Computer Science - Computational Life Sciences (CSLife) - Research area

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  • 2025

    Clustering students’ text form feedback data: comparison of eight vector space models

    Hämäläinen, W., Rybicki, J.-M., Malmi, L., Jung, A. & Pollari-Malmi, K., 24 Jan 2025, ICBDE '24: Proceedings of the 2024 7th International Conference on Big Data and Education. New York: ACM, p. 57-64 8 p.

    Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

    Open Access
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    11 Downloads (Pure)

  • MassSpecGym : A benchmark for the discovery and identification of molecules

    Bushuiev, R., Bushuiev, A., de Jonge, N. F., Young, A., Kretschmer, F., Samusevich, R., Heirman, J., Wang, F., Zhang, L., Dührkop, K., Ludwig, M., Haupt, N. A., Kalia, A., Brungs, C., Schmid, R., Greiner, R., Wang, B., Wishart, D. S., Liu, L. P. & Rousu, J. & 10 others, Bittremieux, W., Rost, H., Mak, T. D., Hassoun, S., Huber, F., van der Hooft, J. J. J., Stravs, M. A., Böcker, S., Sivic, J. & Pluskal, T., 2025, Advances in Neural Information Processing Systems 37 (NeurIPS 2024). Curran Associates Inc., p. 1-18 18 p. (Advances in Neural Information Processing Systems).

    Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

    Open Access
  • 2024

    A General Design Method for Scaffold-Free DNA Wireframe Nanostructures

    Elonen, A., Mohammed, A. & Orponen, P., 2024, Unconventional Computation and Natural Computation - 21st International Conference, UCNC 2024, Proceedings. Cho, D.-J. & Kim, J. (eds.). Springer, p. 178-189 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 14776 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

    1 Citation (Scopus)

  • Automated Rendering of Multi-stranded DNA Complexes with Pseudoknots

    Nowicka, M., Gautam, V. K. & Orponen, P., 2024, Unconventional Computation and Natural Computation - 21st International Conference, UCNC 2024, Proceedings. Cho, D.-J. & Kim, J. (eds.). Springer, p. 190-202 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 14776 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

  • Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops

    Elonen, A. & Orponen, P., Sept 2024, 30th International Conference on DNA Computing and Molecular Programming, DNA 30 2024. Seki, S. & Stewart, J. M. (eds.). Schloss Dagstuhl - Leibniz-Zentrum für Informatik, p. 1-12 12 p. 4. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 314).

    Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

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    16 Downloads (Pure)

  • Estimating treatment effects from single-arm trials via latent-variable modeling

    Haussmann, M., Le, T. M. S., Halla-aho, V., Kurki, S., Leinonen, J., Koskinen, M., Kaski, S. & Lähdesmäki, H., 2024, Proceedings of the 27th International Conference on Artificial Intelligence and Statistics . JMLR, Vol. 238. p. 2926-2934 (Proceedings of Machine Learning Research; vol. 238).

    Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

    Open Access

  • Learning Space-Time Continuous Latent Neural PDEs from Partially Observed States

    Iakovlev, V., Heinonen, M. & Lähdesmäki, H., 2024, Advances in Neural Information Processing Systems 36 (NeurIPS 2023). Curran Associates Inc., 24 p. (Advances in Neural Information Processing Systems; vol. 36).

    Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

    Open Access

  • Optimizing Feature Selection for Unbalanced Metabolomics Data with A Background Factor : A Comparative Study in Parkinson's Disease

    Zhang, Y., Hämäläinen, W., Reinikka, P., Herukka, S. K., Leinonen, V., Lehtonen, M. & Lehtonen, Š., 2024, Proceedings - 2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024. Cannataro, M., Zheng, H., Gao, L., Cheng, J., de Miranda, J. L., Zumpano, E., Hu, X., Cho, Y.-R. & Park, T. (eds.). IEEE, p. 5884-5891 8 p. (Proceedings (IEEE international conference on bioinformatics and biomedicine)).

    Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

    Open Access
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    2 Downloads (Pure)
  • 2023

    Mental Health Coping Stories on Social Media: A Causal-Inference Study of Papageno Effect

    Yuan, Y., Saha, K., Keller, B., Isometsä, E. T. & Aledavood, T., 30 Apr 2023, ACM Web Conference 2023 - Proceedings of the World Wide Web Conference, WWW 2023. ACM, p. 2677–2685

    Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

    Open Access
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    10 Citations (Scopus)
    67 Downloads (Pure)

  • Minority Stress Experienced by LGBTQ Online Communities during the COVID-19 Pandemic

    Yuan, Y., Verma, G., Keller, B. & Aledavood, T., 2 Jun 2023, Proceedings of the Seventeenth International AAAI Conference on Web and Social Media. AAAI Press, p. 936-947 (Proceedings of the International AAAI Conference on Web and Social Media; vol. 17).

    Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

    Open Access
  • 2022

    A Variational Autoencoder for Heterogeneous Temporal and Longitudinal Data

    Öǧretir, M., Ramchandran, S., Papatheodorou, D. & Lähdesmäki, H., 2022, Proceedings - 21st IEEE International Conference on Machine Learning and Applications, ICMLA 2022. Wani, M. A., Kantardzic, M., Palade, V., Neagu, D., Yang, L. & Chan, K.-Y. (eds.). IEEE, p. 1522-1529 8 p.

    Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

    Open Access
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    3 Citations (Scopus)
    100 Downloads (Pure)

  • Learning to Predict Graphs with Fused Gromov-Wasserstein Barycenters

    Brogat-Motte, L., Flamary, R., Brouard, C., Rousu, J. & d'Alché-Buc, F., 2022, Proceedings of the 39th International Conference on Machine Learning, PMLR. JMLR, p. 2321-2335 (Proceedings of Machine Learning Research ; vol. 162).

    Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

    Open Access

  • Variational multiple shooting for Bayesian ODEs with Gaussian processes

    Hedge, P., Yildiz, C., Lähdesmäki, H., Kaski, S. & Heinonen, M., 2022, Proceedings of the 38th Conference on Uncertainty in Artificial Intelligence (UAI 2022), PMLR. JMLR, p. 790-799 (Proceedings of Machine Learning Research ; vol. 180).

    Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

    Open Access
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    1 Citation (Scopus)
    65 Downloads (Pure)
  • 2021

    Continuous-time Model-based Reinforcement Learning

    Yildiz, C., Heinonen, M. & Lähdesmäki, H., 21 Jul 2021, Proceedings of the 38th International Conference on Machine Learning, ICML 2021. JMLR, p. 12009-12018 (Proceedings of Machine Learning Research; vol. 139).

    Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

    Open Access
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    64 Downloads (Pure)

  • Latent Gaussian process with composite likelihoods and numerical quadrature

    Ramchandran, S., Koskinen, M. & Lahdesmaki, H., 2021, 24TH INTERNATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE AND STATISTICS (AISTATS). Banerjee, A. & Fukumizu, K. (eds.). Microtome Publishing, 10 p. (Proceedings of Machine Learning Research; vol. 130).

    Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

    Open Access
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    30 Downloads (Pure)

  • Learning continuous-time PDEs from sparse data with graph neural networks

    Iakovlev, V., Heinonen, M. & Lähdesmäki, H., 2021, International Conference on Learning Representations. OpenReview.net, 15 p.

    Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Professional

    Open Access

  • Longitudinal Variational Autoencoder

    Ramchandran, S., Tikhonov, G., Kujanpaa, K., Koskinen, M. & Lahdesmaki, H., 2021, 24TH INTERNATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE AND STATISTICS (AISTATS). Banerjee, A. & Fukumizu, K. (eds.). Microtome Publishing, 11 p. (Proceedings of Machine Learning Research; vol. 130).

    Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

    Open Access
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    67 Downloads (Pure)
  • 2004

    Balanced data gathering in energy-constrained sensor networks

    Falck, E., Floréen, P., Kaski, P., Kohonen, J. & Orponen, P., 2004, ALGOSENSORS'04, First International Workshop on Algorithmic Aspects of Wireless Sensor Networks, Turku, Suomi, 16.7.2004. Nikoletseas, S. & Rolim, J. D. P. (eds.). Berlin Heidelberg: Springer, p. 59-70

    Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

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    57 Downloads (Pure)
  • 2003

    Multicast time maximization in energy constrained wireless networks

    Floréen, P., Kaski, P., Kohonen, J. & Orponen, P., 2003, DIALM-POMC '03 Joint Workshop on Foundations of Mobile Computing, San Diego, CA, USA, 19.9.2003. Richa, A. & Welch, J. (eds.). ACM, New York: ACM, p. 50-58

    Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

    Open Access
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    49 Citations (Scopus)
    231 Downloads (Pure)