I’m an

Entrepreneur

&

Molecular Designer

interested in the intersection

of AI, biology and physics.


ABOUT ME

Experienced scientific machine learning leader with 8+ years at the forefront of AI-driven drug discovery. Co-founder and Chief R&D Officer of ProteinQure (since 2017), where I lead the Machine Learning (ML) team developing an AI-powered platform for computational peptide/protein design. Achieved breakthrough results including designing an FDA Fast-Track peptide–drug conjugate now in clinical trials against triple-negative breast cancer. Proven track record in executive leadership, technical innovation (generative ML models, multi-objective optimization, quantum algorithms), and strategic partnerships. Honored as an MIT Innovator Under 35 and Forbes 30 Under 30 entrepreneur.


Young man with curly hair smiling, standing in front of a dark background with blue and orange lighting.

LOCATION

Toronto, Canada

TECHNOLOGIES

Python, Bash, Linux
ML: PyTorch, TensorFlow
MLEng: Ray, Flyte, Kubernetes, Docker
MLOps: MLFlow, Optuna, ONNX, TensorRT

FAVOURITE ALGOS

Shor’s Algorithm
Genetic Algorithm
Backpropagation
NSGA-III (multi-objective optimization)

ACADEMIC PUBLICATIONS

7 papers, 1 patent application
Google Scholar
ORCID

CONTACT

hello@markfingerhuth.ai
LinkedIn
Github


SPECIALITIES

  • My work focuses on integrating ML with structural biology, biophysics, and experimental feedback to design peptides and proteins with therapeutic potential. I have experience across the full in silico workflow: structure modelling (AlphaFold, Boltz, Rosetta), docking and molecular dynamics, property prediction (binding affinity, solubility, permeability, serum stability, PK), and closed-loop ML–wet lab cycles. This combination has enabled the discovery of peptides now progressing through clinical development.

  • As a founder and Chief R&D Officer, I’ve built and led interdisciplinary teams across machine learning, computational biology, software engineering, and wet lab science. I focus on creating clear strategy, enabling deep collaboration, and delivering meaningful scientific and business outcomes. I’ve hired and mentored ML teams, secured partnerships with global pharma companies, and driven long-term R&D roadmaps from concept to clinical impact.

  • I build advanced machine learning systems that power real-world drug discovery. My experience spans generative models (diffusion, autoregressive, and geometric deep learning), multi-objective optimization, active learning, and uncertainty-aware prediction. So far, I have led the development of 60+ custom ML models across protein design, property prediction, and experimental decision-making. I specialize in translating cutting-edge research into robust, production-ready tools used by interdisciplinary scientific teams.

  • I have extensive experience architecting and scaling scientific computing systems on the cloud and on-prem. This includes running petascale simulations, deploying multi-GPU training pipelines, orchestrating large-scale Kubernetes workloads, and optimizing inference with ONNX/TensorRT. I’ve designed and implemented infrastructure that processes millions of protein sequences, integrates tightly with ML pipelines, and supports data-driven discovery at industrial scale.

  • I thrive at the interface of research and engineering, driving high-risk, high-impact innovation. I develop next-generation tools that accelerate molecular discovery, including closed-loop ML workflows relying on cloud labs for automated design–make–test-analyze cycles. My team builds peptide-specific ML models that expand the accessible design space to 3500+ non-natural amino acids and enable high-throughput optimization. I have also explored VR-based 3D protein structure analysis for more intuitive interaction with complex molecular geometries. My approach blends rapid prototyping with rigorous scientific validation to push the boundaries of computational drug discovery.


SELECTED ACHIEVEMENTS

2025

First

AI-designed peptide

in clinical trials

2020

Forbes

30 Under 30

Science & Healthcare

2019

MIT

Innovators Under 35