Evidence map›Paper›PMID 40447627›Full record

ArticleScientific data2025

MLOmics: Cancer Multi-Omics Database for Machine Learning.

Ziwei Yang, Rikuto Kotoge, Xihao Piao, Zheng Chen, Lingwei Zhu, Peng Gao, Yasuko Matsubara, Yasushi Sakurai, Jimeng Sun

Abstract readDataset
In one paragraph

Article in Scientific data, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

12 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Ziwei Yang *Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan.ORCID http://orcid.org/0000-0001-9846-840X
Rikuto Kotoge *SANKEN, Osaka University, Osaka, Japan.
Xihao PiaoSANKEN, Osaka University, Osaka, Japan.
Zheng ChenSANKEN, Osaka University, Osaka, Japan. chenz@sanken.osaka-u.ac.jp.ORCID http://orcid.org/0000-0001-6776-7159
Lingwei ZhuIRCN, The University of Tokyo, Tokyo, Japan.
Peng GaoInstitute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.
Yasuko MatsubaraSANKEN, Osaka University, Osaka, Japan.
Yasushi SakuraiSANKEN, Osaka University, Osaka, Japan.
Jimeng SunDepartment of Computer Science, University of Illinois Urbana-Champaign, Champaign, USA.

Funding

MEXT | Japan Society for the Promotion of Science (JSPS) Number JP24K20778JSPSMEXT | JST | Core Research for Evolutional Science and Technology (CREST) JPMJCR23M3
6 · The paper itself

Abstract

Framing the investigation of diverse cancers as a machine learning problem has recently shown significant potential in multi-omics analysis and cancer research. Empowering these successful machine learning models are the high-quality training datasets with sufficient data volume and adequate preprocessing. However, while there exist several public data portals, including The Cancer Genome Atlas (TCGA) multi-omics initiative or open-bases such as the LinkedOmics, these databases are not off-the-shelf for existing machine learning models. In this paper, we introduce MLOmics, an open cancer multi-omics database aiming at serving better the development and evaluation of bioinformatics and machine learning models. MLOmics contains 8,314 patient samples covering all 32 cancer types with four omics types, stratified features, and extensive baselines. Complementary support for downstream analysis and bio-knowledge linking are also included to support interdisciplinary analysis.

Indexed as

Machine LearningNeoplasmsComputational BiologyGenomicsHumansMultiomics

Identifiers

PMID40447627
PMCPMC12125382

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.