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Josef Dean

dblp:335/2041 · DBLP profile ↗
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3ranked-venue papers
0as first author
3since 2021 · last 2025
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 3 · 3 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
2 papers
Bioinformatics and computational biology · 52% Computational science and engineering · 48%
Artificial intelligence
2 papers
Learning theory · 62% Deep learning architectures and training · 38%

Topics — the 6 heaviest of 8, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Machine learning › Learning theory › neural network theory › neural network parameterization
maximal update parameterization
0.912025
u-μP: The Unit-Scaled Maximal Update Parametrization · ICLR 2025
Machine learning › Learning theory › neural network theory
neural network parameterization
0.912025
u-μP: The Unit-Scaled Maximal Update Parametrization · ICLR 2025
Computational science and engineering
foundation models
0.812024
Towards Foundational Models for Molecular Learning on Large-Scale Multi-Task Datasets · ICLR 2024
Bioinformatics and computational biology › molecular informatics › cheminformatics
molecular machine learning
0.812024
Towards Foundational Models for Molecular Learning on Large-Scale Multi-Task Datasets · ICLR 2024
Bioinformatics and computational biology
molecular property prediction
0.812024
Towards Foundational Models for Molecular Learning on Large-Scale Multi-Task Datasets · ICLR 2024
Computational science and engineering › computational chemistry
quantum chemistry
0.712023
Generating QM1B with PySCFIPU · NeurIPS 2023

Methods — techniques the papers use, named apart from their topics

PySCF · 1.3IPU · 1.3multi-task training · 0.8graph neural network · 0.8
YearPublicationVenuePosition
2025 u-μP: The Unit-Scaled Maximal Update Parametrization
Charlie Blake, Constantin Eichenberg, Josef Dean, Lukas Balles, Luke Y. Prince, Björn Deiseroth, Andrés Felipe Cruz-Salinas, Carlo Luschi, Samuel Weinbach, Douglas Orr
ICLR3
2024 Towards Foundational Models for Molecular Learning on Large-Scale Multi-Task Datasets
abstract
Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks. The Graphium library is publicly available on Github and the dataset links are available in Part 1 and Part 2.
Dominique Beaini, Shenyang Huang, Joao Alex Cunha, Gabriela Moisescu-Pareja, Oleksandr Dymov, Samuel Maddrell-Mander, Callum McLean, Frederik Wenkel, Luis Müller, Jama Hussein Mohamud, Ali Parviz, Michael Craig, Michal Koziarski, Jiarui Lu, Zhaocheng Zhu, Cristian Gabellini, Kerstin Kläser 0001, Josef Dean, Cas Wognum, Maciej Sypetkowski, Guillaume Rabusseau, Reihaneh Rabbany, Jian Tang 0005, Christopher Morris 0001, Mirco Ravanelli, Guy Wolf, Prudencio Tossou, Hadrien Mary, Therence Bois, Andrew W. Fitzgibbon, Blazej Banaszewski, Chad Martin, Dominic Masters
ICLR19
2023 Generating QM1B with PySCFIPU
Alexander Mathiasen, Hatem Helal, Kerstin Kläser 0001, Paul Balanca, Josef Dean, Carlo Luschi, Dominique Beaini, Andrew W. Fitzgibbon, Dominic Masters
NeurIPS5