deep learning and surrogate-assisted genetic algorithms

There has recently been great progress in automatic segmentation of medical images with deep learning algorithms. In most works observer variation is acknowledged to be a problem as it makes training data heterogeneous but so far no attempts have been made to explicitly capture this variation. Here, we propose an approach capable of mimicking different styles of segmentation, which potentially can improve quality and clinical acceptance of automatic segmentation methods. In this work, instead of training one neural network on all available data, we train several neural networks on subgroups of data belonging to different segmentation variations separately. Because a priori it may be unclear what styles of segmentation exist in the data and because different styles do not necessarily map one-on-one to different observers, the subgroups should be automatically determined. We achieve this by searching for the best data partition with a genetic algorithm. Therefore, each network can learn a specific style of segmentation from grouped training data. We provide proof of principle results for open-sourced prostate segmentation MRI data with simulated observer variations. Our approach provides an improvement of up to 23% (depending on simulated variations) in terms of Dice and surface Dice coefficients compared to one network trained on all data.Comment: 11 pages, 5 figures, SPIE Medical Imaging Conference - 202