Melissa Humphries

Lauren Elborough, Duncan Taylor, Melissa Humphries

The application of Shapley values to high-dimensional, time-series-like data is computationally challenging - and sometimes impossible. For $N$ inputs the problem is $2^N$ hard. In image processing, clusters of pixels, referred to as superpixels, are used to streamline computations. This research presents an efficient solution for time-seres-like data that adapts the idea of superpixels for Shapley value computation. Motivated by a forensic DNA classification example, the method is applied to multivariate time-series-like data whose features have been classified by a convolutional neural network (CNN). In DNA processing, it is important to identify alleles from the background noise created by DNA extraction and processing. A single DNA profile has $31,200$ scan points to classify, and the classification decisions must be defensible in a court of law. This means that classification is routinely performed by human readers - a monumental and time consuming process. The application of a CNN with fast computation of meaningful Shapley values provides a potential alternative to the classification. This research demonstrates the realistic, accurate and fast computation of Shapley values for this massive task

Duncan Taylor, Melissa Humphries

DNA profiles are made up from multiple series of electrophoretic signal measuring fluorescence over time. Typically, human DNA analysts 'read' DNA profiles using their experience to distinguish instrument noise, artefactual signal, and signal corresponding to DNA fragments of interest. Recent work has developed an artificial neural network, ANN, to carry out the task of classifying fluorescence types into categories in DNA profile electrophoretic signal. But the creation of the necessarily large amount of labelled training data for the ANN is time consuming and expensive, and a limiting factor in the ability to robustly train the ANN. If realistic, prelabelled, training data could be simulated then this would remove the barrier to training an ANN with high efficacy. Here we develop a generative adversarial network, GAN, modified from the pix2pix GAN to achieve this task. With 1078 DNA profiles we train the GAN and achieve the ability to simulate DNA profile information, and then use the generator from the GAN as a 'realism filter' that applies the noise and artefact elements exhibited in typical electrophoretic signal.

Saranzaya Magsarjav, Melissa Humphries, Jonathan Tuke et al.

Topic modelling in Natural Language Processing uncovers hidden topics in large, unlabelled text datasets. It is widely applied in fields such as information retrieval, content summarisation, and trend analysis across various disciplines. However, probabilistic topic models can produce different results when rerun due to their stochastic nature, leading to inconsistencies in latent topics. Factors like corpus shuffling, rare text removal, and document elimination contribute to these variations. This instability affects replicability, reliability, and interpretation, raising concerns about whether topic models capture meaningful topics or just noise. To address these problems, we defined a new stability measure that incorporates accuracy and consistency and uses the generative properties of LDA to generate a new corpus with ground truth. These generated corpora are run through LDA 50 times to determine the variability in the output. We show that LDA can correctly determine the underlying number of topics in the documents. We also find that LDA is more internally consistent, as the multiple reruns return similar topics; however, these topics are not the true topics.