Helsinki Institute for Information Technology (HIIT)

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• Dataset: "Probabilistic Framework for Integration of Mass Spectrum and Retention Time Information in Small Molecule Identification"

  Bach, E. (Creator), Zenodo, 1 Apr 2020

  DOI: 10.5281/zenodo.4305918

  Dataset

• CT Data of a Pen-Spring: Application to Under-Sampled Dynamic X-ray Tomography

  Juurakko, J. (Creator), Purisha, Z. (Creator) & Särkkä, S. (Creator), Zenodo, 3 Jul 2019

  DOI: 10.5281/zenodo.3266936

  Dataset

• aalto-ics-kepaco/msms_rt_score_integration: Relase for the Bioinformatics publication

  Bach, E. (Creator), Zenodo, 2020

  DOI: 10.5281/zenodo.4306269, https://doi.org/10.5281/zenodo.4306270

  Dataset: Software or code

• Result files (ONLYSTEREO): "Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data"

  Bach, E. (Creator), Zenodo, 2022

  DOI: 10.5281/zenodo.6037628

  Dataset

• Data from: Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

  Skwark, M. (Creator), Croucher, N. J. (Contributor), Puranen, S. (Contributor), Chewapreecha, C. (Contributor), Pesonen, M. (Contributor), Xu, Y. (Contributor), Turner, P. (Contributor), Harris, S. R. (Contributor), Beres, S. B. (Contributor), Musser, J. M. (Contributor), Parkhill, J. (Contributor), Bentley, S. D. (Contributor), Aurell, E. (Contributor) & Corander, J. (Contributor), Dryad Digital Repository, 22 Feb 2017

  DOI: 10.5061/dryad.gd14g, https://datadryad.org/resource/doi:10.5061/dryad.gd14g and 3 more links, https://doi.org/10.5061/dryad.gd14g/2, https://doi.org/10.5061/dryad.gd14g/1, https://doi.org/10.5061/dryad.gd14g/3 (show fewer)

  Dataset

• Biological constraints for parameter values of large-scale biologically plausible human Neuroscience models

  Williams, N. (Creator), Ojanperä, A. (Contributor), Siebenhühner, F. (Contributor), Toselli, B. (Contributor), Palva, S. (Contributor), Arnulfo, G. (Contributor), Kaski, S. (Contributor) & Palva, M. (Contributor), Mendeley Data, 2023

  DOI: 10.17632/5kgw7ssbpx.1, https://data.mendeley.com/datasets/5kgw7ssbpx

  Dataset

• aalto-ics-kepaco/lcms2struct_exp: Nature Machine Intelligence

  Bach, E. (Creator), Zenodo, 2022

  DOI: 10.5281/zenodo.7043686, https://zenodo.org/record/7057255

  Dataset: Software or code

• Additional file 2 of Probabilistic modeling methods for cell-free DNA methylation based cancer classification

  Halla-aho, V. (Creator) & Lähdesmäki, H. (Creator), figshare, 5 Apr 2022

  DOI: 10.6084/m9.figshare.19518510, https://springernature.figshare.com/articles/dataset/Additional_file_2_of_Probabilistic_modeling_methods_for_cell-free_DNA_methylation_based_cancer_classification/19518510

  Dataset

• Improving Artificial Teachers by Considering How People Learn and Forget: Dataset

  Nioche, A. (Creator), Murena, P.-A. (Creator), de la Torre-Ortiz, C. (Creator) & Oulasvirta, A. (Creator), Zenodo, 2021

  DOI: 10.5281/zenodo.5536916

  Dataset

• Drug combination data used for comboLTR in "Modeling drug combination effects via latent tensor reconstruction"

  Wang, T. (Creator), Szedmak, S. (Creator), Wang, H. (Creator), Aittokallio, T. (Creator), Pahikkala, T. (Creator), Cichonska, A. (Creator) & Rousu, J. (Creator), Zenodo, 2021

  DOI: 10.5281/zenodo.4625083, https://zenodo.org/record/4625084

  Dataset

• LC-MS² meta data for each MassBank (MB) subset

  Bach, E. (Creator), Zenodo, 2022

  DOI: 10.5281/zenodo.7056047, https://zenodo.org/record/7056047

  Dataset

• LuxHMM: DNA methylation analysis with genome segmentation via hidden Markov model

  Malonzo, M. H. (Creator) & Lähdesmäki, H. (Creator), figshare, 13 Apr 2023

  DOI: 10.6084/m9.figshare.c.6584741, https://springernature.figshare.com/collections/LuxHMM_DNA_methylation_analysis_with_genome_segmentation_via_hidden_Markov_model/6584741

  Dataset

• Protein function prediction through multi-view multi-label latent tensor reconstruction

