Uncertainty quantified deep learning and regression analysis framework for clinical regions of interest segmentation in skin lesions

El Houcine El Fatimi, Shah P*

( *Senior author supervising research)

Accepted: 2024 23rd IEEE ICMLA Machine Learning Conference

Deep learning with uncertainty quantification for predicting Dice coefficient of computational histopathology image segmentation

Audrey Xie, El Fatimi E, Ghosal S, Shah P*

(*Senior author supervising research)

Accepted: 2024 23rd IEEE ICMLA Machine Learning Conference

Responsible deep learning for software as a medical device

Pratik Shah* , Lester J, Delfino J, Pai V

( *Senior author supervising research)

arXiv:2312.13333 [eess.IV]

Biomedical imaging for equitable deep learning, regulatory science, and clinical research

Jenna Lester, Delfino J, Pai V, Shah P*

(*Senior author conceptualizing and leading the session)

IEEE International Symposium on Biomedical Imaging

A deep-learning toolkit for visualization and interpretation of segmented medical images

Sambuddha Ghosal and Shah P*

( *Senior author supervising research)

Cell Reports Methods 1, 100107, 2021

Uncertainty quantified deep learning for predicting dice coefficient of digital histopathology image segmentation

Sambuddha Ghosal, Xie A and Shah P*

( *Senior author supervising research)

arXiv:2011.05791 [stat.ML]

Automated end-to-end deep learning framework for classification and tumor localization from native non-stained pathology images

Akram Bayat, Anderson C, Shah P*^♯

(*Senior author supervising research, ^♯Selected for Deep-dive spotlight session)

SPIE Proceedings. DOI: 10.1117/12.2582303

Use of deep learning to develop and analyze computational hematoxylin and eosin staining of prostate core biopsy images for tumor diagnosis

Aman Rana, Lowe A, Lithgow M, Horback K, Janovitz T, Da Silva A, Tsai H, Shanmugam V, Bayat A, Shah P*

(*Senior author supervising research)

JAMA Network. DOI: 10.1001/jamanetworkopen.2020.5111

Artificial neural networks detect and classify hematologic malignancies or solid tumors using electronic medical records prior to clinical diagnosis

Yujia Zhou, Barnes C, Magoc T, Lipori G, Shah P, Cogle CR

Published at 61st American Society of Hematology Annual Meeting, Orlando, FL

Data science in clinical pharmacology and drug development for improving health outcomes in patients

Pratik Shah, Peck R, Vamvakas S, van der Graaf, Piet H

Clinical Pharmacology and Therapeutics. PMID: 32202650

Improving cancer diagnosis and care: clinical application of computational methods in precision oncology

Proceedings of a Workshop, National Academies of Sciences, Engineering, and Medicine. Washington, DC: The National Academies Press. PMID: 31386317

Artificial intelligence and machine learning in clinical development: a translational perspective

Pratik Shah* et al.

(*Corresponding author)

Nature Digital Medicine. DOI: 10.1038/s41746-019-0148-3

Artificial Intelligence for clinical trial design

Stefan Harrer, Shah P, Antony P, Hu J

Trends in Pharmacological Sciences. PMID: 31326235

Automated process incorporating machine learning segmentation and correlation of oral diseases with systemic health

Gregory Yauney, Rana A, Javia P, Wong L, Muftu A, Shah P*

(*Senior author supervising research)

41st IEEE International Engineering in Medicine and Biology Conference. DOI: 10.1109/EMBC.2019.8857965

Digital reconstruction of teeth using near-infrared light

Keith Angelino, Yauney G, Rana A, Muftu A, Edlund D, Shah P*

(*Senior author supervising research)

41st IEEE International Engineering in Medicine and Biology Conference. DOI: 10.1109/EMBC.2019.8857734

Wearable lab on body: combining sensing of biochemical and digital markers in a wearable device

Pat Pataranutaporn, Jain A, Johnson C, Shah P, Maes P

41st IEEE EMBC Conference. PMID: 31946594

Reinforcement learning with action-derived rewards for chemotherapy and clinical trial dosing regimen selection

Gregory Yauney, Shah P*

(*Senior author supervising research)

Proceedings of the 3rd Machine Learning for Healthcare Conference. PMLR 85:161-226

Computational histological staining and destaining of prostate core biopsy RGB images with generative adversarial neural networks

Aman Rana, Yauney G, Lowe A, Shah P*

(*Senior author supervising research)

17th IEEE International Conference of Machine Learning and Applications. DOI: 10.1109/ICMLA.2018.00133

Machine learning algorithms for classification of microcirculation images from septic and non-septic patients

Perikumar Javia, Rana A, Shapiro NI, Shah P*

(*Senior author supervising research)

17th IEEE International Conference of Machine Learning and Applications. DOI: 10.1109/ICMLA.2018.00097

Technology-enabled examinations of cardiac rhythm, optic nerve, oral health, tympanic membrane, gait and coordination evaluated jointly with routine health screenings: an observational study at the 2015 Kumbh Mela in India

Pratik Shah*^†, Yauney G^†, Gupta O, Patalano V, Mohit M, Merchant R, Subramanian SV

(*Senior author supervising research, ^†Contributed equally)

The British Medical Journal Open. PMID: 29678964

Convolutional neural network for combined classification of fluorescent biomarkers and expert annotations using white light images

