arXiv subjects

Andrew Parnell

Publications and source records attributed to Andrew Parnell.

At least 19 recordsLinked to original sources

arXiv2025

Predicting Mycotoxin Contamination in Irish Oats Using Deep and Transfer Learning

Mycotoxin contamination poses a significant risk to cereal crop quality, food safety, and agricultural productivity. Accurate prediction of mycotoxin levels can support early intervention strategies and reduce economic losses. This study investigates the use of neural networks and transfer learning models to predict mycotoxin contamination in Irish oat crops as a multi-response prediction task. Our dataset comprises oat samples collected in Ireland, containing a mix of environmental, agronomic, and geographical predictors. Five modelling approaches were evaluated: a baseline multilayer perceptron (MLP), an MLP with pre-training, and three transfer learning models; TabPFN, TabNet, and FT-Transformer. Model performance was evaluated using regression (RMSE, $R^2$) and classification (AUC, F1) metrics, with results reported per toxin and on average. Additionally, permutation-based variable importance analysis was conducted to identify the most influential predictors across both prediction tasks. The transfer learning approach TabPFN provided the overall best performance, followed by the baseline MLP. Our variable importance analysis revealed that weather history patterns in the 90-day pre-harvest period were the most important predictors, alongside seed moisture content.

cs.LG↗

arXiv2025

Predicting BVD Re-emergence in Irish Cattle From Highly Imbalanced Herd-Level Data Using Machine Learning Algorithms

Bovine Viral Diarrhoea (BVD) has been the focus of a successful eradication programme in Ireland, with the herd-level prevalence declining from 11.3% in 2013 to just 0.2% in 2023. As the country moves toward BVD freedom, the development of predictive models for targeted surveillance becomes increasingly important to mitigate the risk of disease re-emergence. In this study, we evaluate the performance of a range of machine learning algorithms, including binary classification and anomaly detection techniques, for predicting BVD-positive herds using highly imbalanced herd-level data. We conduct an extensive simulation study to assess model performance across varying sample sizes and class imbalance ratios, incorporating resampling, class weighting, and appropriate evaluation metrics (sensitivity, positive predictive value, F1-score and AUC values). Random forests and XGBoost models consistently outperformed other methods, with the random forest model achieving the highest sensitivity and AUC across scenarios, including real-world prediction of 2023 herd status, correctly identifying 219 of 250 positive herds while halving the number of herds that require compared to a blanket-testing strategy.

cs.LG↗

arXiv2024

Spatio-temporal analysis of extreme winter temperatures in Ireland

We analyse extreme daily minimum temperatures in winter months over the island of Ireland from 1950-2022. We model the marginal distributions of extreme winter minima using a generalised Pareto distribution (GPD), capturing temporal and spatial non-stationarities in the parameters of the GPD. We investigate two independent temporal non-stationarities in extreme winter minima. We model the long-term trend in magnitude of extreme winter minima as well as short-term, large fluctuations in magnitude caused by anomalous behaviour of the jet stream. We measure magnitudes of spatial events with a carefully chosen risk function and fit an r-Pareto process to extreme events exceeding a high-risk threshold. Our analysis is based on synoptic data observations courtesy of Met \'Eireann and the Met Office. We show that the frequency of extreme cold winter events is decreasing over the study period. The magnitude of extreme winter events is also decreasing, indicating that winters are warming, and apparently warming at a faster rate than extreme summer temperatures. We also show that extremely cold winter temperatures are warming at a faster rate than non-extreme winter temperatures. We find that a climate model output previously shown to be informative as a covariate for modelling extremely warm summer temperatures is less effective as a covariate for extremely cold winter temperatures. However, we show that the climate model is useful for informing a non-extreme temperature model.

physics.ao-ph↗

arXiv2024

Generative AI-based data augmentation for improved bioacoustic classification in noisy environments

Obtaining data to train robust artificial intelligence (AI)-based models for species classification can be challenging, particularly for rare species. Data augmentation can boost classification accuracy by increasing the diversity of training data and is cheaper to obtain than expert-labelled data. However, many classic image-based augmentation techniques are not suitable for audio spectrograms. We investigate two generative AI models as data augmentation tools to synthesise spectrograms and supplement audio data: Auxiliary Classifier Generative Adversarial Networks (ACGAN) and Denoising Diffusion Probabilistic Models (DDPMs). The latter performed particularly well in terms of both realism of generated spectrograms and accuracy in a resulting classification task. Alongside these new approaches, we present a new audio data set of 640 hours of bird calls from wind farm sites in Ireland, approximately 800 samples of which have been labelled by experts. Wind farm data are particularly challenging for classification models given the background wind and turbine noise. Training an ensemble of classification models on real and synthetic data combined compared well with highly confident BirdNET predictions. Each classifier we used was improved by including synthetic data, and classification metrics generally improved in line with the amount of synthetic data added. Our approach can be used to augment acoustic signals for more species and other land-use types, and has the potential to bring about advances in our capacity to develop reliable AI-based detection of rare species. Our code is available at https://github.com/gibbona1/SpectrogramGenAI.

