Uncovering hierarchical data structure in single molecule transport

Methods for the analysis, interpretation, and prediction of single-molecule junction conductance behaviour

This article offers a broad overview of measurement methods in the field of molecular electronics, with a particular focus on the most common single-molecule junction fabrication techniques, the challenges in data analysis and interpretation of single-molecule junction current-distance traces, and a summary of simulations and predictive models aimed at establishing robust structure-property relationships of use in the further development of molecular electronics.

Applications of machine learning tools for ultra-sensitive detection of lipoarabinomannan with plasmonic grating biosensors in clinical samples of tuberculosis

Background

Tuberculosis is one of the top ten causes of death globally and the leading cause of death from a single infectious agent. Eradicating the Tuberculosis epidemic by 2030 is one of the top United Nations Sustainable Development Goals. Early diagnosis is essential to achieving this goal because it improves individual prognosis and reduces transmission rates of asymptomatic infected. We aim to support this goal by developing rapid and sensitive diagnostics using machine learning algorithms to minimize the need for expert intervention.

Methods and findings

A single molecule fluorescence immunosorbent assay was used to detect Tuberculosis biomarker lipoarabinomannan from a set of twenty clinical patient samples and a control set of spiked human urine. Tuberculosis status was separately confirmed by GeneXpert MTB/RIF and cell culture. Two machine learning algorithms, an automatic and a semiautomatic model, were developed and trained by the calibrated lipoarabinomannan titration assay data and then tested against the ground truth patient data. The semiautomatic model differed from the automatic model by an expert review step in the former, which calibrated the lower threshold to determine single molecules from background noise. The semiautomatic model was found to provide 88.89% clinical sensitivity, while the automatic model resulted in 77.78% clinical sensitivity.

Conclusions

The semiautomatic model outperformed the automatic model in clinical sensitivity as a result of the expert intervention applied during calibration and both models vastly outperformed manual expert counting in terms of time-to-detection and completion of analysis. Meanwhile, the clinical sensitivity of the automatic model could be improved significantly with a larger training dataset. In short, semiautomatic, and automatic Gaussian Mixture Models have a place in supporting rapid detection of Tuberculosis in resource-limited settings without sacrificing clinical sensitivity.

Trusting our machines: validating machine learning models for single-molecule transport experiments

In this tutorial review, we will describe crucial aspects related to the application of machine learning to help users avoid the most common pitfalls. The examples we present will be based on data from the field of molecular electronics, specifically single-molecule electron transport experiments, but the concepts and problems we explore will be sufficiently general for application in other fields with similar data. In the first part of the tutorial review, we will introduce the field of single-molecule transport, and provide an overview of the most common machine learning algorithms employed. In the second part of the tutorial review, we will show, through examples grounded in single-molecule transport, that the promises of machine learning can only be fulfilled by careful application. We will end the tutorial review with a discussion of where we, as a field, could go from here.

In this tutorial review, we will describe crucial aspects related to the application of machine learning to help users avoid the most common pitfalls.

Using Weakly Supervised Deep Learning to Classify and Segment Single-Molecule Break-Junction Conductance Traces

In order to design molecular electronic devices with high performance and stability, it is crucial to understand their structure-to-property relationships. Single-molecule break junction measurements yield a large number of conductance-distance traces, which are inherently highly stochastic. Here we propose a weakly supervised deep learning algorithm to classify and segment these conductance traces, a method that is mainly based on transfer learning with the pretrain-finetune technique. By exploiting the powerful feature extraction capabilities of the pretrained VGG-16 network, our convolutional neural network model not only achieves high accuracy in the classification of the conductance traces, but also segments precisely the conductance plateau from an entire trace with very few manually labeled traces. Thus, we can produce a more reliable estimation of the junction conductance and quantify the junction stability. These findings show that our model has achieved a better accuracy-to-manpower efficiency balance, opening up the possibility of using weakly supervised deep learning approaches in the studies of single-molecule junctions.

Dissecting Time-Evolved Conductance Behavior of Single Molecule Junctions by Nonparametric Machine Learning

Improved understanding of charge transport in single molecules is essential for utilizing their potential as circuit components at the nanosize limit. However, reliable analyses of varying tunneling current acquired by break junction experiments remain an ongoing challenge to find molecular feature structure-property relationships. In this work, we report on an unsupervised learning approach for investigating molecular signatures in conductance traces. Our hybrid machine learning algorithm compares grids of data in conductance-time domains and judges the similarity without any researcher-crafted parameters to identify fine molecular components that may otherwise be obscured by background fluctuations. We demonstrate its ability for classifying Au-alkanedithiol-Au conductance traces acquired with microfabricated mechanically controllable break junctions. The unbiased procedure was able to not only judge the presence or absence of the carbon chains in the electrode gap but also to identify multiple conductance states of the molecular tunneling junctions with different conformations. This finding may offer a useful tool for studying single-molecule properties using break junction methods.

Deep learning for single-molecule science

Exploring and making predictions based on single-molecule data can be challenging, not only due to the sheer size of the datasets, but also because a priori knowledge about the signal characteristics is typically limited and poor signal-to-noise ratio. For example, hypothesis-driven data exploration, informed by an expectation of the signal characteristics, can lead to interpretation bias or loss of information. Equally, even when the different data categories are known, e.g., the four bases in DNA sequencing, it is often difficult to know how to make best use of the available information content. The latest developments in machine learning (ML), so-called deep learning (DL) offer interesting, new avenues to address such challenges. In some applications, such as speech and image recognition, DL has been able to outperform conventional ML strategies and even human performance. However, to date DL has not been applied much in single-molecule science, presumably in part because relatively little is known about the 'internal workings' of such DL tools within single-molecule science as a field. In this Tutorial, we make an attempt to illustrate in a step-by-step guide how one of those, a convolutional neural network (CNN), may be used for base calling in DNA sequencing applications. We compare it with a SVM as a more conventional ML method, and discuss some of the strengths and weaknesses of the approach. In particular, a 'deep' neural network has many features of a 'black box', which has important implications on how we look at and interpret data.