arXiv subjects

Tanja Alderliesten

Publications and source records attributed to Tanja Alderliesten.

At least 19 recordsLinked to original sources

arXiv2026

Evolving Features vs Evolving Entire Trees with GP for Interpretable Survival Analysis

Survival analysis concerns the task of predicting the time until an event occurs. Often used in the medical field, survival analysis deals with incomplete (i.e., censored) data, for instance, from patients who did not experience the event during the duration of the study. For practical use, both accuracy and interpretability are important. Survival trees are easy-to-follow survival models that split the patient cohort recursively into discrete patient groups. Whilst survival trees can capture complex relationships, they typically need to grow large, threatening interpretability. Moreover, survival trees are often built using greedy approaches that may overlook globally optimal split combinations, limiting predictive performance. Shallow survival trees require expressive, higher-order feature combinations to achieve competitive accuracy. We therefore use genetic programming to multi-objectively evolve inherently inspectable feature sets and study how they interact with different tree induction strategies. We further introduce an evolutionary approach that jointly optimises the survival tree structure and the non-linear split logic. Our findings demonstrate that evolutionary feature construction improves predictive performance across different tree induction strategies on two real-world datasets and two different survival tree depths. Given its speed and flexible presentation, the multi-objective evolution of entire trees likely holds the most future promise.

cs.LG↗

arXiv2026

Parallel Adaptive Multi-Objective Evolutionary Learning of Discretized Bayesian Network Classifiers for Clinical Data

Bayesian Networks (BNs) are of interest from an explainable AI viewpoint, offering transparent probabilistic models for decision support. Baymex is a recently introduced multi-objective evolutionary algorithm for learning discretized BNs, enabling experts to trade-off different objectives of interest, such as likelihood, model complexity, and prior beliefs. While Baymex has been shown to outperform state-of-the-art BN learning approaches, Baymex still 1) requires a lot of computation time and 2) has only been evaluated on synthetic data. To improve scalability, we introduce a parallelization strategy as well as a mechanism that enables adaptively steering optimization toward networks that overfit less. We furthermore reconfigure Baymex to train a BN classifier through multi-objective optimization of cross-entropy loss and the BIC complexity term so as to evaluate its performance on real-world clinical classification tasks. Besides observing speedups up to over 54 times on a 16-core CPU, comparisons against clinically familiar baselines (decision trees, logistic regression, naive Bayes, and random forests) on two open-source (RADCURE and SUPPORT) and one in-house dataset, show that Baymex obtains statistically similar or better predictive performance while producing compact, clinically inspectable BNs. Importantly, Baymex finds multiple plausible BN classifiers that contain predictors consistent with established clinical factors.

cs.LG↗

arXiv2026

Simultaneous Model-Based Evolution of Constants and Expression Structure in GP-GOMEA for Symbolic Regression

Genetic programming (GP) approaches are among the state-of-the-art for symbolic regression, the task of constructing symbolic expressions that fit well with data. To find highly accurate symbolic expressions, both the expression structure and any contained real-valued constants, are important. GP-GOMEA, a modern model-based evolutionary algorithm, is one of the leading algorithms for finding accurate, yet compact expressions. Yet, GP-GOMEA does not perform dedicated constant optimization, but rather uses ephemeral random constants. Hence, the accuracy of GP-GOMEA may well still be improved upon by the incorporation of a constant optimization mechanism. Existing research into mixed discrete-continuous optimization with EAs has shown that a simultaneous and well-integrated approach to optimizing both discrete and continuous parts, leads to the best results on a variety of problems, especially when there are interactions between these parts. In this paper, we therefore propose a novel approach where constants in expressions are optimized at the same time as the expression structure by merging the real-valued variant of GOMEA with GP-GOMEA. The proposed approach is compared to other forms of handling constants in GP-GOMEA, and in the context of other commonly used techniques such as linear scaling, restarts, and constant tuning after GP optimization. Our results indicate that our novel approach generally performs best and confirms the importance of simultaneous constant optimization during evolution.

