Research

I've spent much of my recent career building models that predict complex scientific systems. But prediction and explanation aren't the same objective. I'm interested in how we build AI systems that can move beyond prediction to discover parsimonious explanations: forming hypotheses, designing discriminating experiments, revising models from evidence, and communicating the resulting understanding to humans. I'm interested in the model architectures and training methods that make those capabilities possible.

I came to machine learning from physics and have spent close to a decade doing AI research in industry. At Microsoft Research I was a first author on Aurora, a foundation model for the Earth system published in Nature (2025), contributed to Skala, a deep learning model for quantum chemistry, and worked on few-shot learning and molecular representation. I'm now at the Ellison Institute of Technology, building foundation models for biological sequences: proteins, genetics, and whole-cell behaviour.

I enjoy formulating ideas, and I do the technical work to test them myself: designing models, writing code, and running experiments.

The systems I want to build maintain an internal model of their domain and improve it through interaction with data, tools, simulation, and experiment. Biology is a case in point: to be modellable at all it needs both language and verification in the lab. The representations these systems learn about the world fascinate me in their own right. And whatever modelling paradigm we ultimately choose, we should build systems that are transparent, with true explanation accessible to humans.

Foundation ModelsScientific AIWorld ModelsReasoning SystemsProteins & GenomicsEarth SystemFew-Shot LearningQuantum Chemistry

Experience

Oct 2025 – Present

Research Scientist

Ellison Institute of Technology · Oxford

  • Research lead on foundation models for scientific sequence data, including biological sequences.
  • Focused on architecture, pretraining, and scaling, alongside correct evaluation and data curation.
Feb 2022 – Sep 2025Researcher, Feb 2020 – Jan 2022

Senior Researcher

Microsoft Research AI for Science · Cambridge & Amsterdam

  • First author on Aurora, a large-scale foundation model for the Earth system built on a 3D Swin Transformer backbone with a Perceiver-based encoder, setting a new state of the art for weather forecasting and Earth-system prediction. Published in Nature (2025).
  • Member of the Skala team: deep-learning models for quantum chemistry, including learned exchange-correlation functionals (under review, Nature).
  • Meta-learning, few-shot learning, and graph neural network research including molecular representation learning; publications at NeurIPS and ICLR.
Jan 2019 – Dec 2019

Data Scientist & Researcher

Faculty Science Ltd · London

Apr 2018 – Dec 2018

Visiting Scientist

UCSF Department of Radiology, Brain Networks Laboratory · San Francisco

Sep 2012 – Dec 2017

Research Associate (PhD Student)

University of Cambridge · Cambridge

  • Thesis: “Photon-mediated entanglement of electron spins in a dynamic solid-state environment”

Selected Publications

Full list on Google Scholar →

Foundation Models & Machine Learning

Aurora: A Foundation Model for the Earth SystemNature 2025

C. Bodnar*, W. P. Bruinsma*, A. Lucic*, M. Stanley*, et al.

Nature 641, 1180–1187 (2025)· *equal contribution

Accurate and scalable exchange-correlation with deep learning

G. Luise et al.

arXiv:2506.14665 (2025, under review at Nature)

Hard Meta-Dataset: Towards Understanding Few-Shot Performance on Difficult TasksICLR 2023

S. Basu, J. Bronskill, M. Stanley, D. Massiceti, S. Feizi.

ICLR (2023)

Fake it until you make it? Generative de novo design and virtual screening of synthesizable molecules

M. Stanley, M. Segler.

Current Opinion in Structural Biology 82 (2023)

Re-evaluating Retrosynthesis Algorithms with SyntheseusNeurIPS 2023

K. Maziarz, A. Tripp, G. Liu, M. Stanley, et al.

NeurIPS AI4Science Workshop (2023) / Faraday Discussions 256, 568–586

FS-Mol: A Few-Shot Learning Dataset of MoleculesNeurIPS 2021

M. Stanley, J. Bronskill, K. Maziarz, H. Misztela, J. Lanini, M. Segler, N. Schneider, M. Brockschmidt.

NeurIPS (2021)

Shapley explainability on the data manifoldICLR 2021

C. Frye, D. de Mijolla, M. Stanley, T. Begley, L. Cowton, I. Feige.

ICLR (2021)

Quantum Physics

Phase-tuned entangled state generation between distant spin qubits

R. Stockill*, M. J. Stanley*, L. Huthmacher*, E. Clarke, M. Hugues, A. J. Miller, C. Matthiesen, C. Le Gall, M. Atatüre.

Phys. Rev. Lett. 119, 010503 (2017)· *equal contribution

Controlling the coherence of a diamond spin qubit through its strain environment

M. J. Stanley et al.

Nature Communications 9, 2012 (2018)

Single-photon emission from single-electron transport in a SAW-driven lateral light-emitting diode

M. J. Stanley et al.

Nature Communications 11, 1–7 (2020)

Full counting statistics of quantum dot resonance fluorescence

C. Matthiesen*, M. J. Stanley*, M. Hugues, E. Clarke, M. Atatüre.

Scientific Reports 4, 4911 (2014)· *equal contribution

Education

PhD Physics

University of Cambridge · 2017

MSci Physics · First Class Honours

University of Cambridge · 2011

BA Physics · First Class Honours in all years

University of Cambridge · 2010

Awards

2012EPSRC Doctoral Training Prize
2011Murgoci Prize for Physics (best graduand)
2010Horne Prize for Physical Science
2009Grand Prize Winner, iGEM competition, MIT
2008–09Clare College Scholarships