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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.)

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, Issue 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, Issue 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, Issue 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

netANOVA: novel graph clustering technique with significance assessment via hierarchical ANOVA

Author(s): Diane Duroux, Kristel Van Steen
Published in: Briefings in Bioinformatics, Issue Volume 24, Issue 2,, 2023, Page(s) bbad029, ISSN 1477-4054
Publisher: Oxford University Press
DOI: 10.1093/bib/bbad029

Virtual Biopsy by Using Artificial Intelligence–based Multimodal Modeling of Binational Mammography Data

Author(s): Vesna Barros, Tal Tlusty, Ella Barkan, Efrat Hexter, David Gruen, Michal Guindy, Michal Rosen-Zvi
Published in: Radiology, Issue 00338419, 2022, ISSN 0033-8419
Publisher: Radiological Society of North America
DOI: 10.1148/radiol.220027

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, Issue 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, Issue 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, Issue 23, 2022, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-022-04580-7

Increasing resolution in stress neurobiology: from single cells to complex group behaviors

Author(s): Lucas Miranda, Joeri Bordes, Serena Gasperoni, Juan Pablo Lopez
Published in: Stress, Issue 26(1), 2023, ISSN 1607-8888
Publisher: Taylor & Francis
DOI: 10.1080/10253890.2023.2186141

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, Issue 8/9, 2021, Page(s) e30833, ISSN 2368-7959
Publisher: JMIR Publications
DOI: 10.2196/30833

Higher-order genetic interaction discovery with network-based biological priors

Author(s): Paolo Pellizzoni, Giulia Muzio, Karsten Borgwardt
Published in: Bioinformatics, Issue Volume 39, Issue Supplement_1, 2023, Page(s) i523–i533, ISSN 1367-4811
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btad273

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, Issue 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, Issue 9/3, 2021, Page(s) e24465, ISSN 2291-5222
Publisher: JMIR Publications
DOI: 10.2196/24465

A causal inference approach for estimating effects of non-pharmaceutical interventions during Covid-19 pandemic

Author(s): Vesna Barros , Itay Manes, Victor Akinwande, Celia Cintas, Osnat Bar-Shira, Michal Ozery-Flato, Yishai Shimoni, Michal Rosen-Zvi
Published in: PLOS ONE, Issue 19326203, 2022, Page(s) e0265289, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0265289

Trajectories: a framework for detecting temporal clinical event sequences from health data standardized to the Observational Medical Outcomes Partnership (OMOP) Common Data Model

Author(s): Kadri Künnapuu, Solomon Ioannou, Kadri Ligi, Raivo Kolde, Sven Laur, Jaak Vilo, Peter R Rijnbeek, Sulev Reisberg
Published in: JAMIA Open, Issue 25742531, 2022, Page(s) ooac021, ISSN 2574-2531
Publisher: Oxford University Press
DOI: 10.1093/jamiaopen/ooac021

Targeted Methylation Profiling of Single Laser-Capture Microdissected Post-Mortem Brain Cells by Adapted Limiting Dilution Bisulfite Pyrosequencing (LDBSP)

Author(s): Renzo J. M. Riemens, Gunter Kenis, Jennifer Nolz, Sonia C. Susano Chaves, Diane Duroux, Ehsan Pishva, Diego Mastroeni, Kristel Van Steen, Thomas Haaf, Daniël L. A. van den Hove
Published in: International Journal of Molecular Sciences, Issue 23(24), 2022, Page(s) 15571, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms232415571

networkGWAS: a network-based approach to discover genetic associations

Author(s): Giulia Muzio, Leslie O’Bray, Laetitia Meng-Papaxanthos, Juliane Klatt, Krista Fischer, Karsten Borgwardt
Published in: Bioinformatics, Issue Volume 39, Issue 6, 2023, Page(s) btad370, ISSN 1367-4811
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btad370

Unsupervised Manifold Alignment with Joint Multidimensional Scaling

Author(s): Dexiong Chen, Bowen Fan, Carlos Oliver, Karsten Borgwardt
Published in: The Eleventh International Conference on Learning Representations, Issue 2023, 2023
Publisher: International Conference on Learning Representations
DOI: 10.48550/arxiv.2207.02968

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

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, Issue 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

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