Yuying Xie

Hongzhi Wen, Jiayuan Ding, Wei Jin et al.

Recent advances in multimodal single-cell technologies have enabled simultaneous acquisitions of multiple omics data from the same cell, providing deeper insights into cellular states and dynamics. However, it is challenging to learn the joint representations from the multimodal data, model the relationship between modalities, and, more importantly, incorporate the vast amount of single-modality datasets into the downstream analyses. To address these challenges and correspondingly facilitate multimodal single-cell data analyses, three key tasks have been introduced: $\textit{modality prediction}$, $\textit{modality matching}$ and $\textit{joint embedding}$. In this work, we present a general Graph Neural Network framework $\textit{scMoGNN}$ to tackle these three tasks and show that $\textit{scMoGNN}$ demonstrates superior results in all three tasks compared with the state-of-the-art and conventional approaches. Our method is an official winner in the overall ranking of $\textit{Modality prediction}$ from NeurIPS 2021 Competition, and all implementations of our methods have been integrated into DANCE package~\url{https://github.com/OmicsML/dance}.

Dylan Molho, Jiayuan Ding, Zhaoheng Li et al.

Single-cell technologies are revolutionizing the entire field of biology. The large volumes of data generated by single-cell technologies are high-dimensional, sparse, heterogeneous, and have complicated dependency structures, making analyses using conventional machine learning approaches challenging and impractical. In tackling these challenges, deep learning often demonstrates superior performance compared to traditional machine learning methods. In this work, we give a comprehensive survey on deep learning in single-cell analysis. We first introduce background on single-cell technologies and their development, as well as fundamental concepts of deep learning including the most popular deep architectures. We present an overview of the single-cell analytic pipeline pursued in research applications while noting divergences due to data sources or specific applications. We then review seven popular tasks spanning through different stages of the single-cell analysis pipeline, including multimodal integration, imputation, clustering, spatial domain identification, cell-type deconvolution, cell segmentation, and cell-type annotation. Under each task, we describe the most recent developments in classical and deep learning methods and discuss their advantages and disadvantages. Deep learning tools and benchmark datasets are also summarized for each task. Finally, we discuss the future directions and the most recent challenges. This survey will serve as a reference for biologists and computer scientists, encouraging collaborations.

Hongzhi Wen, Wenzhuo Tang, Wei Jin et al.

Spatially resolved transcriptomics brings exciting breakthroughs to single-cell analysis by providing physical locations along with gene expression. However, as a cost of the extremely high spatial resolution, the cellular level spatial transcriptomic data suffer significantly from missing values. While a standard solution is to perform imputation on the missing values, most existing methods either overlook spatial information or only incorporate localized spatial context without the ability to capture long-range spatial information. Using multi-head self-attention mechanisms and positional encoding, transformer models can readily grasp the relationship between tokens and encode location information. In this paper, by treating single cells as spatial tokens, we study how to leverage transformers to facilitate spatial tanscriptomics imputation. In particular, investigate the following two key questions: (1) $\textit{how to encode spatial information of cells in transformers}$, and (2) $\textit{ how to train a transformer for transcriptomic imputation}$. By answering these two questions, we present a transformer-based imputation framework, SpaFormer, for cellular-level spatial transcriptomic data. Extensive experiments demonstrate that SpaFormer outperforms existing state-of-the-art imputation algorithms on three large-scale datasets while maintaining superior computational efficiency.

Wenzhuo Tang, Hongzhi Wen, Renming Liu et al.

The recent development of multimodal single-cell technology has made the possibility of acquiring multiple omics data from individual cells, thereby enabling a deeper understanding of cellular states and dynamics. Nevertheless, the proliferation of multimodal single-cell data also introduces tremendous challenges in modeling the complex interactions among different modalities. The recently advanced methods focus on constructing static interaction graphs and applying graph neural networks (GNNs) to learn from multimodal data. However, such static graphs can be suboptimal as they do not take advantage of the downstream task information; meanwhile GNNs also have some inherent limitations when deeply stacking GNN layers. To tackle these issues, in this work, we investigate how to leverage transformers for multimodal single-cell data in an end-to-end manner while exploiting downstream task information. In particular, we propose a scMoFormer framework which can readily incorporate external domain knowledge and model the interactions within each modality and cross modalities. Extensive experiments demonstrate that scMoFormer achieves superior performance on various benchmark datasets. Remarkably, scMoFormer won a Kaggle silver medal with the rank of 24/1221 (Top 2%) without ensemble in a NeurIPS 2022 competition. Our implementation is publicly available at Github.

