Microbial Classifier Using Supervised Machine Learning

Resolve Bottlenecks,
Find Innovative Solutions
Generate Solutions

Solution Overview

Problem

Current methods for analyzing microbial composition, particularly in complex microbiota, are cumbersome, slow, and often underestimate absolute population densities, making it difficult to rapidly identify and quantify target microbes in clinical and environmental samples.

Innovation Solution

A computer-implemented method using supervised machine learning, specifically artificial neural networks or random forests, to generate classifiers from flow cytometry data, enabling accurate identification and quantification of target microbes within complex microbial communities.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If supervised machine learning classifiers are used to identify target microbes, then measurement precision and sensitivity are improved, but device complexity increases

Engineering Contradiction:
Improveidentification accuracyVSAvoidclassifier complexity
Core Design Contradiction:
Measurement precisionVSDevice complexity

Solution Approach 1:

The patent applies preliminary action by pre-training machine learning classifiers with extensive flow cytometry data from pure microbial cultures before deploying them for actual sample analysis. This preprocessing step creates ready-to-use classification models that can rapidly identify target microbes in complex samples without requiring complex real-time processing during analysis.

Inventive Principle:
Principle #10Preliminary action

Solution Approach 2:

The patent introduces flow cytometry as an intermediary measurement technique that converts complex microbial identification problems into quantifiable optical signals. By using flow cytometry parameters as intermediate features, the system bridges the gap between simple measurements and complex microbial identification, enabling accurate classification without directly analyzing complex microbial structures.

Inventive Principle:
Principle #24Intermediary (Mediator)

2Productivity

If flow cytometry is used for high-throughput analysis, then productivity is improved, but measurement precision deteriorates due to inability to directly link parameters to microbial identity

Engineering Contradiction:
Improveanalysis throughputVSAvoidspecies identification accuracy
Core Design Contradiction:
ProductivityVSMeasurement precision

Solution Approach 1:

The patent implements feedback by using machine learning classifiers that learn from labeled training data and continuously improve their classification accuracy. The system incorporates feedback loops where classification results are validated against known standards, and the models are refined iteratively to improve species identification precision while maintaining high throughput flow cytometry analysis.

Inventive Principle:
Principle #23Feedback

Solution Approach 2:

The patent applies parameter changes by transforming raw flow cytometry measurements into standardized feature vectors that capture essential microbial characteristics. By changing the parameter representation from raw optical signals to normalized, scaled features, the system maintains the high throughput advantage of flow cytometry while improving the precision of microbial identification through standardized parameter comparison.

Inventive Principle:
Principle #35Parameter changes

Applied Scientific Principles

This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.

Function Achieved in This Case

The method achieves high sensitivity and precision in identifying and quantifying target microbes, with classifiers showing up to 97% accuracy and 90% overall accuracy in recognizing specific bacteria and differentiating closely related species, even in complex backgrounds, and is suitable for diagnosing microbial diseases and detecting contamination.

Implementation Method 1

Cells are detected in FCM on the basis of optical properties (light scatter from cell shape and structures)

Methodology Applied
Scientific EffectLight scatter: Scattering

Implementation Method 2

can further be stained with a plethora of fluorescent dyes that target specific biomolecules (e.g., nucleic acids) or indicate physiological activity

Methodology Applied
Scientific EffectFluorescence: Fluorescence

Data Source

PatentUS20230401449A1Means and methods for classifying microbes
Publication Date: 2023.12.14 UNIVERSITY OF LAUSANNE
  • US20230401449A1 patent drawing
  • US20230401449A1 patent drawing
  • US20230401449A1 patent drawing

AI summary

The invention relates to the field of machine learning and comprises supervised learning. In particular, the invention relates to a computer-implemented method for generating a classifier for at least one target microbe by employing supervised machine learning, e.g., an artificial neural network, a classifier that is obtainable by said method, and applications of the inventive classifier. Thus, the invention further relates to a method for quantifying the abundance of at least one target microbe in a sample, and a method for analyzing the microbial composition in a sample. Further provided herein are diagnostic uses of the classifier, i.e. a method for diagnosing a microbial disease in a subject. In addition, the invention relates to a set of standards comprised in the classifier, a computer-readable storage medium, and/or a kit.