  Armah-Sekum, R. E. (Creator), Szedmak, S. (Creator) & Rousu, J. (Creator), figshare, 3 May 2024

  DOI: 10.6084/m9.figshare.c.7215643.v1, https://springernature.figshare.com/collections/Protein_function_prediction_through_multi-view_multi-label_latent_tensor_reconstruction/7215643/1

  Dataset

• Dataset: "Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data"

  Bach, E. (Creator), Zenodo, 2022

  DOI: 10.5281/zenodo.5854660, https://doi.org/10.1101/2022.02.11.480137

  Dataset

• massbank2db: Build a machine learning ready SQLite database from MassBank

  Bach, E. (Creator), Zenodo, 2022

  DOI: 10.5281/zenodo.7029737

  Dataset: Software or code

• nicholasjclark/mvgam: v1.1.4

  Clark, N. (Creator), Senyondo, H. (Creator) & Vehtari, A. (Creator), Zenodo, 19 Feb 2025

  DOI: 10.5281/zenodo.6918047

  Dataset: Software or code

• Metabolite identification dataset: "Magnitude-Preserving Ranking for Structured Outputs" Brouard et al. (2017)

  Bach, E. (Creator), Zenodo, 2022

  DOI: 10.5281/zenodo.7189944, https://zenodo.org/record/7189944

  Dataset

• Critical Assessment of Small Molecule Identification 2016: automated methods

  Schymanski, E. L. (Creator), Ruttkies, C. (Creator), Krauss, M. (Creator), Brouard, C. (Creator), Kind, T. (Creator), Dührkop, K. (Creator), Allen, F. (Creator), Vaniya, A. (Creator), Verdegem, D. (Creator), Böcker, S. (Creator), Rousu, J. (Creator), Shen, H. (Creator), Tsugawa, H. (Creator), Sajed, T. (Creator), Fiehn, O. (Creator), Ghesquière, B. (Creator) & Neumann, S. (Creator), figshare, 28 Mar 2017

  DOI: 10.6084/m9.figshare.c.3727522.v1, https://figshare.com/collections/Critical_Assessment_of_Small_Molecule_Identification_2016_automated_methods/3727522/1

  Dataset

• Pre-rendered training and testing dataset for the paper Deep Convolutional Reconstruction for Gradient-Domain Rendering

  Kettunen, M. (Creator), Härkönen, E. (Creator) & Lehtinen, J. (Creator), Zenodo, 20 Dec 2019

  DOI: 10.5281/zenodo.3588466

  Dataset

• Pre-configured Mitsuba scenes for the paper Deep Convolutional Reconstruction for Gradient-Domain Rendering

  Kettunen, M. (Creator), Härkönen, E. (Creator) & Lehtinen, J. (Creator), Zenodo, 2019

  DOI: 10.5281/zenodo.3588481

  Dataset

• Additional file 3 of Probabilistic modeling methods for cell-free DNA methylation based cancer classification

  Halla-aho, V. (Creator) & Lähdesmäki, H. (Creator), figshare, 5 Apr 2022

  DOI: 10.6084/m9.figshare.19518513, https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Probabilistic_modeling_methods_for_cell-free_DNA_methylation_based_cancer_classification/19518513

  Dataset

• CamOptimus

  Cankorur-Cetinkaya, A. (Contributor), Dias, J. M. L. (Contributor), Kludas, J. (Creator), Slater, N. K. H. (Contributor), Rousu, J. (Creator), Oliver, S. G. (Contributor) & Dikicioglu, D. (Contributor), Apollo - University of Cambridge Repository , 1 Jan 2016

  DOI: 10.17863/cam.10257, https://www.repository.cam.ac.uk/handle/1810/265930

  Dataset

• 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

• VictoriaLyu/gpstuff: Evaluating Gaussian Process Metamodels and Sequential Designs for Noisy Level Set Estimation V1

  Vehtari, A. (Creator), Vanhatalo, J. (Creator), Sivula, T. (Creator), Solin, A. (Creator), Siivola, E. (Creator), Hartmann, M. (Creator), Steinhart, J. (Creator) & Karikomi, M. (Creator), Zenodo, 2021

  DOI: 10.5281/zenodo.4579993, https://zenodo.org/record/4579994

  Dataset: Software or code

• MassBank/MassBank-data: Release version 2021.12

  Schulze, T. (Creator), Meier, R. (Creator), Alygizakis, N. (Creator), Schymanski, E. (Creator), Bach, E. (Creator), Tanaka, S. (Creator) & Witting, M. (Creator), Zenodo, 2021

  DOI: 10.5281/zenodo.3378723, https://zenodo.org/record/5775684

  Dataset: Software or code