CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data
Centre for Molecular Medicine Norway (NCMM)（挪威分子医学中心（NCMM））；Nordic EMBL Partnership（北欧欧洲分子生物学实验室合作组织）；University of Oslo（奥斯陆大学）；National Taiwan University（国立台湾大学）；Oslo University Hospital（奥斯陆大学医院）；CISPA Helmholtz Center for Information Security（CISPA亥姆霍兹信息安全中心）
Ping-Han Hsieh, Ru-Xiu Hsiao, Katalin Ferenc, Anthony Mathelier, Rebekka Burkholz, Chien-Yu Chen, Geir Kjetil Sandve, Tatiana Belova, Marieke Lydia Kuijjer
Paired single-cell sequencing technologies enable the simultaneous measurement of complementary modalities of molecular data at single-cell resolution. Along with the advances in these technologies, many methods based on variational autoencoders have been developed to integrate these data. However, these methods do not explicitly incorporate prior biological relationships between the data modalities, which could significantly enhance modeling and interpretation. We propose a novel probabilistic learning framework that explicitly incorporates conditional independence relationships between multi-modal data as a directed acyclic graph using a generalized hierarchical variational autoencoder. We demonstrate the versatility of our framework across various applications pertinent to single-cell multi-omics data integration. These include the isolation of common and distinct information from different modalities, modality-specific differential analysis, and integrated cell clustering. We anticipate that the proposed framework can facilitate the construction of highly flexible graphical models that can capture the complexities of biological hypotheses and unravel the connections between different biological data types, such as different modalities of paired single-cell multi-omics data. The implementation of the proposed framework can be found in the repository https://github.com/kuijjerlab/CAVACHON.
Bielefeld University（比勒费尔德大学）；Australian Centre for Robotic Vision（澳大利亚机器人视觉中心）；Queensland University of Technology（昆士兰科技大学）
This contribution comprises the interplay between a multi-modal variational autoencoder and an environment to a perceived environment, on which an agent can act. Furthermore, we conclude our work with a comparison to curiosity-driven learning.
This work gives an in-depth derivation of the trainable evidence lower bound obtained from the marginal joint log-Likelihood with the goal of training a Multi-Modal Variational Autoencoder (M$^2$VAE).
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark（丹麦技术大学诺和诺德基金会生物可持续性中心）；University of Copenhagen（哥本哈根大学）
Multimodal generative models should be able to learn a meaningful latent representation that enables a coherent joint generation of all modalities (e.g., images and text). Many applications also require the ability to accurately sample modalities conditioned on observations of a subset of the modalities. Often not all modalities may be observed for all training data points, so semi-supervised learning should be possible. In this study, we propose a novel product-of-experts (PoE) based variational autoencoder that have these desired properties. We benchmark it against a mixture-of-experts (MoE)…
We investigate deep generative models that can exchange multiple modalities bi-directionally, e.g., generating images from corresponding texts and vice versa. A major approach to achieve this objective is to train a model that integrates all the information of different modalities into a joint representation and then to generate one modality from the corresponding other modality via this joint representation. We simply applied this approach to variational autoencoders (VAEs), which we call a joint multimodal variational autoencoder (JMVAE). However, we found that when this model attempts to ge…
Queen’s University（女王大学）；Azad University（阿扎德大学）；University of Leeds（利兹大学）；KU Leuven（荷语鲁汶大学）；Shenzhen University（深圳大学）
In large studies involving multi protocol Magnetic Resonance Imaging (MRI), it can occur to miss one or more sub-modalities for a given patient owing to poor quality (e.g. imaging artifacts), failed acquisitions, or hallway interrupted imaging examinations. In some cases, certain protocols are unavailable due to limited scan time or to retrospectively harmonise the imaging protocols of two independent studies. Missing image modalities pose a challenge to segmentation frameworks as complementary information contributed by the missing scans is then lost. In this paper, we propose a novel model, …
The University of Hull（赫尔大学）；University of Sunderland（桑德兰大学）
Forecasting short-term motion of nearby vehicles presents an inherently challenging issue as the space of their possible future movements is not strictly limited to a set of single trajectories. Recently proposed techniques that demonstrate plausible results concentrate primarily on forecasting a fixed number of deterministic predictions, or on classifying over a wide variety of trajectories that were previously generated using e.g. dynamic model. This paper focuses on addressing the uncertainty associated with the discussed task by utilising the stochastic nature of generative models in order…
