On Deep Machine Learning Methods for Anomaly Detection within Computer Vision

This thesis concerns deep learning approaches for anomaly detection in images. Anomaly detection addresses how to find any kind of pattern that differs from the regularities found in normal data and is receiving increasingly more attention in deep learning research. This is due in part to its wide set of potential applications ranging from automated CCTV surveillance to quality control across a range of industries. We introduce three original methods for anomaly detection applicable to two specific deployment scenarios. In the first, we detect anomalous activity in potentially crowded scenes through imagery captured via CCTV or other video recording devices. In the second, we segment defects in textures and demonstrate use cases representative of automated quality inspection on industrial production lines. In the context of detecting anomalous activity in scenes, we take an existing state-of-the-art method and introduce several enhancements including the use of a region proposal network for region extraction and a more information-preserving feature preprocessing strategy. This results in a simpler method that is significantly faster and suitable for real-time application. In addition, the increased efficiency facilitates building higher-dimensional models capable of improved anomaly detection performance, which we demonstrate on the pedestrian-based UCSD Ped2 dataset. In the context of texture defect detection, we introduce a method based on the idea of texture restoration that surpasses all state-of-the-art methods on the texture classes of the challenging MVTecAD dataset. In the same context, we additionally introduce a method that utilises transformer networks for future pixel and feature prediction. This novel method is able to perform competitive anomaly detection on most of the challenging MVTecAD dataset texture classes and illustrates both the promise and limitations of state-of-the-art deep learning transformers for the task of texture anomaly detection

Effects of a cognitive acceleration program in a low socio-economic high school in regional Australia

This paper presents research on the effects of a cognitive acceleration intervention in science lessons on low socio-economic students in a government high school in regional Western Australia. Thinking Science Australia is a program currently being implemented in Australian junior high school classes. The research was conducted over two years as a case study in one school with students as they entered high school in Year 8 (n = 71). Findings show that significant cognitive gains were made, with concomitant improvement in the state-wide testing in science when participating students were in Year 9, aged 13 and 14. Teachers reported changes to the ways they teach and described the challenges in implementing the intervention program

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

Short-read, high-throughput sequencing technology cannot identify the chromosomal position of repetitive insertion sequences that typically flank horizontally acquired genes such as bacterial virulence genes and antibiotic resistance genes. The MinION nanopore sequencer can produce long sequencing reads on a device similar in size to a USB memory stick. Here we apply a MinION sequencer to resolve the structure and chromosomal insertion site of a composite antibiotic resistance island in Salmonella Typhi Haplotype 58. Nanopore sequencing data from a single 18-h run was used to create a scaffold for an assembly generated from short-read Illumina data. Our results demonstrate the potential of the MinION device in clinical laboratories to fully characterize the epidemic spread of bacterial pathogens

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century