Gregory Yauney, Angelino K, Edlund D, Shah P*^♯

(*Senior author supervising research, ^♯Selected for oral presentation)

17^th annual IEEE International Conference on BioInformatics and BioEngineering. DOI: 10.1109/BIBE.2017.00-37

Automated segmentation of gingival diseases from oral images

Aman Rana, Yauney G, Wong L, Muftu A, Shah P*

(*Senior author supervising research)

IEEE-NIH 2017 Special Topics Conference on Healthcare Innovations and Point-of-Care Technologies. DOI: 10.1109/HIC.2017.8227605

Clinical validation and assessment of a modular fluorescent imaging system and algorithm for rapid detection and quantification of dental plaque

Pratik Shah*^†, Angelino K^†, Edlund D, Mohit M, Yauney G

(*Senior author supervising research, ^†Contributed equally)

BMC Oral. PMID: 29284461

Detection of biomarkers of periodontal disease in human saliva using stabilized, vertical flow immunoassays

Emma Yee, Lathwal S, Shah P, Sikes H

ACS Sensors. PMID: 29090909

Near-infrared transillumination guides administration of dental 2D radiography and CBCT imaging

Keith Angelino, Edlund D, Bhatia G, Wu S, Shah P*^♯

(*Senior author supervising research, ^♯Selected for oral presentation)

17^th annual IEEE International Conference on BioInformatics and BioEngineering. DOI: 10.1109/BIBE.2017.00-33

Near-infrared imaging for detecting caries and structural deformities in teeth

Keith Angelino, Edlund D and Shah P*

(*Senior author supervising research)

Journal of Translational Engineering in Health and Medicine. PMID: 28507826

Design and preliminary evaluation of a wearable device for mass screening of sleep apnea

Rohan Puri, Athanasios A, Gill N, Sathya S, Rathod G, Wahi A, Satat G, Majmudar M, Shah P*

(*Senior author supervising research)

Conf Proc IEEE Eng Med Biol Soc. PMID: 28268691

Capturing the human body: from VR, consumer, to health applications

Hao Li, Lei W, Swedish T, Shah P, Raskar R

ACM SIGGRAPH Course. DOI: 10.1145/2897826.2927371

Clinical imaging of the human body: for health, visualization and predictive analytics

Ramesh Raskar, Shah P, Swedish T, Mohit M

Computer Vision Pattern Recognition Tutorial

New signaling pathways and metabolites for host: pathogen communication during gastrointestinal infections

Pratik Shah and Hung D

Proceedings of 5^th American Society of Microbiology Conference on Cell-Cell Communication in Bacteria

Regulation of Vibrio cholerae virulence in response to novel host signal

Pratik Shah and Hung D

Gordon Research Conference on Microbial Toxins and Pathogenicity

Polyamine biosynthesis and transport mechanisms are crucial for fitness and pathogenesis of Streptococcus pneumoniae

Pratik Shah*, Nanduri B, Swiatlo E, Ma Y, Pendarvis K

(*Corresponding author)

Microbiology. PMID: 20966092

Misidentification of Candida parapsilosis as C. famata in a clinical case of vertebral osteomyelitis

Mary Jane Burton, Shah P, Swiatlo E

The American Journal of the Medical Sciences. PMID: 20944497

Regulation of Vibrio cholerae virulence gene expression and pathogenesis in microaerophilic growth conditions

Pratik Shah, Oh D, Hung D

Proceedings of Cold Spring Harbor Laboratory, Molecular Genetics of Bacteria and Phage Meeting

Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays

Pratik Shah^†, Kumar R^†, Swiatlo E, Burgess SC, Lawrence ML, Nanduri B

(^†Contributed equally)

BMC Genomics. PMID: 20525227

Mucosal immunization with polyamine transport protein D (PotD) protects mice against nasopharyngeal colonization with Streptococcus pneumoniae

Pratik Shah, Briles DE, King J, Hale Y, Swiatlo E

Experimental Biology and Medicine. PMID: 19176871

Role of polyamine transport in Streptococcus pneumoniae response to physiological stress and murine septicemia

Pratik Shah, Romero DG, Swiatlo E

Microbial Pathogenesis. PMID: 18572376

Differential gene expression in Streptococcus pneumoniae in response to various iron sources

Radha Gupta, Shah P, Swiatlo E

Microbial Pathogenesis. PMID: 19464356

A multifaceted role for polyamines in bacterial pathogens

Pratik Shah*, Swiatlo E

(*Corresponding author)

Molecular Microbiology. PMID: 18405343

Quantitative analysis of Streptococcus pneumoniae TIGR4 response to in vitro iron restriction by 2-D LC ESI MS/MS

Bindu Nanduri, Shah P, Ramkumar M, Allen EB, Swiatlo E, Burgess SC, Lawrence ML

Proteomics. PMID: 18491321

Community-acquired methicillin-resistant Staphylococcus aureus as a cause of Fournier’s Gangrene

Mary Jane Burton, Shah P, Swiatlo E

The American Journal of the Medical Sciences. PMID: 18414076

Cellular location of polyamine transport protein PotD in Streptococcus pneumoniae

Pratik Shah, Marquart M, Quin LR, Swiatlo E

FEMS Microbiology Letters. PMID: 1690772

Immunization with polyamine transport protein PotD protects mice against systemic infection with Streptococcus pneumoniae

Pratik Shah, Swiatlo E

Infection and Immunity. PMID: 16988268