This research attempts to construct a network that can convert online and offline handwritten characters to each other. The proposed network consists of two Variational Auto-Encoders (VAEs) with a shared latent space. The VAEs are trained to generate online and offline handwritten Latin characters simultaneously. In this way, we create a cross-modal VAE (Cross-VAE). During training, the proposed Cross-VAE is trained to minimize the reconstruction loss of the two modalities, the distribution loss of the two VAEs, and a novel third loss called the space sharing loss. This third, space sharing lo…
Seoul National University（首尔国立大学）；University of California, Davis（加州大学戴维斯分校）
Novelty detection using deep generative models such as autoencoder, generative adversarial networks mostly takes image reconstruction error as novelty score function. However, image data, high dimensional as it is, contains a lot of different features other than class information which makes models hard to detect novelty data. The problem gets harder in multi-modal normality case. To address this challenge, we propose a new way of measuring novelty score in multi-modal normality cases using orthogonalized latent space. Specifically, we employ orthogonal low-rank embedding in the latent space t…
University of Illinois, Urbana Champaign（伊利诺伊大学厄巴纳-香槟分校）；LinkedIn Co.（领英公司）
While node semantics have been extensively explored in social networks, little research attention has been paid to profile edge semantics, i.e., social relations. Ideal edge semantics should not only show that two users are connected, but also why they know each other and what they share in common. However, relations in social networks are often hard to profile, due to noisy multi-modal signals and limited user-generated ground-truth labels. In this work, we aim to develop a unified and principled framework that can profile user relations as edge semantics in social networks by integrating mul…
Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State, Georgia Tech, Emory（三机构神经影像与数据科学转化研究中心（TReNDS），佐治亚州立大学、佐治亚理工学院、埃默里大学）；Faculty of Electrical Engineering, Mathematics & Computer Science, TU Delft（代尔夫特理工大学电气工程、数学与计算机科学学院）；Lambert High School（兰伯特高中）
Neuroimaging studies often involve the collection of multiple data modalities. These modalities contain both shared and mutually exclusive information about the brain. This work aims at finding a scalable and interpretable method to fuse the information of multiple neuroimaging modalities using a variational autoencoder (VAE). To provide an initial assessment, this work evaluates the representations that are learned using a schizophrenia classification task. A support vector machine trained on the representations achieves an area under the curve for the classifier's receiver operating characte…
Improving Normative Modeling for Multi-modal Neuroimaging Data using mixture-of-product-of-experts variational autoencoders
Department of Computer Science and Engineering, Washington University in St. Louis, USA（计算机科学与工程系，华盛顿大学圣路易斯分校）；Institute for Informatics, Data Science and Biostatistics, Washington University in St.Louis, USA（信息学、数据科学与生物统计研究所，华盛顿大学圣路易斯分校）；Department of Radiology, Washington University in St.Louis, USA（放射学系，华盛顿大学圣路易斯分校）
The task of predicting stochastic behaviors of road agents in diverse environments is a challenging problem for autonomous driving. To best understand scene contexts and produce diverse possible future states of the road agents adaptively in different environments, a prediction model should be probabilistic, multi-modal, context-driven, and general. We present Conditionalizing Variational AutoEncoders via Hypernetworks (CVAE-H); a conditional VAE that extensively leverages hypernetwork and performs generative tasks for high-dimensional problems like the prediction task. We first evaluate CVAE-…
In this paper, we propose a multimodal transformer using parallel concatenated architecture. Instead of using patches, we use column stripes for images in R, G, B channels as the transformer input. The column stripes keep the spatial relations of original image. We incorporate the multimodal transformer with variational autoencoder for synthetic cross-modal data generation. The multimodal transformer is designed using multiple compression matrices, and it serves as encoders for Parallel Concatenated Variational AutoEncoders (PC-VAE). The PC-VAE consists of multiple encoders, one latent space, …
A Split-Window Transformer for Multi-Model Sequence Spammer Detection using Multi-Model Variational Autoencoder
School of Communications and Information Engineering, Chongqing University of Posts and Telecommunications（重庆邮电大学通信与信息工程学院）；School of Information and Communication Engineering, University of Electronic Science and Technology of China（电子科技大学信息与通信工程学院）
Max Planck Institute for Informatics（马克斯·普朗克信息学研究所）；Bosch Center for Artificial Intelligence（博世人工智能中心）；CISPA Helmholtz Center for Information Security（CISPA亥姆霍兹信息安全中心）
Prediction of future states of the environment and interacting agents is a key competence required for autonomous agents to operate successfully in the real world. Prior work for structured sequence prediction based on latent variable models imposes a uni-modal standard Gaussian prior on the latent variables. This induces a strong model bias which makes it challenging to fully capture the multi-modality of the distribution of the future states. In this work, we introduce Conditional Flow Variational Autoencoders (CF-VAE) using our novel conditional normalizing flow based prior to capture compl…
