arXiv subjects

Peter A. N. Bosman

Publications and source records attributed to Peter A. N. Bosman.

At least 37 records · Page 2Linked to original sources

arXiv2024

Multi-Objective Learning for Deformable Image Registration

Deformable image registration (DIR) involves optimization of multiple conflicting objectives, however, not many existing DIR algorithms are multi-objective (MO). Further, while there has been progress in the design of deep learning algorithms for DIR, there is no work in the direction of MO DIR using deep learning. In this paper, we fill this gap by combining a recently proposed approach for MO training of neural networks with a well-known deep neural network for DIR and create a deep learning based MO DIR approach. We evaluate the proposed approach for DIR of pelvic magnetic resonance imaging (MRI) scans. We experimentally demonstrate that the proposed MO DIR approach -- providing multiple registration outputs for each patient that each correspond to a different trade-off between the objectives -- has additional desirable properties from a clinical use point-of-view as compared to providing a single DIR output. The experiments also show that the proposed MO DIR approach provides a better spread of DIR outputs across the entire trade-off front than simply training multiple neural networks with weights for each objective sampled from a grid of possible values.

eess.IV↗

arXiv2024

Learning Discretized Bayesian Networks with GOMEA

Bayesian networks model relationships between random variables under uncertainty and can be used to predict the likelihood of events and outcomes while incorporating observed evidence. From an eXplainable AI (XAI) perspective, such models are interesting as they tend to be compact. Moreover, captured relations can be directly inspected by domain experts. In practice, data is often real-valued. Unless assumptions of normality can be made, discretization is often required. The optimal discretization, however, depends on the relations modelled between the variables. This complicates learning Bayesian networks from data. For this reason, most literature focuses on learning conditional dependencies between sets of variables, called structure learning. In this work, we extend an existing state-of-the-art structure learning approach based on the Gene-pool Optimal Mixing Evolutionary Algorithm (GOMEA) to jointly learn variable discretizations. The proposed Discretized Bayesian Network GOMEA (DBN-GOMEA) obtains similar or better results than the current state-of-the-art when tasked to retrieve randomly generated ground-truth networks. Moreover, leveraging a key strength of evolutionary algorithms, we can straightforwardly perform DBN learning multi-objectively. We show how this enables incorporating expert knowledge in a uniquely insightful fashion, finding multiple DBNs that trade-off complexity, accuracy, and the difference with a pre-determined expert network.

cs.LG↗

arXiv2024

MultiFIX: An XAI-friendly feature inducing approach to building models from multimodal data

In the health domain, decisions are often based on different data modalities. Thus, when creating prediction models, multimodal fusion approaches that can extract and combine relevant features from different data modalities, can be highly beneficial. Furthermore, it is important to understand how each modality impacts the final prediction, especially in high-stake domains, so that these models can be used in a trustworthy and responsible manner. We propose MultiFIX: a new interpretability-focused multimodal data fusion pipeline that explicitly induces separate features from different data types that can subsequently be combined to make a final prediction. An end-to-end deep learning architecture is used to train a predictive model and extract representative features of each modality. Each part of the model is then explained using explainable artificial intelligence techniques. Attention maps are used to highlight important regions in image inputs. Inherently interpretable symbolic expressions, learned with GP-GOMEA, are used to describe the contribution of tabular inputs. The fusion of the extracted features to predict the target label is also replaced by a symbolic expression, learned with GP-GOMEA. Results on synthetic problems demonstrate the strengths and limitations of MultiFIX. Lastly, we apply MultiFIX to a publicly available dataset for the detection of malignant skin lesions.

cs.AI↗

arXiv2024

Fitness-based Linkage Learning and Maximum-Clique Conditional Linkage Modelling for Gray-box Optimization with RV-GOMEA

For many real-world optimization problems it is possible to perform partial evaluations, meaning that the impact of changing a few variables on a solution's fitness can be computed very efficiently. It has been shown that such partial evaluations can be excellently leveraged by the Real-Valued GOMEA (RV-GOMEA) that uses a linkage model to capture dependencies between problem variables. Recently, conditional linkage models were introduced for RV-GOMEA, expanding its state-of-the-art performance even to problems with overlapping dependencies. However, that work assumed that the dependency structure is known a priori. Fitness-based linkage learning techniques have previously been used to detect dependencies during optimization, but only for non-conditional linkage models. In this work, we combine fitness-based linkage learning and conditional linkage modelling in RV-GOMEA. In addition, we propose a new way to model overlapping dependencies in conditional linkage models to maximize the joint sampling of fully interdependent groups of variables. We compare the resulting novel variant of RV-GOMEA to other variants of RV-GOMEA and VkD-CMA on 12 problems with varying degree of overlapping dependencies. We find that the new RV-GOMEA not only performs best on most problems, also the overhead of learning the conditional linkage models during optimization is often negligible.

