PhD researcher · University of Waterloo

houfu@research:~$ simulate --world --one-system-at-a-time

I build small, working worlds.

I’m Houfu Chen — a digital twin researcher and engineer connecting mechanistic models, noisy sensor data, and machine learning to make complex systems tangible, testable, and understandable.

Explore selected work Start a conversation ↗
  • Python
  • PyTorch
  • COBRApy
  • State-space models
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01 / PROFILE

Engineer by training. Builder by instinct.

I work where models meet reality: noisy signals, heterogeneous environments, and systems that need to stay useful outside a notebook.

I’m a PhD candidate and engineer with one practical obsession: putting a working version of the world in my hands, then using it to ask better questions.

  • 01 Building living digital twins for heterogeneous environments.
  • 02 Integrating machine learning, signal filtering, and probabilistic state estimation.
  • 03 Turning theoretical models into working systems that can be tested against reality.
~/about_me $ ls

Education

  • MEng in Electrical and Computer Engineering University of Toronto (Graduated March 2025)
  • BASc in Nanotechnology Engineering University of Waterloo (Graduated June 2023, With Distinction)
  • Featured alumni in the Data Analytics and Machine Learning Emphasis at UofT. Read more here.

Industry Experience

Teaching & Research

Greenhouse-Level Digital Twin Framework

> Status: Active PhD Research · Prototype Integration

  • Designing a probabilistic state-estimation framework to create a living digital twin of a heterogeneous greenhouse environment.
  • The Core Architecture: Bridging the gap between mechanistic biological predictions and noisy real-world sensor data.
  • Mathematical Frameworks: Implementing dynamic Flux Balance Analysis (dFBA) and Kalman Filtering to continuously track and correct hidden biomass states across multiple spatial zones.
  • Tech Stack: Python, COBRApy, State-Space Models, NumPy, SciPy

System Capabilities

  • [SYS] Languages: Python, C++, JavaScript, TypeScript, Java, C#, R, SQL
  • [ML] Machine Learning: PyTorch, TensorFlow, Scikit-learn, DeepFace, MediaPipe, State-Space Models
  • [DAT] Data & Analysis: Pandas, NumPy, SciPy, COBRApy, Data Visualization
  • [CFG] Frameworks & Tools: React, Node.js, Git, Docker, AWS, Azure, Selenium

02 / EXPERIENCE

Research is the thread. Range is the toolkit.

My current PhD work leads the story; teaching, product engineering, and consulting give me the range to carry ideas into real systems.

~/experience $ ls -l

Management / Consulting

Complaints Management & Operational Consulting @ FAW-Volkswagen

Dispute Resolution, Risk Prevention

May 2024 – July 2025

  • Handled high-risk complaints escalated by frontline agents.
  • Assessed solution fairness and determined fault through cross-functional coordination.
  • Built and maintained QBI Kanban boards to track complaint progress.

CAN Tech Industry

Performance Testing Engineer @ Ford Motor Company

Ubuntu, iperf3, TCP/IP, Selenium

May 2022 – August 2022

QA-Developer @ Manulife

JavaScript, React, WebDriver IO

January 2020 – April 2020

QA Automation Specialist @ Teranet CMS

C#, Selenium

September 2020 – December 2020

Teaching Experience

APS1070 (Foundations of Data Analytics and ML) @ UofT

  • Graded more than 200 projects per term
  • Led 10+ Tutorials per term

MIE370 (Introduction to ML) @ UofT

  • Created 2 Projects, 2 Tutorials, 2 Exam Questions

Research Experience

PhD Researcher @ University of Waterloo

Living Digital Twins, dFBA, State Estimation

Current

  • Developing a living greenhouse twin that connects mechanistic biological models with noisy, heterogeneous sensor data.
  • Supervised by Prof. Nasser Mohieddin Abukhdeir and Prof. Christian Euler in Chemical Engineering.

Research Assistant @ Prof. Yuning Li's Lab, UWaterloo

Chromatography, UV Testing, Organic Solar Cells

May 2019 – August 2019

  • Conducted chromatography and UV testing for organic solar cell research.

03 / SELECTED WORK

Proof lives in the prototype.

Three systems show the same instinct: model the world, test the model, and make the result useful outside a notebook.

~/selected-systems $ inspect

FLAGSHIP RESEARCH · UNIVERSITY OF WATERLOO

A living digital twin for heterogeneous greenhouses

> Active PhD research · prototype integration

  • ProblemGreenhouses are spatially uneven, partially observed, and full of noisy sensor signals.
  • MethodConnect dynamic flux-balance models with Kalman filtering and probabilistic state estimation.
  • Current buildA multi-zone state-estimation framework that continuously corrects hidden biomass states.
  • GoalA twin that keeps updating as the real greenhouse changes — not a one-time simulation.

