arXiv subjects

Sofie Van Hoecke

Publications and source records attributed to Sofie Van Hoecke.

At least 19 recordsLinked to original sources

arXiv2026

Proper Scoring Rules for Right-Censored Survival Data

Proper scoring rules provide a rigorous theoretical basis for the training and evaluation of probabilistic forecasts. In survival analysis, such forecasts describe the distribution of the time until an event occurs. However, this event time is often only partially observed because follow-up may end before the event occurs, resulting in right censoring. We propose a framework for proper scoring of right-censored survival outcomes based on a simple idea: first, map the predictive distribution through the censoring mechanism, then apply the underlying proper score on the induced observed-data law. This yields localized scores for fixed censoring times and marginalized scores when the censoring time is random or only partially observed. The resulting construction recovers familiar right-censored likelihood and IPCW-type criteria within a coherent framework, while also yielding right-censored versions of the CRPS, pinball loss, Brier score, and energy score. We show that the marginalized construction is proper under conditional independent censoring and, for strictly proper base scores, identifies the latent joint CDF on the identifiable region. The same principle also leads to censored engression, a sample-based learning objective for multivariate right-censored survival modeling. In experiments, our scores correctly rank the oracle forecast across several censoring regimes, whereas forecast-dependent plug-in weighted scores can exhibit ranking reversals. Censored engression likewise substantially improves over naive training on censored outcomes.

cs.LG↗

arXiv2026

Conformal Prediction for Dose-Response Models with Continuous Treatments

Understanding the dose-response relation between a continuous treatment and the outcome for an individual can greatly drive decision-making, particularly in areas like personalized drug dosing and personalized healthcare interventions. Point estimates are often insufficient in these high-risk environments, highlighting the need for uncertainty quantification to support informed decisions. Conformal prediction, a distribution-free and model-agnostic method for uncertainty quantification, has seen limited application in continuous treatments or dose-response models. To address this gap, we propose a novel methodology that frames the causal dose-response problem as a covariate shift, leveraging weighted conformal prediction. By incorporating propensity estimation, conformal predictive systems, and likelihood ratios, we present a practical solution for generating prediction intervals for dose-response models. Additionally, our method approximates local coverage for every treatment value by applying kernel functions as weights in weighted conformal prediction. Finally, we use a new synthetic benchmark dataset to demonstrate the significance of covariate shift assumptions in achieving robust prediction intervals for dose-response models.

cs.LG↗

arXiv2025

From Haystack to Needle: Label Space Reduction for Zero-shot Classification

We present Label Space Reduction (LSR), a novel method for improving zero-shot classification performance of Large Language Models (LLMs). LSR iteratively refines the classification label space by systematically ranking and reducing candidate classes, enabling the model to concentrate on the most relevant options. By leveraging unlabeled data with the statistical learning capabilities of data-driven models, LSR dynamically optimizes the label space representation at test time. Our experiments across seven benchmarks demonstrate that LSR improves macro-F1 scores by an average of 7.0% (up to 14.2%) with Llama-3.1-70B and 3.3% (up to 11.1%) with Claude-3.5-Sonnet compared to standard zero-shot classification baselines. To reduce the computational overhead of LSR, which requires an additional LLM call at each iteration, we propose distilling the model into a probabilistic classifier, allowing for efficient inference.

cs.CL↗

arXiv2025

Conformal Convolution and Monte Carlo Meta-learners for Predictive Inference of Individual Treatment Effects

Generating probabilistic forecasts of potential outcomes and individual treatment effects (ITE) is essential for risk-aware decision-making in domains such as healthcare, policy, marketing, and finance. We propose two novel methods: the conformal convolution T-learner (CCT) and the conformal Monte Carlo (CMC) meta-learner, that generate full predictive distributions of both potential outcomes and ITEs. Our approaches combine weighted conformal predictive systems with either analytic convolution of potential outcome distributions or Monte Carlo sampling, addressing covariate shift through propensity score weighting. In contrast to other approaches that allow the generation of potential outcome predictive distributions, our approaches are model agnostic, universal, and come with finite-sample guarantees of probabilistic calibration under knowledge of the propensity score. Regarding estimating the ITE distribution, we formally characterize how assumptions about potential outcomes' noise dependency impact distribution validity and establish universal consistency under independence noise assumptions. Experiments on synthetic and semi-synthetic datasets demonstrate that the proposed methods achieve probabilistically calibrated predictive distributions while maintaining narrow prediction intervals and having performant continuous ranked probability scores. Besides probabilistic forecasting performance, we observe significant efficiency gains for the CCT- and CMC meta-learners compared to other conformal approaches that produce prediction intervals for ITE with coverage guarantees.

