MP
Marie Piraud
cs.CVeess.IVcs.LGcond-mat.quant-gascs.AIbioinformaticscond-mat.dis-nnBraTSDeep Learningmachine learning
On Valency
published · living versionsW_ctyr365s·v1 · currentpublished
Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge
with Spyridon Bakas, Mauricio Reyes, Andras Jakab, Stefan Bauer +422
1 version
Preprints & journals
88 papers in the corpus · 2011–2026A scalable human neuromuscular organoid platform enables lineage-specific analysis of drug responses in spinal muscular atrophy.10.64898/2026.08.23.745904v1 · Lahmann, I., Garcia-Perez, A., El-Shimy, I. A. et al.2026 · 0 citationsbioRxiv
Enhancing Maturation of Human Neuromuscular Organoids via Electrical Stimulation.42325128 · Moysidou, Chrysanthi-Maria, Afonso Martins, Inês, El-Shimy, Ismail Amr et al.2026 · 1 citationAdvanced science (Weinheim, Baden-Wurttemberg, Germany). 2026;13(50):e22762
Lifespan Analysis of the Lung Epithelium Reveals Inflammatory Reprogramming and Regenerative Decline10.64898/2026.06.01.729288v1 · Boosarpu, G., Guenther, E. M., Steinchen, C. et al.2026 · 0 citationsbioRxiv
Fast Cubical Persistent Homology on 2D and 3D Images via Union-Find, Pruning, and Lookup Tables2606.04801v1 · Titouan Le Breton, Karol Szustakowski, Marie Piraud2026 · 0 citationsarXiv
A deep-learning framework reveals whole-body perturbations at cell level.42162424 · Kaltenecker, Doris, Horvath, Izabela, Al-Maskari, Rami et al.2026 · 4 citationsNature. 2026;655(8124):1016-1026
Enhancing efficiency in pediatric brain tumor segmentation using a pathologically diverse single-center clinical dataset.41890357 · Piffer, Arianna, Buchner, Josef Alois, Gennari, Antonio Giulio et al.2026 · 2 citationsNeuro-oncology advances. 2026;8(1):vdag024
GlioMODA: Robust glioma segmentation in clinical routine.41841144 · Canisius, Julian, Buchner, Josef, Rosier, Marcel et al.2026 · 4 citationsNeuro-oncology advances. 2026;8(1):vdag034
Leveraging Multi-Rater Annotations to Calibrate Object Detectors in Microscopy Imaging2601.23007v1 · Francesco Campi, Lucrezia Tondo, Ekin Karabati et al.2026 · 0 citationsarXiv
Cortex-Wide Preservation of Multi-Stimulus Information across Degrees of Network Synchronization10.64898/2025.11.28.690948v1 · Bodea, S. V., Laiz, R. G., Williams, R. H. et al.2025 · 0 citationsbioRxiv
OneProt: Towards multi-modal protein foundation models via latent space alignment of sequence, structure, binding sites and text encoders.41231876 · Flöge, Klemens, Udayakumar, Srisruthi, Sommer, Johanna et al.2025 · 8 citationsPLoS computational biology. 2025;21(11):e1013679
Guided maturation of human neuromuscular organoids via electrical stimulation10.1101/2025.10.30.685366v1 · Moysidou, C.-M., Martins, I. A., El-Shimy, I. A. et al.2025 · 1 citationbioRxiv
Preserving instance continuity and length in segmentation through connectivity-aware loss computation2509.03154v1 · Karol Szustakowski, Luk Frank, Julia Esser et al.2025 · 0 citationsarXiv
Enhancing efficiency in paediatric brain tumour segmentation using a pathologically diverse single-center clinical dataset2507.22152v2 · A. Piffer, J. A. Buchner, A. G. Gennari et al.2025 · 0 citationsarXiv
Forest-Guided Clustering -- Shedding Light into the Random Forest Black Box2507.19455v1 · Lisa Barros de Andrade e Sousa, Gregor Miller, Ronan Le Gleut et al.2025 · 0 citationsarXiv
BrainLesion Suite: A Flexible and User-Friendly Framework for Modular Brain Lesion Image Analysis2507.09036v1 · Florian Kofler, Marcel Rosier, Mehdi Astaraki et al.2025 · 0 citationsarXiv
BraTS orchestrator : Democratizing and Disseminating state-of-the-art brain tumor image analysis2506.13807v1 · Florian Kofler, Marcel Rosier, Mehdi Astaraki et al.2025 · 1 citationarXiv
