PRoBE Laboratory

Pattern Recognition from Biomedical Evidence Laboratory is designed:

    • To harness prior knowledge for effective knowledge discovery from biomedical data.
    • To design and develop novel machine learning algorithms using symbolic, probabilistic and hybrid approaches to solve bioinformatics problems of clinical importance such as biomarker discovery and disease classification.
    • To develop complex pattern recognition tools that can be plugged into computer-aided diagnostic systems to facilitate evidence combination from heterogeneous sources such as data from imaging, de-identified clinical information and biochemical profiling.

Research Mission:


AI approaches to solving real-world problems:

      • Include human in the loop as needed (machine + human combinations)
      • Human interpretable predictive modeling (explainable AI)
      • Integrative model development from diverse data types and knowledge sources (multimodal collective intelligence)

Multimodal Biomedical Dataset Types Analyzed:

  • Proteomic

–Mass Spectral (large/wide/deep)


  • Genomic

–GWAS/SNPs(very large)

–DNA Methylation

–Gene Expression


  • Images

–Cardiac MRI

–Brain fMRI

  • Microbiome
  • Metabolome
  • Exposome
  • Federated Electronic Health Records (EHR)

    Diseases Studied (Biomarker Discovery / Early Detection):

    –Amyotrophic Lateral Sclerosis


    –Lung Cancer

    –Breast Cancer

    –Esophageal Cancer

    –Inflammatory Bowel Diseases Ulcerative Colitis, Crohn’s

    –Coronary Artery Disease

    –Pediatric Cardiomyopathy

    –Helminth’s infections

    –Beryllium Exposure

    –Type 2 Diabetes

    –Cardiovascular Disease

    –Intervertebral Aging

    Grants as a Principal Investigator:


    • NIH/ NIGMS K25 Mentored Quantitative Research Development Award: Intelligent Aids for Proteomic Data Mining (5 years)
    • NIH/NLM R01 Bayesian Rule Learning Methods for Disease Prediction and Biomarker Discovery (3 years)
    • NIH/NIGMS R01 Transfer Rule Learning for Knowledge Based Biomarker Discovery and Predictive Biomedicine (3 years)
    • NIH/NIGMS R01 (Renewal) Transfer Rule Learning with Functional Mapping for Integrative Modeling of Panomics Data (3 years)
    • PHDA Grant: CADidME: Coronary Artery Disease intelligent detection via Metabolomic Expression (1 year)

    Other Notable Research Activities:

    • Investigator: NSF CMU Language Technologies Institute – Biological Language Modeling” (4-5 years)
    • Investigator: TATRC/DoD – Bioinformatics core (3 years)
    • Co-director of Bioinformatics and Biostatistics Core: NCI Hillman Cancer Center – Lung SPORE (Specialized Programs of Research Excellence) (9 years)
    • Inventor: US Patent App. 15/107,444, 2016 – Methods for the detection of esophageal adenocarcinoma

    Current Collaborators:

    Malar Samayamuthu
    Senior Research Scientist

    Edith Luhanga
    Assistant Research Professor

    Current Graduate Students:

    Roy Joy
    (Rafael Ceschin: Primary Advisor)

    Aidan Lakshman
    (Erik Wright: Primary Advisor)

    William Reynolds
    (Rafael Ceschin: Primary Advisor)

    Past Collaborators:

    Bruce G. Buchanan
    Emeritus Distinguished University Professor


    Robert Bowser
    Chief Scientific Officer
    Barrow Neurological Institute

    Michael Becich
    Chairman and Distinguished University Professor

    Gregory Cooper
    Distinguished University Professor and UPMC Endowed Chair

    Ali Zaidi
    Drexel University Professor of Surgery and Medicine

    Jaime Carbonell

    Jill Siegfried

    William Bigbee

    Ashok Panigrahy

    Gwendolyn Sowa

    Nam Vo

    Steve Reis
    Founding Director of Clinical and Translational Science Institute

    David Boone
    Assistant Professor

    Makedonka Mitreva
    McDonnell Genome Institute
    Washington University, St. Loius

    Harry Hochheiser
    Associate Professor

    Blair Jobe

    Featured Post Doctoral Advisees:

    Xinghua Lu

    Guodong Liu

    Mari Mori
    Clinical Geneticist

    Doctoral Student Graduates from PRoBE Lab (dissertations)

    Name                      School                           Year
    Balasubramanian, Jeya     University of Pittsburgh         2020
    Ceschin, Rafael           University of Pittsburgh         2017
    Dougall, David            University of Pittsburgh         2007
    Ganchev, Philip           University of Pittsburgh         2010
    Grover, Himanshu          University of Pittsburgh         2012
    Jordan, Rick              University of Pittsburgh         2016
    Liu, Yan                  Carnegie Mellon University       2006
    Liu, Yuzhe                University of Pittsburgh         2018
    Lopez Pineda, Arturo      University of Pittsburgh         2015
    Lustgarten, Jonathan      University of Pittsburgh         2009
    McDade, Kevin             University of Pittsburgh         2017
    Mitra, Pinaki             University of Pittsburgh         2006
    Ogoe, Henry               University of Pittsburgh         2016