Publications

Search for publications at Department of Computer Science

Below you find a complete list of publications published and edited by scientists at the Department of Computer Science

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Simonsen, M. & Pedersen, C. N. S. (2011). Rapid Computation of Distance Estimators from Nucleotide and Amino Acid Alignments. In Proceedings of the 26th Annual ACM Symposium on Applied Computing Association for Computing Machinery.

Simonsen, M., Thomsen, R., Christensen, M. H. & Pedersen, C. N. S. (2011). GPU-Accelerated High-Accuracy Molecular Docking using Guided Differential Evolution. In GECCO'11 Proceedings of the 13th annual conference on Genetic and evolutionary computation (pp. 1803-1810). Association for Computing Machinery. https://doi.org/10.1145/2001576.2001818

Simonsen, M., Christensen, M. H., Thomsen, R. & Pedersen, C. N. S. (2013). GPU-Accelerated High-Accuracy Molecular Docking using Guided Differential Evolution. In S. tsutsui & P. Collet (Eds.), Massively Parallel Evolutionary Computation on GPGPUs Springer Publishing Company.

Simonsen, M. (2011). Efficient algorithms for tree reconstruction and prediction of molecular interactions. Department of Computer Science, Aarhus University.

Simner, B., Armstrong, A., Bauereiss, T., Campbell, B., Kammar, O., Pichon-Pharabod, J. & Sewell, P. (2025). Precise exceptions in relaxed architectures. In ISCA 2025 - Proceedings of the 52nd Annual International Symposium on Computer Architecture: Proceedings of the 52nd Annual International Symposium on Computer Architecture (pp. 211–224) https://doi.org/10.1145/3695053.3731102

Simmons , R. J. & Zerny, I. (2013). A logical correspondence between natural semantics and abstract machines. In R. Peña & T. Schrijvers (Eds.), Proceedings of the 15th Symposium on Principles and Practice of Declarative Programming, PPDP '13 (pp. 109-119 ). Association for Computing Machinery. https://doi.org/10.1145/2505879.2505899

Simkin, M., Siniscalchi, L. & Yakoubov, S. (2022). On Sufficient Oracles for Secure Computation with Identifiable Abort. In C. Galdi & S. Jarecki (Eds.), Security and Cryptography for Networks - 13th International Conference, SCN 2022, Proceedings (pp. 494-515). Springer. https://doi.org/10.1007/978-3-031-14791-3_22

Simkin, M. (2020). Alice, Bits, and Bob.

Silvestri, C., Lettich, F., Orlando, S. & Jensen, C. S. (2014). GPU-based computing of repeated range queries over moving objects. In Proceedings - 2014 22nd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, PDP 2014 (pp. 640-647). Article 6787342 IEEE Computer Society Press. https://doi.org/10.1109/PDP.2014.27

Silva, G., Lyle, P. J. & Silva, C. (2020). Local Perspectives for Sharing Economy Design on a Remote Tourist Island. In Proceedings of the 32nd Australian Computer-Human Interaction Conference, OzCHI 2020 (pp. 368-378). Association for Computing Machinery. https://doi.org/10.1145/3441000.3441058

Sillasen, M., Daugbjerg, P., Krogh, L. B. & Nielsen, K. (2018). Engineering i skolen - Vidensgrundlag. VIA University College. https://www.ucviden.dk/portal/da/publications/engineering-i-skolen(2d8a5ff9-3ab5-4a10-965f-46ebe403919d).html

Sieczkowski, F., Svendsen, K., Birkedal, L. & Pichon-Pharabod, J. (2015). A separation logic for fictional sequential consistency. In J. Vitek (Ed.), Programming Languages and Systems : 24th European Symposiumon Programming, ESOP 2015 held as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2015 (pp. 736-761). Springer. https://doi.org/10.1007/978-3-662-46669-8_30