Analysis of the MICCAI Brain Tumor Segmentation -- Metastases (BraTS-METS) 2025 Lighthouse Challenge: Brain Metastasis Segmentation on Pre- and Post-treatment MRI2504.12527v3 · Nazanin Maleki, Raisa Amiruddin, Ahmed W. Moawad et al.2025 · 1 citationarXiv
TopEC: prediction of Enzyme Commission classes by 3D graph neural networks and localized 3D protein descriptor.40108108 · van der Weg, Karel, Merdivan, Erinc, Piraud, Marie et al.2025 · 22 citationsNature communications. 2025;16(1):2737
DrugDiff: small molecule diffusion model with flexible guidance towards molecular properties.40001177 · Oestreich, Marie, Merdivan, Erinc, Lee, Michael et al.2025 · 17 citationsJournal of cheminformatics. 2025;17(1):23
Biases in machine-learning models of human single-cell data.39972066 · Willem, Theresa, Shitov, Vladimir A, Luecken, Malte D et al.2025 · 9 citationsNature cell biology. 2025;27(3):384-392
Formation of amyloid-like HTTex1 aggregates in neurons, downregulation of synaptic proteins and early mortality of Huntington's disease flies are causally linked10.1101/2025.02.06.636778v1 · Ast, A., Roth, L., Brusendorf, L. et al.2025 · 0 citationsbioRxiv
The Brain Tumor Segmentation - Metastases (BraTS-METS) Challenge 2023: Brain Metastasis Segmentation on Pre-treatment MRI.37396600 · Moawad, Ahmed W, Janas, Anastasia, Baid, Ujjwal et al.2025 · 4 citationsArXiv. 2024
LungVis 1.0: an automatic AI-powered 3D imaging ecosystem unveils spatial profiling of nanoparticle delivery and acinar migration of lung macrophages.39604430 · Yang, Lin, Liu, Qiongliang, Kumar, Pramod et al.2024 · 24 citationsNature communications. 2024;15(1):10138
The Brain Tumor Segmentation (BraTS) Challenge 2023: Brain MR Image Synthesis for Tumor Segmentation (BraSyn).37608932 · Li, Hongwei Bran, Conte, Gian Marco, Hu, Qingqiao et al.2026 · 21 citationsArXiv. 2024
Probe set selection for targeted spatial transcriptomics.39558096 · Kuemmerle, Louis B, Luecken, Malte D, Firsova, Alexandra B et al.2024 · 57 citationsNature methods. 2024;21(12):2260-2270
OneProt: Towards Multi-Modal Protein Foundation Models2411.04863v3 · Klemens Floge, Srisruthi Udayakumar, Johanna Sommer et al.2024 · 0 citationsarXiv
MultiOrg: A Multi-rater Organoid-detection Dataset2410.14612v2 · Christina Bukas, Harshavardhan Subramanian, Fenja See et al.2024 · 3 citationsarXiv
Radiomics-based prediction of local control in patients with brain metastases following postoperative stereotactic radiotherapy.38813990 · Buchner, Josef A, Kofler, Florian, Mayinger, Michael et al.2024 · 22 citationsNeuro-oncology. 2024;26(9):1638-1650
Deep Learning and 3D Imaging Reveal Whole-Body Alterations in Obesity10.1101/2024.08.18.608300v1 · Kaltenecker, D., Horvath, I., Al-Maskari, R. et al.2024 · 1 citationbioRxiv
BraTS-PEDs: Results of the Multi-Consortium International Pediatric Brain Tumor Segmentation Challenge 20232407.08855v3 · Anahita Fathi Kazerooni, Nastaran Khalili, Xinyang Liu et al.2024 · 20 citationsMachine.Learning.for.Biomedical.Imaging. 3 (2025)
The Brain Tumor Segmentation (BraTS) Challenge 2023: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs).37292481 · Kazerooni, Anahita Fathi, Khalili, Nastaran, Liu, Xinyang et al.2026 · 61 citationsArXiv. 2024
Analysis of the BraTS 2023 Intracranial Meningioma Segmentation Challenge2405.09787v2 · Dominic LaBella, Ujjwal Baid, Omaditya Khanna et al.2024 · 11 citationsMachine.Learning.for.Biomedical.Imaging. 3 (2025)
MISATO: machine learning dataset of protein-ligand complexes for structure-based drug discovery.38730184 · Siebenmorgen, Till, Menezes, Filipe, Benassou, Sabrina et al.2024 · 85 citationsNature computational science. 2024;4(5):367-378