cs.LG↗

arXiv2025

landmarker: a Toolkit for Anatomical Landmark Localization in 2D/3D Images

Anatomical landmark localization in 2D/3D images is a critical task in medical imaging. Although many general-purpose tools exist for landmark localization in classical computer vision tasks, such as pose estimation, they lack the specialized features and modularity necessary for anatomical landmark localization applications in the medical domain. Therefore, we introduce landmarker, a Python package built on PyTorch. The package provides a comprehensive, flexible toolkit for developing and evaluating landmark localization algorithms, supporting a range of methodologies, including static and adaptive heatmap regression. landmarker enhances the accuracy of landmark identification, streamlines research and development processes, and supports various image formats and preprocessing pipelines. Its modular design allows users to customize and extend the toolkit for specific datasets and applications, accelerating innovation in medical imaging. landmarker addresses a critical need for precision and customization in landmark localization tasks not adequately met by existing general-purpose pose estimation tools.

cs.CV↗

arXiv2025

Reliable uncertainty quantification for 2D/3D anatomical landmark localization using multi-output conformal prediction

Automatic anatomical landmark localization in medical imaging requires not just accurate predictions but reliable uncertainty quantification for effective clinical decision support. Current uncertainty quantification approaches often fall short, particularly when combined with normality assumptions, systematically underestimating total predictive uncertainty. This paper introduces conformal prediction as a framework for reliable uncertainty quantification in anatomical landmark localization, addressing a critical gap in automatic landmark localization. We present two novel approaches guaranteeing finite-sample validity for multi-output prediction: Multi-output Regression-as-Classification Conformal Prediction (M-R2CCP) and its variant Multi-output Regression to Classification Conformal Prediction set to Region (M-R2C2R). Unlike conventional methods that produce axis-aligned hyperrectangular or ellipsoidal regions, our approaches generate flexible, non-convex prediction regions that better capture the underlying uncertainty structure of landmark predictions. Through extensive empirical evaluation across multiple 2D and 3D datasets, we demonstrate that our methods consistently outperform existing multi-output conformal prediction approaches in both validity and efficiency. This work represents a significant advancement in reliable uncertainty estimation for anatomical landmark localization, providing clinicians with trustworthy confidence measures for their diagnoses. While developed for medical imaging, these methods show promise for broader applications in multi-output regression problems.

cs.CV↗

arXiv2024

Conformal Predictive Systems Under Covariate Shift

Conformal Predictive Systems (CPS) offer a versatile framework for constructing predictive distributions, allowing for calibrated inference and informative decision-making. However, their applicability has been limited to scenarios adhering to the Independent and Identically Distributed (IID) model assumption. This paper extends CPS to accommodate scenarios characterized by covariate shifts. We therefore propose Weighted CPS (WCPS), akin to Weighted Conformal Prediction (WCP), leveraging likelihood ratios between training and testing covariate distributions. This extension enables the construction of nonparametric predictive distributions capable of handling covariate shifts. We present theoretical underpinnings and conjectures regarding the validity and efficacy of WCPS and demonstrate its utility through empirical evaluations on both synthetic and real-world datasets. Our simulation experiments indicate that WCPS are probabilistically calibrated under covariate shift.

cs.LG↗

arXiv2024

Left-Right Swapping and Upper-Lower Limb Pairing for Robust Multi-Wearable Workout Activity Detection

This work presents the solution of the Signal Sleuths team for the 2024 HASCA WEAR challenge. The challenge focuses on detecting 18 workout activities (and the null class) using accelerometer data from 4 wearables - one worn on each limb. Data analysis revealed inconsistencies in wearable orientation within and across participants, leading to exploring novel multi-wearable data augmentation techniques. We investigate three models using a fixed feature set: (i) "raw": using all data as is, (ii) "left-right swapping": augmenting data by swapping left and right limb pairs, and (iii) "upper-lower limb paring": stacking data by using upper-lower limb pair combinations (2 wearables). Our experiments utilize traditional machine learning with multi-window feature extraction and temporal smoothing. Using 3-fold cross-validation, the raw model achieves a macro F1-score of 90.01%, whereas left-right swapping and upper-lower limb paring improve the scores to 91.30% and 91.87% respectively.