cs.SD↗

arXiv2024

Bayesian Causal Forests for Longitudinal Data: Assessing the Impact of Part-Time Work on Growth in High School Mathematics Achievement

Modelling growth in student achievement is a significant challenge in the field of education. Understanding how interventions or experiences such as part-time work can influence this growth is also important. Traditional methods like difference-in-differences are effective for estimating causal effects from longitudinal data. Meanwhile, Bayesian non-parametric methods have recently become popular for estimating causal effects from single time point observational studies. However, there remains a scarcity of methods capable of combining the strengths of these two approaches to flexibly estimate heterogeneous causal effects from longitudinal data. Motivated by two waves of data from the High School Longitudinal Study, the NCES' most recent longitudinal study which tracks a representative sample of over 20,000 students in the US, our study introduces a longitudinal extension of Bayesian Causal Forests. This model allows for the flexible identification of both individual growth in mathematical ability and the effects of participation in part-time work. Simulation studies demonstrate the predictive performance and reliable uncertainty quantification of the proposed model. Results reveal the negative impact of part time work for most students, but hint at potential benefits for those students with an initially low sense of school belonging. Clear signs of a widening achievement gap between students with high and low academic achievement are also identified. Potential policy implications are discussed, along with promising areas for future research.

stat.ML↗

arXiv2024

Machine Learning Applied to the Detection of Mycotoxin in Food: A Review

Mycotoxins, toxic secondary metabolites produced by certain fungi, pose significant threats to global food safety and public health. These compounds can contaminate a variety of crops, leading to economic losses and health risks to both humans and animals. Traditional lab analysis methods for mycotoxin detection can be time-consuming and may not always be suitable for large-scale screenings. However, in recent years, machine learning (ML) methods have gained popularity for use in the detection of mycotoxins and in the food safety industry in general, due to their accurate and timely predictions. We provide a systematic review on some of the recent ML applications for detecting/predicting the presence of mycotoxin on a variety of food ingredients, highlighting their advantages, challenges, and potential for future advancements. We address the need for reproducibility and transparency in ML research through open access to data and code. An observation from our findings is the frequent lack of detailed reporting on hyperparameters in many studies as well as a lack of open source code, which raises concerns about the reproducibility and optimisation of the ML models used. The findings reveal that while the majority of studies predominantly utilised neural networks for mycotoxin detection, there was a notable diversity in the types of neural network architectures employed, with convolutional neural networks being the most popular.

q-bio.QM↗

arXiv2023

Bayesian Optimisation for Sequential Experimental Design with Applications in Additive Manufacturing

Bayesian optimization (BO) is an approach to globally optimizing black-box objective functions that are expensive to evaluate. BO-powered experimental design has found wide application in materials science, chemistry, experimental physics, drug development, etc. This work aims to bring attention to the benefits of applying BO in designing experiments and to provide a BO manual, covering both methodology and software, for the convenience of anyone who wants to apply or learn BO. In particular, we briefly explain the BO technique, review all the applications of BO in additive manufacturing, compare and exemplify the features of different open BO libraries, unlock new potential applications of BO to other types of data (e.g., preferential output). This article is aimed at readers with some understanding of Bayesian methods, but not necessarily with knowledge of additive manufacturing; the software performance overview and implementation instructions are instrumental for any experimental-design practitioner. Moreover, our review in the field of additive manufacturing highlights the current knowledge and technological trends of BO. This article has a supplementary material online.

cs.LG↗

arXiv2023

Output Feedback Reinforcement Learning with Parameter Optimisation for Temperature Control in a Material Extrusion Additive Manufacturing system

With the rapid development of Additive Manufacturing (AM) comes an urgent need for advanced monitoring and control of the process. Many aspects of the AM process play a significant role in the efficiency, accuracy and repeatability of the process, with temperature regulation being one of the most important ones. In this work, we solve the problem of optimal tracking control for a state space temperature model of a Big Area Additive Manufacturing (BAAM) system. In particular, we address the problem of designing a Linear Quadratic Tracking (LQT) controller when access to the exact system state is not possible, except in the form of measurements. We initially solve the problem with a model-based approach based on reinforcement learning concepts, with state estimation through an observer. We then design a model-free reinforcement-learning based controller with an internal state estimation step and demonstrate its performance through a simulator of the systems' behaviour. Our results showcase the possibility of achieving comparable results while learning optimal policies directly from process data, without the need for an accurate, intricate model of the process. We consider this outcome to be a significant stride towards autonomous intelligent manufacturing.

