Research

Research topics

Our research focuses on computational analysis and understanding of complex natural and social systems. There is a great demand for targeted computational techniques to extract information and insights from rich data collections based on clever combinations of human and machine intelligence. We blend elements from fields such as machine learning/AI, probabilistic programming, statistical ecology, and data science, and drive open developer communities that help to translate latest theoretical advances into accessible methods to inform modeling, experimentation, and decision-making.

Key applications include microbiome research, population cohort studies, and computational social sciences and humanities (SSH). We also coordinate the Open Knowledge Finland Open Science work group, which received Open Science and Research award of the Ministry of Education and Culture in 2017.

Recent publications

Below some examples from recent publications. See ORCID for a full list. Full publication list is also available as bibtex. Copies of most papers are available here.

Computational and data science

Wrangling with Non-Standard Data
Proc. Digital Humanities in the Nordic Countries 2020.
Mäkelä E, Lagus K, Lahti L, Säily T, Tolonen M, Hämäläinen M, Kaislaniemi S, Nevalainen T.
Best long paper in DHN2020.

Three-species Lotka-Volterra model with respect to Caputo and Caputo-Fabrizio fractional operators
Symmetry 2021.
Khalighi M, Eftekhari L, Hosseinpour S, Lahti L.

A hierarchical Ornstein-Uhlenbeck model for stochastic time series analysis
Advances in Intelligent Data Analysis XVII. Lecture Notes in Computer Science 11191. Springer, 2018.
Laitinen V, Lahti L

Retrieval and analysis of Eurostat open data with the eurostat R package
R Journal, 2017.
Lahti L, Huovari J, Kainu M, Biecek P.

Open Data Science
Advances in Intelligent Data Analysis XVII. Lecture Notes in Computer Science 11191:31-39. Springer, India, 2018.
Lahti L.

Microbiome data science

Taxonomic signatures of cause-specific mortality risk in human gut microbiome
Salosensaari A*, Laitinen V*, Havulinna A, Meric G, Cheng S, Perola M, Valsta L, Alfthan G, Inouye M, Watrous JD, Long T, Salido R, Sanders K, Brennan C, Humphrey GC, Sanders JG, Jain M, Jousilahti P, Salomaa V, Knight R, Lahti L*, Niiranen T*.
Nature Communications 12:2671, May 2021.

Modeling spatial patterns in host-associated microbial communities
Ruuskanen M*, Sommeria-Klein G*, Havulinna A, Niiranen T, Lahti L.
Environmental Microbiology 23(5), 2021.

Xylo-oligosaccharides in prevention of hepatic steatosis and adipose tissue inflammation: associating taxonomic and metabolomic patterns in fecal microbiomes with biclustering
Hintikka J, Lensu S, Mäkinen E, Karvinen S, Honkanen M, Linden J, Garrels T, Pekkala S, Lahti L.
International Journal of Environmental Research and Public Health 18(8):4049, April 2021.

Statistical and machine learning techniques in human microbiome studies: contemporary challenges and solutions
Frontiers in Microbiology 2021. Moreno-Indias I, Lahti L, Nedyalkova M, Elbere I, Roshchupkin GV, Adilovic M, Aydemir O, Bakir-Gungor B, Carrillo-de Santa Pau E, D’Elia D, Desai MS, Falquet L, Gundogdu A, Hron K, Klammsteiner T, Lopes MB, Marcos Zambrano LJ, Marques C, Mason M, May P, Pašić L, Pio G, Pongor S, Promponas VJ, Przymus P, Sáez-Rodríguez J, Sampri A, Shigdel R, Stres B, Suharoschi R, Truu J, Truică C-O, Vilne B, Vlachakis DP, Yılmaz E, Zeller G, Zomer A, Gómez-Cabrero D, Claesson M.

Links between gut microbiome composition and fatty liver disease in a large population sample
Gut Microbes 2021.
Ruuskanen MO, Åberg F, Männistö V, Havulinna AS, Méric G, Liu Y, Loomba R, Vázquez-Baeza Y, Tripathi A, Valsta LM, Inouye M, Jousilahti P, Salomaa V, Jain M, Knight R, Lahti L, Niiranen TJ.

Microbial communities as dynamical systems
Current Opinion in Microbiology 2018.
Gonze D, Coyte KZ, Lahti L, Faust K.