cs.NE↗

arXiv2026

Iterated Population Based Training with Task-Agnostic Restarts

Hyperparameter Optimization (HPO) can lift the burden of tuning hyperparameters (HPs) of neural networks. HPO algorithms from the Population Based Training (PBT) family are efficient thanks to dynamically adjusting HPs every few steps of the weight optimization. Recent results indicate that the number of steps between HP updates is an important meta-HP of all PBT variants that can substantially affect their performance. Yet, no method or intuition is available for efficiently setting its value. We introduce Iterated Population Based Training (IPBT), a novel PBT variant that automatically adjusts this HP via restarts that reuse weight information in a task-agnostic way and leverage time-varying Bayesian optimization to reinitialize HPs. Evaluation on 8 image classification and reinforcement learning tasks shows that, on average, our algorithm matches or outperforms 5 previous PBT variants and other HPO algorithms (random search, ASHA, SMAC3), without requiring a budget increase or any changes to its HPs. The source code is available at https://github.com/AwesomeLemon/IPBT.

cs.LG↗

arXiv2026

GP-GOMEA with GPU-Based Fitness Evaluations: Design and Performance Analysis

GP-GOMEA is a state-of-the-art evolutionary algorithm for symbolic regression, known for discovering small and interpretable models. However, its computational cost remains substantial, limiting its applicability to larger datasets and more complex target expressions. In contrast, the rise of modern subsymbolic approaches, particularly deep learning, has been driven largely by the massive parallelism offered by GPUs. In this work, we take the first major step toward a fully GPU-accelerated GP-GOMEA by introducing a GPU-based fitness evaluation scheme. We design a GPU-friendly representation of GP-GOMEA's template-based individuals and a corresponding evaluation strategy that exploits the inherent parallelism of population-based search. This substantially increases evaluation throughput, enabling orders of magnitude more evaluations within the same time budget. Across four standard symbolic regression benchmarks, this increased evaluation capacity yields performance improvements, particularly for larger datasets and larger population sizes. Moreover, the ability to efficiently evaluate much larger datasets and more complex templates enables analyses that were previously infeasible, allowing us to systematically analyze what makes expressions increasingly difficult for GP-GOMEA, providing new insights into how expression structure affects search difficulty. Finally, for the first time, this expanded capability allows a problem-agnostic evolutionary algorithm to reliably regress one of the largest Feynman equations within four hours.

cs.NE↗

arXiv2026

End-user validation of BRIGHT with custom-developed graphical user interface applied to cervical cancer brachytherapy

Multi-objective optimisation using BRIGHT has proven insightful and effective in prostate cancer brachytherapy treatment planning. BRachytherapy via artificially Intelligent GOMEA-Heuristic based Treatment planning (BRIGHT) generates multiple treatment plans, each with a different trade-off between tumour coverage and organs-at-risk sparing. BRIGHT was recently extended to cervical cancer brachytherapy. In this study, we present a novel, custom-developed graphical user interface (GUI) that enables plan navigation, pairwise comparisons, dose distribution visualisation, and possibility for adjustments - essential for efficient clinical use of BRIGHT. End-user validation of BRIGHT with the dedicated GUI was conducted for cervical cancer brachytherapy by emulating clinical practice in ten previously treated patients. A multidisciplinary brachytherapy team used BRIGHT to create new treatment plans. GUI usability was assessed using the System Usability Scale (SUS). BRIGHT plan quality was compared to clinical practice via blinded one-on-one comparisons. The GUI offered helpful features for plan navigation and evaluation, giving users quick insight into whether planning aims are achievable and what treatment options are available. The overall SUS score was 83.3, indicating an 'excellent' system. BRIGHT outperformed clinical practice in five out of ten patients regarding the coverage-sparing trade-off and performed equally well in the remaining five. The BRIGHT plan was preferred over the clinical plan in eight out of ten patients, four of which showed clinically relevant differences. The clinical plan was preferred in two patients, neither with clinically relevant differences. In conclusion, BRIGHT, with its dedicated GUI, is a clinically viable and user-friendly tool for treatment planning in cervical cancer brachytherapy.

