Research

I. AI-Enabled Imaging for Rapid Pathogen Detection

Rapid Salmonella serovar classification using AI-enabled hyperspectral microscopy with different data preprocessing approaches
M Papa, S Bhattacharya, B Park, J Yi
IAFP 2025 (T6-02 Competition Finalist)
Funded by the USDA-ARS
[Conference Page (upcoming), Publisher Page (upcoming)]

Investigating source-specific variations in hyperspectral signatures of Salmonella Infantis
G Kuehnle, M Papa, M Milicevic, B Park, J Yi
IAFP 2025 (P2-85 Competition Finalist)
Funded by the USDA-ARS
[Conference Page (upcoming)]

AI-enabled imaging for pathogen detection under stress conditions: A systematic review
M Papa, G Kuehnle, Y Oh, and J Yi
IAFP 2025 (P2-80) | Pre-registered at PROSPERO
Funded by the MSU Research Foundation Tetrad
[PROSPERO, Conference Page (upcoming), Publisher Page (upcoming)]

Enhancing AI microscopy for foodborne bacterial classification via adversarial domain adaptation across optical and biological variability
S Bhattacharya, A Wasit, M Earles, N Nitin, L Ma, and J Yi
IAFP 2025 (T15-04) | arXiv Preprint
Funded by MSU startup, USDA-NIFA, USDA/NSF AIFS
[ArXiv, Conference Page (upcoming), Publisher Page (upcoming)]

Out-of-distribution generalization of bacterial detection with uncertainty-aware multimodal fusion
T Shin, B Park, J Yi
Funded by the USDA-ARS
[Publisher Page (upcoming)]

Detection of viable but nonculturable E. coli induced by low-level antimicrobials using AI-enabled hyperspectral microscopy
M Papa, A Wasit, J Pecora, TM Bergholz, and J Yi
ASABE 2024 (302-1) | Journal of Food Protection
Funded by MSU Research Foundation Tetrad, MSU Startup
[Conference Page, Publisher Page]

Rapid and data-efficient classification of Salmonella serovars using augmentation and deep learning on hyperspectral microscope images
A Wasit, B Park, and J Yi
IAFP 2024 (P1-295)
Funded by the USDA-ARS, MSU Startup
[Conference Page]

II. Microbiome and Genomic Data Modeling

Improving soil health modeling using imputed microbiome relative abundance data
M Milicevic and J Yi
Inverse Problems Symposium 2025
Funded by MSU startup
[ArXiv (upcoming)]

Genomic and Phenotypic Predictive Modeling of Recurring E. coli Strains
M Milicevic, TM Bergholz and J Yi
Funded by the Center for Produce Safety
[Project Page]

Impact of biotic and abiotic factors on Listeria monocytogenes, Salmonella enterica, and Enterohemorrhagic Escherichia coli in agricultural soil extracts
D Sharma, AL Kraft, JO Owade, M Milicevic, J Yi, and TM Bergholz
Microorganisms
[Publisher Page]

III. Generative AI for Cell Imaging

Label-free prediction of fluorescence markers in bovine satellite cells using deep learning
S Sinha, A Wasit, WS Kim, J Kim, and J Yi
arXiv Preprint
Funded by MSU startup
[ArXiv, Publisher Page (upcoming)]

 

 

Publications

 

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