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PhD Studentship: AI-enhanced Event and Anomaly Detection in Single-molecule Experiments

University of Birmingham - School of Chemistry

Qualification Type: PhD
Location: Birmingham
Funding for: UK Students, EU Students
Funding amount: UKRI stipend and bursary
Hours: Full Time
Placed On: 13th January 2022
Closes: 31st January 2022

Single-molecule measurements, for example current-time or current-distance recordings from single-molecule detectors, usually produce data that are characterised by large variance and high levels of "noise". These characteristics are to some extent intrinsic to the fundamental physical properties of the system under study and they can contain important information about the structure and dynamics of a molecular system. So extracting the full information content of the data, preferably in an unsupervised manner without a priori assumptions, is really critical.

Accordingly, recent years have seen the emergence of advanced data analysis tools in this field, ranging from more conventional dimensionality reduction techniques to Deep Learning and image recognition. This project will build on these advances and explore an entirely new concept: rather than asking what a molecular event might look like, we will ask "what is not background?" (and by implication define what events or "anomalies" in the data are).

We will combine statistical methods and our understanding of single-molecule data with different neural network architectures, such as recurrent neural networks (RNN) and generative adversarial networks (GAN), and develop a toolkit for next-generation single-molecule data analysis.

We are closely aligned with Birmingham's Interdisciplinary Data Science Institute, the School of Mathematics and the Turing Institute, which offer great opportunities for further collaboration. So if you have a background in Chemistry, Physics, Mathematics, Computer Science or a related area, are enthusiastic about working at the interface of Computer Science and Nanoscience and in an interdisciplinary team, then please get in touch and email me directly (t.albrecht@bham.ac.uk)!

References:

Mario Lemmer, Michael S. Inkpen, Katja Kornysheva, Nicholas J. Long & Tim Albrecht, "Unsupervised vector-based classification of single-molecule charge transport data", Nature Comm. 2016, 7, article number: 12922 https://www.nature.com/articles/ncomms12922.

Tim Albrecht, Gregory Slabaugh, Eduardo Alonso & SM Masudur R Al-Arif, "Deep learning for single-molecule science", Nanotechnology 2017, 28, 423001. https://iopscience.iop.org/article/10.1088/1361-6528/aa8334/meta

Anton Vladyka & Tim Albrecht, "Unsupervised classification of single-molecule data with autoencoders and transfer learning", Mach. Learn.: Sci. Technol. 2020, 1, 035013. https://iopscience.iop.org/article/10.1088/2632-2153/aba6f2/meta

Funding Details 

The position is funded for 3.5 years with standard UKRI stipend and bursary.

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