Yuying Xie, Thomas Arildsen, Zheng-Hua Tan

Leveraging the fact that speaker identity and content vary on different time scales, \acrlong{fhvae} (\acrshort{fhvae}) uses different latent variables to symbolize these two attributes. Disentanglement of these attributes is carried out by different prior settings of the corresponding latent variables. For the prior of speaker identity variable, \acrshort{fhvae} assumes it is a Gaussian distribution with an utterance-scale varying mean and a fixed variance. By setting a small fixed variance, the training process promotes identity variables within one utterance gathering close to the mean of their prior. However, this constraint is relatively weak, as the mean of the prior changes between utterances. Therefore, we introduce contrastive learning into the \acrshort{fhvae} framework, to make the speaker identity variables gathering when representing the same speaker, while distancing themselves as far as possible from those of other speakers. The model structure has not been changed in this work but only the training process, thus no additional cost is needed during testing. Voice conversion has been chosen as the application in this paper. Latent variable evaluations include speaker verification and identification for the speaker identity variable, and speech recognition for the content variable. Furthermore, assessments of voice conversion performance are on the grounds of fake speech detection experiments. Results show that the proposed method improves both speaker identity and content feature extraction compared to \acrshort{fhvae}, and has better performance than baseline on conversion.

A. Martina Neuman, Rongrong Wang, Yuying Xie

Graph Neural Networks (GNNs) have emerged as formidable resources for processing graph-based information across diverse applications. While the expressive power of GNNs has traditionally been examined in the context of graph-level tasks, their potential for node-level tasks, such as node classification, where the goal is to interpolate missing node labels from the observed ones, remains relatively unexplored. In this study, we investigate the proficiency of GNNs for such classifications, which can also be cast as a function interpolation problem. Explicitly, we focus on ascertaining the optimal configuration of weights and layers required for a GNN to successfully interpolate a band-limited function over Euclidean cubes. Our findings highlight a pronounced efficiency in utilizing GNNs to generalize a bandlimited function within an $\varepsilon$-error margin. Remarkably, achieving this task necessitates only $O_d((\log\varepsilon^{-1})^d)$ weights and $O_d((\log\varepsilon^{-1})^d)$ training samples. We explore how this criterion stacks up against the explicit constructions of currently available Neural Networks (NNs) designed for similar tasks. Significantly, our result is obtained by drawing an innovative connection between the GNN structures and classical sampling theorems. In essence, our pioneering work marks a meaningful contribution to the research domain, advancing our understanding of the practical GNN applications.

Yuying Xie, Zheng-Hua Tan

Recent advancements in deep learning have significantly impacted the field of speech signal processing, particularly in the analysis and manipulation of complex spectrograms. This survey provides a comprehensive overview of the state-of-the-art techniques leveraging deep neural networks for processing complex spectrograms, which encapsulate both magnitude and phase information. We begin by introducing complex spectrograms and their associated features for various speech processing tasks. Next, we examine the key components and architectures of complex-valued neural networks, which are specifically designed to handle complex-valued data and have been applied to complex spectrogram processing. As recent studies have primarily focused on applying real-valued neural networks to complex spectrograms, we revisit these approaches and their architectural designs. We then discuss various training strategies and loss functions tailored for training neural networks to process and model complex spectrograms. The survey further examines key applications, including phase retrieval, speech enhancement, and speaker separation, where deep learning has achieved significant progress by leveraging complex spectrograms or their derived feature representations. Additionally, we examine the intersection of complex spectrograms with generative models. This survey aims to serve as a valuable resource for researchers and practitioners in the field of speech signal processing, deep learning and related fields.

Wenzhuo Tang, Haitao Mao, Danial Dervovic et al.

