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Advances in spatially-resolved transcriptomics (SRT) technologies have propelled the development of new computational analysis methods to unlock biological insights. As the cost of generating these data decreases, these technologies provide…
Current deep learning-based manifold learning algorithms such as the variational autoencoder (VAE) require fully sampled data to learn the probability density of real-world datasets. Once learned, the density can be used for a variety of…
We present a simple neural rendering architecture that helps variational autoencoders (VAEs) learn disentangled representations. Instead of the deconvolutional network typically used in the decoder of VAEs, we tile (broadcast) the latent…
Information extraction, e.g., attribute value extraction, has been extensively studied and formulated based only on text. However, many attributes can benefit from image-based extraction, like color, shape, pattern, among others. The visual…
Identifying customer segments in retail banking portfolios with different risk profiles can improve the accuracy of credit scoring. The Variational Autoencoder (VAE) has shown promising results in different research domains, and it has been…
Variational autoencoders (VAEs) are among leading approaches to address the problem of learning disentangled representations. Typically a single VAE is used and disentangled representations are sought within its single continuous latent…
With the rapid advancement of Spatial Resolved Transcriptomics (SRT) technology, it is now possible to comprehensively measure gene transcription while preserving the spatial context of tissues. Spatial domain identification and gene…
Variational autoencoders (VAEs) are a popular class of deep generative models with many variants and a wide range of applications. Improvements upon the standard VAE mostly focus on the modelling of the posterior distribution over the…
The discovery of new materials is often constrained by the need for large labelled datasets or expensive simulations. In this study, we explore the use of Disentangling Autoencoders (DAEs) to learn compact and interpretable representations…
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…
High-dimensional clinical data have become invaluable resources for genetic studies, due to their accessibility in biobank-scale datasets and the development of high performance modeling techniques especially using deep learning. Recent…
Data-driven fault diagnostics of safety-critical systems often faces the challenge of a complete lack of labeled data associated with faulty system conditions (i.e., fault types) at training time. Since an unknown number and nature of fault…
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…
Recent advances in explainable machine learning have highlighted the potential of sparse autoencoders in uncovering mono-semantic features in densely encoded embeddings. While most research has focused on Large Language Model (LLM)…
In recent years, the advent of spatial transcriptomics (ST) technology has unlocked unprecedented opportunities for delving into the complexities of gene expression patterns within intricate biological systems. Despite its transformative…
Generative models of observations under interventions have been a vibrant topic of interest across machine learning and the sciences in recent years. For example, in drug discovery, there is a need to model the effects of diverse…
This study introduces SEFI (SEgmentation-Free Integration), a novel method for integrating morphological features of cell nuclei with spatial transcriptomics data. Cell segmentation poses a significant challenge in the analysis of spatial…
While unsupervised variational autoencoders (VAE) have become a powerful tool in neuroimage analysis, their application to supervised learning is under-explored. We aim to close this gap by proposing a unified probabilistic model for…
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…
Quantitative imaging methods, such as magnetic resonance fingerprinting (MRF), aim to extract interpretable pathology biomarkers by estimating biophysical tissue parameters from signal evolutions. However, the pattern-matching algorithms or…