cs.HC↗

arXiv2024

Magnitude and Rotation Invariant Detection of Transportation Modes with Missing Data Modalities

This work presents the solution of the Signal Sleuths team for the 2024 SHL recognition challenge. The challenge involves detecting transportation modes using shuffled, non-overlapping 5-second windows of phone movement data, with exactly one of the three available modalities (accelerometer, gyroscope, magnetometer) randomly missing. Data analysis indicated a significant distribution shift between train and validation data, necessitating a magnitude and rotation-invariant approach. We utilize traditional machine learning, focusing on robust processing, feature extraction, and rotation-invariant aggregation. An ablation study showed that relying solely on the frequently used signal magnitude vector results in the poorest performance. Conversely, our proposed rotation-invariant aggregation demonstrated substantial improvement over using rotation-aware features, while also reducing the feature vector length. Moreover, z-normalization proved crucial for creating robust spectral features.

cs.LG↗

arXiv2024

Addressing Data Quality Challenges in Observational Ambulatory Studies: Analysis, Methodologies and Practical Solutions for Wrist-worn Wearable Monitoring

Chronic disease management and follow-up are vital for realizing sustained patient well-being and optimal health outcomes. Recent advancements in wearable sensing technologies, particularly wrist-worn devices, offer promising solutions for longitudinal patient follow-up by shifting from subjective, intermittent self-reporting to objective, continuous monitoring. However, collecting and analyzing wearable data presents unique challenges, such as data entry errors, non-wear periods, missing wearable data, and wearable artifacts. We therefore present an in-depth exploration of data analysis challenges tied to wrist-worn wearables and ambulatory label acquisition, using two real-world datasets (i.e., mBrain21 and ETRI lifelog2020). We introduce novel practical countermeasures, including participant compliance visualizations, interaction-triggered questionnaires to assess personal bias, and an optimized wearable non-wear detection pipeline. Further, we propose a visual analytics approach to validate processing pipelines using scalable tools such as tsflex and Plotly-Resampler. Lastly, we investigate the impact of missing wearable data on "window-of-interest" analysis methodologies. Prioritizing transparency and reproducibility, we offer open access to our detailed code examples, facilitating adaptation in future wearable research. In conclusion, our contributions provide actionable approaches for wearable data collection and analysis in chronic disease management.

cs.CE↗

arXiv2023

tsdownsample: high-performance time series downsampling for scalable visualization

Interactive line chart visualizations greatly enhance the effective exploration of large time series. Although downsampling has emerged as a well-established approach to enable efficient interactive visualization of large datasets, it is not an inherent feature in most visualization tools. Furthermore, there is no library offering a convenient interface for high-performance implementations of prominent downsampling algorithms. To address these shortcomings, we present tsdownsample, an open-source Python package specifically designed for CPU-based, in-memory time series downsampling. Our library focuses on performance and convenient integration, offering optimized implementations of leading downsampling algorithms. We achieve this optimization by leveraging low-level SIMD instructions and multithreading capabilities in Rust. In particular, SIMD instructions were employed to optimize the argmin and argmax operations. This SIMD optimization, along with some algorithmic tricks, proved crucial in enhancing the performance of various downsampling algorithms. We evaluate the performance of tsdownsample and demonstrate its interoperability with an established visualization framework. Our performance benchmarks indicate that the algorithmic runtime of tsdownsample approximates the CPU's memory bandwidth. This work marks a significant advancement in bringing high-performance time series downsampling to the Python ecosystem, enabling scalable visualization. The open-source code can be found at https://github.com/predict-idlab/tsdownsample

