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Esa Pitkänen

@epitkanen.bsky.social
83 followers 285 following 11 posts

FIMM-EMBL Group Leader at @fimm-uh.bsky.social‬ | @mlbiomed.bsky.social‬ | mlbiomed.net

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Reposted by Esa Pitkänen
Machine Learning in Biomedicine @mlbiomed.bsky.social · 04/09/2026
Yrjö Koski presented his work at IEEE CIBCB 2026 titled NanoDS: Accurate simulation of nanopore sequencing data with distribution approximations 🧬💻 cibcb2026.dib.uth.gr
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Esa Pitkänen @epitkanen.bsky.social · 02/09/2026
A lot of exciting science at @eccb-europe.bsky.social in Geneva, where @mlbiomed.bsky.social researchers Guangzhao Cheng, Daniyar Karabayev, Nora Schreiber, Arina Tagmazian and Hanna Nebelung presented their posters. Photo by Kira Detrois - thanks!
MLBioMed researchers Guangzhao Cheng, Daniyar Karabayev, Nora Schreiber, Arina Tagmazian, Hanna Nebelung and Esa Pitkänen at the ECCB 2026 conference.
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Esa Pitkänen @epitkanen.bsky.social · 01/09/2026
Can domain-specific foundation models compete with large pan-tissue models? Yes. HistoEncoder, trained on prostate tissue, matches H-Optimus-1, UNI2-h, Virchow2 and CONCH v1.5 in cancer detection and grading, while being much smaller and 3–5× faster. doi.org/10.1016/j.jp...
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Esa Pitkänen @epitkanen.bsky.social · 16/06/2026
Really happy to see this one out! Great work by @lalangohr.bsky.social, Ilse Kaaja and the whole team. 🩸🧬 @mlbiomed.bsky.social @fimm-uh.bsky.social
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Reposted by Esa Pitkänen
Institute for Molecular Medicine Finland (FIMM) @fimm-uh.bsky.social · 24/03/2026
Upcoming FIMM dissertation! 📢 MSc Veera Timonen from @epitkanen.bsky.social's group will defend her doctoral dissertation "Multimodal investigation of hematological features in healthy blood donors" @helsinki.fi on 27 March at 13:00. Welcome! 🔗 tapahtumat.helsinki.fi/en-FI/page/6...
Promotional poster for a doctoral dissertation featuring a teal background with a diagonal banner reading “Doctoral Dissertation.” The name Veera Timonen is prominently displayed alongside the thesis title, “Multimodal investigation of hematological features in healthy blood donors.” The event details are listed: 27 March 2026 at 13:00, Biomedicum Helsinki, Lecture hall 2. The opponent is Guillaume Jacquemet from the University of Turku & Åbo Akademi, Finland.

On the right side, there is a circular portrait of a blonde woman wearing glasses and a black top, set within a white-bordered frame. At the bottom are institutional logos for the University of Helsinki and FIMM (Institute for Molecular Medicine Finland, HiLIFE unit).
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Esa Pitkänen @epitkanen.bsky.social · 05/03/2026
Our new preprint: dual-task learning in >17k cancer WGS. Somatic variant models can transfer across datasets, but dataset shift strongly affects performance. Cross-cohort validation is essential. www.medrxiv.org/content/10.6... @fimm-uh.bsky.social @mlbiomed.bsky.social
medrxiv.org
Pan-cancer tumour classification and risk stratification from whole-genome somatic variants via dual-task representation learning
Tumour typing from whole-genome sequencing is increasingly accurate, yet molecular subtyping from somatic variants remains challenging because of tumour heterogeneity and inconsistent clinical annotat...
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Reposted by Esa Pitkänen
Nordic EMBL Partnership for Molecular Medicine @nordicembl.bsky.social · 14/01/2026
📢As part of the Nordic EMBL Partnership for Molecular Medicine, @fimm-uh.bsky.social is now recruiting doctoral researchers in the FIMM-EMBL International PhD Programme. tinyurl.com/553jzfuy Deadline for application February 6, 2026 👇
tinyurl.com
FIMM-EMBL International PhD Programme | HiLIFE – Helsinki Institute of Life Science | University of Helsinki
As part of the Nordic EMBL Partnership for Molecular Medicine, outstanding doctoral researchers are recruited to the institute-level rotation programme through the annual call. The recruited doctoral ...
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Esa Pitkänen @epitkanen.bsky.social · 20/11/2025
Grateful to @syopasaatio.bsky.social and donors for supporting our work at @mlbiomed.bsky.social! Thanks to this grant, we can develop new computational approaches for multimodal precision oncology. @fimm-uh.bsky.social
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Esa Pitkänen @epitkanen.bsky.social · 06/11/2025
Excited to share our latest pre-print on profiling DNA adducts with nanopore sequencing! This study was led by Yrjö Koski, who developed a computational toolkit called IonStats, and identified several compound-specific effects caused by genotoxic compounds. www.biorxiv.org/content/10.1...
biorxiv.org
Compound-specific DNA adduct profiling with nanopore sequencing and IonStats
Covalently bound DNA adducts are mutation precursors that contribute to aging and diseases such as cancer. Accurate detection of adducts in the genome will shed light on tumorigenesis. Commonly used a...
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