• Targeted Branching for the Maximum Independent Set Problem Using Graph Neural Networks 

  Langedal, Kenneth; Hespe, Demian; Sanders, Peter (Journal article; Peer reviewed, 2024)

  Identifying a maximum independent set is a fundamental NP-hard problem. This problem has several real-world applications and requires finding the largest possible set of vertices not adjacent to each other in an undirected ...

• Graph Neural Networks in Algorithm Engineering 

  Langedal, Kenneth (Doctoral thesis, 2025-03-27)

  Graf Nevrale Nettverk (GNN) er ny teknologi innen kunstig intelligens. GNN viderefører de vellykkede ideene fra konvensjonell dyplæring til å fungere på grafer. For ulike grafteoretiske problemer har GNN blitt et nytt ...

• PACE Solver Description: LUNCH - Linear Uncrossing Heuristics 

  Langedal, Kenneth; Bentert, Matthias; Blanco, Thorgal; Drange, Pål Grønås (Journal article; Peer reviewed, 2024)

  The 2024 PACE challenge is on One-Sided Crossing Minimization: Given a bipartite graph with one fixed and one free layer, compute an ordering of the vertices in the free layer that minimizes the number of edge crossings ...

• The category of iterative sets in homotopy type theory and univalent foundations 

  Gratzer, Daniel; Gylterud, Håkon Robbestad; Mörtberg, Anders; Stenholm, Elisabeth (Journal article; Peer reviewed, 2024)

  When working in homotopy type theory and univalent foundations, the traditional role of the category of sets, Set, is replaced by the category hSet of homotopy sets (h-sets); types with h-propositional identity types. Many ...

• First-Order Temporal Logic on Finite Traces: Semantic Properties, Decidable Fragments, and Applications 

  Artale, Alessandro; Mazzullo, Andrea; Ozaki Rivera Castillo, Ana Helena (Journal article; Peer reviewed, 2024)

  Formalisms based on temporal logics interpreted over finite strict linear orders, known in the literature as finite traces, have been used for temporal specification in automated planning, process modelling, (runtime) ...

• Tool-Augmented Human Creativity 

  Hole, Kjell Jørgen (Journal article; Peer reviewed, 2024)

  Creativity is the hallmark of human intelligence. Roli et al. (Frontiers in Ecology and Evolution 9:806283, 2022) state that algorithms cannot achieve human creativity. This paper analyzes cooperation between humans and ...

• The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update 

  Abueg, Linelle Ann L.; Afgan, Enis; Allart, Olivier; Awan, Ahmed H.; Bacon, Wendi A.; Baker, Dannon; Bassetti, Madeline; Batut, Bérénice; Bernt, Matthias; Blankenberg, Daniel; Bombarely, Aureliano; Bretaudeau, Anthony; Bromhead, Catherine J.; Burke, Melissa L.; Capon, Patrick K.; Čech, Martin; Chavero-Díez, María; Chilton, John M.; Collins, Tyler J.; Coppens, Frederik; Coraor, Nate; Cuccuru, Gianmauro; Cumbo, Fabio; Davis, John; De Geest, Paul F.; de Koning, Willem; Demko, Martin; DeSanto, Assunta; Begines, José Manuel Domínguez; Doyle, Maria A.; Droesbeke, Bert; Erxleben-Eggenhofer, Anika; Föll, Melanie C.; Formenti, Giulio; Fouilloux, Anne; Gangazhe, Rendani; Genthon, Tanguy; Goecks, Jeremy; Gonzalez Beltran, Alejandra N.; Goonasekera, Nuwan A.; Goué, Nadia; Griffin, Timothy J.; Grüning, Björn A.; Guerler, Aysam; Gundersen, Sveinung; Gustafsson, Ove Johan Ragnar; Hall, Christina; Harrop, Thomas W.; Hecht, Helge; Heidari, Alireza; Heisner, Tillman; Heyl, Florian; Hiltemann, Saskia; Hotz, Hans-Rudolf; Hyde, Cameron J.; Jagtap, Pratik D.; Jakiela, Julia; Johnson, James E.; Joshi, Jayadev; Jossé, Marie; Jum’ah, Khaled; Kalaš, Matúš; Kamieniecka, Katarzyna; Kayikcioglu, Tunc; Konkol, Markus; Kostrykin, Leonid; Kucher, Natalie; Kumar, Anup; Kuntz, Mira; Lariviere, Delphine; Lazarus, Ross; Le Bras, Yvan; Le Corguillé, Gildas; Lee, Justin; Leo, Simone; Liborio, Leandro; Libouban, Romane; López Tabernero, David; Lopez-Delisle, Lucille; Los, Laila S.; Mahmoud, Alexandru; Makunin, Igor; Marin, Pierre; Mehta, Subina; Mok, Winnie; Moreno, Pablo A.; Morier-Genoud, François; Mosher, Stephen; Müller, Teresa; Nasr, Engy; Nekrutenko, Anton; Nelson, Tiffanie M.; Oba, Asime J.; Ostrovsky, Alexander; Polunina, Polina V.; Poterlowicz, Krzysztof; Price, Elliott J.; Price, Gareth R.; Rasche, Helena; Raubenolt, Bryan; Royaux, Coline; Sargent, Luke; Savage, Michelle T.; Savchenko, Volodymyr; Savchenko, Denys; Schatz, Michael C.; Seguineau, Pauline; Serrano-Solano, Beatriz; Soranzo, Nicola; Srikakulam, Sanjay Kumar; Suderman, Keith; Syme, Anna E.; Tangaro, Marco Antonio; Tedds, Jonathan A.; Tekman, Mehmet; Thang, Wai Cheng; Thanki, Anil S.; Uhl, Michael; van den Beek, Marius; Varshney, Deepti; Vessio, Jenn; Videm, Pavankumar; Von Kuster, Greg; Watson, Gregory R.; Whitaker-Allen, Natalie; Winter, Uwe; Wolstencroft, Martin; Zambelli, Federico; Zierep, Paul; Zoabi, Rand (Journal article; Peer reviewed, 2024)

  Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform ...

• Integration of graph neural networks and genome-scale metabolic models for predicting gene essentiality 

  Hasibi, Ramin; Michoel, Tom Luk R; Oyarzún, Diego A. (Journal article; Peer reviewed, 2024)

  Genome-scale metabolic models are powerful tools for understanding cellular physiology. Flux balance analysis (FBA), in particular, is an optimization-based approach widely employed for predicting metabolic phenotypes. In ...

• Poly(U) polymerase activity in Caenorhabditis elegans regulates abundance and tailing of sRNA and mRNA 

  Kelley, Leanne H.; Caldas, Ian V.; Sullenberger, Matthew T.; Yongblah, Kevin E.; Niazi, Adnan Muhammad; Iyer, Anoop; Li, Yini; Tran, Patrick Minty; Valen, Eivind; Ahmed-Braimah, Yasir H.; Maine, Eleanor M. (Journal article; Peer reviewed, 2024)

  Terminal nucleotidyltransferases add nucleotides to the 3′ end of RNA to modify their stability and function. In Caenorhabditis elegans, the terminal uridyltransferases/poly(U) polymerases PUP-1 (aka CID-1, CDE-1), PUP-2, ...

• Mapping Graphs to Trees : Partition Trees, Leaf Powers and Decompositions 

  Høgemo, Svein (Doctoral thesis, 2025-02-27)

  Mange anvendelsar i informatikken kan kokast ned til å finne struktur i datamengder. Datamengder kan gjerne framstillast som grafar, og mange slags strukturar kan framstillast som tre. Difor er det ofte ønskjeleg å overføre ...

• Electricity demand forecasting at distribution and household levels using explainable causal graph neural network 

  Miraki, Amir; Parviainen, Pekka; Arghandeh, Reza (Journal article; Peer reviewed, 2024)

  Forecasting electricity demand is an essential part of the smart grid to ensure a stable and reliable power grid. With the increasing integration of renewable energy resources into the grid, forecasting the demand for ...

• Comprehensive contact tracing during an outbreak of alpha-variant SARS-CoV-2 in a rural community reveals less viral genomic diversity and higher household secondary attack rates than expected 

  Sivertsen, Audun; Mortensen, Nicolay; Solem, Unni; Valen, Eivind; Bullita, Marie Francoise; Wensaas, Knut-Arne; Litleskare, Sverre; Rørtveit, Guri; Grewal, Harleen; Ulvestad, Elling (Journal article; Peer reviewed, 2024)

  Sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes throughout the COVID-19 pandemic has generated a wealth of data on viral evolution across populations, but only a few studies have so far ...

• Explorations of Physical Attacks Against Embedded Systems and Their Defences 

  Askeland, Amund (Doctoral thesis, 2025-02-05)

  Til dagleg omgir me oss med hundrevis av elektroniske system. Desse systema, som gjerne blir kalla innvevde system, finst i bilane me køyrer, i kritisk infrastruktur, og i heimane våre. Som brukarar tek me ofte for gitt ...

• Who Watches the Watchers: Attacking Glitch Detection Circuits 

  Askeland, Amund; Petkova-Nikova, Svetla Iordanova; Nikov, Ventzislav (Journal article, 2024)

  Over the last decades, fault injection attacks have been demonstrated to be an effective method for breaking the security of electronic devices. Some types of fault injection attacks, like clock and voltage glitching, ...

