Machine learning for automatic analysis of affective behaviour

The automated analysis of affect has been gaining rapidly increasing attention by researchers over the past two decades, as it constitutes a fundamental step towards achieving next-generation computing technologies and integrating them into everyday life (e.g. via affect-aware, user-adaptive interfaces, medical imaging, health assessment, ambient intelligence etc.). The work presented in this thesis focuses on several fundamental problems manifesting in the course towards the achievement of reliable, accurate and robust affect sensing systems. In more detail, the motivation behind this work lies in recent developments in the field, namely (i) the creation of large, audiovisual databases for affect analysis in the so-called ''Big-Data`` era, along with (ii) the need to deploy systems under demanding, real-world conditions. These developments led to the requirement for the analysis of emotion expressions continuously in time, instead of merely processing static images, thus unveiling the wide range of temporal dynamics related to human behaviour to researchers. The latter entails another deviation from the traditional line of research in the field: instead of focusing on predicting posed, discrete basic emotions (happiness, surprise etc.), it became necessary to focus on spontaneous, naturalistic expressions captured under settings more proximal to real-world conditions, utilising more expressive emotion descriptions than a set of discrete labels. To this end, the main motivation of this thesis is to deal with challenges arising from the adoption of continuous dimensional emotion descriptions under naturalistic scenarios, considered to capture a much wider spectrum of expressive variability than basic emotions, and most importantly model emotional states which are commonly expressed by humans in their everyday life. In the first part of this thesis, we attempt to demystify the quite unexplored problem of predicting continuous emotional dimensions. This work is amongst the first to explore the problem of predicting emotion dimensions via multi-modal fusion, utilising facial expressions, auditory cues and shoulder gestures. A major contribution of the work presented in this thesis lies in proposing the utilisation of various relationships exhibited by emotion dimensions in order to improve the prediction accuracy of machine learning methods - an idea which has been taken on by other researchers in the field since. In order to experimentally evaluate this, we extend methods such as the Long Short-Term Memory Neural Networks (LSTM), the Relevance Vector Machine (RVM) and Canonical Correlation Analysis (CCA) in order to exploit output relationships in learning. As it is shown, this increases the accuracy of machine learning models applied to this task. The annotation of continuous dimensional emotions is a tedious task, highly prone to the influence of various types of noise. Performed real-time by several annotators (usually experts), the annotation process can be heavily biased by factors such as subjective interpretations of the emotional states observed, the inherent ambiguity of labels related to human behaviour, the varying reaction lags exhibited by each annotator as well as other factors such as input device noise and annotation errors. In effect, the annotations manifest a strong spatio-temporal annotator-specific bias. Failing to properly deal with annotation bias and noise leads to an inaccurate ground truth, and therefore to ill-generalisable machine learning models. This deems the proper fusion of multiple annotations, and the inference of a clean, corrected version of the ``ground truth'' as one of the most significant challenges in the area. A highly important contribution of this thesis lies in the introduction of Dynamic Probabilistic Canonical Correlation Analysis (DPCCA), a method aimed at fusing noisy continuous annotations. By adopting a private-shared space model, we isolate the individual characteristics that are annotator-specific and not shared, while most importantly we model the common, underlying annotation which is shared by annotators (i.e., the derived ground truth). By further learning temporal dynamics and incorporating a time-warping process, we are able to derive a clean version of the ground truth given multiple annotations, eliminating temporal discrepancies and other nuisances. The integration of the temporal alignment process within the proposed private-shared space model deems DPCCA suitable for the problem of temporally aligning human behaviour; that is, given temporally unsynchronised sequences (e.g., videos of two persons smiling), the goal is to generate the temporally synchronised sequences (e.g., the smile apex should co-occur in the videos). Temporal alignment is an important problem for many applications where multiple datasets need to be aligned in time. Furthermore, it is particularly suitable for the analysis of facial expressions, where the activation of facial muscles (Action Units) typically follows a set of predefined temporal phases. A highly challenging scenario is when the observations are perturbed by gross, non-Gaussian noise (e.g., occlusions), as is often the case when analysing data acquired under real-world conditions. To account for non-Gaussian noise, a robust variant of Canonical Correlation Analysis (RCCA) for robust fusion and temporal alignment is proposed. The model captures the shared, low-rank subspace of the observations, isolating the gross noise in a sparse noise term. RCCA is amongst the first robust variants of CCA proposed in literature, and as we show in related experiments outperforms other, state-of-the-art methods for related tasks such as the fusion of multiple modalities under gross noise. Beyond private-shared space models, Component Analysis (CA) is an integral component of most computer vision systems, particularly in terms of reducing the usually high-dimensional input spaces in a meaningful manner pertaining to the task-at-hand (e.g., prediction, clustering). A final, significant contribution of this thesis lies in proposing the first unifying framework for probabilistic component analysis. The proposed framework covers most well-known CA methods, such as Principal Component Analysis (PCA), Linear Discriminant Analysis (LDA), Locality Preserving Projections (LPP) and Slow Feature Analysis (SFA), providing further theoretical insights into the workings of CA. Moreover, the proposed framework is highly flexible, enabling novel CA methods to be generated by simply manipulating the connectivity of latent variables (i.e. the latent neighbourhood). As shown experimentally, methods derived via the proposed framework outperform other equivalents in several problems related to affect sensing and facial expression analysis, while providing advantages such as reduced complexity and explicit variance modelling.Open Acces