The Brain Tumor Segmentation in Pediatrics (BraTS-PEDs) Challenge: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs)2404.15009v4 · Anahita Fathi Kazerooni, Nastaran Khalili, Xinyang Liu et al.2024 · 11 citationsarXiv
Virtual reality-empowered deep-learning analysis of brain cells.38649742 · Kaltenecker, Doris, Al-Maskari, Rami, Negwer, Moritz et al.2024 · 38 citationsNature methods. 2024;21(7):1306-1315
Denoising Diffusion Models for 3D Healthy Brain Tissue Inpainting2403.14499v1 · Alicia Durrer, Julia Wolleb, Florentin Bieder et al.2024 · 20 citationsarXiv
TopEC: Improved classification of enzyme function by a localized 3D protein descriptor and 3D Graph Neural Networks10.1101/2024.01.31.578271v1 · van der Weg, K., Merdivan, E., Piraud, M. et al.2024 · 2 citationsbioRxiv
Improved prediction of bacterial CRISPRi guide efficiency from depletion screens through mixed-effect machine learning and data integration.38200565 · Yu, Yanying, Gawlitt, Sandra, de Andrade E Sousa, Lisa Barros et al.2024 · 26 citationsGenome biology. 2024;25(1):13
Panoptica -- instance-wise evaluation of 3D semantic and instance segmentation maps2312.02608v1 · Florian Kofler, Hendrik Moller, Josef A. Buchner et al.2023 · 2 citationsarXiv
Identifying core MRI sequences for reliable automatic brain metastasis segmentation.37678623 · Buchner, Josef A, Peeken, Jan C, Etzel, Lucas et al.2026 · 17 citationsRadiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology. 2023;188:109901
Formate promotes invasion and metastasis in reliance on lipid metabolism.37651228 · Delbrouck, Catherine, Kiweler, Nicole, Chen, Oleg et al.2023 · 20 citationsCell reports. 2023;42(9):113034
Providing AI expertise as an infrastructure in academia.37602219 · Piraud, Marie, Camero, Andrés, Götz, Markus et al.2023 · 3 citationsPatterns (New York, N.Y.). 2023;4(8):100819
Framing image registration as a landmark detection problem for label-noise-aware task representation (HitR)2308.01318v2 · Diana Waldmannstetter, Ivan Ezhov, Benedikt Wiestler et al.2023 · 0 citationsarXiv
Whole-body cellular mapping in mouse using standard IgG antibodies.37430076 · Mai, Hongcheng, Luo, Jie, Hoeher, Luciano et al.2024 · 122 citationsNature biotechnology. 2024;42(4):617-627
The Brain Tumor Segmentation (BraTS-METS) Challenge 2023: Brain Metastasis Segmentation on Pre-treatment MRI2306.00838v3 · Ahmed W. Moawad, Anastasia Janas, Ujjwal Baid et al.2023 · 40 citationsarXiv
The Brain Tumor Segmentation (BraTS) Challenge 2023: Glioma Segmentation in Sub-Saharan Africa Patient Population (BraTS-Africa)2305.19369v1 · Maruf Adewole, Jeffrey D. Rudie, Anu Gbadamosi et al.2023 · 41 citationsarXiv
The Brain Tumor Segmentation (BraTS) Challenge 2023: Glioma Segmentation in Sub-Saharan Africa Patient Population (BraTS-Africa).37396608 · Adewole, Maruf, Rudie, Jeffrey D, Gbdamosi, Anu et al.2026 · 3 citationsArXiv. 2023
Echo2Pheno: a deep-learning application to uncover echocardiographic phenotypes in conscious mice.37221250 · Bukas, Christina, Galter, Isabella, da Silva-Buttkus, Patricia et al.2023 · 7 citationsMammalian genome : official journal of the International Mammalian Genome Society. 2023;34(2):200-215
Cytokine signaling converging on IL11 in ILD fibroblasts provokes aberrant epithelial differentiation signatures.37266432 · Kastlmeier, Miriam T, Gonzalez-Rodriguez, Erika, Cabanis, Phoebe et al.2023 · 22 citationsFrontiers in immunology. 2023;14:1128239
The Brain Tumor Segmentation (BraTS) Challenge: Local Synthesis of Healthy Brain Tissue via Inpainting2305.08992v3 · Florian Kofler, Felix Meissen, Felix Steinbauer et al.2023 · 5 citationsarXiv
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