ishanu chattopadhyay
Digital Twin of the Human Microbiome
University of Chicago Medicine
Nicholas Sizemore
Kaitlyn Oliphant
Erika Claud
pip install qbiome
import qbiome
from qbiome.data_formatter import DataFormatter
from qbiome.quantizer import Quantizer
from qbiome.qnet_orchestrator import QnetOrchestrator
from qbiome.forecaster import Forecaster
mathematics
computer science
social science
medicine
AI/ML learning theory and applications
Complex systems
Implication of AI in Future of Societay
University of Chicago Medicine
The Laboratory for Zero Knowledge Discovery
THE PROBLEM
Can microbial assay from gut actionably
pre-empt developmental markers?
Assuming a 1000 species ecosystem, and 1 successful experiment every day to discern a single two-way relationship, we would need 1,368 years to go through all possibilities. If we look for 3 way interactions, we would need 454,844 years
This is a general method!
E-Net
recursive forest
E-distance
a biologically informed, adaptive distance between strains
smaller distances imply a quatitatively high probability of spontaneous jump
$$J \textrm{ is the Jensen-Shannon divergence }$$
Sanov's Theorem & Pinsker's Inequality
Theorem
stable profile \(x_{h}\), "well-adapted" \(\Rightarrow Pr(x_h\rightarrow x_h) \approx 1 \)
For "new" profile \(x_{a}\), \( \displaystyle \theta(x_{a},x_{h}) \approx 0 \)
Assume:
Then, we have:
we can tell if new profile will be stable
A Math Solution to a Hard Biological Problem
Biology-aware Perturbations to "reconstruct" missing data
sample
?
Can i meaningfully perturb aundunce values?
Can we fill them in if they are missing?
Risk of Time-stamped Microbial Profile to lead to Developmental Deficit
The Zero Profile
Actinobacteria 30
Bacilli 30
Bacteroidia 30
Coriobacteria 32
Gammaproteobacteria 32
AHCTG
SHCTG
All patients All Entities
Feeding Variables added
Ability to "fill in" missing data is equivalent to making trajectory forecasts
Our risk measure is highly predictive and actionable
Which entities are most predictive?
Supplantation MUST be personalized
Supplantation MUST be personalized
Network Interpretations?
Effect of Clinical Variables
Future
Concretely answer the question: "what is a healthy microbiome?"
Explicit supplantation profiles that are tuned to individual ecosystems
Bioreactor experiments