Computational strategies for single-cell multi-omics integration

Single-cell omics technologies are currently solving biological and medical problems that earlier have remained elusive, such as discovery of new cell types, cellular differentiation trajectories and communication networks across cells and tissues. Current advances especially in single-cell multi-omics hold high potential for breakthroughs by integration of multiple different omics layers. To pair with the recent biotechnological developments, many computational approaches to process and analyze single-cell multi-omics data have been proposed. In this review, we first introduce recent developments in single-cell multi-omics in general and then focus on the available data integration strategies. The integration approaches are divided into three categories: early, intermediate, and late data integration. For each category, we describe the underlying conceptual principles and main characteristics, as well as provide examples of currently available tools and how they have been applied to analyze single-cell multi-omics data. Finally, we explore the challenges and prospective future directions of single-cell multi-omics data integration, including examples of adopting multi-view analysis approaches used in other disciplines to single-cell multi-omics.</p

Data-Driven Representation Learning in Multimodal Feature Fusion

abstract: Modern machine learning systems leverage data and features from multiple modalities to gain more predictive power. In most scenarios, the modalities are vastly different and the acquired data are heterogeneous in nature. Consequently, building highly effective fusion algorithms is at the core to achieve improved model robustness and inferencing performance. This dissertation focuses on the representation learning approaches as the fusion strategy. Specifically, the objective is to learn the shared latent representation which jointly exploit the structural information encoded in all modalities, such that a straightforward learning model can be adopted to obtain the prediction. We first consider sensor fusion, a typical multimodal fusion problem critical to building a pervasive computing platform. A systematic fusion technique is described to support both multiple sensors and descriptors for activity recognition. Targeted to learn the optimal combination of kernels, Multiple Kernel Learning (MKL) algorithms have been successfully applied to numerous fusion problems in computer vision etc. Utilizing the MKL formulation, next we describe an auto-context algorithm for learning image context via the fusion with low-level descriptors. Furthermore, a principled fusion algorithm using deep learning to optimize kernel machines is developed. By bridging deep architectures with kernel optimization, this approach leverages the benefits of both paradigms and is applied to a wide variety of fusion problems. In many real-world applications, the modalities exhibit highly specific data structures, such as time sequences and graphs, and consequently, special design of the learning architecture is needed. In order to improve the temporal modeling for multivariate sequences, we developed two architectures centered around attention models. A novel clinical time series analysis model is proposed for several critical problems in healthcare. Another model coupled with triplet ranking loss as metric learning framework is described to better solve speaker diarization. Compared to state-of-the-art recurrent networks, these attention-based multivariate analysis tools achieve improved performance while having a lower computational complexity. Finally, in order to perform community detection on multilayer graphs, a fusion algorithm is described to derive node embedding from word embedding techniques and also exploit the complementary relational information contained in each layer of the graph.Dissertation/ThesisDoctoral Dissertation Electrical Engineering 201

Multi-view Data Analysis

Multi-view data analysis is a key technology for making effective decisions by leveraging information from multiple data sources. The process of data acquisition across various sensory modalities gives rise to the heterogeneous property of data. In my thesis, multi-view data representations are studied towards exploiting the enriched information encoded in different domains or feature types, and novel algorithms are formulated to enhance feature discriminability. Extracting informative data representation is a critical step in visual recognition and data mining tasks. Multi-view embeddings provide a new way of representation learning to bridge the semantic gap between the low-level observations and high-level human comprehensible knowledge benefitting from enriched information in multiple modalities.Recent advances on multi-view learning have introduced a new paradigm in jointly modeling cross-modal data. Subspace learning method, which extracts compact features by exploiting a common latent space and fuses multi-view information, has emerged proiminent among different categories of multi-view learning techniques. This thesis provides novel solutions in learning compact and discriminative multi-view data representations by exploiting the data structures in low dimensional subspace. We also demonstrate the performance of the learned representation scheme on a number of challenging tasks in recognition, retrieval and ranking problems.The major contribution of the thesis is a unified solution for subspace learning methods, which is extensible for multiple views, supervised learning, and non-linear transformations. Traditional statistical learning techniques including Canonical Correlation Analysis, Partial Least Square regression and Linear Discriminant Analysis are studied by constructing graphs of specific forms under the same framework. Methods using non-linear transforms based on kernels and (deep) neural networks are derived, which lead to superior performance compared to the linear ones. A novel multi-view discriminant embedding method is proposed by taking the view difference into consideration. Secondly, a multiview nonparametric discriminant analysis method is introduced by exploiting the class boundary structure and discrepancy information of the available views. This allows for multiple projecion directions, by relaxing the Gaussian distribution assumption of related methods. Thirdly, we propose a composite ranking method by keeping a close correlation with the individual rankings for optimal rank fusion. We propose a multi-objective solution to ranking problems by capturing inter-view and intra-view information using autoencoderlike networks. Finally, a novel end-to-end solution is introduced to enhance joint ranking with minimum view-specific ranking loss, so that we can achieve the maximum global view agreements within a single optimization process.In summary, this thesis aims to address the challenges in representing multi-view data across different tasks. The proposed solutions have shown superior performance in numerous tasks, including object recognition, cross-modal image retrieval, face recognition and object ranking