Sieczkowski, F., Bizjak, A. & Birkedal, L. (2015). ModuRes: A Coq Library for Modular Reasoning About Concurrent Higher-Order Imperative Programming Languages. In C. Urban & X. Zhang (Eds.), Interactive Theorem Proving: 6th International Conference, ITP 2015, Nanjing, China, August 24-27, 2015, Proceedings (pp. 375-390). Springer. https://doi.org/10.1007/978-3-319-22102-1_25

Sieczkowski, F., Stepanenko, S., Sterling, J. & Birkedal, L. (2024). The Essence of Generalized Algebraic Data Types. Proceedings of the ACM on Programming Languages , 8(POPL), 695-723. https://doi.org/10.1145/3632866

Sidorenco, N., Oechsner, S. & Spitters, B. (2021). Formal security analysis of MPC-in-the-head zero-knowledge protocols. In Proceedings - 2021 IEEE 34th Computer Security Foundations Symposium, CSF 2021 (pp. 607-620). IEEE. https://doi.org/10.1109/CSF51468.2021.00050

Šidlauskas, D., Šaltenis, S. & Jensen, C. S. (2012). Parallel main-memory indexing for moving-object query and update workloads. In Proceedings of the 2012 ACM SIGMOD International Conference on Management of Data (pp. 37-48 ). Association for Computing Machinery. https://doi.org/10.1145/2213836.2213842

Šidlauskas, D., Jensen, C. S. & Šaltenis , S. (2012). A comparison of the use of virtual versus physical snapshots for supporting update-intensive workloads. In Proceedings of the Eighth International Workshop on Data Management on New Hardware: DaMoN '12 (pp. 1-8). Association for Computing Machinery. https://doi.org/10.1145/2236584.2236585

Sidlauskas, D., Ross, K. A., Jensen, C. S. & Saltenis, S. (2011). Thread-Level Parallel Indexing of Update Intensive Moving-Object Workloads. Lecture Notes in Computer Science, 6849, 186-204. https://doi.org/10.1007/978-3-642-22922-0_12

Sidlauskas, D., Saltenis, S. & Jensen, C. S. (2014). Processing of extreme moving-object update and query workloads in main memory. V L D B Journal, 23(5), 817-841. https://doi.org/10.1007/s00778-014-0353-2

Sidlauskas, D. & Jensen, C. S. (2014). Spatial joins in main memory: Implementation matters! Proceedings of the VLDB Endowment, 8(1), 97-100. http://www.vldb.org/pvldb/vol8/p97-sidlauskas.pdf

Sidenmark, L., Clarke, C., Zhang, X., Phu, J. & Gellersen, H. (2020). Outline Pursuits: Gaze-assisted Selection of Occluded Objects in Virtual Reality. In CHI 2020 - Proceedings of the 2020 CHI Conference on Human Factors in Computing Systems Article 3376438 Association for Computing Machinery. https://doi.org/10.1145/3313831.3376438

Sidenmark, L., Potts, D., Bapisch, B. & Gellersen, H. (2021). Radi-Eye: Hands-Free Radial Interfaces for 3D Interaction using Gaze-Activated Head-Crossing. In CHI 2021 - Proceedings of the 2021 CHI Conference on Human Factors in Computing Systems: Making Waves, Combining Strengths Article 740 Association for Computing Machinery. https://doi.org/10.1145/3411764.3445697

Sidenmark, L., Clarke, C., Newn, J., Lystbæk, M. N., Pfeuffer, K. & Gellersen, H. (2023). Vergence Matching: Inferring Attention to Objects in 3D Environments for Gaze-Assisted Selection. In CHI '23: Proceedings of the 2023 CHI Conference on Human Factors in Computing Systems Article 257 Association for Computing Machinery. https://doi.org/10.1145/3544548.3580685

Sidenmark, L., Lystbæk, M. N. & Gellersen, H. (2023). GE-Simulator: An Open-Source Tool for Simulating Real-Time Errors for HMD-based Eye Trackers. In S. N. Spencer (Ed.), Proceedings of the 2023 Symposium on Eye Tracking Research and Applications (pp. 1-6). Article 8 Association for Computing Machinery. https://doi.org/10.1145/3588015.3588417

