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Objective: fMRI and derived measures such as functional connectivity (FC) have been used to predict brain age, general fluid intelligence, psychiatric disease status, and preclinical neurodegenerative disease. However, it is not always…
Unsupervised disentangled representation learning from the unlabelled audio data, and high fidelity audio generation have become two linchpins in the machine learning research fields. However, the representation learned from an unsupervised…
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…
Finding an interpretable non-redundant representation of real-world data is one of the key problems in Machine Learning. Biological neural networks are known to solve this problem quite well in unsupervised manner, yet unsupervised…
Sparse autoencoders (SAEs) emerged as a promising tool for mechanistic interpretability of transformer-based foundation models. Very recently, SAEs were also adopted for the visual domain, enabling the discovery of visual concepts and their…
Histopathology images are crucial to the study of complex diseases such as cancer. The histologic characteristics of nuclei play a key role in disease diagnosis, prognosis and analysis. In this work, we propose a sparse Convolutional…
Recently, deep learning becomes the main focus of machine learning research and has greatly impacted many important fields. However, deep learning is criticized for lack of interpretability. As a successful unsupervised model in deep…
Estimating an individual's potential response to continuously varied treatments is crucial for addressing causal questions across diverse domains, from healthcare to social sciences. However, existing methods are limited either to…
We present Universal Sparse Autoencoders (USAEs), a framework for uncovering and aligning interpretable concepts spanning multiple pretrained deep neural networks. Unlike existing concept-based interpretability methods, which focus on a…
Diffusion-based representation learning has achieved substantial attention due to its promising capabilities in latent representation and sample generation. Recent studies have employed an auxiliary encoder to identify a corresponding…
Generative Adversarial Networks (GANs) have been used in many different applications to generate realistic synthetic data. We introduce a novel GAN with Autoencoder (GAN-AE) architecture to generate synthetic samples for variable length,…
In this paper, we introduce a novel normative modeling approach that incorporates focal loss and adversarial autoencoders (FAAE) for Alzheimer's Disease (AD) diagnosis and biomarker identification. Our method is an end-to-end approach that…
Variational autoencoders are prominent generative models for modeling discrete data. However, with flexible decoders, they tend to ignore the latent codes. In this paper, we study a VAE model with a deterministic decoder (DD-VAE) for…
Deep generative models have made tremendous advances in image and signal representation learning and generation. These models employ the full Euclidean space or a bounded subset as the latent space, whose flat geometry, however, is often…
Health disparities, or inequalities between different patient demographics, are becoming crucial in medical decision-making, especially in Electronic Health Record (EHR) predictive modeling. To ensure the fairness of sensitive attributes,…
Recent advances in Explainable AI (XAI) increased the demand for deployment of safe and interpretable AI models in various industry sectors. Despite the latest success of deep neural networks in a variety of domains, understanding the…
Understanding the structure of complex, nonstationary, high-dimensional time-evolving signals is a central challenge in scientific data analysis. In many domains, such as speech and biomedical signal processing, the ability to learn…
Autoencoder (AE) is the key to the success of latent diffusion models for image and video generation, reducing the denoising resolution and improving efficiency. However, the power of AE has long been underexplored in terms of network…
Phenotype-based screening has attracted much attention for identifying cell-active compounds. Transcriptional and proteomic profiles of cell population or single cells are informative phenotypic measures of cellular responses to…
Recent work (Bengio et al., 2013) has shown howDenoising Auto-Encoders(DAE) become gener-ative models as a density estimator. However,in practice, the framework suffers from a mixingproblem in the MCMC sampling process and nodirect method…