Research output per year
Research output per year
Personal profile
Artistic and research interests
I work on computational biology and probabilistic machine learning with applications in biomedicine.
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):
Keywords
- Computational biology
- Machine learning
- Deep generative models
- Bioinformatics
- Artificial intelligence
- Probabilistic modelling
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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
Research output
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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) -
A comparative study of clinical trial and real-world data in patients with diabetic kidney disease
Kurki, S., Halla-aho, V., Haussmann, M., Lähdesmäki, H., Leinonen, J. V. & Koskinen, M., 19 Jan 2024, In: Scientific Reports. 14, 1, 1731.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile7 Citations (Scopus)22 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 -
Latent variable model for high-dimensional point process with structured missingness
Sinelnikov, M., Haussmann, M. & Lähdesmäki, H., 2024, In: Proceedings of Machine Learning Research. 235, p. 45525-45543 19 p.Research output: Contribution to journal › Conference article › Scientific › peer-review
Open AccessFile20 Downloads (Pure) -
Learning conditional variational autoencoders with missing covariates
Ramchandran, S., Tikhonov, G., Lönnroth, O., Tiikkainen, P. & Lähdesmäki, H., Mar 2024, In: Pattern Recognition. 147, 110113.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile9 Citations (Scopus)127 Downloads (Pure)
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AI assisted Health Lähdesmäki: Trustworthy AI-assisted phenotyping, prediction and treatment design using large-scale health data
Lähdesmäki, H. (Principal investigator)
01/01/2024 → 31/12/2026
Project: Academy of Finland: Other research funding
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-: Finnish Center for Artificial Intelligence
Lähdesmäki, H. (Principal investigator)
01/01/2023 → 31/12/2026
Project: Academy of Finland: Other research funding
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Heal-Art jatko: Immunoregulation and Therapeutic Precision in Rheumatoid Arthritis
Lähdesmäki, H. (Principal investigator)
01/01/2021 → 31/12/2022
Project: Academy of Finland: Other research funding
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-: Bridging the Reality Gap in Autonomous Learning
Lähdesmäki, H. (Principal investigator)
01/01/2020 → 31/12/2022
Project: Academy of Finland: Other research funding
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FCAI: Finnish Center for Artificial Intelligence (FCAI)
Lähdesmäki, H. (Principal investigator)
01/01/2019 → 31/12/2022
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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Additional file 4 of Probabilistic modeling methods for cell-free DNA methylation based cancer classification
Halla-aho, V. (Creator) & Lähdesmäki, H. (Creator), figshare, 2022
DOI: 10.6084/m9.figshare.19518516, https://springernature.figshare.com/articles/dataset/Additional_file_4_of_Probabilistic_modeling_methods_for_cell-free_DNA_methylation_based_cancer_classification/19518516
Dataset
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A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways
Äijö, T. (Creator), Huang, Y.-H. (Contributor), Mannerström, H. (Creator), Chavez, L. (Contributor), Tsagaratou, A. (Contributor), Rao, A. (Contributor) & Lähdesmäki, H. (Creator), figshare, 1 Jan 2016
DOI: 10.6084/m9.figshare.c.3604346.v1, https://figshare.com/collections/A_probabilistic_generative_model_for_quantification_of_DNA_modifications_enables_analysis_of_demethylation_pathways/3604346/1
Dataset
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Probabilistic modeling methods for cell-free DNA methylation based cancer classification
Halla-aho, V. (Creator) & Lähdesmäki, H. (Contributor), figshare, 1 Jan 2022
DOI: 10.6084/m9.figshare.c.5931075.v1, https://springernature.figshare.com/collections/Probabilistic_modeling_methods_for_cell-free_DNA_methylation_based_cancer_classification/5931075/1 and 4 more links, https://springernature.figshare.com/articles/dataset/Additional_file_2_of_Probabilistic_modeling_methods_for_cell-free_DNA_methylation_based_cancer_classification/19518510/1, https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Probabilistic_modeling_methods_for_cell-free_DNA_methylation_based_cancer_classification/19518513/1, https://springernature.figshare.com/articles/dataset/Additional_file_4_of_Probabilistic_modeling_methods_for_cell-free_DNA_methylation_based_cancer_classification/19518516/1, https://springernature.figshare.com/articles/journal_contribution/Additional_file_1_of_Probabilistic_modeling_methods_for_cell-free_DNA_methylation_based_cancer_classification/19518507/1 (show fewer)
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
Prizes
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Elias Tillandz prize 2012 for article
Lähdesmäki, H. (Recipient), 2012
Prize: Award or honor granted for a specific work
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Elias Tillandz prize 2013 for article
Lähdesmäki, H. (Recipient), 2013
Prize: Award or honor granted for a specific work
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IARIA Best Paper Award for our paper
Lähdesmäki, H. (Recipient), 2008
Prize: Award or honor granted for a specific work
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Tampere Science Foundation award for the best doctoral thesis
Lähdesmäki, H. (Recipient), 2005
Prize: Award or honor granted for a specific work
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The first position in the 5th Dialogue for Reverse Engineering Assessments and Methods (DREAM)
Lähdesmäki, H. (Recipient), 16 Nov 2010
Prize: Award or honor granted for a specific work
Activities
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Faster Bayesian inference in Joint Species Distribution Models
Tikhonov, G. (Speaker), Vanhatalo, J. (Contributor), Ovaskainen, O. (Contributor) & Lähdesmäki, H. (Contributor)
22 Jun 2020 → 26 Jun 2020Activity: Talk or presentation types › Conference presentation
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International Workshop on Machine Learning in Systems Biology
Lähdesmäki, H. (Member)
3 Sept 2016 → 4 Sept 2016Activity: Participating in or organising an event types › Membership of an organizing committee or other positions of trust of a conference or a seminar
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Foreign Organisation
Lähdesmäki, H. (Visiting researcher)
18 May 2016Activity: Visiting an external institution types › Visiting an external academic institution
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Foreign Organisation
Lähdesmäki, H. (Visiting researcher)
30 Mar 2016 → 3 Apr 2016Activity: Visiting an external institution types › Visiting an external academic institution
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Foreign Organisation
Lähdesmäki, H. (Visiting researcher)
17 May 2016Activity: Visiting an external institution types › Visiting an external academic institution
Press/Media
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Research Findings from Aalto University Update Understanding of Machine Learning (EPIC-TRACE: predicting TCR binding to unseen epitopes using attention and contextualized embeddings)
27/12/2023
1 item of Media coverage
Press/Media: Media appearance
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University of Turku and Abo Akademi University Researchers Target Type 1 Diabetes (Serum APOC1 levels are decreased in young autoantibody positive children who rapidly progress to type 1 diabetes)
10/10/2023
1 item of Media coverage
Press/Media: Media appearance
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Research Data from University of Turku and Abo Akademi University Update Understanding of Data Analytics (Permutation-based significance analysis reduces the type 1 error rate in bisulphite sequencing data analysis of human umbilical cord blood ...)
05/10/2023
1 item of Media coverage
Press/Media: Media appearance
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Aalto University: Scientists Unravel The Effects Of New Medication For Advanced Melanoma With The Help Of AI
03/03/2023
1 item of Media coverage
Press/Media: Media appearance
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Scientists unravel the effects of new medication for advanced melanoma with the help of AI
02/03/2023
2 items of Media coverage
Press/Media: Media appearance