Build Tracker
Methods and software in development
Snapshots of current methods and tools, with brief notes on where they are in the development pipeline.
Stage 1
In development
Survival methodology
DeSurv Platform
Efficient survival estimators pairing de-biased gradients with flexible machine-learning bases for biomarker-rich trials.
Adaptive trial core
ADAPT Statistical Hub
evolveTrial and evolveBO packages for adaptive monitoring and automated operating-characteristic tuning for the ARPA-H ADAPT platform.
Patient communication
TrialMatch LLM
Fine-tuned language model translating pancreatic cancer eligibility criteria into bilingual summaries with transparent inclusion/exclusion logic.
Stage 2
Pilot deployment
Missing data
dlGLM Package
Deep-learning generalized linear models for non-ignorable missing data used in ADAPT analytics and shared-resource consults.
Stromal genomics
DeCAF Classifier
Transcriptomic classifier of pancreatic tumor and stromal interaction states informing biomarker analyses for PDAC trials.
Clinical registries
NIMIWAE Package
Deep-learning imputation methods for EHR labs and longitudinal clinical data supporting Lineberger analytics.
Stage 3
Community adoption
Epigenomics
epigraHMM
Multi-condition epigenomic discovery pipeline used for ATAC/ChIP analyses at UNC Lineberger.
RNA-seq suite
FSCseq + CompDTUReg
Subtype discovery and differential transcript usage suite with reproducible vignettes, used in SPORE core analyses.
Clinical diagnostics
PurIST Clinical Pipeline
Single-sample PDAC classifier developed with the Yeh laboratory, with CLIA reporting used in UNC Molecular Diagnostics and PANCREAS trial evaluations.
Journeys
Code-to-clinic stories
Diagnostics
PurIST → cooperative trials
Developed with the Yeh laboratory from initial prototype to CLIA-certified assay informing UNC Molecular Diagnostics reports and PANCREAS trial subtyping.
Epigenomics
epigraHMM → NIH consortia
Used by UNC/TBCRC teams to harmonize ATAC/ChIP analyses for cell-state discovery.
Missing data
dlGLM → ARPA-H analytics
Deployed in ADAPT analytics with containerized builds on Lineberger HPC; next milestone is an external validation manuscript.
Collaboration & access
Projects are co-developed with Gillings trainees, UNC Lineberger oncologists, Alliance cooperative groups, and other collaborators. Documentation lives in GitHub repos and lab wikis.