Publications

Learning to accelerate distributed ADMM using graph neural networks

Doerks, Henri; Häusner, Paul; Hernández Escobar, Daniel; Sjölund, Jens

Part of Proceedings of The 8th Annual Learning for Dynamics and Control Conference, p. 1995-2020, 2026

Conference paper

Stochastic activator-inhibitor models: long-range cellular patterning from local kinetics and mechanochemical coupling

Blom, Erik; Menz, Gesina; Engblom, Stefan

Manuscript (preprint)

SLAM-AGS: Slide-Label Aware Multi-Task Pretraining Using Adaptive Gradient Surgery in Computational Cytology

Acerbis, Marco; Chatterjee, Swarnadip; Avenel, Christophe; Lindblad, Joakim

Part of 2026 IEEE 23rd International Symposium on Biomedical Imaging (ISBI), 2026

Conference paper

• DOI for SLAM-AGS: Slide-Label Aware Multi-Task Pretraining Using Adaptive Gradient Surgery in Computational Cytology

Group Equivariant Diffusion for Anomaly Detection in Computational Cytology

Chatterjee, Swarnadip; Sivakumar, Ssharvien Kumar; Mukhopadhyay, Anirban

Manuscript (preprint)

Learning Multimodal Normality Representations for Abnormal Cell Detection in Cytology and Single-Cell Microscopy

Chatterjee, Swarnadip; Lindblad, Joakim

Manuscript (preprint)

Needle in a Haystack: One-Class Representation Learning for Detecting Rare Malignant Cells in Computational Cytology

Chatterjee, Swarnadip; Basic, Vladimir; Capitanio, Arrigo; Göksel, Orcun et al.

Manuscript (preprint)

Learning from Normality in Computational Cytology: Deep Learning Methods for Rare Abnormal Cell Detection in Monomodal and Multimodal Cytology Images

Chatterjee, Swarnadip

2026

Doctoral thesis, comprehensive summary

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Delays in Spiking Neural Networks: A State Space Model Approach

Karilanova, Sanja; Dey, Subhrakanti; Özcelikkale, Ayca

2026

Conference paper

Time-Varying Deep State Space Models forSequences with Switching Dynamics

Karilanova, Sanja; Dey, Subhrakanti; Özcelikkale, Ayca

2026

Conference paper

Bridging Spiking Neural Networks and Deep State-Space Models

Karilanova, Sanja

2026

Doctoral thesis, comprehensive summary

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Federated Learning of Spiking Neural Networks under Heterogeneous Temporal Resolutions

Karilanova, Sanja; Dey, Subhrakanti; Özcelikkale, Ayca

Manuscript (preprint)

Efficient Modeling of Ion Diffusion in Solid-state Electrolyte Materials

Gustafsson, Hannes

2026

Doctoral thesis, comprehensive summary

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Investigating configuration entropy in ceramic superionic conductors

Schwarz, Fabian; Gustafsson, Hannes; Mace, Amber

Manuscript (preprint)

Impact of Carrier Concentration, Framework Potential and Structural Variations on Li-Diffusivity in Li_1+xAl_xTi_2–xPO₄

Gustafsson, Hannes; Schwarz, Fabian; Alex, Tamme; Mace, Amber

Manuscript (preprint)

Feynman integrals and modular forms

Sohnle, Yoann

2026

Doctoral thesis, comprehensive summary

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Parameters, Potentials and Probabilistic Methods in Molecular Modeling

Nordman, Alfred Torsten

2026

Doctoral thesis, comprehensive summary

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Bayesian Modeling of Polarizable Water: Lessons for Force Field Development

Nordman, Alfred T.; Engblom, Stefan; van der Spoel, David

Part of Journal of Chemical Theory and Computation, p. 5435-5447, 2026

Article in journal

• DOI for Bayesian Modeling of Polarizable Water: Lessons for Force Field Development
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Systematic Increase of Force Field Accuracy using the Alexandria Chemistry Toolkit

Nordman, Alfred T.; Rosenbaum, Måns K.; van der Spoel, David

Manuscript (preprint)

Robust Learning from Distributed and Heterogeneous Data

Ju, Li

2026

Doctoral thesis, comprehensive summary

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Canonical differential equations and intersection matrices

Duhr, Claude; Maggio, Sara; Porkert, Franziska; Semper, Cathrin et al.