Analyzing Multimodal Integration in the Variational Autoencoder from an Information-Theoretic Perspective
Hamburg University of Technology（汉堡工业大学）；Humboldt-Universität zu Berlin（柏林洪堡大学）；Federal Institute for Materials Research and Testing（联邦材料研究与测试研究所）；Santa Fe Institute（圣塔菲研究所）；Leipzig University（莱比锡大学）
Multi-modal Gaussian Process Variational Autoencoders for Neural and Behavioral Data
Fordham University（福特汉姆大学）；Georgia Institute of Technology（佐治亚理工学院）；Icahn School of Medicine at Mount Sinai（Mount Sinai医学院）；University of California, San Diego（加州大学圣地亚哥分校）
We investigate deep generative models that can exchange multiple modalities bi-directionally, e.g., generating images from corresponding texts and vice versa. Recently, some studies handle multiple modalities on deep generative models, such as variational autoencoders (VAEs). However, these models typically assume that modalities are forced to have a conditioned relation, i.e., we can only generate modalities in one direction. To achieve our objective, we should extract a joint representation that captures high-level concepts among all modalities and through which we can exchange them bi-direc…
Multimodal learning is a framework for building models that make predictions based on different types of modalities. Important challenges in multimodal learning are the inference of shared representations from arbitrary modalities and cross-modal generation via these representations; however, achieving this requires taking the heterogeneous nature of multimodal data into account. In recent years, deep generative models, i.e., generative models in which distributions are parameterized by deep neural networks, have attracted much attention, especially variational autoencoders, which are suitable…
Multimodal Variational Autoencoder for Low-cost Cardiac Hemodynamics Instability Detection
University of Sheffield（谢菲尔德大学）；IITRAM（印度理工学院拉杰科德校区）；Sheffield Teaching Hospitals（谢菲尔德教学医院）；INSIGNEO, Institute for in Silico Medicine, University of Sheffield（谢菲尔德大学INSIGNEO计算机医学研究所）
In today's day and age when almost every industry has an online presence with users interacting in online marketplaces, personalized recommendations have become quite important. Traditionally, the problem of collaborative filtering has been tackled using Matrix Factorization which is linear in nature. We extend the work of [11] on using variational autoencoders (VAEs) for collaborative filtering with implicit feedback by proposing a hybrid, multi-modal approach. Our approach combines movie embeddings (learned from a sibling VAE network) with user ratings from the Movielens 20M dataset and appl…
A comprehensive understanding of vision and language and their interrelation are crucial to realize the underlying similarities and differences between these modalities and to learn more generalized, meaningful representations. In recent years, most of the works related to Text-to-Image synthesis and Image-to-Text generation, focused on supervised generative deep architectures to solve the problems, where very little interest was placed on learning the similarities between the embedding spaces across modalities. In this paper, we propose a novel self-supervised deep learning based approach tow…
The detection of anomalous executions is valuable for reducing potential hazards in assistive manipulation. Multimodal sensory signals can be helpful for detecting a wide range of anomalies. However, the fusion of high-dimensional and heterogeneous modalities is a challenging problem. We introduce a long short-term memory based variational autoencoder (LSTM-VAE) that fuses signals and reconstructs their expected distribution. We also introduce an LSTM-VAE-based detector using a reconstruction-based anomaly score and a state-based threshold. For evaluations with 1,555 robot-assisted feeding exe…
University of Science and Technology of China（中国科学技术大学）
Currently, almost all the multi-track music generation models use the Convolutional Neural Network (CNN) to build the generative model, while the Recurrent Neural Network (RNN) based models can not be applied in this task. In view of the above problem, this paper proposes a RNN-based Hierarchical Multi-modal Fusion Generation Variational Autoencoder (VAE) network, MIDI-Sandwich2, for multi-track symbolic music generation. Inspired by VQ-VAE2, MIDI-Sandwich2 expands the dimension of the original hierarchical model by using multiple independent Binary Variational Autoencoder (BVAE) models withou…
Saarland University（萨尔大学）；MPI for Software Systems（马克斯·普朗克软件系统研究所）
A number of variational autoencoders (VAEs) have recently emerged with the aim of modeling multimodal data, e.g., to jointly model images and their corresponding captions. Still, multimodal VAEs tend to focus solely on a subset of the modalities, e.g., by fitting the image while neglecting the caption. We refer to this limitation as modality collapse. In this work, we argue that this effect is a consequence of conflicting gradients during multimodal VAE training. We show how to detect the sub-graphs in the computational graphs where gradients conflict (impartiality blocks), as well as how to l…
