Varner Lab — Cornell University

Mathematical models for markets and molecules.

The Varner Lab builds mathematical models and computational tools at the intersection of engineering, data science, and applied mathematics — spanning quantitative finance and machine learning today, on a deep foundation in systems and synthetic biology.

Quantitative Finance Machine Learning Systems Biology Cell-Free Systems
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70+
Peer-reviewed publications
20+
Open-source repositories
1997
Publishing since
Research

Two domains, one approach.

A consistent toolkit — mechanistic modeling, ensemble parameter estimation, and machine learning — applied to systems as different as a financial market and a living cell.

01 Current focus

Quantitative Finance & Machine Learning

Methods from engineering, statistics, and machine learning applied to financial systems — agent-based market simulations, transformer models for financial time series, and regime-aware models of risk and return.

  • Agent-based market simulation
  • Transformer models for time series
  • Regime models & value-at-risk
  • Options pricing & portfolio optimization
02 Foundation

Systems & Synthetic Biology

Two decades building predictive, mechanistic models of biological systems — metabolic networks, signal transduction, the coagulation and complement cascades, and cell-free protein synthesis.

  • Metabolic & constraint-based models
  • Signal transduction networks
  • Coagulation & complement cascades
  • Cell-free protein synthesis
Selected Work

Recent & notable.

All 70+ publications →
2026 · arXiv
Stochastic Attention via Langevin Dynamics on the Modern Hopfield Energy
Alswaidan A, Varner JD
2026 · PNAS (sub.)
Training-Free Generation of Protein Sequences from Small Family Alignments via Stochastic Attention
Varner JD
2026 · npj Syst. Biol.
Validated Synthetic Patient Generation for Small Longitudinal Cohorts: Coagulation Dynamics Across Pregnancy
Varner JD, Bravo MC, McBride C, Orfeo T, Bernstein I
2026 · arXiv
BSTModelKit.jl: Constructing, solving, and analyzing Biochemical Systems Theory models
Vadhin S, Varner JD
2024 · arXiv
MarketGPT: Developing a pre-trained transformer (GPT) for modeling financial time series
Wheeler A, Varner JD
2000 · Nature Biotech.
A mathematical model of caspase function in apoptosis
Fussenegger M, Bailey JE, Varner JD
01

Publications

Peer-reviewed articles and preprints, 1997–present, with links to code and data.

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02

Software

Open-source packages and models for finance, simulation, and computational biology.

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03

Teaching

Courses in computational thinking, machine learning, and quantitative finance.

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