Part of Journal of High Energy Physics (JHEP), 2026

Article in journal

• DOI for Canonical differential equations and intersection matrices
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OneFlowSBI: One Model, Many Queries for Simulation-Based Inference

Nautiyal, Mayank; Ju, Li; Ernfors, Melker; Hagland, Klara et al.

Manuscript (preprint)

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Epistemic Uncertainty Quantification for Pre-trained VLMs via Riemannian Flow Matching

Ju, Li; Nautiyal, Mayank; Hellander, Andreas; Vats, Ekta et al.

Manuscript (preprint)

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Electric double layer at the metal-oxide/electrolyte interface

Knijff, Lisanne; Jia, Mei; Zhang, Chao

Part of Encyclopedia of Solid Liquid Interfaces, p. 567-575, Elsevier, 2023

Chapter in book

• DOI for Electric double layer at the metal-oxide/electrolyte interface

An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation

Kříž, Kristian; Schmidt, Lisa; Andersson, Alfred T.; Walz, Marie-Madeleine et al.

Part of Journal of Chemical Information and Modeling, p. 412-431, 2023

Article, review/survey

• DOI for An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation
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Meshfree RBF-FD methods for numerical simulation of PDE problems

Larsson, Elisabeth; Mavrič, Bostjan; Michael, Andreas; Pooladi, Fatemeh et al.

Part of 9th European Thermal Sciences Conference (Eurotherm 2024) 10/06/2024 - 13/06/2024 Lake Bled, Slovenia, 2024

Conference paper

• DOI for Meshfree RBF-FD methods for numerical simulation of PDE problems
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Sampling string vacua using generative models

Walden, Moritz; Larfors, Magdalena

Part of Machine Learning, 2026

Article in journal

• DOI for Sampling string vacua using generative models
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Image-based metrics in ultrasound for estimation of global speed of sound

Denkin, Roman; Göksel, Orcun

Part of Ultrasonics, 2026

Article in journal

• DOI for Image-based metrics in ultrasound for estimation of global speed of sound
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Zero-shot Temporal Resolution Domain Adaptation for Spiking Neural Networks

Karilanova, Sanja; Fabre, Maxime; Neftci, Emre; Özçelikkale, Ayça

Part of Neural Networks, 2026

Article in journal

• DOI for Zero-shot Temporal Resolution Domain Adaptation for Spiking Neural Networks
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State-Space Model Inspired Multiple-Input Multiple-Output Spiking Neurons

Karilanova, Sanja; Dey, Subhrakanti; Özcelikkale, Ayca

Part of 2025 Neuro Inspired Computational Elements (NICE), 2025

Conference paper

• DOI for State-Space Model Inspired Multiple-Input Multiple-Output Spiking Neurons
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Low-Bit Data Processing Using Multiple-Output Spiking Neurons With Non-Linear Reset Feedback

Karilanova, Sanja; Dey, Subhrakanti; Özcelikkale, Ayca

Part of IEEE Journal on Selected Topics in Signal Processing, p. 1172-1186, 2025

Article in journal

• DOI for Low-Bit Data Processing Using Multiple-Output Spiking Neurons With Non-Linear Reset Feedback
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Bayesian three-point water models

Nordman, Alfred T.; Engblom, Stefan; Van der Spoel, David

Part of npj Computational Materials, 2025

Article in journal

• DOI for Bayesian three-point water models
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Computationally Efficient DFT-Based Sampling of Ion Diffusion in Crystalline Solids

Gustafsson, Hannes; Schwarz, Fabian; Smolders, Thijs J. A. M.; Barthel, Senja et al.

Part of Journal of Chemical Theory and Computation, p. 8669-8682, 2025

Article in journal

• DOI for Computationally Efficient DFT-Based Sampling of Ion Diffusion in Crystalline Solids
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From asymptotic distribution and vague convergence to uniform convergence, with numerical applications

Barbarino, Giovanni; Ekström, Sven-Erik; Garoni, Carlo; Meadon, David et al.

Part of Journal of Numerical Mathematics, p. 21-60, 2026

Article in journal

• DOI for From asymptotic distribution and vague convergence to uniform convergence, with numerical applications
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Sound Speed Approximation Using B-mode Image Alignment with Steered Focused Transmits

Bezek, Can Deniz; Koudelka, Paul; Denkin, Roman; Göksel, Orcun

Part of 2025 IEEE International Ultrasonics Symposium (IUS), p. 1-4, 2025

Conference paper

• DOI for Sound Speed Approximation Using B-mode Image Alignment with Steered Focused Transmits

Exploiting the Asymmetric Uncertainty Structure of Pre-trained VLMs on the Unit Hypersphere

Ju, Li; Andersson, Max; Fredriksson, Stina; Glöckner, Edward et al.

