Andrew Tran

Experience

1. Present

   

   Alkera AI (opens in new tab) — Co-founder / CTO

   • Creating the next-generation data IDE.
2. Oct 2022 – Apr 2026

   

   Gerstein Lab, Yale University (opens in new tab) — Research Assistant

   New Haven, CT

   • Developed multi-modal RNA, DNA, protein, and small molecule bio LLM reasoning models.
3. May 2025 – Aug 2025

   

   Hudson River Trading (opens in new tab) — Software Engineer Intern

   New York, NY

   • Designed a FUSE filesystem in C++ for efficiently serving source files and built Python tooling for analyzing resource usage across a distributed compute cluster.
4. May 2024 – Apr 2025

   

   Ramp (opens in new tab) — Software Engineer Intern

   New York, NY

   • Led development of a card delivery platform to increase usage of card payments across the product.

Selected Projects

• GPU Topology-Aware PyTorch Model Partitioning Engine → (opens in new tab)

  Python · PyTorch · PyTorch Distributed

  Designed a system to automatically partition PyTorch computation graphs based on GPU network topology.

• Neural Clipping Search for Differentially Private Stochastic Gradient Descent → (opens in new tab)

  Python · PyTorch

  Bayesian optimization for discovering adaptive gradient clipping functions that improve convergence for neural network training that preserves privacy.

• Single-Cell Chemical Perturbation Hybrid Graph Neural Network → (opens in new tab)

  Python · PyTorch · PyTorch Geometric

  Combined variational autoencoders and graph neural networks to predict differential gene expression from chemical perturbations.

• Keyboard Video to Text → (opens in new tab)

  Python · HuggingFace · OpenCV

  Designed a model to predict the text typed from an overhead video of typing on a keyboard.

Publications

• MolLM: A unified language model for integrating biomedical text with 2D and 3D molecular representations

  Bioinformatics, June 2024

  Xiangru Tang, Andrew Tran, et al.

  Paper: MolLM: A unified language model for integrating biomedical text with 2D and 3D molecular representations → (opens in new tab)

Education

Sep 2022 – May 2026

Yale University (opens in new tab)

B.S./M.S. in Computer Science; Certificate in Data Science

Selected coursework

Trustworthy Machine Learning, Probabilistic Machine Learning, Theory of Statistics, Deep Learning on Graphs, Natural Language Processing, Distributed Systems, Operating Systems, Computer Architecture, Computer Networks, Compilers.