cs.NE↗

arXiv2024

Improving the efficiency of GP-GOMEA for higher-arity operators

Deploying machine learning models into sensitive domains in our society requires these models to be explainable. Genetic Programming (GP) can offer a way to evolve inherently interpretable expressions. GP-GOMEA is a form of GP that has been found particularly effective at evolving expressions that are accurate yet of limited size and, thus, promote interpretability. Despite this strength, a limitation of GP-GOMEA is template-based. This negatively affects its scalability regarding the arity of operators that can be used, since with increasing operator arity, an increasingly large part of the template tends to go unused. In this paper, we therefore propose two enhancements to GP-GOMEA: (i) semantic subtree inheritance, which performs additional variation steps that consider the semantic context of a subtree, and (ii) greedy child selection, which explicitly considers parts of the template that in standard GP-GOMEA remain unused. We compare different versions of GP-GOMEA regarding search enhancements on a set of continuous and discontinuous regression problems, with varying tree depths and operator sets. Experimental results show that both proposed search enhancements have a generally positive impact on the performance of GP-GOMEA, especially when the set of operators to choose from is large and contains higher-arity operators.

cs.NE↗

arXiv2024

A Tournament of Transformation Models: B-Spline-based vs. Mesh-based Multi-Objective Deformable Image Registration

The transformation model is an essential component of any deformable image registration approach. It provides a representation of physical deformations between images, thereby defining the range and realism of registrations that can be found. Two types of transformation models have emerged as popular choices: B-spline models and mesh models. Although both models have been investigated in detail, a direct comparison has not yet been made, since the models are optimized using very different optimization methods in practice. B-spline models are predominantly optimized using gradient-descent methods, while mesh models are typically optimized using finite-element method solvers or evolutionary algorithms. Multi-objective optimization methods, which aim to find a diverse set of high-quality trade-off registrations, are increasingly acknowledged to be important in deformable image registration. Since these methods search for a diverse set of registrations, they can provide a more complete picture of the capabilities of different transformation models, making them suitable for a comparison of models. In this work, we conduct the first direct comparison between B-spline and mesh transformation models, by optimizing both models with the same state-of-the-art multi-objective optimization method, the Multi-Objective Real-Valued Gene-pool Optimal Mixing Evolutionary Algorithm (MO-RV-GOMEA). The combination with B-spline transformation models, moreover, is novel. We experimentally compare both models on two different registration problems that are both based on pelvic CT scans of cervical cancer patients, featuring large deformations. Our results, on three cervical cancer patients, indicate that the choice of transformation model can have a profound impact on the diversity and quality of achieved registration outcomes.

cs.CV↗

arXiv2023

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).

cs.LG↗

arXiv2023

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.

cs.LG↗

arXiv2023

A Joint Python/C++ Library for Efficient yet Accessible Black-Box and Gray-Box Optimization with GOMEA

Exploiting knowledge about the structure of a problem can greatly benefit the efficiency and scalability of an Evolutionary Algorithm (EA). Model-Based EAs (MBEAs) are capable of doing this by explicitly modeling the problem structure. The Gene-pool Optimal Mixing Evolutionary Algorithm (GOMEA) is among the state-of-the-art of MBEAs due to its use of a linkage model and the optimal mixing variation operator. Especially in a Gray-Box Optimization (GBO) setting that allows for partial evaluations, i.e., the relatively efficient evaluation of a partial modification of a solution, GOMEA is known to excel. Such GBO settings are known to exist in various real-world applications to which GOMEA has successfully been applied. In this work, we introduce the GOMEA library, making existing GOMEA code in C++ accessible through Python, which serves as a centralized way of maintaining and distributing code of GOMEA for various optimization domains. Moreover, it allows for the straightforward definition of BBO as well as GBO fitness functions within Python, which are called from the C++ optimization code for each required (partial) evaluation. We describe the structure of the GOMEA library and how it can be used, and we show its performance in both GBO and Black-Box Optimization (BBO).

cs.NE↗

arXiv2023

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.

cs.NE↗

arXiv2023

Convolutions, Transformers, and their Ensembles for the Segmentation of Organs at Risk in Radiation Treatment of Cervical Cancer

