Quality control (QC) has long been considered essential to guarantee the reliability of neuroimaging studies. It is particularly important for fetal brain MRI, where large and unpredictable fetal motion can lead to substantial artifacts in the acquired images. Existing methods for fetal brain quality assessment operate at the \textit{slice} level, and fail to get a comprehensive picture of the quality of an image, that can only be achieved by looking at the \textit{entire} brain volume. In this work, we propose FetMRQC, a machine learning framework for automated image quality assessment tailored to fetal brain MRI, which extracts an ensemble of quality metrics that are then used to predict experts' ratings. Based on the manual ratings of more than 1000 low-resolution stacks acquired across two different institutions, we show that, compared with existing quality metrics, FetMRQC is able to generalize out-of-domain, while being interpretable and data efficient. We also release a novel manual quality rating tool designed to facilitate and optimize quality rating of fetal brain images. Our tool, along with all the code to generate, train and evaluate the model is available at //github.com/Medical-Image-Analysis-Laboratory/fetal_brain_qc/ .
Contrastive learning (CL) has emerged as a promising technique for improving recommender systems, addressing the challenge of data sparsity by leveraging self-supervised signals from raw data. Integration of CL with graph convolutional network (GCN)-based collaborative filterings (CFs) has been explored in recommender systems. However, current CL-based recommendation models heavily rely on low-pass filters and graph augmentations. In this paper, we propose a novel CL method for recommender systems called the reaction-diffusion graph contrastive learning model (RDGCL). We design our own GCN for CF based on both the diffusion, i.e., low-pass filter, and the reaction, i.e., high-pass filter, equations. Our proposed CL-based training occurs between reaction and diffusion-based embeddings, so there is no need for graph augmentations. Experimental evaluation on 6 benchmark datasets demonstrates that our proposed method outperforms state-of-the-art CL-based recommendation models. By enhancing recommendation accuracy and diversity, our method brings an advancement in CL for recommender systems.
Quantifying the uncertainty of predictions is a core problem in modern statistics. Methods for predictive inference have been developed under a variety of assumptions, often -- for instance, in standard conformal prediction -- relying on the invariance of the distribution of the data under special groups of transformations such as permutation groups. Moreover, many existing methods for predictive inference aim to predict unobserved outcomes in sequences of feature-outcome observations. Meanwhile, there is interest in predictive inference under more general observation models (e.g., for partially observed features) and for data satisfying more general distributional symmetries (e.g., rotationally invariant or coordinate-independent observations in physics). Here we propose SymmPI, a methodology for predictive inference when data distributions have general group symmetries in arbitrary observation models. Our methods leverage the novel notion of distributional equivariant transformations, which process the data while preserving their distributional invariances. We show that SymmPI has valid coverage under distributional invariance and characterize its performance under distribution shift, recovering recent results as special cases. We apply SymmPI to predict unobserved values associated to vertices in a network, where the distribution is unchanged under relabelings that keep the network structure unchanged. In several simulations in a two-layer hierarchical model, and in an empirical data analysis example, SymmPI performs favorably compared to existing methods.
There is an overgrowing demand for data sharing in academia and industry. However, such sharing has issues with personal privacy and data confidentiality. One option is to share only synthetically-generated versions of the real data. Generative Adversarial Network (GAN) is a recently-popular technique that can be used for this purpose. Relational databases usually have multiple tables that are related to each other. So far, the use of GANs has essentially focused on generating single tables. This paper presents Incremental Relational Generator (IRG), which uses GANs to synthetically generate interrelated tables. Given an empirical relational database, IRG can generate a synthetic version that can be safely shared. IRG generates the tables in some sequential order. The key idea is to construct a context, based on the tables generated so far, when using a GAN to generate the next table. Experiments with public datasets and private student data show that IRG outperforms state-of-the-art in terms of statistical properties and query results.
Deep learning has been the mainstream technique in natural language processing (NLP) area. However, the techniques require many labeled data and are less generalizable across domains. Meta-learning is an arising field in machine learning studying approaches to learn better learning algorithms. Approaches aim at improving algorithms in various aspects, including data efficiency and generalizability. Efficacy of approaches has been shown in many NLP tasks, but there is no systematic survey of these approaches in NLP, which hinders more researchers from joining the field. Our goal with this survey paper is to offer researchers pointers to relevant meta-learning works in NLP and attract more attention from the NLP community to drive future innovation. This paper first introduces the general concepts of meta-learning and the common approaches. Then we summarize task construction settings and application of meta-learning for various NLP problems and review the development of meta-learning in NLP community.
