Eric Y. Kim1,2

1Independent Researcher · 2Previously: Stanford, Google, NGeneBioAI

Keywords:

Data-driven | Hypothesis-based | Self-directed

Abstract:

Engineering next-generation AI systems that understand and operate within specialized scientific contexts.

About Me

ML Research Engineer specializing in domain-specific AI agents for scientific research. Currently advancing CRISPR protein engineering with AlphaFold3 while building agentic systems that understand and operate within specialized scientific contexts. Creator of ChatSQ, a platform enabling researchers to deploy custom AI agents tailored to their specific domains - like multi-omics analysis agents that integrate and visualize complex biological data. I combine deep learning expertise (transformer architectures, protein design models) with 16 years of Google engineering rigor to tackle complex scaling and biological challenges. My unique strength lies in bridging cutting-edge ML research with practical scientific applications, developing both novel models (SAN transformer for proteomics, patent pending) and intuitive tools that empower researchers. Actively seeking collaborations in protein engineering, computational biology, and next-generation scientific AI agents.

PyTorch Transformers LLMs Agentic AI RAG AlphaFold3 ESM/ESM-C ProteinMPNN RFDiffusion Proteomics CRISPR Python TypeScript C++ Distributed Systems HPC/GPU ETL Pipelines

Projects

Experience

Independent Researcher

w/ Prof. Yongsub Kim, Univ. of Ulsan College of Medicine
November 2024 - Present
  • Developing novel methods to improve CRISPR-Cas9 protein functionality, utilizing AlphaFold3 for structure prediction and deep learning models for sequence optimization
  • Engineered and optimized a high-throughput AlphaFold3 inference pipeline on HPC infrastructure, increasing GPU utilization from 60% to ~100% via strategic job batching and scheduling
  • Leading the evaluation of competing protein design methodologies (EvolvePro, ProteinMPNN, RFdiffusion) to identify optimal strategies for enhancing CRISPR-Cas9 gene-editing efficacy

ML Research Engineer

NGeneBioAI

San Diego, CA
July 2022 - September 2024
  • ChatSQ: Sole architect and developer of an AI-powered data analysis platform providing a Jupyter-like environment with local file access and support for custom, domain-specific agents
  • SAN (Spectrum is All you Need) [Patent Pending]: Designed and implemented a novel transformer-based model for ID-free classification of proteomic samples from Data Independent Acquisition (DIA) spectra
  • Work selected for prestigious oral presentation at the HUPO World Congress 2022

Software Engineer, Efficiency team

Google

Kirkland, WA
July 2016 - June 2022
  • Saved 6% of CPU fleet-wide for Google Maps frontend by conducting large-scale RPC trace analysis to identify and eliminate a critical thread-starvation hotspot
  • Designed and launched a novel A/B testing framework capable of measuring CPU or latency regressions with 1% accuracy using a minimal task set (8 tasks), enabling faster and more precise experimentation
  • Improved fleet stability and security by developing and deploying a new memory protection method across more than 10 core services
  • Led open-ended performance analyses across Google's services, identifying optimization opportunities in CPU, memory, and latency

Software Engineer, DoubleClick For Advertisers

Google

New York, NY
October 2011 - June 2016
  • Reduced end-to-end ad trafficking-to-serving latency by 90% (from 20 minutes to 2 minutes) by designing and implementing an instant build and serving pipeline
  • Successfully migrated a legacy build and ad serving system to Google's modern, scalable infrastructure

Software Engineer, CJK & Korean search team

Google

Mountain View, CA
January 2006 - September 2011
  • Tech Lead for the launch of experimental Universal Search and Trending Queries for Korean search users
  • Key contributor to growing the Google Seoul office, conducting over 100 technical interviews and performing due diligence for potential acquisitions
  • Internationalized Google Video for global audiences and localized the Q&A search feature for the Korean market

Education

M.S. in Computer Science

Stanford University

2004 - 2005

    M.S. in Electrical Engineering

    Stanford University

    2000 - 2002

      B.S. in Electrical Engineering

      Seoul National University

      1996 - 2000
      • Summa Cum Laude