eess.SP↗

arXiv2023

MinMaxLTTB: Leveraging MinMax-Preselection to Scale LTTB

Visualization plays an important role in analyzing and exploring time series data. To facilitate efficient visualization of large datasets, downsampling has emerged as a well-established approach. This work concentrates on LTTB (Largest-Triangle-Three-Buckets), a widely adopted downsampling algorithm for time series data point selection. Specifically, we propose MinMaxLTTB, a two-step algorithm that marks a significant enhancement in the scalability of LTTB. MinMaxLTTB entails the following two steps: (i) the MinMax algorithm preselects a certain ratio of minimum and maximum data points, followed by (ii) applying the LTTB algorithm on only these preselected data points, effectively reducing LTTB's time complexity. The low computational cost of the MinMax algorithm, along with its parallelization capabilities, facilitates efficient preselection of data points. Additionally, the competitive performance of MinMax in terms of visual representativeness also makes it an effective reduction method. Experiments show that MinMaxLTTB outperforms LTTB by more than an order of magnitude in terms of computation time. Furthermore, preselecting a small multiple of the desired output size already provides similar visual representativeness compared to LTTB. In summary, MinMaxLTTB leverages the computational efficiency of MinMax to scale LTTB, without compromising on LTTB's favored visualization properties. The accompanying code and experiments of this paper can be found at https://github.com/predict-idlab/MinMaxLTTB.

cs.HC↗

arXiv2023

Data Point Selection for Line Chart Visualization: Methodological Assessment and Evidence-Based Guidelines

Time series visualization plays a crucial role in identifying patterns and extracting insights across various domains. However, as datasets continue to grow in size, visualizing them effectively becomes challenging. Downsampling, which involves data aggregation or selection, is a well-established approach to overcome this challenge. This work focuses on data selection algorithms, which accomplish downsampling by selecting values from the original time series. Despite their widespread adoption in visualization platforms and time series databases, there is limited literature on the evaluation of these techniques. To address this, we propose an extensive metrics-based evaluation methodology. Our methodology analyzes visual representativeness by assessing how well a downsampled time series line chart visually approximates the original data. Moreover, our methodology includes a novel concept called "visual stability", which captures visual changes when updating (streaming) or interacting with the visualization (panning and zooming). We evaluated four data point selection algorithms across three open-source visualization toolkits using our proposed methodology, considering various figure-drawing properties. Following the analysis of our findings, we formulated a set of evidence-based guidelines for line chart visualization at scale with downsampling. To promote reproducibility and enable the qualitative evaluation of new advancements in time series data point selection, we have made our methodology and results openly accessible. The proposed evaluation methodology, along with the obtained insights from this study, establishes a foundation for future research in this domain.

cs.HC↗

arXiv2022

Do Not Sleep on Traditional Machine Learning: Simple and Interpretable Techniques Are Competitive to Deep Learning for Sleep Scoring

Over the last few years, research in automatic sleep scoring has mainly focused on developing increasingly complex deep learning architectures. However, recently these approaches achieved only marginal improvements, often at the expense of requiring more data and more expensive training procedures. Despite all these efforts and their satisfactory performance, automatic sleep staging solutions are not widely adopted in a clinical context yet. We argue that most deep learning solutions for sleep scoring are limited in their real-world applicability as they are hard to train, deploy, and reproduce. Moreover, these solutions lack interpretability and transparency, which are often key to increase adoption rates. In this work, we revisit the problem of sleep stage classification using classical machine learning. Results show that competitive performance can be achieved with a conventional machine learning pipeline consisting of preprocessing, feature extraction, and a simple machine learning model. In particular, we analyze the performance of a linear model and a non-linear (gradient boosting) model. Our approach surpasses state-of-the-art (that uses the same data) on two public datasets: Sleep-EDF SC-20 (MF1 0.810) and Sleep-EDF ST (MF1 0.795), while achieving competitive results on Sleep-EDF SC-78 (MF1 0.775) and MASS SS3 (MF1 0.817). We show that, for the sleep stage scoring task, the expressiveness of an engineered feature vector is on par with the internally learned representations of deep learning models. This observation opens the door to clinical adoption, as a representative feature vector allows to leverage both the interpretability and successful track record of traditional machine learning models.