cs.NE↗

arXiv2026

Introns and Templates Matter: Rethinking Linkage in GP-GOMEA

GP-GOMEA is among the state-of-the-art for symbolic regression, especially when it comes to finding small and potentially interpretable solutions. A key mechanism employed in any GOMEA variant is the exploitation of linkage, the dependencies between variables, to ensure efficient evolution. In GP-GOMEA, mutual information between node positions in GP trees has so far been used to learn linkage. For this, a fixed expression template is used. This however leads to introns for expressions smaller than the full template. As introns have no impact on fitness, their occurrences are not directly linked to selection. Consequently, introns can adversely affect the extent to which mutual information captures dependencies between tree nodes. To overcome this, we propose two new measures for linkage learning, one that explicitly considers introns in mutual information estimates, and one that revisits linkage learning in GP-GOMEA from a grey-box perspective, yielding a measure that needs not to be learned from the population but is derived directly from the template. Across five standard symbolic regression problems, GP-GOMEA achieves substantial improvements using both measures. We also find that the newly learned linkage structure closely reflects the template linkage structure, and that explicitly using the template structure yields the best performance overall.

cs.NE↗

arXiv2025

Sharing Knowledge without Sharing Data: Stitches can improve ensembles of disjointly trained models

Deep learning has been shown to be very capable at performing many real-world tasks. However, this performance is often dependent on the presence of large and varied datasets. In some settings, like in the medical domain, data is often fragmented across parties, and cannot be readily shared. While federated learning addresses this situation, it is a solution that requires synchronicity of parties training a single model together, exchanging information about model weights. We investigate how asynchronous collaboration, where only already trained models are shared (e.g. as part of a publication), affects performance, and propose to use stitching as a method for combining models. Through taking a multi-objective perspective, where performance on each parties' data is viewed independently, we find that training solely on a single parties' data results in similar performance when merging with another parties' data, when considering performance on that single parties' data, while performance on other parties' data is notably worse. Moreover, while an ensemble of such individually trained networks generalizes better, performance on each parties' own dataset suffers. We find that combining intermediate representations in individually trained models with a well placed pair of stitching layers allows this performance to recover to a competitive degree while maintaining improved generalization, showing that asynchronous collaboration can yield competitive results.

cs.LG↗

arXiv2025

Automated and Interpretable Survival Analysis from Multimodal Data

Accurate and interpretable survival analysis remains a core challenge in oncology. With growing multimodal data and the clinical need for transparent models to support validation and trust, this challenge increases in complexity. We propose an interpretable multimodal AI framework to automate survival analysis by integrating clinical variables and computed tomography imaging. Our MultiFIX-based framework uses deep learning to infer survival-relevant features that are further explained: imaging features are interpreted via Grad-CAM, while clinical variables are modeled as symbolic expressions through genetic programming. Risk estimation employs a transparent Cox regression, enabling stratification into groups with distinct survival outcomes. Using the open-source RADCURE dataset for head and neck cancer, MultiFIX achieves a C-index of 0.838 (prediction) and 0.826 (stratification), outperforming the clinical and academic baseline approaches and aligning with known prognostic markers. These results highlight the promise of interpretable multimodal AI for precision oncology with MultiFIX.

cs.AI↗

arXiv2025

PISA: An AI Pipeline for Interpretable-by-design Survival Analysis Providing Multiple Complexity-Accuracy Trade-off Models

Survival analysis is central to clinical research, informing patient prognoses, guiding treatment decisions, and optimising resource allocation. Accurate time-to-event predictions not only improve quality of life but also reveal risk factors that shape clinical practice. For these models to be relevant in healthcare, interpretability is critical: predictions must be traceable to patient-specific characteristics, and risk factors should be identifiable to generate actionable insights for both clinicians and researchers. Traditional survival models often fail to capture non-linear interactions, while modern deep learning approaches, though powerful, are limited by poor interpretability. We propose a Pipeline for Interpretable Survival Analysis (PISA) - a pipeline that provides multiple survival analysis models that trade off complexity and performance. Using multiple-feature, multi-objective feature engineering, PISA transforms patient characteristics and time-to-event data into multiple survival analysis models, providing valuable insights into the survival prediction task. Crucially, every model is converted into simple patient stratification flowcharts supported by Kaplan-Meier curves, whilst not compromising on performance. While PISA is model-agnostic, we illustrate its flexibility through applications of Cox regression and shallow survival trees, the latter avoiding proportional hazards assumptions. Applied to two clinical benchmark datasets, PISA produced interpretable survival models and intuitive stratification flowcharts whilst achieving state-of-the-art performances. Revisiting a prior departmental study further demonstrated its capacity to automate survival analysis workflows in real-world clinical research.

