Toxicity Analysis Trees for Molecule Fragment Risk Prediction

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Solution Overview

Problem

Conventional methods for determining molecule toxicity require physical synthesis and testing on cell cultures, consuming significant resources and time, especially for multiple molecules at various doses, and lack comprehensive characterization of toxicity dimensions.

Innovation Solution

A system utilizing machine learning models, particularly toxicity prediction models, generates toxicity dose-response curves and toxicity analysis trees to predict molecule toxicity without physical synthesis, incorporating diverse training data from images and biochemical assays to provide thorough toxicity characterization.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If physical synthesis and cell culture testing are used to determine molecule toxicity, then accurate toxicity measurement is achieved, but resource consumption and time requirements increase significantly

Engineering Contradiction:
Improvetoxicity measurement accuracyVSAvoidtoxicity assessment efficiency
Core Design Contradiction:
Measurement precisionVSProductivity

Solution Approach 1:

The system performs preliminary toxicity assessments using machine learning models trained on historical toxicity data before physical synthesis and cell culture testing. This preliminary action filters out molecules with predicted high toxicity, reducing the number of molecules requiring resource-intensive physical testing while maintaining accurate toxicity measurement for final decisions.

Inventive Principle:
Principle #10Preliminary action

Solution Approach 2:

The system creates computational copies of molecules and uses virtual screening through machine learning models to predict toxicity characteristics. These digital twins allow rapid assessment of multiple molecular variants without physical synthesis, preserving measurement accuracy through validated predictive algorithms while dramatically improving productivity.

Inventive Principle:
Principle #26Copying

2Loss of information

If physical synthesis and testing are performed for multiple molecules at various doses, then comprehensive toxicity characterization is achieved, but resource consumption increases

Engineering Contradiction:
Improvetoxicity characterization completenessVSAvoidresource consumption
Core Design Contradiction:
Loss of informationVSLoss of substance

Solution Approach 1:

The system segments the toxicity assessment process into computational prediction stages and physical validation stages. Machine learning models perform initial comprehensive toxicity characterization across multiple doses and molecular variants, identifying key toxicity patterns. Physical resources are then concentrated only on molecules requiring final validation, reducing overall resource consumption while maintaining characterization completeness.

Inventive Principle:
Principle #1Segmentation

Solution Approach 2:

The system uses parameter changes in molecular structure (in silico modifications) to explore toxicity relationships across multiple doses and molecular variants. By computationally varying molecular parameters and predicting toxicity outcomes, the system achieves comprehensive characterization without proportionally increasing physical resource consumption, focusing wet lab resources only on promising candidates.

Inventive Principle:
Principle #35Parameter changes

3Productivity

If machine learning models are used to predict toxicity, then productivity is improved, but measurement precision may be compromised

Engineering Contradiction:
Improvetoxicity prediction speedVSAvoidtoxicity prediction accuracy
Core Design Contradiction:
ProductivityVSMeasurement precision

Solution Approach 1:

The system implements feedback loops where machine learning toxicity predictions are continuously refined using results from physical cell culture testing. Predicted toxicity values feed back into model retraining, improving measurement precision over time. This feedback mechanism allows the system to maintain high productivity through computational prediction while progressively achieving accuracy comparable to physical testing.

Inventive Principle:
Principle #23Feedback

Solution Approach 2:

The machine learning models perform preliminary toxicity screening at high speed, identifying molecules with acceptable toxicity profiles. These preliminary predictions are then validated with high-precision physical testing only for molecules passing the computational filter. This two-stage approach maintains both productivity (through rapid initial screening) and measurement precision (through targeted physical validation).

Inventive Principle:
Principle #10Preliminary action

Data Source

PatentUS20260004888A1Identifying drivers of molecule toxicity using toxicity analysis trees
Publication Date: 2026.01.01 AXIOMBIO INC
  • US20260004888A1 patent drawing
  • US20260004888A1 patent drawing
  • US20260004888A1 patent drawing

AI summary

Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for predicting toxicity of a molecule. In one aspect, a method comprises: obtaining data identifying an input molecule; generating data defining a toxicity analysis tree for the input molecule; and processing the toxicity analysis tree to generate a respective toxicity score for each of a plurality of molecule fragments in the input molecule that characterizes an impact of the molecule fragment on a toxicity of the input molecule.