Representation Learning for Words and Entities

This thesis presents new methods for unsupervised learning of distributed representations of words and entities from text and knowledge bases. The first algorithm presented in the thesis is a multi-view algorithm for learning representations of words called Multiview Latent Semantic Analysis (MVLSA). By incorporating up to 46 different types of co-occurrence statistics for the same vocabulary of english words, I show that MVLSA outperforms other state-of-the-art word embedding models. Next, I focus on learning entity representations for search and recommendation and present the second method of this thesis, Neural Variational Set Expansion (NVSE). NVSE is also an unsupervised learning method, but it is based on the Variational Autoencoder framework. Evaluations with human annotators show that NVSE can facilitate better search and recommendation of information gathered from noisy, automatic annotation of unstructured natural language corpora. Finally, I move from unstructured data and focus on structured knowledge graphs. I present novel approaches for learning embeddings of vertices and edges in a knowledge graph that obey logical constraints.Comment: phd thesis, Machine Learning, Natural Language Processing, Representation Learning, Knowledge Graphs, Entities, Word Embeddings, Entity Embedding

Graph Deep Learning: Methods and Applications

The past few years have seen the growing prevalence of deep neural networks on various application domains including image processing, computer vision, speech recognition, machine translation, self-driving cars, game playing, social networks, bioinformatics, and healthcare etc. Due to the broad applications and strong performance, deep learning, a subfield of machine learning and artificial intelligence, is changing everyone\u27s life.Graph learning has been another hot field among the machine learning and data mining communities, which learns knowledge from graph-structured data. Examples of graph learning range from social network analysis such as community detection and link prediction, to relational machine learning such as knowledge graph completion and recommender systems, to mutli-graph tasks such as graph classification and graph generation etc.An emerging new field, graph deep learning, aims at applying deep learning to graphs. To deal with graph-structured data, graph neural networks (GNNs) are invented in recent years which directly take graphs as input and output graph/node representations. Although GNNs have shown superior performance than traditional methods in tasks such as semi-supervised node classification, there still exist a wide range of other important graph learning problems where either GNNs\u27 applicabilities have not been explored or GNNs only have less satisfying performance.In this dissertation, we dive deeper into the field of graph deep learning. By developing new algorithms, architectures and theories, we push graph neural networks\u27 boundaries to a much wider range of graph learning problems. The problems we have explored include: 1) graph classification; 2) medical ontology embedding; 3) link prediction; 4) recommender systems; 5) graph generation; and 6) graph structure optimization.We first focus on two graph representation learning problems: graph classification and medical ontology embedding.For graph classification, we develop a novel deep GNN architecture which aggregates node features through a novel SortPooling layer that replaces the simple summing used in previous works. We demonstrate its state-of-the-art graph classification performance on benchmark datasets. For medical ontology embedding, we propose a novel hierarchical attention propagation model, which uses attention mechanism to learn embeddings of medical concepts from hierarchically-structured medical ontologies such as ICD-9 and CCS. We validate the learned embeddings on sequential procedure/diagnosis prediction tasks with real patient data.Then we investigate GNNs\u27 potential for predicting relations, specifically link prediction and recommender systems. For link prediction, we first develop a theory unifying various traditional link prediction heuristics, and then design a framework to automatically learn suitable heuristics from a given network based on GNNs. Our model shows unprecedented strong link prediction performance, significantly outperforming all traditional methods. For recommender systems, we propose a novel graph-based matrix completion model, which uses a GNN to learn graph structure features from the bipartite graph formed by user and item interactions. Our model not only outperforms various matrix completion baselines, but also demonstrates excellent transfer learning ability -- a model trained on MovieLens can be directly used to predict Douban movie ratings with high performance.Finally, we explore GNNs\u27 applicability to graph generation and graph structure optimization. We focus on a specific type of graphs which usually carry computations on them, namely directed acyclic graphs (DAGs). We develop a variational autoencoder (VAE) for DAGs and prove that it can injectively map computations into a latent space. This injectivity allows us to perform optimization in the continuous latent space instead of the original discrete structure space. We then apply our VAE to two types of DAGs, neural network architectures and Bayesian networks. Experiments show that our model not only generates novel and valid DAGs, but also finds high-quality neural architectures and Bayesian networks through performing Bayesian optimization in its latent space