Xavier Coubez

Annika Stein, Xavier Coubez, Spandan Mondal et al.

Deep learning is a standard tool in the field of high-energy physics, facilitating considerable sensitivity enhancements for numerous analysis strategies. In particular, in identification of physics objects, such as jet flavor tagging, complex neural network architectures play a major role. However, these methods are reliant on accurate simulations. Mismodeling can lead to non-negligible differences in performance in data that need to be measured and calibrated against. We investigate the classifier response to input data with injected mismodelings and probe the vulnerability of flavor tagging algorithms via application of adversarial attacks. Subsequently, we present an adversarial training strategy that mitigates the impact of such simulated attacks and improves the classifier robustness. We examine the relationship between performance and vulnerability and show that this method constitutes a promising approach to reduce the vulnerability to poor modeling.

Rohit Agarwal, Aman Sinha, Ayan Vishwakarma et al.

Modeling irregularly-sampled time series (ISTS) is challenging because of missing values. Most existing methods focus on handling ISTS by converting irregularly sampled data into regularly sampled data via imputation. These models assume an underlying missing mechanism, which may lead to unwanted bias and sub-optimal performance. We present SLAN (Switch LSTM Aggregate Network), which utilizes a group of LSTMs to model ISTS without imputation, eliminating the assumption of any underlying process. It dynamically adapts its architecture on the fly based on the measured sensors using switches. SLAN exploits the irregularity information to explicitly capture each sensor's local summary and maintains a global summary state throughout the observational period. We demonstrate the efficacy of SLAN on two public datasets, namely, MIMIC-III, and Physionet 2012.

Tristan Kirscher, Alexandra Ertl, Klaus Maier-Hein et al.

Pancreatic ductal adenocarcinoma (PDAC) segmentation on contrast-enhanced CT is inherently ambiguous: inter-rater disagreement among experts reflects genuine uncertainty rather than annotation noise. Standard deep learning approaches assume a single ground truth, producing probabilistic outputs that can be poorly calibrated and difficult to interpret under such ambiguity. We present TwinTrack, a framework that addresses this gap through post-hoc calibration of ensemble segmentation probabilities to the empirical mean human response (MHR) -the fraction of expert annotators labeling a voxel as tumor. Calibrated probabilities are thus directly interpretable as the expected proportion of annotators assigning the tumor label, explicitly modeling inter-rater disagreement. The proposed post-hoc calibration procedure is simple and requires only a small multi-rater calibration set. It consistently improves calibration metrics over standard approaches when evaluated on the MICCAI 2025 CURVAS-PDACVI multi-rater benchmark.

Aman Sinha, Timothee Mickus, Marianne Clausel et al.

The success of pretrained language models (PLMs) across a spate of use-cases has led to significant investment from the NLP community towards building domain-specific foundational models. On the other hand, in mission critical settings such as biomedical applications, other aspects also factor in-chief of which is a model's ability to produce reasonable estimates of its own uncertainty. In the present study, we discuss these two desiderata through the lens of how they shape the entropy of a model's output probability distribution. We find that domain specificity and uncertainty awareness can often be successfully combined, but the exact task at hand weighs in much more strongly.

Tristan Kirscher, Sylvain Faisan, Xavier Coubez et al.

Pediatric medical imaging presents unique challenges due to significant anatomical and developmental differences compared to adults. Direct application of segmentation models trained on adult data often yields suboptimal performance, particularly for small or rapidly evolving structures. To address these challenges, several strategies leveraging the nnU-Net framework have been proposed, differing along four key axes: (i) the fingerprint dataset (adult, pediatric, or a combination thereof) from which the Training Plan -including the network architecture-is derived; (ii) the Learning Set (adult, pediatric, or mixed), (iii) Data Augmentation parameters, and (iv) the Transfer learning method (finetuning versus continual learning). In this work, we introduce PSAT (Pediatric Segmentation Approaches via Adult Augmentations and Transfer learning), a systematic study that investigates the impact of these axes on segmentation performance. We benchmark the derived strategies on two pediatric CT datasets and compare them with state-of-theart methods, including a commercial radiotherapy solution. PSAT highlights key pitfalls and provides actionable insights for improving pediatric segmentation. Our experiments reveal that a training plan based on an adult fingerprint dataset is misaligned with pediatric anatomy-resulting in significant performance degradation, especially when segmenting fine structures-and that continual learning strategies mitigate institutional shifts, thus enhancing generalization across diverse pediatric datasets. The code is available at https://github.com/ICANS-Strasbourg/PSAT.

Aman Sinha, Bogdan-Valentin Popescu, Xavier Coubez et al.

Language models (LMs) capabilities have grown with a fast pace over the past decade leading researchers in various disciplines, such as biomedical research, to increasingly explore the utility of LMs in their day-to-day applications. Domain specific language models have already been in use for biomedical natural language processing (NLP) applications. Recently however, the interest has grown towards medical language models and their understanding capabilities. In this paper, we investigate the medical conceptual grounding of various language models against expert clinicians for identification of hallmarks of immunotherapy in breast cancer abstracts. Our results show that pre-trained language models have potential to outperform large language models in identifying very specific (low-level) concepts.