Deep human face analysis and modelling

Human face appearance and motion play a significant role in creating the complex social environments of human civilisation. Humans possess the capacity to perform facial analysis and come to conclusion such as the identity of individuals, understanding emotional state and diagnosing diseases. The capacity though is not universal for the entire population, where there are medical conditions such prosopagnosia and autism which can directly affect facial analysis capabilities of individuals, while other facial analysis tasks require specific traits and training to perform well. This has lead to the research of facial analysis systems within the computer vision and machine learning fields over the previous decades, where the aim is to automate many facial analysis tasks to a level similar or surpassing humans. While breakthroughs have been made in certain tasks with the emergence of deep learning methods in the recent years, new state-of-the-art results have been achieved in many computer vision and machine learning tasks. Within this thesis an investigation into the use of deep learning based methods for facial analysis systems takes place, following a review of the literature specific facial analysis tasks, methods and challenges are found which form the basis for the research findings presented. The research presented within this thesis focuses on the tasks of face detection and facial symmetry analysis specifically for the medical condition facial palsy. Firstly an initial approach to face detection and symmetry analysis is proposed using a unified multi-task Faster R-CNN framework, this method presents good accuracy on the test data sets for both tasks but also demonstrates limitations from which the remaining chapters take their inspiration. Next the Integrated Deep Model is proposed for the tasks of face detection and landmark localisation, with specific focus on false positive face detection reduction which is crucial for accurate facial feature extraction in the medical applications studied within this thesis. Evaluation of the method on the Face Detection Dataset and Benchmark and Annotated Faces in-the-Wild benchmark data sets shows a significant increase of over 50% in precision against other state-of-the-art face detection methods, while retaining a high level of recall. The task of facial symmetry and facial palsy grading are the focus of the finals chapters where both geometry-based symmetry features and 3D CNNs are applied. It is found through evaluation that both methods have validity in the grading of facial palsy. The 3D CNNs are the most accurate with an F1 score of 0.88. 3D CNNs are also capable of recognising mouth motion for both those with and without facial palsy with an F1 score of 0.82

A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Modules

Studies of the relationship between DNA variation and gene expression variation, often referred to as “expression quantitative trait loci (eQTL) mapping”, have been conducted in many species and resulted in many significant findings. Because of the large number of genes and genetic markers in such analyses, it is extremely challenging to discover how a small number of eQTLs interact with each other to affect mRNA expression levels for a set of co-regulated genes. We present a Bayesian method to facilitate the task, in which co-expressed genes mapped to a common set of markers are treated as a module characterized by latent indicator variables. A Markov chain Monte Carlo algorithm is designed to search simultaneously for the module genes and their linked markers. We show by simulations that this method is more powerful for detecting true eQTLs and their target genes than traditional QTL mapping methods. We applied the procedure to a data set consisting of gene expression and genotypes for 112 segregants of S. cerevisiae. Our method identified modules containing genes mapped to previously reported eQTL hot spots, and dissected these large eQTL hot spots into several modules corresponding to possibly different biological functions or primary and secondary responses to regulatory perturbations. In addition, we identified nine modules associated with pairs of eQTLs, of which two have been previously reported. We demonstrated that one of the novel modules containing many daughter-cell expressed genes is regulated by AMN1 and BPH1. In conclusion, the Bayesian partition method which simultaneously considers all traits and all markers is more powerful for detecting both pleiotropic and epistatic effects based on both simulated and empirical data

Constraints on the χ_(c1) versus χ_(c2) polarizations in proton-proton collisions at √s = 8 TeV

The polarizations of promptly produced χ_(c1) and χ_(c2) mesons are studied using data collected by the CMS experiment at the LHC, in proton-proton collisions at √s=8  TeV. The χ_c states are reconstructed via their radiative decays χ_c → J/ψγ, with the photons being measured through conversions to e⁺e⁻, which allows the two states to be well resolved. The polarizations are measured in the helicity frame, through the analysis of the χ_(c2) to χ_(c1) yield ratio as a function of the polar or azimuthal angle of the positive muon emitted in the J/ψ → μ⁺μ⁻ decay, in three bins of J/ψ transverse momentum. While no differences are seen between the two states in terms of azimuthal decay angle distributions, they are observed to have significantly different polar anisotropies. The measurement favors a scenario where at least one of the two states is strongly polarized along the helicity quantization axis, in agreement with nonrelativistic quantum chromodynamics predictions. This is the first measurement of significantly polarized quarkonia produced at high transverse momentum