Research output per year
Research output per year
Personal profile
Expertise related to UN Sustainable Development Goals
In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):
Education/Academic qualification
Doctoral degree, Engineering and Technology, University of Helsinki
Award Date: 15 Feb 2013
Fingerprint
Dive into the research topics where Markus Heinonen is active. These topic labels come from the works of this person. Together they form a unique fingerprint.
- 1 Similar Profiles
Collaborations and top research areas from the last five years
Recent external collaboration on country/territory level. Dive into details by clicking on the dots or
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Balancing Imbalanced Toxicity Models : Using MolBERT with Focal Loss
Masood, M. A., Kaski, S., Ceulemans, H., Herman, D. & Heinonen, M., 2025, AI in Drug Discovery - 1st International Workshop, AIDD 2024, Held in Conjunction with ICANN 2024, Proceedings. Clevert, D.-A., Wand, M., Schmidhuber, J., Malinovská, K. & Tetko, I. V. (eds.). Springer, p. 82-97 16 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 14894 LNCS).Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review
Open AccessFile38 Downloads (Pure) -
Improving robustness to corruptions with multiplicative weight perturbations
Trinh, T., Heinonen, M., Acerbi, L. & Kaski, S., 2025, Advances in Neural Information Processing Systems 37 (NeurIPS 2024). Globerson, A., Mackey, L., Belgrave, D., Fan, A., Paquet, U., Tomczak, J. & Zhang, C. (eds.). Curran Associates Inc., (Advances in Neural Information Processing Systems; vol. 37).Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review
Open Access -
Probabilistic analysis of spatial viscoelastic cues in 3D cell culture using magnetic microrheometry
Arasalo, O., Lehtonen, A. J., Kielosto, M., Heinonen, M. & Pokki, J., 21 Jan 2025, In: Biophysical Journal. 124, 2, p. 351-362 12 p.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile4 Downloads (Pure) -
Single-cell analysis of aplastic anemia reveals a convergence of NK and NK-like CD8+ T cells with a disease-associated TCR signature
Lundgren, S., Huuhtanen, J., Keränen, M., Feng, X., Patel, B. A., Ryland, G. L., Fox, L. C., Bravo-Perez, C., Clemente, M., Kerr, C., Walldin, G., Dufva, O., Zaimoku, Y., Tuononen, T., Myllymäki, M., Ebeling, F., Jokinen, E., Heinonen, M., Kasanen, T. & Klievink, J. & 14 others, , 26 Feb 2025, In: SCIENCE TRANSLATIONAL MEDICINE. 17, 787, p. 1-17 17 p., eadl6758.Research output: Contribution to journal › Article › Scientific › peer-review
1 Citation (Scopus)1 Downloads (Pure) -
Towards Interpretable Models of Chemist Preferences for Human-in-the-Loop Assisted Drug Discovery
Nahal, Y., Heinonen, M., Kabeshov, M., Janet, J. P., Nittinger, E., Engkvist, O. & Kaski, S., 2025, AI in Drug Discovery - 1st International Workshop, AIDD 2024, Held in Conjunction with ICANN 2024, Proceedings. Clevert, D.-A., Wand, M., Schmidhuber, J., Malinovská, K. & Tetko, I. V. (eds.). Springer, p. 58-70 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 14894 LNCS).Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review
Open AccessFile1 Citation (Scopus)28 Downloads (Pure)
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Heinonen Markus/ AT jatko: Deep learning with differential equations
Heinonen, M. (Principal investigator)
01/09/2023 → 31/08/2025
Project: Academy of Finland: Other research funding
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Heinonen Markus AT-palkka: Deep learning with differential equations
Heinonen, M. (Principal investigator)
01/09/2020 → 31/08/2025
Project: Academy of Finland: Other research funding
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-: Deep learning with differential equations
Heinonen, M. (Principal investigator)
01/09/2020 → 31/08/2023
Project: Academy of Finland: Other research funding
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Next-generation statistical learning for synthetic enzyme engineering
Heinonen, M. (Principal investigator)
01/09/2016 → 31/08/2019
Project: Academy of Finland: Other research funding
Datasets
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Additional file 2 of Modeling binding specificities of transcription factor pairs with random forests
