Method and system for predicting a phenotypic feature of a host based on a microbiome of the host

Patent metadata

Field	Value
Publication number	US-2024212789-A1
Application number	US-202118288833-A
Country	US
Kind code	A1
Filing date	Aug 3, 2021
Priority date	May 19, 2021
Publication date	Jun 27, 2024
Grant date	—

Abstract

A method for predicting a phenotypic feature of a host based on a microbiome of the host by means of a data processing system includes providing or collecting microbiome-specific data and host-specific data, joining the microbiome-specific data and the host-specific data by computing a joint representation, and predicting the phenotypic feature on the basis of the joint representation by means of at least one machine learning model or machine learning algorithm. The method can be used to support the development of optimized immunotherapies.

First claim

1 : A method for predicting a phenotypic feature of a host based on a microbiome of the host by a data processing system, the method comprising:
providing or collecting microbiome-specific data and host-specific data; joining the microbiome-specific data and the host-specific data by computing a joint representation; and predicting the phenotypic feature on the basis of the joint representation using at least one machine learning model or machine learning algorithm.

2 : The method according to claim 1 , wherein the microbiome-specific data and the host-specific data comprise microbiome-specific data modalities and host-specific data modalities.

3 : The method according to claim 2 , wherein the provided or collected microbiome-specific and host-specific data or data modalities are provided or collected from one or more databases, wherein for each set of data or data modalities a certain target phenotypic feature to be predicted and/or a ground truth phenotypic feature is also stored in the database.

4 : The method according to claim 1 , wherein the method supports regression and/or classification tasks, wherein the result of predicting the phenotypic feature is a regression or a classification.

5 : The method according to claim 2 , wherein the method comprises encoding all provided microbiome-specific and host-specific data or data modalities with at least one stochastic encoder to a definable space, wherein the at least one stochastic encoder comprises a derivable parametric function capable of learning time series.

6 : The method according to claim 5 , wherein the joint representation results from the encoding and is modeled for encompassing at least one interaction between single data or single data modalities.

7 : The method according to claim 1 , wherein at least one machine learning model or at least one machine learning algorithm learns to predict the phenotypic feature via multimodal learning and/or is designed for a multimodal variational approximation via a product of single-modality posteriors.

8 : The method according to claim 2 , wherein a training phase of the at least one machine learning process or machine learning algorithm with the microbiome-specific and host-specific data or data modalities comprises collecting a target phenotypic ground truth associated with the microbiome-specific and host-specific data or data modalities.

9 : The method according to claim 8 , wherein the training phase further comprises computing single-modality posteriors via stochastic encoding functions.

10 : The method according to claim 9 , wherein the single-modality posteriors of the various data or data modalities are joined in a multimodal joint posterior distribution, wherein the joint posterior distribution or joint representation is used to operate the phenotypic prediction using a decoder.

11 : The method according to claim 8 , wherein the training phase further comprises training the machine learning model or machine learning algorithm by minimizing an objective function which accounts for an error score between prediction and ground truth.

12 : The method according to claim 1 , wherein the method comprises an inference phase comprising collecting microbiome-specific and host-specific input data or input data modalities for a new host, computing single-modality posteriors via stochastic encoding functions on the basis of the input data or input data modalities, joining the single-modality posteriors of the various data or data modalities in a multimodal joint posterior distribution or joint representation and using the multimodal joint posterior distribution or joint representation to operate the phenotypic prediction with the decoder.

13 : The method according to any claim 1 , wherein the method is model/algorithm-agnostic and/or phenotype-agnostic.

14 : The method according to claim 2 , wherein the data or data modalities or input data or input data modalities comprise at least one species-level relative abundance profile, at least one strain-level marker profile and/or at least one host data modality.

15 : A data processing system for carrying out a method for predicting a phenotypic feature of a host based on a microbiome of the host, the system:
providing or collecting means for providing or collecting microbiome-specific data and host-specific data; joining means for joining the microbiome-specific data and the host-specific data by computing a joint representation; and predicting means for predicting the phenotypic feature on the basis of the joint representation by means of at least one machine learning model or machine learning algorithm.

16 : The method according to claim 1 , wherein the method provides support for development of optimized immunotherapies for personalized cancer vaccines.

Assignees

• NEC Laboratories Europe GmbH

Inventors

• Grazioli Filippo
• Meiser Andrea
• Pileggi Giampaolo
• Siarheyeu Raman

Classifications

• G16B40/20

  Supervised data analysis · CPC title

• Y02A90/10

  Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation · CPC title

• G16B20/00 Primary

  ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations · CPC title