Evidence map›Paper›PMID 38729933›Full record

ArticleNature communications2024

VOLTA: an enVironment-aware cOntrastive ceLl represenTation leArning for histopathology.

Ramin Nakhli, Katherine Rich, Allen Zhang, Amirali Darbandsari, Elahe Shenasa, Amir Hadjifaradji, Sidney Thiessen, Katy Milne, Steven J M Jones, Jessica N McAlpine and 4 more

Abstract read
In one paragraph

Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Article
  5. Article
  6. Review
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

14 authors.

Ramin Nakhli *School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.ORCID http://orcid.org/0000-0001-6463-4465
Katherine Rich *Bioinformatics Graduate Program, University of British Columbia, Vancouver, Canada.
Allen ZhangDepartment of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
Amirali DarbandsariDepartment of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC, Canada.
Elahe ShenasaDepartment of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
Amir HadjifaradjiSchool of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
Sidney ThiessenDeeley Research Centre, BC Cancer Agency, Victoria, BC, Canada.
Katy MilneDeeley Research Centre, BC Cancer Agency, Victoria, BC, Canada.ORCID http://orcid.org/0000-0001-5616-1821
Steven J M JonesCanada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, Canada.ORCID http://orcid.org/0000-0003-3394-2208
Jessica N McAlpineDepartment of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada.ORCID http://orcid.org/0000-0001-6003-485X
Brad H NelsonDeeley Research Centre, BC Cancer Agency, Victoria, BC, Canada.
C Blake GilksDepartment of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
Hossein FarahaniSchool of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.ORCID http://orcid.org/0000-0002-9503-1875
Ali BashashatiSchool of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada. ali.bashashati@ubc.ca.ORCID http://orcid.org/0000-0002-4212-7224

Funding

Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada) Project GrantGouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada) Discovery GrantMichael Smith Foundation for Health Research (MSFHR) Scholar ProgramTerry Fox Research Institute (Institut de Recherche Terry Fox) Program Project
6 · The paper itself

Abstract

In clinical oncology, many diagnostic tasks rely on the identification of cells in histopathology images. While supervised machine learning techniques necessitate the need for labels, providing manual cell annotations is time-consuming. In this paper, we propose a self-supervised framework (enVironment-aware cOntrastive cell represenTation learning: VOLTA) for cell representation learning in histopathology images using a technique that accounts for the cell's mutual relationship with its environment. We subject our model to extensive experiments on data collected from multiple institutions comprising over 800,000 cells and six cancer types. To showcase the potential of our proposed framework, we apply VOLTA to ovarian and endometrial cancers and demonstrate that our cell representations can be utilized to identify the known histotypes of ovarian cancer and provide insights that link histopathology and molecular subtypes of endometrial cancer. Unlike supervised models, we provide a framework that can empower discoveries without any annotation data, even in situations where sample sizes are limited.

Indexed as

Endometrial NeoplasmsOvarian NeoplasmsAlgorithmsFemaleHumansImage Processing, Computer-AssistedMachine LearningSupervised Machine Learning

Identifiers

PMID38729933
PMCPMC11087497

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

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.