Segmentation of regions of interest in images of patients, is a crucial step in many medical procedures. Deep neural networks have proven to be particularly adept at this task. However, a key question is what type of deep neural network to choose, and whether making a certain choice makes a difference. In this work, we will answer this question for the task of segmentation of the Organs At Risk (OARs) in radiation treatment of cervical cancer (i.e., bladder, bowel, rectum, sigmoid) in Magnetic Resonance Imaging (MRI) scans. We compare several state-of-the-art models belonging to different architecture categories, as well as a few new models that combine aspects of several state-of-the-art models, to see if the results one gets are markedly different. We visualize model predictions, create all possible ensembles of models by averaging their output probabilities, and calculate the Dice Coefficient between predictions of models, in order to understand the differences between them and the potential of possible combinations. The results show that small improvements in metrics can be achieved by advancing and merging architectures, but the predictions of the models are quite similar (most models achieve on average more than 0.8 Dice Coefficient when compared to the outputs of other models). However, the results from the ensemble experiments indicate that the best results are obtained when the best performing models from every category of the architectures are combined.

eess.IV↗

arXiv2023

MOREA: a GPU-accelerated Evolutionary Algorithm for Multi-Objective Deformable Registration of 3D Medical Images

Finding a realistic deformation that transforms one image into another, in case large deformations are required, is considered a key challenge in medical image analysis. Having a proper image registration approach to achieve this could unleash a number of applications requiring information to be transferred between images. Clinical adoption is currently hampered by many existing methods requiring extensive configuration effort before each use, or not being able to (realistically) capture large deformations. A recent multi-objective approach that uses the Multi-Objective Real-Valued Gene-pool Optimal Mixing Evolutionary Algorithm (MO-RV-GOMEA) and a dual-dynamic mesh transformation model has shown promise, exposing the trade-offs inherent to image registration problems and modeling large deformations in 2D. This work builds on this promise and introduces MOREA: the first evolutionary algorithm-based multi-objective approach to deformable registration of 3D images capable of tackling large deformations. MOREA includes a 3D biomechanical mesh model for physical plausibility and is fully GPU-accelerated. We compare MOREA to two state-of-the-art approaches on abdominal CT scans of 4 cervical cancer patients, with the latter two approaches configured for the best results per patient. Without requiring per-patient configuration, MOREA significantly outperforms these approaches on 3 of the 4 patients that represent the most difficult cases.

cs.CV↗

arXiv2023

Bi-objective optimization of organ properties for the simulation of intracavitary brachytherapy applicator placement in cervical cancer

Validation of deformable image registration techniques is extremely important, but hard, especially when complex deformations or content mismatch are involved. These complex deformations and content mismatch, for example, occur after the placement of an applicator for brachytherapy for cervical cancer. Virtual phantoms could enable the creation of validation data sets with ground truth deformations that simulate the large deformations that occur between image acquisitions. However, the quality of the multi-organ Finite Element Method (FEM)-based simulations is dependent on the patient-specific external forces and mechanical properties assigned to the organs. A common approach to calibrate these simulation parameters is through optimization, finding the parameter settings that optimize the match between the outcome of the simulation and reality. When considering inherently simplified organ models, we hypothesize that the optimal deformations of one organ cannot be achieved with a single parameter setting without compromising the optimality of the deformation of the surrounding organs. This means that there will be a trade-off between the optimal deformations of adjacent organs, such as the vagina-uterus and bladder. This work therefore proposes and evaluates a multi-objective optimization approach where the trade-off between organ deformations can be assessed after optimization. We showcase what the extent of the trade-off looks like when bi-objectively optimizing the patient-specific mechanical properties and external forces of the vagina-uterus and bladder for FEM-based simulations.

physics.med-ph↗

arXiv2023

Clinically Acceptable Segmentation of Organs at Risk in Cervical Cancer Radiation Treatment from Clinically Available Annotations

Deep learning models benefit from training with a large dataset (labeled or unlabeled). Following this motivation, we present an approach to learn a deep learning model for the automatic segmentation of Organs at Risk (OARs) in cervical cancer radiation treatment from a large clinically available dataset of Computed Tomography (CT) scans containing data inhomogeneity, label noise, and missing annotations. We employ simple heuristics for automatic data cleaning to minimize data inhomogeneity and label noise. Further, we develop a semi-supervised learning approach utilizing a teacher-student setup, annotation imputation, and uncertainty-guided training to learn in presence of missing annotations. Our experimental results show that learning from a large dataset with our approach yields a significant improvement in the test performance despite missing annotations in the data. Further, the contours generated from the segmentation masks predicted by our model are found to be equally clinically acceptable as manually generated contours.

eess.IV↗

arXiv2023

Automatic Landmarks Correspondence Detection in Medical Images with an Application to Deformable Image Registration

