Mathematical Modelling and Machine Learning Methods for Bioinformatics and Data Science Applications

Mathematical modeling is routinely used in physical and engineering sciences to help understand complex systems and optimize industrial processes. Mathematical modeling differs from Artificial Intelligence because it does not exclusively use the collected data to describe an industrial phenomenon or process, but it is based on fundamental laws of physics or engineering that lead to systems of equations able to represent all the variables that characterize the process. Conversely, Machine Learning methods require a large amount of data to find solutions, remaining detached from the problem that generated them and trying to infer the behavior of the object, material or process to be examined from observed samples. Mathematics allows us to formulate complex models with effectiveness and creativity, describing nature and physics. Together with the potential of Artificial Intelligence and data collection techniques, a new way of dealing with practical problems is possible. The insertion of the equations deriving from the physical world in the data-driven models can in fact greatly enrich the information content of the sampled data, allowing to simulate very complex phenomena, with drastically reduced calculation times. Combined approaches will constitute a breakthrough in cutting-edge applications, providing precise and reliable tools for the prediction of phenomena in biological macro/microsystems, for biotechnological applications and for medical diagnostics, particularly in the field of precision medicine

Video Content Understanding Using Text

The rise of the social media and video streaming industry provided us a plethora of videos and their corresponding descriptive information in the form of concepts (words) and textual video captions. Due to the mass amount of available videos and the textual data, today is the best time ever to study the Computer Vision and Machine Learning problems related to videos and text. In this dissertation, we tackle multiple problems associated with the joint understanding of videos and text. We first address the task of multi-concept video retrieval, where the input is a set of words as concepts, and the output is a ranked list of full-length videos. This approach deals with multi-concept input and prolonged length of videos by incorporating multi-latent variables to tie the information within each shot (short clip of a full-video) and across shots. Secondly, we address the problem of video question answering, in which, the task is to answer a question, in the form of Fill-In-the-Blank (FIB), given a video. Answering a question is a task of retrieving a word from a dictionary (all possible words suitable for an answer) based on the input question and video. Following the FIB problem, we introduce a new problem, called Visual Text Correction (VTC), i.e., detecting and replacing an inaccurate word in the textual description of a video. We propose a deep network that can simultaneously detect an inaccuracy in a sentence while benefiting 1D-CNNs/LSTMs to encode short/long term dependencies, and fix it by replacing the inaccurate word(s). Finally, as the last part of the dissertation, we propose to tackle the problem of video generation using user input natural language sentences. Our proposed video generation method constructs two distributions out of the input text, corresponding to the first and last frames latent representations. We generate high-fidelity videos by interpolating latent representations and a sequence of CNN based up-pooling blocks

