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To interpret the genetic profile present in a patient sample, it is necessary to know which mutations have important roles in the development of the corresponding cancer type. Named entity recognition is a core step in the text mining…

Cancer is a complex disease with significant social and economic impact. Advancements in high-throughput molecular assays and the reduced cost for performing high-quality multi-omics measurements have fuelled insights through machine…

Is there really much more to say about sparse autoencoders (SAEs)? Autoencoders in general, and SAEs in particular, represent deep architectures that are capable of modeling low-dimensional latent structure in data. Such structure could…

Masked Autoencoders (MAEs) have emerged as a dominant strategy for self-supervised representation learning in natural images, where models are pre-trained to reconstruct masked patches with a pixel-wise mean squared error (MSE) between…

Unsupervised learning can leverage large-scale data sources without the need for annotations. In this context, deep learning-based auto encoders have shown great potential in detecting anomalies in medical images. However, state-of-the-art…

We propose SAHMM-VAE, a source-wise adaptive Hidden Markov prior variational autoencoder for unsupervised blind source separation. Instead of treating the latent prior as a single generic regularizer, the proposed framework assigns each…

Deep generative models have emerged as influential instruments for data generation and manipulation. Enhancing the controllability of these models by selectively modifying data attributes has been a recent focus. Variational Autoencoders…

Masked Autoencoders (MAE) based on a reconstruction task have risen to be a promising paradigm for self-supervised learning (SSL) and achieve state-of-the-art performance across different benchmark datasets. However, despite its impressive…

Extracting compact, physically interpretable representations from high-dimensional scientific data is a persistent challenge due to the complex, nonlinear structures inherent in physical systems. We propose a Gaussian Mixture Variational…

To achieve high-levels of autonomy, modern robots require the ability to detect and recover from anomalies and failures with minimal human supervision. Multi-modal sensor signals could provide more information for such anomaly detection…

Effective treatment for rectal cancer relies on accurate lymph node metastasis (LNM) staging. However, radiological criteria based on lymph node (LN) size, shape and texture morphology have limited diagnostic accuracy. In this work, we…

Variational autoencoder (VAE) is a popular method for drug discovery and there had been a great deal of architectures and pipelines proposed to improve its performance. But the VAE model itself suffers from deficiencies such as poor…

Traditional transformer-based semantic segmentation relies on quantized embeddings. However, our analysis reveals that autoencoder accuracy on segmentation mask using quantized embeddings (e.g. VQ-VAE) is 8% lower than continuous-valued…

In this tutorial, we explore Variational Autoencoders (VAEs), an essential framework for unsupervised learning, particularly suited for high-dimensional datasets such as neuroimaging. By integrating deep learning with Bayesian inference,…

Here we propose the Reweighted Autoencoded Variational Bayes for Enhanced Sampling (RAVE) method, a new iterative scheme that uses the deep learning framework of variational autoencoders to enhance sampling in molecular simulations. RAVE…

Affective video facial analysis (AVFA) has emerged as a key research field for building emotion-aware intelligent systems, yet this field continues to suffer from limited data availability. In recent years, the self-supervised learning…

Masked Autoencoders (MAEs) trained on audio spectrogram patches have emerged as a prominent approach for learning self-supervised audio representations. While several recent papers have evaluated key aspects of training MAEs on audio data,…

Classical methods for model order selection often fail in scenarios with low SNR or few snapshots. Deep learning-based methods are promising alternatives for such challenging situations as they compensate lack of information in the…

Deep learning has gained significant attention in medical image segmentation. However, the limited availability of annotated training data presents a challenge to achieving accurate results. In efforts to overcome this challenge, data…

We investigated the adaptation and performance of Masked Autoencoders (MAEs) with Vision Transformer (ViT) architectures for self-supervised representation learning on one-dimensional (1D) ultrasound signals. Although MAEs have demonstrated…