Publications

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

Menz, Gesina; Engblom, Stefan

Part of Bulletin of Mathematical Biology, 2025

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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

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• DOI for Learning group invariant Calabi-Yau metrics by fundamental domain projections
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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

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• DOI for Spectral properties of flipped Toeplitz matrices and computational applications
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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

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• DOI for PiNN: Equivariant Neural Network Suite for Modeling Electrochemical Systems
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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

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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

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Probabilistic Models of Genetic Variability in Sequence Evolution

Müller-Widmann, Rebekka

2025

Doctoral thesis, comprehensive summary

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Probabilistic models of codon sequence evolution during speciation

Müller-Widmann, Rebekka; Mugal, Carina F.; Kaj, Ingemar

Manuscript (preprint)

Signatures of GC-biased gene conversion across different time scales display the underlying recombination hotspot dynamics

Müller-Widmann, Rebekka; Kaj, Ingemar; Mugal, Carina F.

Manuscript (preprint)

Detection of Extremely Sparse Key Instances in Whole Slide Cytology Images via Self-supervised One-class Representation Learning

Chatterjee, Swarnadip; Göksel, Orcun; Sladoje, Nataša; Lindblad, Joakim

Part of Pattern Recognition, p. 408-421, 2024

Conference paper

• DOI for Detection of Extremely Sparse Key Instances in Whole Slide Cytology Images via Self-supervised One-class Representation Learning

Matrix-less spectral approximation for large structured matrices

Barbarino, Giovanni; Claesson, Melker; Ekström, Sven-Erik; Garoni, Carlo et al.

Part of BIT Numerical Mathematics, 2025

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Dipole and Charge Prediction for Electrochemical Systems from Atomistic Machine Learning

Knijff, Lisanne

2025

Doctoral thesis, comprehensive summary

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PiNN: equivariant neural network suite for modelling electrochemical systems

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

2024

Article in journal

• DOI for PiNN: equivariant neural network suite for modelling electrochemical systems

InfoHier: Hierarchical Information Extraction via Encoding and Embedding

Zhang, Tianru; Ju, Li; Singh, Prashant; Toor, Salman

Manuscript (preprint)

Modeling of Nanomaterials for Supercapacitors: Beyond Carbon Electrodes

Bi, Sheng; Knijff, Lisanne; Lian, Xiliang; van Hees, Alicia et al.

Part of ACS Nano, p. 19931-19949, 2024

Article, review/survey

• DOI for Modeling of Nanomaterials for Supercapacitors: Beyond Carbon Electrodes
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Federated learning for predicting compound mechanism of action based on image-data from cell painting

Ju, Li; Hellander, Andreas; Spjuth, Ola

Part of Artificial Intelligence in the Life Sciences, 2024

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• DOI for Federated learning for predicting compound mechanism of action based on image-data from cell painting
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Accelerating Fair Federated Learning: Adaptive Federated Adam

Ju, Li; Zhang, Tianru; Toor, Salman; Hellander, Andreas

Part of IEEE Transactions on Machine Learning in Communications and Networking, p. 1017-1032, 2024

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• DOI for Accelerating Fair Federated Learning: Adaptive Federated Adam
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The soaring kite: a tale of two punctured tori

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

Part of Journal of High Energy Physics (JHEP), 2024

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"The six blind men and the elephant": An Interdisciplinary Selection of Measurement Features

Ellingsen, Ask; Lundholm, Douglas; Magnot, Jean-Pierre

Part of Geometric Methods in Physics XL, p. 275-307, 2024

Conference paper

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Computer Vision and Explainability in Human-Human and Human-Robot Interaction

Fraile, Marc

2024

Doctoral thesis, comprehensive summary

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Are We Friends: End-to-End Prediction of Child Rapport in Guided Play

Fraile, Marc; Varni, Giovanna; Lindblad, Joakim; Sladoje, Nataša et al.

2024

Conference paper

UpStory: the Uppsala Storytelling dataset

Fraile, Marc; Calvo-Barajas, Natalia; Apeiron, Anastasia Sophia; Varni, Giovanna et al.

