Literature DB >> 35788277

Application of non-negative matrix factorization in oncology: one approach for establishing precision medicine.

Ryuji Hamamoto1, Ken Takasawa2, Hidenori Machino2, Kazuma Kobayashi1, Satoshi Takahashi2, Amina Bolatkan2, Norio Shinkai3, Akira Sakai3, Rina Aoyama4, Masayoshi Yamada5, Ken Asada2, Masaaki Komatsu2, Koji Okamoto1, Hirokazu Kameoka6, Syuzo Kaneko1.   

Abstract

The increase in the expectations of artificial intelligence (AI) technology has led to machine learning technology being actively used in the medical field. Non-negative matrix factorization (NMF) is a machine learning technique used for image analysis, speech recognition, and language processing; recently, it is being applied to medical research. Precision medicine, wherein important information is extracted from large-scale medical data to provide optimal medical care for every individual, is considered important in medical policies globally, and the application of machine learning techniques to this end is being handled in several ways. NMF is also introduced differently because of the characteristics of its algorithms. In this review, the importance of NMF in the field of medicine, with a focus on the field of oncology, is described by explaining the mathematical science of NMF and the characteristics of the algorithm, providing examples of how NMF can be used to establish precision medicine, and presenting the challenges of NMF. Finally, the direction regarding the effective use of NMF in the field of oncology is also discussed.
© The Author(s) 2022. Published by Oxford University Press.

Entities:  

Keywords:  NMF; machine learning; meta-analysis; omics analysis; single-cell analysis

Mesh:

Year:  2022        PMID: 35788277      PMCID: PMC9294421          DOI: 10.1093/bib/bbac246

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN: 1467-5463            Impact factor:   13.994


  111 in total

Review 1.  Machine Learning in Medical Imaging.

Authors:  Maryellen L Giger
Journal:  J Am Coll Radiol       Date:  2018-02-02       Impact factor: 5.532

2.  SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes.

Authors:  Marc Elosua-Bayes; Paula Nieto; Elisabetta Mereu; Ivo Gut; Holger Heyn
Journal:  Nucleic Acids Res       Date:  2021-05-21       Impact factor: 16.971

3.  A fresh look at somatic mutations in cancer.

Authors:  Dávid Szüts
Journal:  Science       Date:  2022-04-21       Impact factor: 47.728

4.  Analyses of microstructural variation in the human striatum using non-negative matrix factorization.

Authors:  Corinne Robert; Raihaan Patel; Nadia Blostein; Chrisopher J Steele; M Mallar Chakravarty
Journal:  Neuroimage       Date:  2021-11-27       Impact factor: 6.556

Review 5.  High-dimensional role of AI and machine learning in cancer research.

Authors:  Enrico Capobianco
Journal:  Br J Cancer       Date:  2022-01-10       Impact factor: 9.075

6.  The single-cell pathology landscape of breast cancer.

Authors:  Hartland W Jackson; Jana R Fischer; Vito R T Zanotelli; H Raza Ali; Robert Mechera; Savas D Soysal; Holger Moch; Simone Muenst; Zsuzsanna Varga; Walter P Weber; Bernd Bodenmiller
Journal:  Nature       Date:  2020-01-20       Impact factor: 49.962

7.  Semi-automated brain tumor segmentation on multi-parametric MRI using regularized non-negative matrix factorization.

Authors:  Nicolas Sauwen; Marjan Acou; Diana M Sima; Jelle Veraart; Frederik Maes; Uwe Himmelreich; Eric Achten; Sabine Van Huffel
Journal:  BMC Med Imaging       Date:  2017-05-04       Impact factor: 1.930

8.  An integrated multi-omics analysis identifies prognostic molecular subtypes of non-muscle-invasive bladder cancer.

Authors:  Sia Viborg Lindskrog; Frederik Prip; Philippe Lamy; Ann Taber; Clarice S Groeneveld; Karin Birkenkamp-Demtröder; Jørgen Bjerggaard Jensen; Trine Strandgaard; Iver Nordentoft; Emil Christensen; Mateo Sokac; Nicolai J Birkbak; Lasse Maretty; Gregers G Hermann; Astrid C Petersen; Veronika Weyerer; Marc-Oliver Grimm; Marcus Horstmann; Gottfrid Sjödahl; Mattias Höglund; Torben Steiniche; Karin Mogensen; Aurélien de Reyniès; Roman Nawroth; Brian Jordan; Xiaoqi Lin; Dejan Dragicevic; Douglas G Ward; Anshita Goel; Carolyn D Hurst; Jay D Raman; Joshua I Warrick; Ulrika Segersten; Danijel Sikic; Kim E M van Kessel; Tobias Maurer; Joshua J Meeks; David J DeGraff; Richard T Bryan; Margaret A Knowles; Tatjana Simic; Arndt Hartmann; Ellen C Zwarthoff; Per-Uno Malmström; Núria Malats; Francisco X Real; Lars Dyrskjøt
Journal:  Nat Commun       Date:  2021-04-16       Impact factor: 17.694

9.  Predicting Deep Learning Based Multi-Omics Parallel Integration Survival Subtypes in Lung Cancer Using Reverse Phase Protein Array Data.

Authors:  Satoshi Takahashi; Ken Asada; Ken Takasawa; Ryo Shimoyama; Akira Sakai; Amina Bolatkan; Norio Shinkai; Kazuma Kobayashi; Masaaki Komatsu; Syuzo Kaneko; Jun Sese; Ryuji Hamamoto
Journal:  Biomolecules       Date:  2020-10-19

10.  Assessing Versatile Machine Learning Models for Glioma Radiogenomic Studies across Hospitals.

Authors:  Risa K Kawaguchi; Masamichi Takahashi; Mototaka Miyake; Manabu Kinoshita; Satoshi Takahashi; Koichi Ichimura; Ryuji Hamamoto; Yoshitaka Narita; Jun Sese
Journal:  Cancers (Basel)       Date:  2021-07-19       Impact factor: 6.639

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