Single-Cell Similarity Encoding for Histopathology Classification
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Solution Overview
Problem
Existing automated tools for cell identification in histopathology images lack accurate, generalizable, and scalable approaches for single cell analysis, with supervised learning requiring extensive manual annotations and unsupervised methods being prone to bias and uncertainty.
Innovation Solution
A machine learning-based method that uses a self-supervised deep learning pipeline to classify single cells by training a network to differentiate similar and dissimilar images without external class labels, utilizing a small set of reference images and sub-patches to reduce annotation burden and improve accuracy.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If supervised deep learning models are used for cell identification, then accuracy is improved, but the time required for training and the amount of manual annotations required increases significantly
Solution Approach 1:
The patent applies preliminary action by pre-training a deep learning model on large-scale unsupervised data (such as ImageNet) to learn general visual features and representations before fine-tuning on the specific task of cell identification in histopathology images. This pre-training phase occurs before any manual annotations are required for the target domain, allowing the model to start with a solid foundation of visual processing capabilities that reduces the need for extensive manual annotations and training time on the specific medical imaging task.
Solution Approach 2:
The patent uses copying by transferring pre-trained model weights and architectural designs from general-purpose computer vision models to the specific domain of histopathology image analysis. Instead of training a deep learning model from scratch on annotated medical images, the approach copies and adapts pre-existing models that have already learned effective feature representations from large amounts of unlabeled natural images, thereby significantly reducing the annotation burden and training requirements for the specialized medical application.
2Ease of operation
If unsupervised learning methods are used for cell identification, then the annotation burden is reduced, but the predictions have high uncertainty and clustering is prone to bias
Solution Approach 1:
The patent applies self-service by using the model's own pre-trained representations and embeddings to automatically generate pseudo-labels for training data without requiring manual annotations. The system leverages its pre-existing knowledge from pre-training to self-generate training labels through techniques such as consistency regularization and self-training, where the model confidently predicts labels for data it is uncertain about and uses these predictions to refine its own training set, thereby reducing dependence on external human annotation while maintaining reliable predictions.
Solution Approach 2:
The patent implements feedback mechanisms where the model continuously refines its predictions by comparing them against consistency constraints and using performance metrics to guide further training. The system incorporates feedback loops that adjust model parameters based on prediction confidence and consistency across multiple passes, gradually improving reliability while operating without manual annotations. This feedback-driven refinement allows the unsupervised approach to achieve reliable predictions by iteratively correcting and improving its own output.
Data Source
AI summary
Methods and systems for analysing the cellular composition of a sample are described, comprising: providing an image of the sample in which a plurality of cellular populations are associated with respective signals and classifying a plurality of query cells in the image between a plurality of classes corresponding to respective cellular populations in the plurality of cellular populations. This is performed by providing a query single cell image to an encoder module of a machine learning model to produce a feature vector for the query image, and assigning the query cell to one of the plurality of classes based on the feature vector for the query image and feature vectors produced by the encoder module for each of a plurality of reference single cell images. The machine leaning model comprises: the encoder module, configured to take as input a single cell image and to produce as output a feature vector the single cell image, and a similarity module configured to take as input a pair of feature vectors for a pair of single cell images and to produce as output a score indicative of the similarity between the single cell images. Thus, the machine learning model can be obtained without the need for an extensively annotated dataset. The methods find use in the analysis of multiplex immunohistochemistry/immunofluorescence in a variety of clinical contexts.