Multi-modal generative models represent an important family of deep models, whose goal is to facilitate representation learning on data with multiple views or modalities. However, current deep multi-modal models focus on the inference of shared representations, while neglecting the important private aspects of data within individual modalities. In this paper, we introduce a disentangled multi-modal variational autoencoder (DMVAE) that utilizes disentangled VAE strategy to separate the private and shared latent spaces of multiple modalities. We specifically consider the instance where the laten…
We propose a novel approach to train a multi-modal policy from mixed demonstrations without their behavior labels. We develop a method to discover the latent factors of variation in the demonstrations. Specifically, our method is based on the variational autoencoder with a categorical latent variable. The encoder infers discrete latent factors corresponding to different behaviors from demonstrations. The decoder, as a policy, performs the behaviors accordingly. Once learned, the policy is able to reproduce a specific behavior by simply conditioning on a categorical vector. We evaluate our meth…
Variation Autoencoder (VAE) has become a powerful tool in modeling the non-linear generative process of data from a low-dimensional latent space. Recently, several studies have proposed to use VAE for unsupervised clustering by using mixture models to capture the multi-modal structure of latent representations. This strategy, however, is ineffective when there are outlier data samples whose latent representations are meaningless, yet contaminating the estimation of key major clusters in the latent space. This exact problem arises in the context of resting-state fMRI (rs-fMRI) analysis, where c…
In this paper we present a a deep generative model for lossy video compression. We employ a model that consists of a 3D autoencoder with a discrete latent space and an autoregressive prior used for entropy coding. Both autoencoder and prior are trained jointly to minimize a rate-distortion loss, which is closely related to the ELBO used in variational autoencoders. Despite its simplicity, we find that our method outperforms the state-of-the-art learned video compression networks based on motion compensation or interpolation. We systematically evaluate various design choices, such as the use of…
University of Oxford（牛津大学）；Alan Turing Institute（艾伦·图灵研究所）；University of Cambridge（剑桥大学）
Learning generative models that span multiple data modalities, such as vision and language, is often motivated by the desire to learn more useful, generalisable representations that faithfully capture common underlying factors between the modalities. In this work, we characterise successful learning of such models as the fulfillment of four criteria: i) implicit latent decomposition into shared and private subspaces, ii) coherent joint generation over all modalities, iii) coherent cross-generation across individual modalities, and iv) improved model learning for individual modalities through m…
DMMRL: Disentangled Multi-Modal Representation Learning via Variational Autoencoders for Molecular Property Prediction
Guangxi Key Lab of Human-machine Interaction and Intelligent Decision（广西人机交互与智能决策重点实验室）；Nanning Normal University（南宁师范大学）；College of Big Data and Software Engineering（大数据与软件工程学院）；Zhejiang Wanli University（浙江万里大学）
Autoencoders have been widely used for dimensional reduction and feature extraction. Various types of autoencoders have been proposed by introducing regularization terms. Most of these regularizations improve representation learning by constraining the weights in the encoder part, which maps input into hidden nodes and affects the generation of features. In this study, we show that a constraint to the decoder can also significantly improve its performance because the decoder determines how the latent variables contribute to the reconstruction of input. Inspired by the structural modal analysis…
Recent developments in high throughput profiling of individual neurons have spurred data driven exploration of the idea that there exist natural groupings of neurons referred to as cell types. The promise of this idea is that the immense complexity of brain circuits can be reduced, and effectively studied by means of interactions between cell types. While clustering of neuron populations based on a particular data modality can be used to define cell types, such definitions are often inconsistent across different characterization modalities. We pose this issue of cross-modal alignment as an opt…
Kiel University（基尔大学）；ZBW – Leibniz Information Centre for Economics（ZBW——莱布尼茨经济信息中心）
We present multi-modal adversarial autoencoders for recommendation and evaluate them on two different tasks: citation recommendation and subject label recommendation. We analyze the effects of adversarial regularization, sparsity, and different input modalities. By conducting 408 experiments, we show that adversarial regularization consistently improves the performance of autoencoders for recommendation. We demonstrate, however, that the two tasks differ in the semantics of item co-occurrence in the sense that item co-occurrence resembles relatedness in case of citations, yet implies diversity…
