Antonio Fonseca
Staff Machine Learning Scientist at Matterworks
Cambridge, Massachusetts, United States
Summary
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Senior🎓
Top SchoolAntonio Fonseca is a Staff Machine Learning Scientist with a decade of experience building AI systems at the intersection of computational neuroscience, protein design, and robotics. Currently leading ML and AI development at Matterworks, he previously drove large-scale generative protein pipelines at Gensaic that produced millions of candidate therapeutics and scaffolded thousands of proteins per hour. His PhD research at Yale produced foundation models for fMRI (BrainLM), continuous spatiotemporal transformers, and Neural Integro-Differential Equations, demonstrating strengths in self-supervised learning and modeling complex continuous dynamics. Antonio pairs deep academic rigor with hands-on engineering—developing hardware/software for behavioral neuroscience, high-throughput validation pipelines, and automation systems since early roles in robotics and reliability engineering. Based in Cambridge, MA, he blends mechatronics and neuroscience training to tackle problems that require both wet-lab sensibilities and production-grade ML infrastructure. Colleagues value him for shipping ambitious research-to-production projects that uncover interpretable latent structure in messy biological data.
10 years of coding experience
11 years of employment as a software developer
High school, High school at Guaracy Silveira Technical SchoolMaintenance Electrician Industrial Electronics Technology/Technician, Maintenance Electrician Industrial Electronics Technology/Technician at SENAI (National Service of Industrial Learning)Automation Instrumentation and Robotic Engineering Mechatronics Robotics and Automation Engineering, Automation Instrumentation and Robotic Engineering Mechatronics Robotics and Automation Engineering at Universidade Federal do ABCMaster's degree Microelectronics, Master's degree Microelectronics at Federal University of Rio Grande do SulDoctor of Philosophy - PhD Neuroscience, Doctor of Philosophy - PhD Neuroscience at Yale School of MedicineMechanical Engineering Mechatronics Robotics and Automation Engineering, Mechanical Engineering Mechatronics Robotics and Automation Engineering at Laurentian University/Université Laurentienne
English, Portuguese, Spanish, French
Github Skills (69)
computer-vision10
blast9
python9
sequence-to-sequence9
pytorch9
machine-learning9
bioinformatics9
artificial-intelligence9
metagenomics9
ai8
genomics8
clustering8
ecology8
taxonomy8
protein-structure8
Programming languages (6)
Github contributions (5)
ahof1704/VocalMat
Aug 2016 - Sep 2020
Analysis of ultrasonic vocalizations from mice using computer vision and machine learning
Contributions:95 commits, 2 PRs, 83 pushes in 4 years 1 month
computer-visionmachine-learning
ahof1704/ahof1704.github.io
Sep 2021 - Jun 2024
Contributions:88 pushes, 1 branch in 2 years 9 months
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