stat.ML↗

arXiv2022

Perfectly predicting ICU length of stay: too good to be true

A paper of Alsinglawi et al was recently accepted and published in Scientific Reports. In this paper, the authors aim to predict length of stay (LOS), discretized into either long (> 7 days) or short stays (< 7 days), of lung cancer patients in an ICU department using various machine learning techniques. The authors claim to achieve perfect results with an Area Under the Receiver Operating Characteristic curve (AUROC) of 100% with a Random Forest (RF) classifier with ADASYN class balancing over sampling technique, which if accurate could have significant implications for hospital management. However, we have identified several methodological flaws within the manuscript which cause the results to be overly optimistic and would have serious consequences if used in a clinical practice. Moreover, the reporting of the methodology is unclear and many important details are missing from the manuscript, which makes reproduction extremely difficult. We highlight the effect these oversights have had on the result and provide a more believable result of 88.91% AUROC when these oversights are corrected.

cs.LG↗

arXiv2022

Plotly-Resampler: Effective Visual Analytics for Large Time Series

Visual analytics is arguably the most important step in getting acquainted with your data. This is especially the case for time series, as this data type is hard to describe and cannot be fully understood when using for example summary statistics. To realize effective time series visualization, four requirements have to be met; a tool should be (1) interactive, (2) scalable to millions of data points, (3) integrable in conventional data science environments, and (4) highly configurable. We observe that open source Python visualization toolkits empower data scientists in most visual analytics tasks, but lack the combination of scalability and interactivity to realize effective time series visualization. As a means to facilitate these requirements, we created Plotly-Resampler, an open source Python library. Plotly-Resampler is an add-on for Plotly's Python bindings, enhancing line chart scalability on top of an interactive toolkit by aggregating the underlying data depending on the current graph view. Plotly-Resampler is built to be snappy, as the reactivity of a tool qualitatively affects how analysts visually explore and analyze data. A benchmark task highlights how our toolkit scales better than alternatives in terms of number of samples and time series. Additionally, Plotly-Resampler's flexible data aggregation functionality paves the path towards researching novel aggregation techniques. Plotly-Resampler's integrability, together with its configurability, convenience, and high scalability, allows to effectively analyze high-frequency data in your day-to-day Python environment.

cs.HC↗

arXiv2022

Powershap: A Power-full Shapley Feature Selection Method

Feature selection is a crucial step in developing robust and powerful machine learning models. Feature selection techniques can be divided into two categories: filter and wrapper methods. While wrapper methods commonly result in strong predictive performances, they suffer from a large computational complexity and therefore take a significant amount of time to complete, especially when dealing with high-dimensional feature sets. Alternatively, filter methods are considerably faster, but suffer from several other disadvantages, such as (i) requiring a threshold value, (ii) not taking into account intercorrelation between features, and (iii) ignoring feature interactions with the model. To this end, we present powershap, a novel wrapper feature selection method, which leverages statistical hypothesis testing and power calculations in combination with Shapley values for quick and intuitive feature selection. Powershap is built on the core assumption that an informative feature will have a larger impact on the prediction compared to a known random feature. Benchmarks and simulations show that powershap outperforms other filter methods with predictive performances on par with wrapper methods while being significantly faster, often even reaching half or a third of the execution time. As such, powershap provides a competitive and quick algorithm that can be used by various models in different domains. Furthermore, powershap is implemented as a plug-and-play and open-source sklearn component, enabling easy integration in conventional data science pipelines. User experience is even further enhanced by also providing an automatic mode that automatically tunes the hyper-parameters of the powershap algorithm, allowing to use the algorithm without any configuration needed.

cs.LG↗

arXiv2022

R-GCN: The R Could Stand for Random

The inception of the Relational Graph Convolutional Network (R-GCN) marked a milestone in the Semantic Web domain as a widely cited method that generalises end-to-end hierarchical representation learning to Knowledge Graphs (KGs). R-GCNs generate representations for nodes of interest by repeatedly aggregating parameterised, relation-specific transformations of their neighbours. However, in this paper, we argue that the the R-GCN's main contribution lies in this "message passing" paradigm, rather than the learned weights. To this end, we introduce the "Random Relational Graph Convolutional Network" (RR-GCN), which leaves all parameters untrained and thus constructs node embeddings by aggregating randomly transformed random representations from neighbours, i.e., with no learned parameters. We empirically show that RR-GCNs can compete with fully trained R-GCNs in both node classification and link prediction settings.

cs.LG↗