Supervised by Prof. Nasser Mohieddin Abukhdeir and Prof. Christian Euler · Chemical Engineering

ROUTING SYSTEM · OPEN NOTEBOOK

Building Smart Evacuation Maps

  • ProblemShortest-path routing can create unsafe crowd concentration during majority evacuations.
  • MethodCombine Dijkstra routing, ant-colony-inspired optimization, and LLM-assisted decisions.
  • EvidenceOutperformed simple Dijkstra in the tested majority-evacuation scenarios.
GitHub ↗ Build note ↗

PHYSICAL COMPUTING · LIGHT

S.W.I.M (Sequential Wave Imprinting Machine)

  • IdeaMove a one-dimensional light source through space to imprint a two-dimensional image.
  • BuildArduino, addressable LEDs, and time-lapse photography turn digital pixels into a physical trace.
  • ContextHardware project sponsored by Prof. Steve Mann.
GitHub ↗
Sequential Wave Imprinting Machine light pattern S.W.I.M. hardware experiment in motion

~/experiments $ ls --compact

Older experiments stay available without competing with the research story.

Multimodal emotion analysisDeepFace · MediaPipe · Ollama ↗ Personal finance trackerLocal-first · OFX/QFX → Autonomous retrieval robotLEGO Mindstorms · 3rd place ↗ Matrix calculatorPython · GUI ↗

04 / LIVE LAB

Useful tools, built in public.

A growing shelf of focused browser tools: read, reflect, track, play, and leave a signal.

~/live-lab $ ls --available

SWIPE TO BROWSE →

A neon cellular butterfly from Conway’s Game of Life FLAGSHIP · LIVE
[##]
game_of_life.exe
Draw patterns, watch them evolve, and turn them into music. Explore a sandbox, 11 leaderboard challenges, and a Music Box sequencer.
flagship sandbox challenges music
JS · PWA · leaderboard → play ↗
[📖]
reading_room.app
A private bilingual reader with local OCR, PDF and text import, line-by-line translation, paragraph notes, and portable backups.
local-first OCR FR → EN
Browser · private → open
[✎]
journal_intime.app
A calm space for small reflections and daily signals, designed to make writing feel lighter and more immediate.
reflection daily weather-aware
Journal · browser → write
[$]
fin_tracker.app
A teachable personal finance tracker for categorizing transactions, seeing patterns, and keeping private data under your control.
insights categories privacy
Data · local → track
[✉]
message_box.app
A low-friction way to leave a private note, question, or hello without needing to open an email client.
direct private no login
Inbox · async → leave a note
[◎]
attachment_quiz.app
An 18-question attachment-style explorer with a clear Anxiety × Avoidance visualization, shareable results, and compare mode.
visualization shareable compare
18 questions → explore

05 / NOTES & LIFE

There’s more than one mode.

Notes from the PhD journey, private-by-design experiments, and ideas I’m still turning over.

~/personal_logs $ ls -a

Interdisciplinary PhD Journey

Status: Current PhD @ University of Waterloo

  • Research Focus: Digital Twins & Systems Architecture
  • Department: Chemical Engineering
  • Supervisors: Prof. Nasser Mohieddin Abukhdeir & Prof. Christian Euler

Knowledge Base

A collection of my thoughts, articles, and book notes.

  • Computer Vision & AI: Notes from recent deep dives.
  • Algorithms: Problem-solving patterns and optimizations.
  • How to Be an Imperfectionist: Key takeaways on productivity.

Salle de lecture — bilingual reading room

A private reader for books I’m working through in French: import a passage, interleave English line by line, and attach notes to any paragraph.

  • Local OCR extracts highlighted text from screenshots
  • PDF and text import stay in the browser
  • Paragraph notes, markdown export, and JSON backup
→ Enter the reading room

~/life $ ./game_life --launch

Game Life

9 games · 3 co-op

A whole arcade with its own home — cellular automata, AI board games, a torch-lit roguelike maze, a plant-metabolism farming sim, and real-time co-op.

  • game_of_life.exe
  • gomoku.exe
  • labyrinth.exe
  • grow_a_tomato.exe
  • tomatoswipe.exe
  • sudoku.exe
  • keep_up.exe
  • lander.exe
  • tether.exe
Life is a game — enjoy every piece of it. Don’t be afraid. Don’t rush.
→ Enter the arcade ↗

Attachment Style Quiz

Discover your attachment style — Secure, Anxious, Avoidant, or Fearful — through 18 questions inspired by “Attached” by Levine & Heller.

  • 2D scatter plot visualization on Anxiety × Avoidance axes
  • Shareable result links
  • Compare mode: plot two people on the same chart
→ Take the quiz

06 / CONTACT

Let’s make something useful.

I’m open to research collaborations, technical conversations, and ambitious systems problems — especially where modeling, sensing, and machine learning overlap.

Email Houfu