Signatures of ecological processes in microbial community time series
Microbiome, 2018.
Faust K, Bauchinger F, Laroche B, de Buyl S, Lahti L, Washburne AD, Gonze D, Widder S.

Multi-stability and the origin of microbial community types
ISME Journal 2017.
Faust K, Gonze D, Lahti L, Raes J.

Linking statistical and ecological theory: Hubbell’s unified neutral theory of biodiversity as a hierarchical Dirichlet process
Proceedings of the IEEE 2017.
Harris K, Parsons TL, Ijaz UZ, Lahti L, Holmes I, Quince C.

Computational humanities

Corpus Linguistics and Eighteenth Century Collections Online (ECCO)
Tolonen M, Mäkelä E, Ijaz A, Lahti L.
Research in Corpus Linguistics 9/1:19-34, 2021.

Examining the Early Modern Canon: The English Short Title Catalogue and Large-Scale Patterns of Cultural Production
In: Baird I. (eds) Data Visualization in Enlightenment Literature and Culture. Palgrave Macmillan, Cham. pp. 63-119, 2021. Tolonen M, Hill MJ, Ijaz AZ, Vaara V, Lahti L.

Quantifying bias and uncertainty in historical data collections with probabilistic programming
CEUR Workshop Proc. on Computational Humanities Research, 2020.
Lahti L, Mäkelä E, Tolonen M.

Bibliographic Data Science and the History of the Book (c. 1500-1800)
Cataloging and classification quarterly, 2019.
Lahti L, Marjanen J, Roivainen H, Tolonen M.

A Quantitative Approach to Book-Printing in Sweden and Finland, 1640–1828
Historical Methods: A Journal of Quantitative and Interdisciplinary History, 2019.
Tolonen M*, Lahti L*, Roivainen H, Marjanen J.

A National Public Sphere? Analyzing the Language, Location, and Form of Newspapers in Finland, 1771–1917
Journal of European Periodical Studies, 2019.
Marjanen J, Vaara V, Kanner A, Roivainen H, Mäkelä E, Lahti L, Tolonen M.

Open science

Alchemy & algorithms: perspectives on the philosophy and history of open science
RIO Journal 2017.
Lahti L, da Silva F, Laine MP, Lähteenoja V, Tolonen M.

Open education and educational resources. National policy and executive plan by the higher education and research community for 2021-2025 - Policy component 1: Open access to educational resources
Responsible Research Series 16:2020. Helsinki, Finland. Published by the Committee for Public Information (TJNK) and Federation of Finnish Learned Societies (TSV) .

Open Research Policy / Avoimen tutkimuksen politiikka
University of Turku, OpenUTU work group, 2018.

Opening academic publishing: development and application of systematic evaluation criteria. Report on the openness of major scientific publishers
Finnish IT Center for Science (CSC) and Ministry of Education and Culture, Open Science and Research Initiative (ATT). 2018.
Björk A, Paavolainen J-M, Ropponen T, Laakso M, Lahti L.

Opinion pieces (in Finnish)

Aatehistoria ja digitaalisten aineistojen mahdollisuudet
Ennen & Nyt (Finland) 2015.
Tolonen M, Lahti L.

Avoimuus voi vahvistaa päätöksenteon tieteellistä pohjaa
Invited opinion piece: University of Helsinki, ThinkOpen blog. August 2020.
Lahti L.

Päätös epidemialaskelmien salaamisesta vastoin valtioneuvoston avoimuuslinjausta
Invited perspective, Open Knowledge Finland blog. July 2020.
Lahti L.

Lähdekoodin sisältämien yksityiskohtien avoimuus on keskeistä päätöksenteon läpinäkyvyydelle
HS Mielipide. June 2020.
Lahti L.

Tietopyyntö THL:n epidemialaskelmien lähdekoodeista
Open Knowledge Finland ry. (Freedom of Information request)
Invited perspective, Open Knowledge Finland blog. June 2020.
Lahti L, Toikkanen T.

Päätöksenteossa käytettävien laskentamallien tulisi olla lähtökohtaisesti avoimia
Helsingin Sanomat (HS Mielipide / researcher position statement). May 2020.
Lahti L, Wallgren T, Kulmala M.

Funding and support

The work has been supported by University of Turku, Academy of Finland, European Union (COST / H2020), foundations, and other sources.