math.OC↗

arXiv2023

Data-driven Linear Quadratic Tracking based Temperature Control of a Big Area Additive Manufacturing System

Designing efficient closed-loop control algorithms is a key issue in Additive Manufacturing (AM), as various aspects of the AM process require continuous monitoring and regulation, with temperature being a particularly significant factor. Here we study closed-loop control of a state space temperature model with a focus on both model-based and data-driven methods. We demonstrate these approaches using a simulator of the temperature evolution in the extruder of a Big Area Additive Manufacturing system (BAAM). We perform an in-depth comparison of the performance of these methods using the simulator. We find that we can learn an effective controller using solely simulated process data. Our approach achieves parity in performance compared to model-based controllers and so lessens the need for estimating a large number of parameters of the intricate and complicated process model. We believe this result is an important step towards autonomous intelligent manufacturing.

math.OC↗

arXiv2023

reslr: An R package for relative sea level modelling

We present reslr, an R package to perform Bayesian modelling of relative sea level data. We include a variety of different statistical models previously proposed in the literature, with a unifying framework for loading data, fitting models, and summarising the results. Relative sea-level data often contain measurement error in multiple dimensions and so our package allows for these to be included in the statistical models. When plotting the output sea level curves, the focus is often on comparing rates of change, and so our package allows for computation of the derivative of sea level curves with appropriate consideration of the uncertainty. We provide a large example dataset from the Atlantic coast of North America and show some of the results that might be obtained from our package.

stat.AP↗

arXiv2023

SERT: A Transfomer Based Model for Spatio-Temporal Sensor Data with Missing Values for Environmental Monitoring

Environmental monitoring is crucial to our understanding of climate change, biodiversity loss and pollution. The availability of large-scale spatio-temporal data from sources such as sensors and satellites allows us to develop sophisticated models for forecasting and understanding key drivers. However, the data collected from sensors often contain missing values due to faulty equipment or maintenance issues. The missing values rarely occur simultaneously leading to data that are multivariate misaligned sparse time series. We propose two models that are capable of performing multivariate spatio-temporal forecasting while handling missing data naturally without the need for imputation. The first model is a transformer-based model, which we name SERT (Spatio-temporal Encoder Representations from Transformers). The second is a simpler model named SST-ANN (Sparse Spatio-Temporal Artificial Neural Network) which is capable of providing interpretable results. We conduct extensive experiments on two different datasets for multivariate spatio-temporal forecasting and show that our models have competitive or superior performance to those at the state-of-the-art.

cs.LG↗

arXiv2023

Hierarchical Embedded Bayesian Additive Regression Trees

We propose a simple yet powerful extension of Bayesian Additive Regression Trees which we name Hierarchical Embedded BART (HE-BART). The model allows for random effects to be included at the terminal node level of a set of regression trees, making HE-BART a non-parametric alternative to mixed effects models which avoids the need for the user to specify the structure of the random effects in the model, whilst maintaining the prediction and uncertainty calibration properties of standard BART. Using simulated and real-world examples, we demonstrate that this new extension yields superior predictions for many of the standard mixed effects models' example data sets, and yet still provides consistent estimates of the random effect variances. In a future version of this paper, we outline its use in larger, more advanced data sets and structures.

stat.ME↗

arXiv2023

Inference for extreme spatial temperature events in a changing climate with application to Ireland

We investigate the changing nature of the frequency, magnitude and spatial extent of extreme temperatures in Ireland from 1931 to 2022. We develop an extreme value model that captures spatial and temporal non-stationarity in extreme daily maximum temperature data. We model the tails of the marginal variables using the generalised Pareto distribution and the spatial dependence of extreme events by a semi-parametric Brown-Resnick r-generalised Pareto process, with parameters of each model allowed to change over time. We use weather station observations for modelling extreme events since data from climate models (not conditioned on observational data) can over-smooth these events and have trends determined by the specific climate model configuration. However, climate models do provide valuable information about the detailed physiography over Ireland and the associated climate response. We propose novel methods which exploit the climate model data to overcome issues linked to the sparse and biased sampling of the observations. Our analysis identifies a temporal change in the marginal behaviour of extreme temperature events over the study domain, which is much larger than the change in mean temperature levels over this time window. We illustrate how these characteristics result in increased spatial coverage of the events that exceed critical temperatures.