Manuscript (preprint)

Super Yang-Mills on branched covers and weighted projective spaces

Mauch, Roman; Ruggeri, Lorenzo

Part of Journal of High Energy Physics (JHEP), 2024

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Demo Abstract: Blades: A Unified Benchmark Suite for Byzantine-Resilient in Federated Learning

Li, Shenghui; Ngait, Edith C. -H.; Ye, Fanghua; Ju, Li et al.

Part of 9TH ACM/IEEE CONFERENCE ON INTERNET OF THINGS DESIGN AND IMPLEMENTATION, IOTDI 2024, p. 229-230, 2024

Conference paper

• DOI for Demo Abstract: Blades: A Unified Benchmark Suite for Byzantine-Resilient in Federated Learning

Blades: A Unified Benchmark Suite for Byzantine Attacks and Defenses in Federated Learning

Li, Shenghui; Ngai, Edith C. H.; Ye, Fanghua; Ju, Li et al.

Part of 2024 IEEE/ACM Ninth International Conference on Internet-of-Things Design and Implementation (IoTDI), p. 158-169, 2024

Conference paper

• DOI for Blades: A Unified Benchmark Suite for Byzantine Attacks and Defenses in Federated Learning

A Wright-Fisher graph model and the impact of directional selection on genetic variation

Kaj, Ingemar; Mugal, Carina F.; Müller-Widmann, Rebekka

Part of Theoretical Population Biology, p. 13-24, 2024

Article in journal

• DOI for A Wright-Fisher graph model and the impact of directional selection on genetic variation
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The β maps: Strong clustering and distribution results on the complex unit circle

Schiavoni-Piazza, Alec J. A.; Meadon, David; Serra, Stefano

Part of Linear Algebra and its Applications, p. 365-383, 2024

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• DOI for The β maps: Strong clustering and distribution results on the complex unit circle
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Modeling and Estimation of Impulsive Biomedical Systems

Runvik, Håkan

2023

Licentiate thesis, comprehensive summary

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Robust One-Step Estimation of Impulsive Time Series

Runvik, Håkan; Medvedev, Alexander

Manuscript (preprint)

• DOI for Robust One-Step Estimation of Impulsive Time Series

Spike timing–based coding in neuromimetic tactile system enables dynamic object classification

Chen, Libo; Karilanova, Sanja; Chaki, Soumi; Wen, Chenyu et al.

Part of Science, p. 660-665, 2024

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• DOI for Spike timing–based coding in neuromimetic tactile system enables dynamic object classification
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Reversible Hydration Enabling High-Rate Aqueous Li-Ion Batteries

Zhang, Leiting; Kühling, Franziska; Mattsson, Agnes-Matilda; Knijff, Lisanne et al.

Part of ACS Energy Letters, p. 959-966, 2024

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• DOI for Reversible Hydration Enabling High-Rate Aqueous Li-Ion Batteries
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Predicting Ion Diffusion from the Shape of Potential Energy Landscapes

Gustafsson, Hannes; Kozdra, Melania; Smit, Berend; Barthel, Senja et al.

Part of Journal of Chemical Theory and Computation, p. 18-29, 2024

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• DOI for Predicting Ion Diffusion from the Shape of Potential Energy Landscapes
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Cycles in Impulsive Goodwin's Oscillators of arbitrary order☆

Proskurnikov, Anton V.; Runvik, Håkan; Medvedev, Alexander

Part of Automatica, 2024

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PiNNwall: Heterogeneous Electrode Models from Integrating Machine Learning and Atomistic Simulation

Dufils, Thomas; Knijff, Lisanne; Shao, Yunqi; Zhang, Chao

Part of Journal of Chemical Theory and Computation, p. 5199-5209, 2023

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• DOI for PiNNwall: Heterogeneous Electrode Models from Integrating Machine Learning and Atomistic Simulation
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Investigating the Relevance of Contextual Information Towards Improving Deep CNN Based Oral Cancer Screening on Whole Slide Cytology Samples