Models for natural language and images benefit from data scaling behavior: the more data fed into the model, the better they perform. This 'better with more' phenomenon enables the effectiveness of large-scale pre-training on vast amounts of data. However, current graph pre-training methods struggle to scale up data due to heterogeneity across graphs. To achieve effective data scaling, we aim to develop a general model that is able to capture diverse data patterns of graphs and can be utilized to adaptively help the downstream tasks. To this end, we propose UniAug, a universal graph structure augmentor built on a diffusion model. We first pre-train a discrete diffusion model on thousands of graphs across domains to learn the graph structural patterns. In the downstream phase, we provide adaptive enhancement by conducting graph structure augmentation with the help of the pre-trained diffusion model via guided generation. By leveraging the pre-trained diffusion model for structure augmentation, we consistently achieve performance improvements across various downstream tasks in a plug-and-play manner. To the best of our knowledge, this study represents the first demonstration of a data-scaling graph structure augmentor on graphs across domains.

Runze Su, Fei Tao, Xudong Liu et al.

The applications of short-term user-generated video (UGV), such as Snapchat, and Youtube short-term videos, booms recently, raising lots of multimodal machine learning tasks. Among them, learning the correspondence between audio and visual information from videos is a challenging one. Most previous work of the audio-visual correspondence(AVC) learning only investigated constrained videos or simple settings, which may not fit the application of UGV. In this paper, we proposed new principles for AVC and introduced a new framework to set sight of videos' themes to facilitate AVC learning. We also released the KWAI-AD-AudVis corpus which contained 85432 short advertisement videos (around 913 hours) made by users. We evaluated our proposed approach on this corpus, and it was able to outperform the baseline by 23.15% absolute difference.

He Lyu, Ningyu Sha, Shuyang Qin et al.

This paper extends robust principal component analysis (RPCA) to nonlinear manifolds. Suppose that the observed data matrix is the sum of a sparse component and a component drawn from some low dimensional manifold. Is it possible to separate them by using similar ideas as RPCA? Is there any benefit in treating the manifold as a whole as opposed to treating each local region independently? We answer these two questions affirmatively by proposing and analyzing an optimization framework that separates the sparse component from the manifold under noisy data. Theoretical error bounds are provided when the tangent spaces of the manifold satisfy certain incoherence conditions. We also provide a near optimal choice of the tuning parameters for the proposed optimization formulation with the help of a new curvature estimation method. The efficacy of our method is demonstrated on both synthetic and real datasets.

Anna Little, Yuying Xie, Qiang Sun

Classical multidimensional scaling is an important dimension reduction technique. Yet few theoretical results characterizing its statistical performance exist. This paper provides a theoretical framework for analyzing the quality of embedded samples produced by classical multidimensional scaling. This lays the foundation for various downstream statistical analyses, and we focus on clustering noisy data. Our results provide scaling conditions on the sample size, ambient dimensionality, between-class distance, and noise level under which classical multidimensional scaling followed by a distance-based clustering algorithm can recover the cluster labels of all samples with high probability. Numerical simulations confirm these scaling conditions are near-sharp. Applications to both human genomics data and natural language data lend strong support to the methodology and theory.

Yuying Xie, Yufeng Liu, William Valdar

Gaussian graphical models are widely used to represent conditional dependence among random variables. In this paper, we propose a novel estimator for data arising from a group of Gaussian graphical models that are themselves dependent. A motivating example is that of modeling gene expression collected on multiple tissues from the same individual: here the multivariate outcome is affected by dependencies acting not only at the level of the specific tissues, but also at the level of the whole body; existing methods that assume independence among graphs are not applicable in this case. To estimate multiple dependent graphs, we decompose the problem into two graphical layers: the systemic layer, which affects all outcomes and thereby induces cross- graph dependence, and the category-specific layer, which represents graph-specific variation. We propose a graphical EM technique that estimates both layers jointly, establish estimation consistency and selection sparsistency of the proposed estimator, and confirm by simulation that the EM method is superior to a simple one-step method. We apply our technique to mouse genomics data and obtain biologically plausible results.