1,721,064 research outputs found
AI3SD Video: How to detect unexpected features & physical processes in single-molecule data
No full textThis talk forms part of the ML4MC (Machine Learning for Materials and Chemicals Series which has been organised as a joint venture between the Artificial Intelligence for Scientific Discovery Network+ (AI3SD) and the Directed Assembly Network. This series ran over summer 2021 and covers topics that encompass our overlapping Network interests of AI, Machine Learning, Artificial Photosynthesis, Biomimetic Materials, Crystal Design & Engineering, Materials, Molecules, Photochemistry, Photocatalysis and Supramolecular Chemistry. This video was the sixth talk in the ML4MC series and formed part of the session "Research Talks"
AI3SD Video: Event detection in single-molecule data – how to find molecular signatures without (too many) prior assumptions
No full textData from single-molecule experiments, such as from current-time or conductance-distance spectroscopy or sensors, are often “noisy” and characterised by complex molecular behaviour. In some cases, extracting the physically relevant information may be based on supervised approaches, i.e. where labelled data are available for training. In other cases, such data are either not available or it may simply be undesirable to make a priori assumptions about the molecular characteristics, for example to prevent loss of information and expectation bias.[1,2] This may require unsupervised methods or alternative approaches that put an emphasis on “what is not background?”, rather than “what does an event look like?”. In my talk, I will discuss some of the approaches we have taken, including some based on image recognition networks (AlexNet, VGG16),[3,4] and show those can be used to extract not only physically meaningful characteristics, but also previously unknown molecular behaviour.[1] M. Lemmer et al., “Unsupervised vector-based classification of single-molecule charge transport data”, Nat. Commun. 2016, 7, art. no. 12922[2] T. Albrecht et al., “Deep learning for single-molecule science”, Nanotechnol. 2017, 28, 423001.[3] A. Vladyka, T. Albrecht, “Unsupervised classification of single-molecule data with autoencoders and transfer learning”, Machin. Learn.: Sci. Technol. 2020, 1, 035013.[4] C. Weaver et al., “Unsupervised Classification of Voltammetric Data with Image Recognition and Dimensionality Reduction” (in preparation
AI3SD Video: When charge transport data are a worm – a transfer learning approach for unsupervised data classification
No full textAdvanced data analysis methodologies, and in particular dimensionality reduction techniques, are now used more and more widely in the single-molecule charge transport community. They allow for comprehensive exploration of large datasets, where data display significant variance and sometimes contain (unknown) sub-populations. To this end, unsupervised approaches, which do not rely on class labels or pre-defined expectations can be advantageous. Multi-Parameter Vector Classification (MPVC) is one example and PCA-based methods have also been employed in this context [1,2,3]. We have recently shown how Transfer Learning may be employed to identify and quantify hidden features in single-molecule charge transport data [3]. Using open-access neural networks such as AlexNet, trained on millions of seemingly unrelated image data, feature recognition then does not require network training with application-specific data. Instead, the network recognises features in the input that it had learned in other contexts and, for example, identifies different shapes in conductance-distance traces as images of different worm species. Thus, our results show how Deep Learning methodologies can readily be employed for unsupervised data classification, even if the amount of problem-specific, ‘own’ data is limited.[1] M Lemmer, MS Inkpen, K Kornysheva, NJ Long, T Albrecht, “Unsupervised vector-based classification of single-molecule charge transport data”, Nat. Comm. 2016, 7, 12922.[2] T Albrecht, G Slabaugh, E Alonso, SMMR Al-Arif, “Deep learning for single-molecule science”, Nanotechnology 2017, 28 (42), 423001.[3] A Vladyka, T Albrecht, “Unsupervised classification of single-molecule data with autoencoders and transfer learning”, Mach. Learn.: Sci. Technol. 2020, 1, 035013
AI3SD Project: Application of Capsule Net for automated DNA sequencing using tunnelling spectroscopy
No full textIn this project, we take the next step for quantum tunnelling-based biosensing and sequencing to become promising contender for label-free ‘next-next’ generation sequencing of biopolymers.This could be achieved by combining state-of-the-art surface chemistry, nanoscience and chemical sensing with Capsule Nets (CN) as a novel Deep Learning methodology, to maximise the extraction of information from the tunnelling data. Our results to date show a moderate improvement in detection accuracy when using Capsule Nets, compared to Convolutional Neural Networks. CapsNets were however superior when dealing with incomplete data, for examplewhen recognising events at the edges of the recording window, which could partly offset the increased computational cost. Ongoing work beyond this project now aims to further explore this aspect and support our findings with increasing amounts of experimental data. In addition, the project has allowed us to explore a new approach to data classification of single-molecule charge transport data using Transfer Learning and Image Recognition Networks (IRN). In this context, the feature extractor of IRNs trained on millions of (unrelated) image data is used to recognise characteristics in conductance-distance or current-time data, which are then clustered and interpreted. This means that no charge transport data are required for training the feature extractor, removing the need for large, application-specific training data
Humans of AI3SD: Professor Tim Albrecht
No full textThis interview forms part of our Humans of AI3SD Series. Professor Tim Albrecht, a Professor of Physical Chemistry at the University of Birmingham was interviewed by Michelle Pauli at our AI3SD Network+ Conference in 2019. Tim is a PI on one of the funding projects from AI3SD-FundingCall1
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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