stat.ME↗

arXiv2023

Bayesian Causal Forests for Multivariate Outcomes: Application to Irish Data From an International Large Scale Education Assessment

Bayesian Causal Forests (BCF) is a causal inference machine learning model based on a highly flexible non-parametric regression and classification tool called Bayesian Additive Regression Trees (BART). Motivated by data from the Trends in International Mathematics and Science Study (TIMSS), which includes data on student achievement in both mathematics and science, we present a multivariate extension of the BCF algorithm. With the help of simulation studies we show that our approach can accurately estimate causal effects for multiple outcomes subject to the same treatment. We also apply our model to Irish data from TIMSS 2019. Our findings reveal the positive effects of having access to a study desk at home (Mathematics ATE 95% CI: [0.20, 11.67]) while also highlighting the negative consequences of students often feeling hungry at school (Mathematics ATE 95% CI: [-11.15, -2.78] , Science ATE 95% CI: [-10.82,-1.72]) or often being absent (Mathematics ATE 95% CI: [-12.47, -1.55]).

stat.ML↗

arXiv2023

A noisy-input generalised additive model for relative sea-level change along the Atlantic coast of North America

We propose a Bayesian, noisy-input, spatial-temporal generalised additive model to examine regional relative sea-level (RSL) changes over time. The model provides probabilistic estimates of component drivers of regional RSL change via the combination of a univariate spline capturing a common regional signal over time, random slopes and intercepts capturing site-specific (local), long-term linear trends and a spatial-temporal spline capturing residual, non-linear, local variations. Proxy and instrumental records of RSL and corresponding measurement errors inform the model and a noisy-input method accounts for proxy temporal uncertainties. Results focus on the decomposition of RSL over the past 3000 years along the Atlantic coast of North America.

stat.AP↗

arXiv2022

NEAL: An open-source tool for audio annotation

Passive acoustic monitoring is used widely in ecology, biodiversity, and conservation studies. Data sets collected via acoustic monitoring are often extremely large and built to be processed automatically using Artificial Intelligence and Machine learning models, which aim to replicate the work of domain experts. These models, being supervised learning algorithms, need to be trained on high quality annotations produced by experts. Since the experts are often resource-limited, a cost-effective process for annotating audio is needed to get maximal use out of the data. We present an open-source interactive audio data annotation tool, NEAL (Nature+Energy Audio Labeller). Built using R and the associated Shiny framework, the tool provides a reactive environment where users can quickly annotate audio files and adjust settings that automatically change the corresponding elements of the user interface. The app has been designed with the goal of having both expert birders and citizen scientists contribute to acoustic annotation projects. The popularity and flexibility of R programming in bioacoustics means that the Shiny app can be modified for other bird labelling data sets, or even to generic audio labelling tasks. We demonstrate the app by labelling data collected from wind farm sites across Ireland.

cs.SD↗

arXiv2022

Optimal age-specific vaccination control for COVID-19: an Irish case study

The outbreak of a novel coronavirus causing severe acute respiratory syndrome in December 2019 has escalated into a worldwide pandemic. In this work, we propose a compartmental model to describe the dynamics of transmission of infection and use it to obtain the optimal vaccination control. The model accounts for the various stages of the vaccination and the optimisation is focused on minimising the infections to protect the population and relieve the healthcare system. As a case study we selected the Republic of Ireland. We use data provided by Ireland's COVID-19 Data-Hub and simulate the evolution of the pandemic with and without the vaccination in place for two different scenarios, one representative of a national lockdown situation and the other indicating looser restrictions in place. One of the main findings of our work is that the optimal approach would involve a vaccination programme where the older population is vaccinated in larger numbers earlier while simultaneously part of the younger population also gets vaccinated to lower the risk of transmission between groups. We compare our simulated results with that of the vaccination policy taken by the Irish government to explore the advantages of our optimisation method. Our comparison suggests that a similar reduction in cases may have been possible even with a reduced set of vaccinations being available for use.

math.OC↗

arXiv2022

vivid: An R package for Variable Importance and Variable Interactions Displays for Machine Learning Models

We present vivid, an R package for visualizing variable importance and variable interactions in machine learning models. The package provides a range of displays including heatmap and graph-based displays for viewing variable importance and interaction jointly and partial dependence plots in both a matrix layout and an alternative layout emphasizing important variable subsets. With the intention of increasing a machine learning models' interpretability and making the work applicable to a wider readership, we discuss the design choices behind our implementation by focusing on the package structure and providing an in-depth look at the package functions and key features. We also provide a practical illustration of the software in use on a data set.

stat.CO↗