2025

Conference paper

On canonical differential equations for Calabi-Yau multi-scale Feynman integrals

Maggio, Sara; Sohnle, Yoann

Part of Journal of High Energy Physics (JHEP), 2025

Article in journal

• DOI for On canonical differential equations for Calabi-Yau multi-scale Feynman integrals
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Evolutionary machine learning of physics-based force fields in high-dimensional parameter-space

Van der Spoel, David; Marrades, Julián; Kriz, Kristian; Hosseini, A. Najla et al.

Part of Digital Discovery, p. 1925-1935, 2025

Article in journal

• DOI for Evolutionary machine learning of physics-based force fields in high-dimensional parameter-space
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Dipole orientation of hydrated gas phase proteins

Agelii, Harald; Jakobsson, Ellen L. S.; De Santis, Emiliano; Elfrink, Gideon et al.

Part of Physical Chemistry, Chemical Physics - PCCP, 2025

Article in journal

• DOI for Dipole orientation of hydrated gas phase proteins
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Looping the loops: a tale of elliptic dual Feynman integrals

Giroux, Mathieu; Pokraka, Andrzej; Porkert, Franziska; Sohnle, Yoann

Part of 16th International Symposium on Radiative Corrections, 2024

Conference paper

• DOI for Looping the loops: a tale of elliptic dual Feynman integrals
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Interpretable neural network predictions of high-intensity femtosecond x-ray free-electron laser pulses using sulfur K-shell emission spectra

Agelii, Harald; Bellisario, Alfredo; Caleman, Carl; Timneanu, Nicusor et al.

Part of Physical Review Research, 2025

Article in journal

• DOI for Interpretable neural network predictions of high-intensity femtosecond x-ray free-electron laser pulses using sulfur K-shell emission spectra

Image-based tissue characterization with sound speed

Denkin, Roman; Göksel, Orcun

2025

Conference paper

Modelling Population-Level Hes1 Dynamics: Insights from a Multi-framework Approach

Menz, Gesina; Engblom, Stefan

Part of Bulletin of Mathematical Biology, 2025

Article in journal

• DOI for Modelling Population-Level Hes1 Dynamics: Insights from a Multi-framework Approach
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Learning group invariant Calabi-Yau metrics by fundamental domain projections

Hendi, Yacoub; Larfors, Magdalena; Walden, Moritz

Part of Machine Learning, 2025

Article in journal

• DOI for Learning group invariant Calabi-Yau metrics by fundamental domain projections
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PiNN: Equivariant Neural Network Suite for Modeling Electrochemical Systems

Li, Jichen; Knijff, Lisanne; Zhang, Zhan-Yun; Andersson, Linnéa et al.

Part of Journal of Chemical Theory and Computation, p. 1382-1395, 2025

Article in journal

• DOI for PiNN: Equivariant Neural Network Suite for Modeling Electrochemical Systems
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Spectral properties of flipped Toeplitz matrices and computational applications

Barbarino, Giovanni; Ekström, Sven-Erik; Garoni, Carlo; Meadon, David et al.

Part of Applied Mathematics and Computation, 2025

Article in journal

• DOI for Spectral properties of flipped Toeplitz matrices and computational applications
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Topics in Cohomological Field Theory: Let's Twist Again!

Mauch, Roman

2025

Doctoral thesis, comprehensive summary

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The Equivariant B model

Festuccia, Guido; Mauch, Roman; Zabzine, Maxim

Part of Journal of High Energy Physics (JHEP), 2025

Article in journal

• DOI for The Equivariant B model
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Codimension-Two Defects and SYM on Orbifolds

Mauch, Roman; Ruggeri, Lorenzo

Part of Journal of High Energy Physics (JHEP), 2025

Article in journal

• DOI for Codimension-Two Defects and SYM on Orbifolds
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From 5d flat connections to 4d fluxes (the art of slicing the cone)

Lundin, Jim; Mauch, Roman; Ruggeri, Lorenzo

Part of Journal of High Energy Physics (JHEP), 2023

Article in journal

• DOI for From 5d flat connections to 4d fluxes (the art of slicing the cone)
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Probabilistic Models of Genetic Variability in Sequence Evolution

Müller-Widmann, Rebekka

2025

Doctoral thesis, comprehensive summary

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