Sidenmark, L., Prummer, F., Newn, J. & Gellersen, H. (2023). Comparing Gaze, Head and Controller Selection of Dynamically Revealed Targets in Head-Mounted Displays. IEEE Transactions on Visualization and Computer Graphics, 29(11), 4740-4750. https://doi.org/10.1109/TVCG.2023.3320235

Shyam, S. (2026). Algorithms and Complexity for Constrained Fair Division, Discrepancy, and Packing. [PhD dissertation, Aarhus University].

Shokeen, E., Jensen, A. V., Iversen, O. S., Lunding, M. S., Petersen, M. G. & Bilstrup, K.-E. K. (2026). Beyond Isolated Interventions: An Ecological and Infrastructural Synthesis of K–12 Cybersecurity Education Research. ACM Transactions on Computing Education. Advance online publication. https://doi.org/10.1145/3819079

Shin, S., Na, I. & Elmqvist, N. (2025). Drillboards: Adaptive Visualization Dashboards for Dynamic Personalization of Visualization Experiences. IEEE Transactions on Visualization and Computer Graphics, 31(10), 7196-7210. https://doi.org/10.1109/TVCG.2025.3542606

Shin, Y. (2018). External Memory Algorithms for Massive Terrains and Polygons. Aarhus Universitet.

Shin, S., Hong, S. & Elmqvist, N. (2025). Visualizationary: Automating Design Feedback for Visualization Designers Using Large Language Models. IEEE Transactions on Visualization and Computer Graphics, 31(10), 8796-8813. https://doi.org/10.1109/TVCG.2025.3579700

Shi, Z., Mathur, U. & Pavlogiannis, A. (2024). Optimistic Prediction of Synchronization-Reversal Data Races. In ICSE 2024 - Proceedings of the 46th IEEE/ACM International Conference on Software Engineering: Proceedings of the IEEE/ACM 46th International Conference on Software Engineering (pp. 1-13). Article 134 Association for Computing Machinery. https://doi.org/10.1145/3597503.3639099

Shi, Z., Møldrup, L., Mathur, U. & Pavlogiannis, A. (2026). The Complexity of Testing Message-Passing Concurrency. Proceedings of the ACM on Programming Languages , 10, 1-32. https://doi.org/10.1145/3776643

Sheng, Q. Z., Wang, G., Jensen, C. S. & Xu, G. (Eds.) (2012). Web Technologies and Applications: 14th Asia-Pacific Web Conference, APWeb 2012, Kunming, China, April 11-13, 2012. Proceedings. Springer. Lecture Notes in Computer Science Vol. 7235 https://doi.org/10.1007/978-3-642-29253-8

Sheng, Q. Z., Wang, G. & Jensen, C. S. (2012). Message from the Program Chairs. In Web Technologies and Applications: 14th Asia-Pacific Web Conference, APWeb 2012, Kunming, China, April 11-13, 2012. Proceedings (pp. VI). Springer. https://doi.org/10.1007/978-3-642-29253-8

Shapiro, D., Buscher, M., Ørbæk, P., Mogensen, P. H. & Christensen, M. (2005). Spatial Computing and Ambient Collaborative Environments for Design and Construction. In Proceedings of the 3rd international conference on innovation in architecture, engineering and construction (pp. 199-210)

Shao, J., Tan, Y., Gao, L., Yang, Q., Plant, C. & Assent, I. (2019). Synchronization-based clustering on evolving data stream. Information Sciences, 501, 573-587. https://doi.org/10.1016/j.ins.2018.09.035

Shaik, I. & Pol, J. V. D. (2021). Classical Planning as QBF without Grounding (extended version). (pp. 1-17). https://arxiv.org/abs/2106.10138

