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Machine Learning Frontiers in Precision Medicine

Deliverables

Software implementing the method developed

ESR 9: Software implementing the method developed

1st summer school

1st summer school

Systematic review on existing methods

ESR 9: Systematic review on existing methods

2nd summer school

2nd summer school

Methodology to embed sparse somatic genetic profiles

ESR 5: Methodology to embed sparse somatic genetic profiles

Comparison of methods for network analysis of individual omics data

ESR 12: Comparison of methods for network analysis of individual comics data

Publication describing the application of current causal inference tools to a representative use-case

ESR 14: Publication describing the application of current causal inference tools to a representative use-case

Deep learning methods to find molecular components relevant for signaling that define functions that can be related to phenotypes (disease, drug response, etc.)

ESR 9: Deep learning methods to find molecular components relevant for signaling that define functions that can be related to phenotypes (disease, drug response, etc.)

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Publications

Prediction of recovery from multiple organ dysfunction syndrome in pediatric sepsis patients

Author(s): Bowen Fan, Juliane Klatt, Michael M. Moor, Latasha A. Daniels, Swiss Pediatric Sepsis Study, Lazaro N. Sanchez-Pinto, Philipp K. A. Agyeman, Luregn J. Schlapbach, Karsten M. Borgwardt
Published in: Bioinformatics, 38 (Supplement_1), 2022, Page(s) i101–i108, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btac229

Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data

Author(s): Pelin Gundogdu, Carlos Loucera, Inmaculada Alamo-Alvarez, Joaquin Dopazo, Isabel Nepomuceno
Published in: BioData Mining, 15, 2022, ISSN 1756-0381
Publisher: BioMed Central
DOI: 10.1186/s13040-021-00285-4

Systematic Review of Functional MRI Applications for Psychiatric Disease Subtyping

Author(s): Lucas Miranda, Riya Paul, Benno Pütz, Nikolaos Koutsouleris, Bertram Müller-Myhsok
Published in: Frontiers in Psychiatry, 12, 2021, ISSN 1664-0640
Publisher: Frontiers Research Foundation
DOI: 10.3389/fpsyt.2021.665536

Biological network analysis with deep learning

Author(s): Giulia Muzio, Leslie O’Bray, Karsten Borgwardt
Published in: Briefings in Bioinformatics, 2020, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbaa257

AI-assisted tracking of worldwide non-pharmaceutical interventions for COVID-19

Author(s): Parthasarathy Suryanarayanan, Ching-Huei Tsou, Ananya Poddar, Diwakar Mahajan, Bharath Dandala, Piyush Madan, Anshul Agrawal, Charles Wachira, Osebe Mogaka Samuel, Osnat Bar-Shira, Clifton Kipchirchir, Sharon Okwako, William Ogallo, Fred Otieno, Timothy Nyota, Fiona Matu, Vesna Resende Barros, Daniel Shats, Oren Kagan, Sekou Remy, Oliver Bent, Pooja Guhan, Shilpa Mahatma, Aisha Walcott-Bryant, Div
Published in: Scientific Data, 8/1, 2021, ISSN 2052-4463
Publisher: Springer
DOI: 10.1038/s41597-021-00878-y

Interpretable network-guided epistasis detection

Author(s): Diane Duroux; Héctor Climente-González; Chloé-Agathe Azencott; Kristel Van Steen
Published in: Gigascience, 11, 2022, Page(s) giab093, ISSN 2047-217X
Publisher: Oxford University Press
DOI: 10.1101/2020.09.24.310136

Detecting gene–gene interactions from GWAS using diffusion kernel principal components

Author(s): Andrew Walakira, Junior Ocira, Diane Duroux, Ramouna Fouladi, Miha Moškon, Damjana Rozman, Kristel Van Steen
Published in: BMC Bioinformatics, 23, 2022, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-022-04580-7

Shift in Social Media App Usage During COVID-19 Lockdown and Clinical Anxiety Symptoms: Machine Learning–Based Ecological Momentary Assessment Study

Author(s): Jihan Ryu, Emese Sükei, Agnes Norbury, Shelley H Liu, Juan José Campaña-Montes, Enrique Baca-Garcia, Antonio Artés, M Mercedes Perez-Rodriguez
Published in: JMIR Mental Health, 8/9, 2021, Page(s) e30833, ISSN 2368-7959
Publisher: JMIR Publications
DOI: 10.2196/30833

Quantification of tumor heterogeneity: from data acquisition to metric generation

Author(s): Aditya Kashyap, Maria Anna Rapsomaniki, Vesna Barros, Anna Fomitcheva-Khartchenko, Adriano Luca Martinelli, Antonio Foncubierta Rodriguez, Maria Gabrani, Michal Rosen-Zvi, Govind Kaigala
Published in: Trends in Biotechnology, Volume 40, Issue 6, 2022, Page(s) 647-676, ISSN 0968-0004
Publisher: Elsevier BV
DOI: 10.1016/j.tibtech.2021.11.006

Predicting Emotional States Using Behavioral Markers Derived From Passively Sensed Data: Data-Driven Machine Learning Approach

Author(s): Emese Sükei, Agnes Norbury, M Mercedes Perez-Rodriguez, Pablo M Olmos, Antonio Artés
Published in: JMIR mHealth and uHealth, 9/3, 2021, Page(s) e24465, ISSN 2291-5222
Publisher: JMIR Publications
DOI: 10.2196/24465

Network Aggregation to Enhance Results Derived from Multiple Analytics

Author(s): Diane Duroux, Héctor Climente-González, Lars Wienbrandt, Kristel Van Steen
Published in: Artificial Intelligence Applications and Innovations - 16th IFIP WG 12.5 International Conference, AIAI 2020, Neos Marmaras, Greece, June 5–7, 2020, Proceedings, Part I, 583, 2020, Page(s) 128-140, ISBN 978-3-030-49160-4
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-49161-1_12

The Case of Missed Cancers: Applying AI as a Radiologist's Safety Net

Author(s): Michal Chorev, Yoel Shoshan, Ayelet Akselrod-Ballin, Adam Spiro, Shaked Naor, Alon Hazan, Vesna Barros, Iuliana Weinstein, Esma Herzel, Varda Shalev, Michal Guindy, Michal Rosen-Zvi
Published in: Medical Image Computing and Computer Assisted Intervention – MICCAI 2020, 2020, Page(s) 220-229
Publisher: Springer
DOI: 10.5281/zenodo.4076797