Antikainen, A. A. (Creator), Heinonen, M. (Creator) & Lähdesmäki, H. (Creator), figshare, 6 Jun 2022
DOI: 10.6084/m9.figshare.20003421, https://springernature.figshare.com/articles/dataset/Additional_file_2_of_Modeling_binding_specificities_of_transcription_factor_pairs_with_random_forests/20003421
Dataset
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Genome wide analysis of protein production load in Trichoderma reesei
Pakula, T. M. (Contributor), Nygren, H. (Contributor), Barth, D. (Contributor), Heinonen, M. (Contributor), Castillo, S. (Contributor), Penttilä, M. (Creator) & Arvas, M. (Contributor), figshare, 1 Jan 2016
DOI: 10.6084/m9.figshare.c.3603251.v1, https://figshare.com/collections/Genome_wide_analysis_of_protein_production_load_in_Trichoderma_reesei/3603251/1
Dataset
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Modeling binding specificities of transcription factor pairs with random forests
Antikainen, A. A. (Creator), Heinonen, M. (Creator) & Lähdesmäki, H. (Creator), figshare, 2022
DOI: 10.6084/m9.figshare.c.6031779.v1, https://springernature.figshare.com/collections/Modeling_binding_specificities_of_transcription_factor_pairs_with_random_forests/6031779/1 and 2 more links, https://doi.org/10.6084/m9.figshare.20003418.v1, https://doi.org/10.6084/m9.figshare.20003421.v1 (show fewer)
Dataset
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Human-in-the-loop active learning for goal-oriented molecule generation
Nahal, Y. (Creator), Menke, J. (Creator), Martinelli, J. (Creator), Heinonen, M. (Creator), Kabeshov, M. (Creator), Janet, J. P. (Creator), Nittinger, E. (Creator), Engkvist, O. (Creator) & Kaski, S. (Creator), figshare, 10 Dec 2024
DOI: 10.6084/m9.figshare.c.7577679.v1, https://springernature.figshare.com/collections/Human-in-the-loop_active_learning_for_goal-oriented_molecule_generation/7577679/1
Dataset
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Human-in-the-loop assisted de novo molecular design
Sundin, I. (Creator), Voronov, A. (Creator), Xiao, H. (Creator), Papadopoulos, K. (Creator), Bjerrum, E. J. (Creator), Heinonen, M. (Creator), Patronov, A. (Creator), Kaski, S. (Creator) & Engkvist, O. (Creator), figshare, 13 Aug 2024
DOI: 10.6084/m9.figshare.c.6582620, https://springernature.figshare.com/collections/Human-in-the-loop_assisted_de_novo_molecular_design/6582620
Dataset
Activities
- 3 Visiting an external academic institution
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University of California, San Francisco
Heinonen, M. (Visiting researcher)
9 Jan 2017 → 24 Feb 2017Activity: Visiting an external institution types › Visiting an external academic institution
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University of California, San Francisco
Heinonen, M. (Visiting researcher)
31 Jul 2017 → 25 Aug 2017Activity: Visiting an external institution types › Visiting an external academic institution
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Telecom ParisTech
Heinonen, M. (Visiting researcher)
1 Jan 2013 → 30 Dec 2014Activity: Visiting an external institution types › Visiting an external academic institution
Press/Media
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Aalto University Reports Findings in Bioinformatics (TCRconv: Predicting recognition between T cell receptors and epitopes using contextualized motifs)
19/12/2022
1 item of Media coverage
Press/Media: Media appearance
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Strengthening nonparametric Bayesian methods with structured kernels
09/11/2022
1 item of Media coverage
Press/Media: Media appearance
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Differential Equations for Machine Learning
14/01/2022
1 item of Media coverage
Press/Media: Media appearance
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Artificial Intelligence Model Predicts Which Immune System Key Opens the Locks of Coronavirus
30/04/2021
1 item of Media coverage
Press/Media: Media appearance
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Aalto University team wins AI research award
Lähdesmäki, H., Heinonen, M. & Kaski, S.
24/04/2019
1 item of Media coverage
Press/Media: Media appearance