Shaik, I. & van de Pol, J. (2022). Classical Planning as QBF without Grounding. In A. Kumar, S. Thiebaux, P. Varakantham & W. Yeoh (Eds.), Proceedings of the 32nd International Conference on Automated Planning and Scheduling, ICAPS 2022 (pp. 329-337). AAAI Press. https://doi.org/10.1609/icaps.v32i1.19817

Shaik, I., Heisinger, M., Seidl, M. & Pol, J. V. D. (2023). Validation of QBF Encodings with Winning Strategies. Leibniz International Proceedings in Informatics, 271. https://doi.org/10.4230/LIPIcs.SAT.2023.24

Shaik, I. & van de Pol, J. (2023). Concise QBF Encodings for Games on a Grid (extended version). https://doi.org/10.48550/arXiv.2303.16949

Shaik, I., Mayer-Eichberger, V., van de Pol, J. & Saffidine, A. (2023). Implicit State and Goals in QBF Encodings for Positional Games (extended version). https://doi.org/10.48550/arXiv.2301.07345

Shaik, I. & van de Pol, J. (2023). Optimal Layout Synthesis for Quantum Circuits as Classical Planning. In 2023 IEEE/ACM International Conference on Computer Aided Design (ICCAD) IEEE. https://doi.org/10.1109/ICCAD57390.2023.10323924

Shaik, I. & Van de Pol, J. (2024). Optimal Layout Synthesis for Deep Quantum Circuits on NISQ Processors with 100+ Qubits. In S. Chakraborty & J.-H. R. Jiang (Eds.), 27th International Conference on Theory and Applications of Satisfiability Testing, SAT 2024 Article 26 Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.SAT.2024.26

Shaik, I. & Pol, J. V. D. (2024). Optimal Layout-Aware CNOT Circuit Synthesis with Qubit Permutation. In U. Endriss, F. S. Melo, K. Bach, A. Bugarin-Diz, J. M. Alonso-Moral, S. Barro & F. Heintz (Eds.), ECAI 2024 - 27th European Conference on Artificial Intelligence, 19-24 October 2024, Santiago de Compostela, Spain - Including 13th Conference on Prestigious Applications of Intelligent Systems (PAIS 2024) (pp. 4207-4215). IOS Press. https://doi.org/10.3233/FAIA240993

Shaik, I. (2023). Concise Encodings for Planning and 2-Player Games. [PhD dissertation, Aarhus University]. Aarhus Universitet.

Shaik, I., Mayer-Eichberger, V., van de Pol, J. & Saffidine, A. (2024). Implicit QBF Encodings for Positional Games. In M. Hartisch, C.-H. Hsueh & J. Schaeffer (Eds.), Advances in Computer Games - 18th International Conference, ACG 2023, Revised Selected Papers (pp. 133-145). Springer. https://doi.org/10.1007/978-3-031-54968-7_12

Shaik, I. & van de Pol, J. (2025). CNOT-Optimal Clifford Synthesis as SAT. In J. Berg, J. Nordstrom & J. Nordstrom (Eds.), 28th International Conference on Theory and Applications of Satisfiability Testing, SAT 2025 Article 28 Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.SAT.2025.28

S. Fitzgerald, J., Gorm Larsen, P., Tjell, S. & Verhoef, M. (2007). Validation Support for Distributed Real-Time Embedded Systems in VDM++. In Proceedings of the Tenth IEEE International Symposium on High Assurance Software Engineering (HASE 2007) (pp. 331-340). IEEE Computer Society Press.

Sergey, I. & Clark, D. (2012). A correspondence between type checking via reduction and type checking via evaluation. Information Processing Letters, 112(1-2), 13-20. https://doi.org/10.1016/j.ipl.2011.10.008

Sergey, I., Midtgaard, J. & Clarke, D. (2012). Calculating Graph Algorithms for Dominance and Shortest Path. Lecture Notes in Computer Science, 7342, 132-156. https://doi.org/10.1007/978-3-642-31113-0_8

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Marianne Dammand Iversen

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