Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

Equipment

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Statistical and machine learning challenges in classification and integration of molecular and genomic data

2016/23/D/ST6/03613

Keywords:

classification integrative genomics cancer statistical learning machine learning empirical bayes bootstrap

Descriptors:

  • ST6_11: Machine learning, statistical data processing and applications using signal processing (e.g. speech, image, video)
  • NZ2_8: Computational biology
  • NZ2_9: Systems biology

Panel:

ST6 - Computer science and informatics: informatics and information systems, computer science, scientific computing, intelligent systems

Host institution :

Uniwersytet Warszawski, Wydział Matematyki, Informatyki i Mechaniki

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr Neo Christopher Chung 

Number of co-investigators in the project: 2

Call: SONATA 12 - announced on 2016-09-15

Amount awarded: 424 029 PLN

Project start date (Y-m-d): 2017-08-03

Project end date (Y-m-d): 2021-02-02

Project duration:: 42 months (the same as in the proposal)

Project status: Project settled

Project description

Download the project description in a pdf file

Note - project descriptions were prepared by the authors of the applications themselves and placed in the system in an unchanged form.

Equipment purchased [PL]

  1. 27" Monitor (Dell UltraSharp U2717D) (2 450 PLN)
  2. Macbook Pro 15' 2.7 GHz (13 899 PLN)
  3. Network-attached storage (NAS).

Information in the final report

  • Publication in academic press/journals (6)
  • Articles in post-conference publications (3)
  1. Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data
    Authors:
    Neo Christopher Chung, Błażej Miasojedow, Michał Startek, Anna Gambin
    Academic press:
    BMC Bioinformatics (rok: 2019, tom: 20, strony: 644), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    0.1186/s12859-019-3118-5 - link to the publication
  2. Deep learning in oncological radiomics and challenges of interpretability and data harmonization
    Authors:
    Panagiotis Papadimitroulas, Lennart Brocki, Neo Christopher Chung, Wistan Marchadour, Franck Vermet, Laurent Gaubert, Vasilis Eleftheriadis, Dimitris Plachouris, Dimitris Visvikis, George Kagadis, Mathieu Hatt
    Academic press:
    Physica Medica (rok: 2021, ), Wydawca: Elsevier
    Status:
    Accepted for publication
    DOI:
    None - link to the publication
  3. Statistical significance of cluster membership for unsupervised evaluation of cell identities
    Authors:
    Neo Christopher Chung
    Academic press:
    Bioinformatics (rok: 2020, tom: 36, strony: 3107-3114), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btaa087 - link to the publication
  4. Identifying temporal molecular signatures underlying cardiovascular diseases: A data science platform
    Authors:
    Neo Christopher Chung, Howard Choi, Ding Wang, Bilal Mirza, Alexander R Pelletier, Dibakar Sigdel, Wei Wang, Peipei Ping
    Academic press:
    Journal of Molecular and Cellular Cardiology (rok: 2020, tom: 145, strony: 54-58), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.yjmcc.2020.05.020 - link to the publication
  5. Truncated robust principal component analysis and noise reduction for single cell RNA-seq data
    Authors:
    Krzysztof Gogolewski, Maciej Sykulski, Neo Christopher Chung, Anna Gambin
    Academic press:
    Journal of Computational Biology (rok: 2019, tom: 26, strony: 782-793), Wydawca: Mary Ann Liebert
    Status:
    Published
    DOI:
    10.1089/cmb.2018.0255 - link to the publication
  6. Unsupervised Classification of Multi-Omics Data during Cardiac Remodeling using Deep Learning
    Authors:
    Neo Christopher Chung, Bilal Mirza, Howard Choi, Jie Wang, Ding Wang, Peipei Ping, Wei Wang
    Academic press:
    Methods (rok: 2019, tom: 166, strony: 66-73), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.ymeth.2019.03.004 - link to the publication
  1. Concept Saliency Maps to Visualize Relevant Features in Deep Generative Models
    Authors:
    Lennart Brocki, Neo Christopher Chung
    Conference:
    18th IEEE International Conference On Machine Learning And Applications (ICMLA) (rok: 2019, ), Wydawca: IEEE Xplore
    Data:
    konferencja 43815
    Status:
    Published
  2. Input Bias in Rectified Gradients and Modified Saliency Maps
    Authors:
    Lennart Brocki, Neo Christopher Chung
    Conference:
    2021 IEEE International Conference on Big Data and Smart Computing (rok: 2021, ), Wydawca: IEEE Xplore
    Data:
    konferencja 17/01
    Status:
    Accepted for publication
  3. Truncated Robust Principal Component Analysis and Noise Reduction for Single Cell RNA-seq Data
    Authors:
    Krzysztof Gogolewski, Maciej Sykulski, Neo Christopher Chung, Anna Gambin
    Conference:
    International Symposium on Bioinformatics Research and Applications (rok: 2018, ), Wydawca: Springer
    Data:
    konferencja 08/06 - 11/06
    Status:
    Published

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