Evidence map›Paper›PMID 38176354›Full record

ArticleMedical image analysis2024

Attention De-sparsification Matters: Inducing diversity in digital pathology representation learning.

Saarthak Kapse, Srijan Das, Jingwei Zhang, Rajarsi R Gupta, Joel Saltz, Dimitris Samaras, Prateek Prasanna

Abstract read
In one paragraph

Article in Medical image analysis, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Hard Negative Sample Mining for Whole Slide Image Classification.Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention · 2024
    Article
  4. SI-MIL: Taming Deep MIL for Self-Interpretability in Gigapixel Histopathology.Proceedings. IEEE Computer Society Conference on Computer Vision and Pattern Recognition · 2024
    Article
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

7 authors.

Saarthak KapseStony Brook University, 100 Nicolls Rd, Stony Brook, NY, 11794, USA. Electronic address: saarthak.kapse@stonybrook.edu.
Srijan DasUNC Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA.
Jingwei ZhangStony Brook University, 100 Nicolls Rd, Stony Brook, NY, 11794, USA.
Rajarsi R GuptaStony Brook University, 100 Nicolls Rd, Stony Brook, NY, 11794, USA.
Joel SaltzStony Brook University, 100 Nicolls Rd, Stony Brook, NY, 11794, USA.
Dimitris SamarasStony Brook University, 100 Nicolls Rd, Stony Brook, NY, 11794, USA.
Prateek PrasannaStony Brook University, 100 Nicolls Rd, Stony Brook, NY, 11794, USA. Electronic address: prateek.prasanna@stonybrook.edu.

Funding

TCIA Sustainment and Scalability - Platforms for Quantitative Imaging Informatics in Precision MedicineU24CA215109 · NCI · UNIV OF ARKANSAS FOR MED SCIS · PI BANERJEE, IMON, PRIOR, FRED WILLIAM · 2017 to 2021
$8.5M
Methods and Tools for Integrating Pathomics Data into Cancer RegistriesUH3CA225021 · NCI · STATE UNIVERSITY NEW YORK STONY BROOK · PI CLIFFORD, GARI DAVID, DURBIN, ERIC B. · 2020 to 2022
$1.9M
Methods and Tools for Integrating Pathomics Data into Cancer RegistriesUG3CA225021 · NCI · STATE UNIVERSITY NEW YORK STONY BROOK · PI DURBIN, ERIC B., FORAN, DAVID J · 2018 to 2019
$815k
IMAT-ITCR Collaboration: Combining FIBI and topological data analysis: Synergistic approaches for tumor structural microenvironment explorationR21CA258493 · NCI · STATE UNIVERSITY NEW YORK STONY BROOK · PI CHEN, CHAO, PRASANNA, PRATEEK · 2022 to 2023
$467k
NCI NIH HHS R21 CA258493NCI NIH HHS U24 CA215109NCI NIH HHS UG3 CA225021NCI NIH HHS UH3 CA225021
6 · The paper itself

Abstract

We propose DiRL, a Diversity-inducing Representation Learning technique for histopathology imaging. Self-supervised learning (SSL) techniques, such as contrastive and non-contrastive approaches, have been shown to learn rich and effective representations of digitized tissue samples with limited pathologist supervision. Our analysis of vanilla SSL-pretrained models' attention distribution reveals an insightful observation: sparsity in attention, i.e, models tends to localize most of their attention to some prominent patterns in the image. Although attention sparsity can be beneficial in natural images due to these prominent patterns being the object of interest itself, this can be sub-optimal in digital pathology; this is because, unlike natural images, digital pathology scans are not object-centric, but rather a complex phenotype of various spatially intermixed biological components. Inadequate diversification of attention in these complex images could result in crucial information loss. To address this, we leverage cell segmentation to densely extract multiple histopathology-specific representations, and then propose a prior-guided dense pretext task, designed to match the multiple corresponding representations between the views. Through this, the model learns to attend to various components more closely and evenly, thus inducing adequate diversification in attention for capturing context-rich representations. Through quantitative and qualitative analysis on multiple tasks across cancer types, we demonstrate the efficacy of our method and observe that the attention is more globally distributed.

Indexed as

Image Processing, Computer-AssistedMachine LearningPathologyHumansPhenotypeCell segmentationComputational pathologySelf supervised learningVision Transformer

Identifiers

PMID38176354
PMCPMC11150864

What OpenQuestion holds

Textmetadata
LicenceTDM
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.