Towards Video Transformers for Automatic Human Analysis

[eng] With the aim of creating artificial systems capable of mirroring the nuanced understanding and interpretative powers inherent to human cognition, this thesis embarks on an exploration of the intersection between human analysis and Video Transformers. The objective is to harness the potential of Transformers, a promising architectural paradigm, to comprehend the intricacies of human interaction, thus paving the way for the development of empathetic and context-aware intelligent systems. In order to do so, we explore the whole Computer Vision pipeline, from data gathering, to deeply analyzing recent developments, through model design and experimentation. Central to this study is the creation of UDIVA, an expansive multi-modal, multi-view dataset capturing dyadic face-to-face human interactions. Comprising 147 participants across 188 sessions, UDIVA integrates audio-visual recordings, heart-rate measurements, personality assessments, socio- demographic metadata, and conversational transcripts, establishing itself as the largest dataset for dyadic human interaction analysis up to this date. This dataset provides a rich context for probing the capabilities of Transformers within complex environments. In order to validate its utility, as well as to elucidate Transformers' ability to assimilate diverse contextual cues, we focus on addressing the challenge of personality regression within interaction scenarios. We first adapt an existing Video Transformer to handle multiple contextual sources and conduct rigorous experimentation. We empirically observe a progressive enhancement in model performance as more context is added, reinforcing the potential of Transformers to decode intricate human dynamics. Building upon these findings, the Dyadformer emerges as a novel architecture, adept at long-range modeling of dyadic interactions. By jointly modeling both participants in the interaction, as well as embedding multi- modal integration into the model itself, the Dyadformer surpasses the baseline and other concurrent approaches, underscoring Transformers' aptitude in deciphering multifaceted, noisy, and challenging tasks such as the analysis of human personality in interaction. Nonetheless, these experiments unveil the ubiquitous challenges when training Transformers, particularly in managing overfitting due to their demand for extensive datasets. Consequently, we conclude this thesis with a comprehensive investigation into Video Transformers, analyzing topics ranging from architectural designs and training strategies, to input embedding and tokenization, traversing through multi-modality and specific applications. Across these, we highlight trends which optimally harness spatio-temporal representations that handle video redundancy and high dimensionality. A culminating performance comparison is conducted in the realm of video action classification, spotlighting strategies that exhibit superior efficacy, even compared to traditional CNN-based methods.[cat] Aquesta tesi busca crear sistemes artificials que reflecteixin les habilitats de comprensió i interpretació humanes a través de l'ús de Transformers per a vídeo. L'objectiu és utilitzar aquestes arquitectures per comprendre millor la interacció humana i desenvolupar sistemes intel·ligents i conscients de l'entorn. Això implica explorar àmplies àrees de la Visió per Computador, des de la recopilació de dades fins a l'anàlisi de l'estat de l'art i la prova experimental d'aquests models. Una part essencial d'aquest estudi és la creació d'UDIVA, un ampli conjunt de dades multimodal i multivista que enregistra interaccions humanes cara a cara. Amb 147 participants i 188 sessions, UDIVA inclou contingut audiovisual, freqüència cardíaca, perfils de personalitat, dades sociodemogràfiques i transcripcions de les converses. És el conjunt de dades més gran conegut per a l'anàlisi de la interacció humana diàdica i proporciona un context ric per a l'estudi de les capacitats dels Transformers en entorns complexos. Per tal de validar la seva utilitat i les habilitats dels Transformers, ens centrem en la regressió de la personalitat. Inicialment, adaptem un Transformer de vídeo per integrar diverses fonts de context. Mitjançant experiments exhaustius, observem millores progressives en els resultats amb la inclusió de més context, confirmant la capacitat dels Transformers. Motivats per aquests resultats, desenvolupem el Dyadformer, una arquitectura per interaccions diàdiques de llarga duració. Aquesta nova arquitectura considera simultàniament els dos participants en la interacció i incorpora la multimodalitat en un sol model. El Dyadformer supera la nostra proposta inicial i altres treballs similars, destacant la capacitat dels Transformers per abordar tasques complexes. No obstant això, aquestos experiments revelen reptes d'entrenament dels Transformers, com el sobreajustament, per la seva necessitat de grans conjunts de dades. La tesi conclou amb una anàlisi profunda dels Transformers per a vídeo, incloent dissenys arquitectònics, estratègies d'entrenament, preprocessament de vídeos, tokenització i multimodalitat. S'identifiquen tendències per gestionar la redundància i alta dimensionalitat de vídeos i es realitza una comparació de rendiment en la classificació d'accions a vídeo, destacant estratègies d'eficàcia superior als mètodes tradicionals basats en convolucions

When I Look into Your Eyes: A Survey on Computer Vision Contributions for Human Gaze Estimation and Tracking

The automatic detection of eye positions, their temporal consistency, and their mapping into a line of sight in the real world (to find where a person is looking at) is reported in the scientific literature as gaze tracking. This has become a very hot topic in the field of computer vision during the last decades, with a surprising and continuously growing number of application fields. A very long journey has been made from the first pioneering works, and this continuous search for more accurate solutions process has been further boosted in the last decade when deep neural networks have revolutionized the whole machine learning area, and gaze tracking as well. In this arena, it is being increasingly useful to find guidance through survey/review articles collecting most relevant works and putting clear pros and cons of existing techniques, also by introducing a precise taxonomy. This kind of manuscripts allows researchers and technicians to choose the better way to move towards their application or scientific goals. In the literature, there exist holistic and specifically technological survey documents (even if not updated), but, unfortunately, there is not an overview discussing how the great advancements in computer vision have impacted gaze tracking. Thus, this work represents an attempt to fill this gap, also introducing a wider point of view that brings to a new taxonomy (extending the consolidated ones) by considering gaze tracking as a more exhaustive task that aims at estimating gaze target from different perspectives: from the eye of the beholder (first-person view), from an external camera framing the beholder’s, from a third-person view looking at the scene where the beholder is placed in, and from an external view independent from the beholder