stat.AP↗

arXiv2025

Dealing with Segmentation Errors in Needle Reconstruction for MRI-Guided Brachytherapy

Brachytherapy involves bringing a radioactive source near tumor tissue using implanted needles. Image-guided brachytherapy planning requires amongst others, the reconstruction of the needles. Manually annotating these needles on patient images can be a challenging and time-consuming task for medical professionals. For automatic needle reconstruction, a two-stage pipeline is commonly adopted, comprising a segmentation stage followed by a post-processing stage. While deep learning models are effective for segmentation, their results often contain errors. No currently existing post-processing technique is robust to all possible segmentation errors. We therefore propose adaptations to existing post-processing techniques mainly aimed at dealing with segmentation errors and thereby improving the reconstruction accuracy. Experiments on a prostate cancer dataset, based on MRI scans annotated by medical professionals, demonstrate that our proposed adaptations can help to effectively manage segmentation errors, with the best adapted post-processing technique achieving median needle-tip and needle-bottom point localization errors of $1.07$ (IQR $\pm 1.04$) mm and $0.43$ (IQR $\pm 0.46$) mm, respectively, and median shaft error of $0.75$ (IQR $\pm 0.69$) mm with 0 false positive and 0 false negative needles on a test set of 261 needles.

eess.IV↗

arXiv2025

More Efficient Real-Valued Gray-Box Optimization through Incremental Distribution Estimation in RV-GOMEA

The Gene-pool Optimal Mixing EA (GOMEA) family of EAs offers a specific means to exploit problem-specific knowledge through linkage learning, i.e., inter-variable dependency detection, expressed using subsets of variables, that should undergo joint variation. Such knowledge can be exploited if faster fitness evaluations are possible when only a few variables are changed in a solution, enabling large speed-ups. The recent-most version of Real-Valued GOMEA (RV-GOMEA) can learn a conditional linkage model during optimization using fitness-based linkage learning, enabling fine-grained dependency exploitation in learning and sampling a Gaussian distribution. However, while the most efficient Gaussian-based EAs, like NES and CMA-ES, employ incremental learning of the Gaussian distribution rather than performing full re-estimation every generation, the recent-most RV-GOMEA version does not employ such incremental learning. In this paper, we therefore study whether incremental distribution estimation can lead to efficiency enhancements of RV-GOMEA. We consider various benchmark problems with varying degrees of overlapping dependencies. We find that, compared to RV-GOMEA and VKD-CMA-ES, the required number of evaluations to reach high-quality solutions can be reduced by a factor of up to 1.5 if population sizes are tuned problem-specifically, while a reduction by a factor of 2-3 can be achieved with generic population-sizing guidelines.

cs.NE↗

arXiv2025

A Step towards Interpretable Multimodal AI Models with MultiFIX

Real-world problems are often dependent on multiple data modalities, making multimodal fusion essential for leveraging diverse information sources. In high-stakes domains, such as in healthcare, understanding how each modality contributes to the prediction is critical to ensure trustworthy and interpretable AI models. We present MultiFIX, an interpretability-driven multimodal data fusion pipeline that explicitly engineers distinct features from different modalities and combines them to make the final prediction. Initially, only deep learning components are used to train a model from data. The black-box (deep learning) components are subsequently either explained using post-hoc methods such as Grad-CAM for images or fully replaced by interpretable blocks, namely symbolic expressions for tabular data, resulting in an explainable model. We study the use of MultiFIX using several training strategies for feature extraction and predictive modeling. Besides highlighting strengths and weaknesses of MultiFIX, experiments on a variety of synthetic datasets with varying degrees of interaction between modalities demonstrate that MultiFIX can generate multimodal models that can be used to accurately explain both the extracted features and their integration without compromising predictive performance.