Purpose: Deformable Image Registration (DIR) can benefit from additional guidance using corresponding landmarks in the images. However, the benefits thereof are largely understudied, especially due to the lack of automatic landmark detection methods for three-dimensional (3D) medical images. Approach: We present a Deep Convolutional Neural Network (DCNN), called DCNN-Match, that learns to predict landmark correspondences in 3D images in a self-supervised manner. We trained DCNN-Match on pairs of Computed Tomography (CT) scans containing simulated deformations. We explored five variants of DCNN-Match that use different loss functions and assessed their effect on the spatial density of predicted landmarks and the associated matching errors. We also tested DCNN-Match variants in combination with the open-source registration software Elastix to assess the impact of predicted landmarks in providing additional guidance to DIR. Results: We tested our approach on lower-abdominal CT scans from cervical cancer patients: 121 pairs containing simulated deformations and 11 pairs demonstrating clinical deformations. The results showed significant improvement in DIR performance when landmark correspondences predicted by DCNN-Match were used in the case of simulated (p = $0e^0$) as well as clinical deformations (p = 0.030). We also observed that the spatial density of the automatic landmarks with respect to the underlying deformation affect the extent of improvement in DIR. Finally, DCNN-Match was found to generalize to Magnetic Resonance Imaging (MRI) scans without requiring retraining, indicating easy applicability to other datasets. Conclusions: DCNN-Match learns to predict landmark correspondences in 3D medical images in a self-supervised manner, which can improve DIR performance.

cs.CV↗

arXiv2022

Obtaining Smoothly Navigable Approximation Sets in Bi-Objective Multi-Modal Optimization

Even if a Multi-modal Multi-Objective Evolutionary Algorithm (MMOEA) is designed to find solutions well spread over all locally optimal approximation sets of a Multi-modal Multi-objective Optimization Problem (MMOP), there is a risk that the found set of solutions is not smoothly navigable because the solutions belong to various niches, reducing the insight for decision makers. To tackle this issue, a new MMOEAs is proposed: the Multi-Modal Bézier Evolutionary Algorithm (MM-BezEA), which produces approximation sets that cover individual niches and exhibit inherent decision-space smoothness as they are parameterized by Bézier curves. MM-BezEA combines the concepts behind the recently introduced BezEA and MO-HillVallEA to find all locally optimal approximation sets. When benchmarked against the MMOEAs MO_Ring_PSO_SCD and MO-HillVallEA on MMOPs with linear Pareto sets, MM-BezEA was found to perform best in terms of best hypervolume.

cs.NE↗

arXiv2022

Heed the Noise in Performance Evaluations in Neural Architecture Search

Neural Architecture Search (NAS) has recently become a topic of great interest. However, there is a potentially impactful issue within NAS that remains largely unrecognized: noise. Due to stochastic factors in neural network initialization, training, and the chosen train/validation dataset split, the performance evaluation of a neural network architecture, which is often based on a single learning run, is also stochastic. This may have a particularly large impact if a dataset is small. We therefore propose to reduce this noise by evaluating architectures based on average performance over multiple network training runs using different random seeds and cross-validation. We perform experiments for a combinatorial optimization formulation of NAS in which we vary noise reduction levels. We use the same computational budget for each noise level in terms of network training runs, i.e., we allow less architecture evaluations when averaging over more training runs. Multiple search algorithms are considered, including evolutionary algorithms which generally perform well for NAS. We use two publicly available datasets from the medical image segmentation domain where datasets are often limited and variability among samples is often high. Our results show that reducing noise in architecture evaluations enables finding better architectures by all considered search algorithms.

cs.NE↗

arXiv2022

Evolutionary Neural Cascade Search across Supernetworks

To achieve excellent performance with modern neural networks, having the right network architecture is important. Neural Architecture Search (NAS) concerns the automatic discovery of task-specific network architectures. Modern NAS approaches leverage supernetworks whose subnetworks encode candidate neural network architectures. These subnetworks can be trained simultaneously, removing the need to train each network from scratch, thereby increasing the efficiency of NAS. A recent method called Neural Architecture Transfer (NAT) further improves the efficiency of NAS for computer vision tasks by using a multi-objective evolutionary algorithm to find high-quality subnetworks of a supernetwork pretrained on ImageNet. Building upon NAT, we introduce ENCAS - Evolutionary Neural Cascade Search. ENCAS can be used to search over multiple pretrained supernetworks to achieve a trade-off front of cascades of different neural network architectures, maximizing accuracy while minimizing FLOPs count. We test ENCAS on common computer vision benchmarks (CIFAR-10, CIFAR-100, ImageNet) and achieve Pareto dominance over previous state-of-the-art NAS models up to 1.5 GFLOPs. Additionally, applying ENCAS to a pool of 518 publicly available ImageNet classifiers leads to Pareto dominance in all computation regimes and to increasing the maximum accuracy from 88.6% to 89.0%, accompanied by an 18\% decrease in computation effort from 362 to 296 GFLOPs. Our code is available at https://github.com/AwesomeLemon/ENCAS

cs.CV↗