Chatterjee, Swarnadip; Sladoje, Nataša; Lindblad, Joakim

2023

Conference paper

A case study in designing trustworthy interactions: implications for socially assistive robotics

Zhong, Mengyu; Fraile, Marc; Castellano, Ginevra; Winkle, Katie

Part of Frontiers in Computer Science, 2023

Article in journal

• DOI for A case study in designing trustworthy interactions: implications for socially assistive robotics
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A numerical investigation of some RBF-FD error estimates

Larsson, Elisabeth; Mavrič, Boštjan; Michael, Andreas; Pooladi, Fatemeh

Part of Dolomites Research Notes on Approximation, p. 78-95, 2022

Article in journal

• DOI for A numerical investigation of some RBF-FD error estimates

DCNN based Oral Cancer Screening using Whole Slide Cytology Images: Effect of Increased Patch Size

Chatterjee, Swarnadip; Sladoje, Nataša; Lindblad, Joakim

2022

Conference paper

End-to-End Learning and Analysis of Infant Engagement During Guided Play: Prediction and Explainability

Fraile, Marc; Fawcett, Christine; Lindblad, Joakim; Sladoje, Nataša et al.

Part of ICMI '22, p. 444-454, 2022

Conference paper

• DOI for End-to-End Learning and Analysis of Infant Engagement During Guided Play: Prediction and Explainability
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Impulsive time series modeling with application to luteinizing hormone data

Runvik, Håkan; Medvedev, Alexander

Part of Frontiers in Endocrinology, 2022

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• DOI for Impulsive time series modeling with application to luteinizing hormone data
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Input Sequence and Parameter Estimation in Impulsive Biomedical Models

Runvik, Håkan; Medvedev, Alexander

Part of 2022 European Control Conference (ECC), p. 253-258, 2022

Conference paper

• DOI for Input Sequence and Parameter Estimation in Impulsive Biomedical Models

An efficient linked list for molecular simulations on a spherical surface

Vélez Ramirez, Esteban; Elvingson, Christer

Part of Journal of Physics A, 2022

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• DOI for An efficient linked list for molecular simulations on a spherical surface
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Index of the transversally elliptic complex in Pestunization

Mauch, Roman; Ruggeri, Lorenzo

Part of Journal of Physics A, 2022

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• DOI for Index of the transversally elliptic complex in Pestunization
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Finite-field coupling via learning the charge response kernel

Shao, Yunqi; Andersson, Linnéa; Knijff, Lisanne; Zhang, Chao

Part of Electronic Structure, 2022

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• DOI for Finite-field coupling via learning the charge response kernel
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A Nearly Neutral Model of Molecular Signatures of Natural Selection after Change in Population Size

Müller, Rebekka; Kaj, Ingemar; Mugal, Carina

Part of Genome Biology and Evolution, 2022

Article in journal

• DOI for A Nearly Neutral Model of Molecular Signatures of Natural Selection after Change in Population Size
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Bayesian Monitoring of COVID-19 in Sweden

Marin, Robin; Runvik, Håkan; Medvedev, Alexander; Engblom, Stefan

Part of Epidemics, 2023

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• DOI for Bayesian Monitoring of COVID-19 in Sweden
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Proactive Autoscaling for Edge Computing Systems with Kubernetes

Ju, Li; Singh, Prashant; Toor, Salman

2021

Conference paper

• DOI for Proactive Autoscaling for Edge Computing Systems with Kubernetes

Machine learning inference of molecular dipole moment in liquid water

Knijff, Lisanne; Zhang, Chao

Part of Machine Learning, 2021

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• DOI for Machine learning inference of molecular dipole moment in liquid water
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Automatic Analysis of Infant Engagement during Play: An End-to-end Learning and Explainable AI Pilot Experiment

Fraile, Marc; Lindblad, Joakim; Fawcett, Christine; Sladoje, Natasa et al.

Part of Companion Publication of the 2021 International Conference on Multimodal Interaction, p. 403-407, 2021

Conference paper

• DOI for Automatic Analysis of Infant Engagement during Play: An End-to-end Learning and Explainable AI Pilot Experiment
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