Context-aware Facial Inpainting with GANs

Facial inpainting is a difficult problem due to the complex structural patterns of a face image. Using irregular hole masks to generate contextualised features in a face image is becoming increasingly important in image inpainting. Existing methods generate images using deep learning models, but aberrations persist. The reason for this is that key operations are required for feature information dissemination, such as feature extraction mechanisms, feature propagation, and feature regularizers, are frequently overlooked or ignored during the design stage. A comprehensive review is conducted to examine existing methods and identify the research gaps that serve as the foundation for this thesis. The aim of this thesis is to develop novel facial inpainting algorithms with the capability of extracting contextualised features. First, Symmetric Skip Connection Wasserstein GAN (SWGAN) is proposed to inpaint high-resolution face images that are perceptually consistent with the rest of the image. Second, a perceptual adversarial Network (RMNet) is proposed to include feature extraction and feature propagation mechanisms that target missing regions while preserving visible ones. Third, a foreground-guided facial inpainting method is proposed with occlusion reasoning capability, which guides the model toward learning contextualised feature extraction and propagation while maintaining fidelity. Fourth, V-LinkNet is pro-posed that takes into account of the critical operations for information dissemination. Additionally, a standard protocol is introduced to prevent potential biases in performance evaluation of facial inpainting algorithms. The experimental results show V-LinkNet achieved the best results with SSIM of 0.96 on the standard protocol. In conclusion, generating facial images with contextualised features is important to achieve realistic results in inpainted regions. Additionally, it is critical to consider the standard procedure while comparing different approaches. Finally, this thesis outlines the new insights and future directions of image inpainting

Appearance Modelling and Reconstruction for Navigation in Minimally Invasive Surgery

Minimally invasive surgery is playing an increasingly important role for patient care. Whilst its direct patient benefit in terms of reduced trauma, improved recovery and shortened hospitalisation has been well established, there is a sustained need for improved training of the existing procedures and the development of new smart instruments to tackle the issue of visualisation, ergonomic control, haptic and tactile feedback. For endoscopic intervention, the small field of view in the presence of a complex anatomy can easily introduce disorientation to the operator as the tortuous access pathway is not always easy to predict and control with standard endoscopes. Effective training through simulation devices, based on either virtual reality or mixed-reality simulators, can help to improve the spatial awareness, consistency and safety of these procedures. This thesis examines the use of endoscopic videos for both simulation and navigation purposes. More specifically, it addresses the challenging problem of how to build high-fidelity subject-specific simulation environments for improved training and skills assessment. Issues related to mesh parameterisation and texture blending are investigated. With the maturity of computer vision in terms of both 3D shape reconstruction and localisation and mapping, vision-based techniques have enjoyed significant interest in recent years for surgical navigation. The thesis also tackles the problem of how to use vision-based techniques for providing a detailed 3D map and dynamically expanded field of view to improve spatial awareness and avoid operator disorientation. The key advantage of this approach is that it does not require additional hardware, and thus introduces minimal interference to the existing surgical workflow. The derived 3D map can be effectively integrated with pre-operative data, allowing both global and local 3D navigation by taking into account tissue structural and appearance changes. Both simulation and laboratory-based experiments are conducted throughout this research to assess the practical value of the method proposed

Gaze-Based Human-Robot Interaction by the Brunswick Model

We present a new paradigm for human-robot interaction based on social signal processing, and in particular on the Brunswick model. Originally, the Brunswick model copes with face-to-face dyadic interaction, assuming that the interactants are communicating through a continuous exchange of non verbal social signals, in addition to the spoken messages. Social signals have to be interpreted, thanks to a proper recognition phase that considers visual and audio information. The Brunswick model allows to quantitatively evaluate the quality of the interaction using statistical tools which measure how effective is the recognition phase. In this paper we cast this theory when one of the interactants is a robot; in this case, the recognition phase performed by the robot and the human have to be revised w.r.t. the original model. The model is applied to Berrick, a recent open-source low-cost robotic head platform, where the gazing is the social signal to be considered