Deep neural networks (DNNs) have become a proven and indispensable machine learning tool. As a black-box model, it remains difficult to diagnose what aspects of the model's input drive the decisions of a DNN. In countless real-world domains, from legislation and law enforcement to healthcare, such diagnosis is essential to ensure that DNN decisions are driven by aspects appropriate in the context of its use. The development of methods and studies enabling the explanation of a DNN's decisions has thus blossomed into an active, broad area of research. A practitioner wanting to study explainable deep learning may be intimidated by the plethora of orthogonal directions the field has taken. This complexity is further exacerbated by competing definitions of what it means ``to explain'' the actions of a DNN and to evaluate an approach's ``ability to explain''. This article offers a field guide to explore the space of explainable deep learning aimed at those uninitiated in the field. The field guide: i) Introduces three simple dimensions defining the space of foundational methods that contribute to explainable deep learning, ii) discusses the evaluations for model explanations, iii) places explainability in the context of other related deep learning research areas, and iv) finally elaborates on user-oriented explanation designing and potential future directions on explainable deep learning. We hope the guide is used as an easy-to-digest starting point for those just embarking on research in this field.
With the advances of data-driven machine learning research, a wide variety of prediction problems have been tackled. It has become critical to explore how machine learning and specifically deep learning methods can be exploited to analyse healthcare data. A major limitation of existing methods has been the focus on grid-like data; however, the structure of physiological recordings are often irregular and unordered which makes it difficult to conceptualise them as a matrix. As such, graph neural networks have attracted significant attention by exploiting implicit information that resides in a biological system, with interactive nodes connected by edges whose weights can be either temporal associations or anatomical junctions. In this survey, we thoroughly review the different types of graph architectures and their applications in healthcare. We provide an overview of these methods in a systematic manner, organized by their domain of application including functional connectivity, anatomical structure and electrical-based analysis. We also outline the limitations of existing techniques and discuss potential directions for future research.
Deep Learning has implemented a wide range of applications and has become increasingly popular in recent years. The goal of multimodal deep learning is to create models that can process and link information using various modalities. Despite the extensive development made for unimodal learning, it still cannot cover all the aspects of human learning. Multimodal learning helps to understand and analyze better when various senses are engaged in the processing of information. This paper focuses on multiple types of modalities, i.e., image, video, text, audio, body gestures, facial expressions, and physiological signals. Detailed analysis of past and current baseline approaches and an in-depth study of recent advancements in multimodal deep learning applications has been provided. A fine-grained taxonomy of various multimodal deep learning applications is proposed, elaborating on different applications in more depth. Architectures and datasets used in these applications are also discussed, along with their evaluation metrics. Last, main issues are highlighted separately for each domain along with their possible future research directions.
Recently, the emergence of pre-trained models (PTMs) has brought natural language processing (NLP) to a new era. In this survey, we provide a comprehensive review of PTMs for NLP. We first briefly introduce language representation learning and its research progress. Then we systematically categorize existing PTMs based on a taxonomy with four perspectives. Next, we describe how to adapt the knowledge of PTMs to the downstream tasks. Finally, we outline some potential directions of PTMs for future research. This survey is purposed to be a hands-on guide for understanding, using, and developing PTMs for various NLP tasks.
UMAP (Uniform Manifold Approximation and Projection) is a novel manifold learning technique for dimension reduction. UMAP is constructed from a theoretical framework based in Riemannian geometry and algebraic topology. The result is a practical scalable algorithm that applies to real world data. The UMAP algorithm is competitive with t-SNE for visualization quality, and arguably preserves more of the global structure with superior run time performance. Furthermore, UMAP has no computational restrictions on embedding dimension, making it viable as a general purpose dimension reduction technique for machine learning.
Spectral clustering is a leading and popular technique in unsupervised data analysis. Two of its major limitations are scalability and generalization of the spectral embedding (i.e., out-of-sample-extension). In this paper we introduce a deep learning approach to spectral clustering that overcomes the above shortcomings. Our network, which we call SpectralNet, learns a map that embeds input data points into the eigenspace of their associated graph Laplacian matrix and subsequently clusters them. We train SpectralNet using a procedure that involves constrained stochastic optimization. Stochastic optimization allows it to scale to large datasets, while the constraints, which are implemented using a special-purpose output layer, allow us to keep the network output orthogonal. Moreover, the map learned by SpectralNet naturally generalizes the spectral embedding to unseen data points. To further improve the quality of the clustering, we replace the standard pairwise Gaussian affinities with affinities leaned from unlabeled data using a Siamese network. Additional improvement can be achieved by applying the network to code representations produced, e.g., by standard autoencoders. Our end-to-end learning procedure is fully unsupervised. In addition, we apply VC dimension theory to derive a lower bound on the size of SpectralNet. State-of-the-art clustering results are reported on the Reuters dataset. Our implementation is publicly available at //github.com/kstant0725/SpectralNet .