About me

I am a Machine Learning engineer and researcher, with a particular interest in Physical AI, AI4Science and Reinforcement Learning. In the past I co-founded inductiva.ai , a cloud-HPC platform for engineers, and I was one of the initial team members of the AlphaFold project at Google DeepMind . Prior to that, I worked in the Query Formulation team at Microsoft Bing and did research in Machine Learning and Computer Vision at Idiap Research Institute and École Polytechnique Fédérale de Lausane , both in Switzerland. I did my undergraduate studies in Informatics and Computing Engineering at FEUP , in Portugal, where I am originally from.

You can connect with me via my LinkedIn profile.

News

Mar 2026
I am launching AI4Science Studio, a boutique AI studio focused on challenging R&D projects in Physical AI and AI for Science. I am accepting inquiries for project partnerships starting in May 2026. Feel free to reach out via LinkedIn.
Mar 2026
Released fastflowlm-docker, a Docker container for running LLMs on AMD Ryzen AI NPU under Linux. The official support was limited to Windows, but Claude Opus 4.6 figured out how to build it succesfully in Linux!

Blog

"Live as if you were to die tomorrow. Learn as if you were to live forever." Mahatma Gandhi

Check out my blog where I share thoughts and ideas and things I am learning about at each moment. Here are some recent and old highlights:

Equivariance in Neural Networks: A Free Lunch That Isn't
The Future of AI is Physical: Simulation is Key
2024 Nobel Prize in Chemistry: AlphaFold
AI-Driven Drug Discovery: Why Molecular Dynamics Simulations Matter
All Blog Posts →

Podcast interviews

Podcast 45 graus with José Maria Pimentel, 2025 (in Portuguese)
Bitalk podcast, Nov 2024 (in Portuguese)

Round Table discussions

Deep Learning Sessions Portugal, 2023
Deep Learning Sessions Portugal, 2022

Talks

Machine Learning for Science and Engineering Summer School, 2025
Deep Learning for NIR Chemometrics workshop, University of Algarve, 2024
The Science Circle, hosted by Jousef Murad, 2022

Publications

"Truth is what stands the test of experience." Albert Einstein

Main publications are listed below, but see also my Google Scholar profile for an up to date list.

AlphaFold 1 / Computational Biology

Nature
Improved protein structure prediction using potentials from deep learning
Andrew W Senior, Richard Evans, John Jumper, James Kirkpatrick, Laurent Sifre, Tim Green, Chongli Qin, Augustin Žídek, Alexander WR Nelson, Alex Bridgland, Hugo Penedones, Stig Petersen, Karen Simonyan, Steve Crossan, Pushmeet Kohli, David T Jones, David Silver, Koray Kavukcuoglu, Demis Hassabis
Nature journal, 15 Jan 2020
Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13)
Andrew W Senior, Richard Evans, John Jumper, James Kirkpatrick, Laurent Sifre, Tim Green, Chongli Qin, Augustin Žídek, Alexander WR Nelson, Alex Bridgland, Hugo Penedones, Stig Petersen, Karen Simonyan, Steve Crossan, Pushmeet Kohli, David T Jones, David Silver, Koray Kavukcuoglu, Demis Hassabis
Proteins: Structure, Function, and Bioinformatics, 2019

Reinforcement Learning

NeurIPS
Hugo Penedones, Carlos Riquelme, Damien Vincent, Hartmut Maennel, Timothy Mann, André Barreto, Sylvain Gelly, Gergely Neu
NeurIPS, December 2019
H. Penedones, D. Vincent, Hartmut Maennel, S. Gelly, T. Mann, A. Barreto
July 2018
T. Mann, H. Penedones, S. Mannor, T. Hester
December 2016

AI & Numerical Simulation

Rodrigo Valério, Hugo Penedones, Luís Sarmento
6th FOAM@Iberia Conference, Oct 2024
Luís Sarmento, Hugo Penedones, Sérgio Santos, Paulo Barbosa
COCE 2024, Valencia, Spain, Nov 2024
Bruno Alves Ribeiro, João Alves Ribeiro, Hugo Penedones, Luís Sarmento, Jorge Belinha, Miguel Anibal Bessa, Sérgio Tavares, Faez Ahmed
Workshop on Machine Learning for Materials, ICLR 2023

AI for Mathematics

Augusto Peres, Eduardo Dias, Luís Sarmento, Hugo Penedones
arXiv, January 2022

Computer Vision

H. Penedones, R. Collobert, F. Fleuret, D. Grangier
Idiap Research Report, 2011
H. Penedones, F. Fleuret
Idiap Internal Research Report, 2009

AI for Space

H. Penedones, B. Sousa, A. Donati, J. Martinez-Heras
SpaceOps 2008 Conference Proceedings, Heidelberg, Germany

Book

"Courage is not the absence of fear. It is acting in spite of it." Mark Twain
Cover of 'A Nossa Vez', a book by Hugo Penedones

In 2011, I wrote a book in Portuguese, expressing my views of the world. In a collection of very small chapters, I touch a wide range of topics, such as: democracy, economy, education, entrepreneurship, transparency, sustainability, peace, etc.

If you are interested, you can read the full book in digital formats for free, or order a paperback copy.

    Open-source projects

    "What I cannot create, I do not understand." Richard Feynman
    "Write programs that do one thing and do it well. Write programs to work together." Doug McIlroy

    I enjoy building tools and exploring interesting problems through code. Here are some of my public projects on GitHub:

    Python GUI to annotate face landmarks. Points can be predicted by pre-existing ML model, users just needs to apply small fixes.
    Lua code for learning pose-aware visual representations to improve object classification accuracy. Code for the research paper "Improving Object Classification using Pose Information".
    Convolutional Neural Networks for handwritten digit recognition using Torch7 and Lua.
    A Lua Torch package for evaluating machine learning binary classifiers via ROC curves.
    K-d tree implementation in C++ for efficient nearest neighbour search in multi-dimensional spaces.
    Machine learning algorithms implemented in C++. A collection of ML algorithms from scratch for educational and research purposes.
    Simple particle filter tracker in C++. Implementation of particle filtering for object tracking in computer vision.
    A fast Sudoku solver implemented in C with a Python wrapper. Demonstrates efficient constraint satisfaction problem solving.
    Interactive, zoomable fractals using PyGame. Explore the beauty of mathematical fractals with real-time rendering.
    A character-based n-grams language model for probabilistic query autocomplete. Given a text prefix, it suggests the most likely completions based on a trained model.
    Docker container for running large language models on AMD Ryzen AI NPU under Linux using FastFlowLM. Built entirely by Claude AI via GitHub Copilot CLI.

    Competitive Programming

    Data structures and algorithms useful for programming competitions. A collection of competitive programming utilities and problem-solving patterns.
    My solutions to a set of competitive programming problems.