Regression transformer enables concurrent sequence regression and generation for molecular language modelling

J Born, M Manica - Nature Machine Intelligence, 2023 - nature.com
Despite tremendous progress of generative models in the natural sciences, their
controllability remains challenging. One fundamentally missing aspect of molecular or …

Aligning optimization trajectories with diffusion models for constrained design generation

G Giannone, A Srivastava… - Advances in Neural …, 2023 - proceedings.neurips.cc
Generative models have significantly influenced both vision and language domains,
ushering in innovative multimodal applications. Although these achievements have …

Foundation model for material science

S Takeda, A Kishimoto, L Hamada, D Nakano… - Proceedings of the …, 2023 - ojs.aaai.org
Foundation models (FMs) are achieving remarkable successes to realize complex
downstream tasks in domains including natural language and visions. In this paper, we …

Chemical representation learning for toxicity prediction

J Born, G Markert, N Janakarajan, TB Kimber… - Digital …, 2023 - pubs.rsc.org
Undesired toxicity is a major hindrance to drug discovery and largely responsible for high
attrition rates in early stages. This calls for new, reliable, and interpretable molecular …

On the choice of active site sequences for kinase-ligand affinity prediction

J Born, Y Shoshan, T Huynh, WD Cornell… - Journal of chemical …, 2022 - ACS Publications
Recent work showed that active site rather than full-protein-sequence information improves
predictive performance in kinase-ligand binding affinity prediction. To refine the notion of an …

Standardizing chemical compounds with language models

MT Cretu, A Toniato, A Thakkar… - Machine Learning …, 2023 - iopscience.iop.org
With the growing amount of chemical data stored digitally, it has become crucial to represent
chemical compounds accurately and consistently. Harmonized representations facilitate the …

Automated patent classification for crop protection via domain adaptation

D Christofidellis, MM Lehmann, T Luksch… - Applied AI …, 2023 - Wiley Online Library
Patents show how technology evolves in most scientific fields over time. The best way to use
this valuable knowledge base is to use efficient and effective information retrieval and …

[PDF][PDF] Accelerating scientific discovery using domain adaptive language modelling

D Christofidellis - 2023 - pureadmin.qub.ac.uk
Scientific discovery is the process of successful scientific inquiry that allows us to develop
new technologies, solve practical problems, and aid decision-making. This process is a non …

Domain-agnostic and Multi-level Evaluation of Generative Models

GA Tadesse, J Born, C Cintas, W Ogallo… - arxiv preprint arxiv …, 2023 - arxiv.org
While the capabilities of generative models heavily improved in different domains (images,
text, graphs, molecules, etc.), their evaluation metrics largely remain based on simplified …