cs.NE↗

arXiv2025

Thinking Outside the Template with Modular GP-GOMEA

The goal in Symbolic Regression (SR) is to discover expressions that accurately map input to output data. Because often the intent is to understand these expressions, there is a trade-off between accuracy and the interpretability of expressions. GP-GOMEA excels at producing small SR expressions (increasing the potential for interpretability) with high accuracy, but requires a fixed tree template, which limits the types of expressions that can be evolved. This paper presents a modular representation for GP-GOMEA that allows multiple trees to be evolved simultaneously that can be used as (functional) subexpressions. While each tree individually is constrained to a (small) fixed tree template, the final expression, if expanded, can exhibit a much larger structure. Furthermore, the use of subexpressions decomposes the original regression problem and opens the possibility for enhanced interpretability through the piece-wise understanding of small subexpressions. We compare the performance of GP-GOMEA with and without modular templates on a variety of datasets. We find that our proposed approach generally outperforms single-template GP-GOMEA and can moreover uncover ground-truth expressions underlying synthetic datasets with modular subexpressions at a faster rate than GP-GOMEA without modular subexpressions.

cs.NE↗

arXiv2025

Multi-Objective Deep-Learning-based Biomechanical Deformable Image Registration with MOREA

When choosing a deformable image registration (DIR) approach for images with large deformations and content mismatch, the realism of found transformations often needs to be traded off against the required runtime. DIR approaches using deep learning (DL) techniques have shown remarkable promise in instantly predicting a transformation. However, on difficult registration problems, the realism of these transformations can fall short. DIR approaches using biomechanical, finite element modeling (FEM) techniques can find more realistic transformations, but tend to require much longer runtimes. This work proposes the first hybrid approach to combine them, with the aim of getting the best of both worlds. This hybrid approach, called DL-MOREA, combines a recently introduced multi-objective DL-based DIR approach which leverages the VoxelMorph framework, called DL-MODIR, with MOREA, an evolutionary algorithm-based, multi-objective DIR approach in which a FEM-like biomechanical mesh transformation model is used. In our proposed hybrid approach, the DL results are used to smartly initialize MOREA, with the aim of more efficiently optimizing its mesh transformation model. We empirically compare DL-MOREA against its components, DL-MODIR and MOREA, on CT scan pairs capturing large bladder filling differences of 15 cervical cancer patients. While MOREA requires a median runtime of 45 minutes, DL-MOREA can already find high-quality transformations after 5 minutes. Compared to the DL-MODIR transformations, the transformations found by DL-MOREA exhibit far less folding and improve or preserve the bladder contour distance error.

cs.CV↗

arXiv2024

Hyperparameter-Free Medical Image Synthesis for Sharing Data and Improving Site-Specific Segmentation

Sharing synthetic medical images is a promising alternative to sharing real images that can improve patient privacy and data security. To get good results, existing methods for medical image synthesis must be manually adjusted when they are applied to unseen data. To remove this manual burden, we introduce a Hyperparameter-Free distributed learning method for automatic medical image Synthesis, Sharing, and Segmentation called HyFree-S3. For three diverse segmentation settings (pelvic MRIs, lung X-rays, polyp photos), the use of HyFree-S3 results in improved performance over training only with site-specific data (in the majority of cases). The hyperparameter-free nature of the method should make data synthesis and sharing easier, potentially leading to an increase in the quantity of available data and consequently the quality of the models trained that may ultimately be applied in the clinic. Our code is available at https://github.com/AwesomeLemon/HyFree-S3

cs.CV↗

arXiv2024

Stitching for Neuroevolution: Recombining Deep Neural Networks without Breaking Them

Traditional approaches to neuroevolution often start from scratch. This becomes prohibitively expensive in terms of computational and data requirements when targeting modern, deep neural networks. Using a warm start could be highly advantageous, e.g., using previously trained networks, potentially from different sources. This moreover enables leveraging the benefits of transfer learning (in particular vastly reduced training effort). However, recombining trained networks is non-trivial because architectures and feature representations typically differ. Consequently, a straightforward exchange of layers tends to lead to a performance breakdown. We overcome this by matching the layers of parent networks based on their connectivity, identifying potential crossover points. To correct for differing feature representations between these layers we employ stitching, which merges the networks by introducing new layers at crossover points. To train the merged network, only stitching layers need to be considered. New networks can then be created by selecting a subnetwork by choosing which stitching layers to (not) use. Assessing their performance is efficient as only their evaluation on data is required. We experimentally show that our approach enables finding networks that represent novel trade-offs between performance and computational cost, with some even dominating the original networks.

cs.NE↗

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↗