• Single-Cell Gene-Regulatory Networks of Advanced Symptomatic Atherosclerosis 

  Mocci, Giuseppe; Sukhavasi, Katyayani; Örd, Tiit; Bankier, Sean Alexander; Singha, Prosanta; Arasu, Uma Thanigai; Agbabiaje, Olayinka Oluwasegun; Mäkinen, Petri; Ma, Lijiang; Hodonsky, Chani J.; Aherrahrou, Redouane; Muhl, Lars; Liu, Jianping; Gustafsson, Sonja; Byandelger, Byambajav; Wang, Ying; Koplev, Simon; Lendahl, Urban; Owens, Gary K.; Leeper, Nicholas J.; Pasterkamp, Gerard; Vanlandewijck, Michael; Michoel, Tom; Ruusalepp, Arno; Hao, Ke; Ylä-Herttuala, Seppo; Väli, Marika; Järve, Heli; Mokry, Michal; Civelek, Mete; Miller, Clint J.; Kovacic, Jason C.; Kaikkonen, Minna U.; Betsholtz, Christer; Björkegren, Johan L.M. (Journal article; Peer reviewed, 2024)

  Background: While our understanding of the single-cell gene expression patterns underlying the transformation of vascular cell types during the progression of atherosclerosis is rapidly improving, the clinical and ...

• Automated cell type annotation and exploration of single-cell signaling dynamics using mass cytometry 

  Kleftogiannis, Dimitrios; Gavasso, Sonia; Tislevoll, Benedicte Sjo; van der Meer, Nisha; Motzfeldt, Inga Kirstine Flaaten; Hellesøy, Monica; Gullaksen, Stein-Erik; Griessinger, Emmanuel; Fagerholt, Oda Helen Eck; Lenartova, Andrea; Fløisand, Yngvar; Schuringa, Jan Jacob; Gjertsen, Bjørn Tore; Jonassen, Inge (Journal article; Peer reviewed, 2024)

  Mass cytometry by time-of-flight (CyTOF) is an emerging technology allowing for in-depth characterization of cellular heterogeneity in cancer and other diseases. Unfortunately, high-dimensional analyses of CyTOF data remain ...

• On planarity of graphs in homotopy type theory 

  Cubides, Jonathan Steven Prieto; Gylterud, Håkon Robbestad (Journal article; Peer reviewed, 2024)

  In this paper, we present a constructive and proof-relevant development of graph theory, including the notion of maps, their faces and maps of graphs embedded in the sphere, in homotopy type theory (HoTT). This allows us ...

• PRPF8-mediated dysregulation of hBrr2 helicase disrupts human spliceosome kinetics and 5´-splice-site selection causing tissue-specific defects 

  Atkinson, Robert; Georgiou, Maria; Yang, Chunbo; Szymanska, Katarzyna; Lahat, Albert; Vasconcelos, Elton J. R.; Ji, Yanlong; Moya Molina, Marina; Collin, Joseph; Queen, Rachel; Dorgau, Birthe; Watson, Avril; Kurzawa-Akanbi, Marzena; Laws, Ross; Saxena, Abhijit; Shyan Beh, Chia; Siachisumo, Chileleko; Görtler, Franziska Stilla Maria; Karwatka, Magdalena; Davey, Tracey; Inglehearn, Chris F.; McKibbin, Martin; Lührmann, Reinhard; Steel, David H.; Elliott, David J.; Armstrong, Lyle; Urlaub, Henning; Ali, Robin R.; Grellscheid, Sushma Nagaraja; Johnson, Colin A.; Mozaffari-Jovin, Sina; Lako, Majlinda (Journal article; Peer reviewed, 2024)

  The carboxy-terminus of the spliceosomal protein PRPF8, which regulates the RNA helicase Brr2, is a hotspot for mutations causing retinitis pigmentosa-type 13, with unclear role in human splicing and tissue-specificity ...

• The Structure of Paradoxes in a Logic of Sentential Operators 

  Walicki, Michal (Journal article; Peer reviewed, 2024)

  Any language L of classical logic, of first- or higher-order, is expanded with sentential quantifiers and operators. The resulting language L+, capable of self-reference without arithmetic or syntax encoding, can serve as ...

• XNLP-Completeness for Parameterized Problems on Graphs with a Linear Structure 

  Bodlaender, Hans L.; Groenland, Carla; Jacob, Hugo; Jaffke, Lars; Lima, Paloma T. (Journal article; Peer reviewed, 2024)

  In this paper, we showcase the class XNLP as a natural place for many hard problems parameterized by linear width measures. This strengthens existing W[1]-hardness proofs for these problems, since XNLP-hardness implies ...

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