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Latent variable models such as the Variational Auto-Encoder (VAE) have become a go-to tool for analyzing biological data, especially in the field of single-cell genomics. One remaining challenge is the interpretability of latent variables…

Genomics · Quantitative Biology 2023-02-20 Romain Lopez , Nataša Tagasovska , Stephen Ra , Kyunghyn Cho , Jonathan K. Pritchard , Aviv Regev

The task of causal representation learning aims to uncover latent higher-level causal variables that affect lower-level observations. Identifying the true latent causal variables from observed data, while allowing instantaneous causal…

Machine Learning · Computer Science 2026-02-19 Yuhang Liu , Zhen Zhang , Dong Gong , Mingming Gong , Biwei Huang , Anton van den Hengel , Kun Zhang , Javen Qinfeng Shi

Modeling spillover effects from observational data is an important problem in economics, business, and other fields of research. % It helps us infer the causality between two seemingly unrelated set of events. For example, if consumer…

Machine Learning · Computer Science 2018-10-04 Vineeth Rakesh , Ruocheng Guo , Raha Moraffah , Nitin Agarwal , Huan Liu

We propose a variational autoencoder (VAE) approach for parameter estimation in nonlinear mixed-effects models based on ordinary differential equations (NLME-ODEs) using longitudinal data from multiple subjects. In moderate dimensions,…

Methodology · Statistics 2026-02-11 Zhe Li , Mélanie Prague , Rodolphe Thiébaut , Quentin Clairon

Continuous treatment effect estimation holds significant practical importance across various decision-making and assessment domains, such as healthcare and the military. However, current methods for estimating dose-response curves hinge on…

Machine Learning · Computer Science 2024-06-05 Ruijing Cui , Jianbin Sun , Bingyu He , Kewei Yang , Bingfeng Ge

Variational autoencoders (VAEs) are widely used deep generative models capable of learning unsupervised latent representations of data. Such representations are often difficult to interpret or control. We consider the problem of…

Machine Learning · Computer Science 2018-12-18 Jack Klys , Jake Snell , Richard Zemel

Disentangled representation learning aims to learn low-dimensional representations where each dimension corresponds to an underlying generative factor. While the Variational Auto-Encoder (VAE) is widely used for this purpose, most existing…

Machine Learning · Computer Science 2024-12-31 Di Fan , Yannian Kou , Chuanhou Gao

Recent advances in electron, scanning probe, optical, and chemical imaging and spectroscopy yield bespoke data sets containing the information of structure and functionality of complex systems. In many cases, the resulting data sets are…

Materials Science · Physics 2024-11-15 Yongtao Liu , Bryan D Huey , Maxim A. Ziatdinov , Sergei V. Kalinin

In causality, estimating the effect of a treatment without confounding inference remains a major issue because requires to assess the outcome in both case with and without treatment. Not being able to observe simultaneously both of them,…

Machine Learning · Computer Science 2021-12-09 Celine Beji , Florian Yger , Jamal Atif

Conditional variational autoencoders (CVAEs) are versatile deep generative models that extend the standard VAE framework by conditioning the generative model with auxiliary covariates. The original CVAE model assumes that the data samples…

Machine Learning · Statistics 2022-03-03 Siddharth Ramchandran , Gleb Tikhonov , Otto Lönnroth , Pekka Tiikkainen , Harri Lähdesmäki

Variational autoencoders (VAEs) employ Bayesian inference to interpret sensory inputs, mirroring processes that occur in primate vision across both ventral (Higgins et al., 2021) and dorsal (Vafaii et al., 2023) pathways. Despite their…

Machine Learning · Computer Science 2024-12-10 Hadi Vafaii , Dekel Galor , Jacob L. Yates

Predicting the distribution of outcomes under hypothetical interventions is crucial across healthcare, economics, and policy-making. However, existing methods often require restrictive assumptions, and are typically limited by the lack of…

Machine Learning · Computer Science 2025-08-11 Andreas Sauter , Saber Salehkaleybar , Aske Plaat , Erman Acar

The ability to record activities from hundreds of neurons simultaneously in the brain has placed an increasing demand for developing appropriate statistical techniques to analyze such data. Recently, deep generative models have been…

Machine Learning · Statistics 2020-11-11 Ding Zhou , Xue-Xin Wei

Variational Auto-Encoders (VAEs) have been widely applied for learning compact, low-dimensional latent representations of high-dimensional data. When the correlation structure among data points is available, previous work proposed…

Machine Learning · Computer Science 2019-12-20 Da Tang , Dawen Liang , Nicholas Ruozzi , Tony Jebara

Estimating treatment effects, especially individualized treatment effects (ITE), using observational data is challenging due to the complex situations of confounding bias. Existing approaches for estimating treatment effects from…

Machine Learning · Statistics 2022-07-26 Zheng Feng , Mattia Prosperi , Jiang Bian

Learning disentanglement aims at finding a low dimensional representation which consists of multiple explanatory and generative factors of the observational data. The framework of variational autoencoder (VAE) is commonly used to…

Machine Learning · Computer Science 2023-12-20 Mengyue Yang , Furui Liu , Zhitang Chen , Xinwei Shen , Jianye Hao , Jun Wang

Estimating long-term causal effects by combining long-term observational and short-term experimental data is a crucial but challenging problem in many real-world scenarios. In existing methods, several ideal assumptions, e.g. latent…

Machine Learning · Computer Science 2025-05-12 Ruichu Cai , Junjie Wan , Weilin Chen , Zeqin Yang , Zijian Li , Peng Zhen , Jiecheng Guo

Although the Conditional Variational AutoEncoder (CVAE) model can generate more diversified responses than the traditional Seq2Seq model, the responses often have low relevance with the input words or are illogical with the question. A…

Computation and Language · Computer Science 2022-10-12 Jiayi Liu , Wei Wei , Zhixuan Chu , Xing Gao , Ji Zhang , Tan Yan , Yulin Kang

Optimal computations under uncertainty require an adequate probabilistic representation about beliefs. Deep generative models, and specifically Variational Autoencoders (VAEs), have the potential to meet this demand by building latent…

Estimating long-term causal effects based on short-term surrogates is a significant but challenging problem in many real-world applications, e.g., marketing and medicine. Despite its success in certain domains, most existing methods…

Machine Learning · Computer Science 2023-11-22 Ruichu Cai , Weilin Chen , Zeqin Yang , Shu Wan , Chen Zheng , Xiaoqing Yang , Jiecheng Guo