Related papers: Reconstructing Isoform Graphs from RNA-Seq data
Although RNA-Seq data provide unprecedented isoform-level expression information, detection of alternative isoform regulation (AIR) remains difficult, particularly when working with an incomplete transcript annotation. We introduce…
Graph-structured data exhibit substantial heterogeneity in where their predictive signals originate: in some domains, node-level semantics dominate, while in others, structural patterns play a central role. This structure-semantics…
Limited data and low dose constraints are common problems in a variety of tomographic reconstruction paradigms which lead to noisy and incomplete data. Over the past few years sinogram denoising has become an essential pre-processing step…
Motivation: Measurements of gene expression over time enable the reconstruction of transcriptional networks. However, Bayesian networks and many other current reconstruction methods rely on assumptions that conflict with the differential…
Graph Neural Networks (GNN) exhibit superior performance in graph representation learning, but their inference cost can be high, due to an aggregation operation that can require a memory fetch for a very large number of nodes. This…
Graph Neural Networks (GNNs) are de facto solutions to structural data learning. However, it is susceptible to low-quality and unreliable structure, which has been a norm rather than an exception in real-world graphs. Existing graph…
Sampling-based algorithms are classical approaches to perform Bayesian inference in inverse problems. They provide estimators with the associated credibility intervals to quantify the uncertainty on the estimators. Although these methods…
Recent works have investigated the role of graph bottlenecks in preventing long-range information propagation in message-passing graph neural networks, causing the so-called `over-squashing' phenomenon. As a remedy, graph rewiring…
Graph condensation, which reduces the size of a large-scale graph by synthesizing a small-scale condensed graph as its substitution, has immediate benefits for various graph learning tasks. However, existing graph condensation methods rely…
Classical nonlinear dimensionality reduction (NLDR) techniques like t-SNE, Isomap, and LLE excel at creating low-dimensional embeddings for data visualization but fundamentally lack the ability to map these embeddings back to the original…
Score-based generative models (SGMs) have recently shown promising results for image reconstruction on simulated positron emission tomography (PET) datasets. In this work we have developed and implemented practical methodology for 3D image…
Single-cell RNA sequencing (scRNA-seq) technology provides high-throughput gene expression data to study the cellular heterogeneity and dynamics of complex organisms. Graph neural networks (GNNs) have been widely used for automatic cell…
The advent of Graph Neural Networks (GNNs) has revolutionized the field of machine learning, offering a novel paradigm for learning on graph-structured data. Unlike traditional neural networks, GNNs are capable of capturing complex…
Graph neural networks have been successful for machine learning, as well as for combinatorial and graph problems such as the Subgraph Isomorphism Problem and the Traveling Salesman Problem. We describe an approach for computing graph…
The problem of estimating the structure of a graph from observed data is of growing interest in the context of high-throughput genomic data, and single-cell RNA sequencing in particular. These, however, are challenging applications, since…
Alternative splicing of gene transcripts greatly expands the functional capacity of the genome, and certain splice isoforms may indicate specific disease states such as cancer. Splice junction microarrays interrogate thousands of splice…
In the presence of recombination, the evolutionary relationships between a set of sampled genomes cannot be described by a single genealogical tree. Instead, the genomes are related by a complex, interwoven collection of genealogies…
Fluorescence microscopy images usually show severe anisotropy in axial versus lateral resolution. This hampers downstream processing, i.e. the automatic extraction of quantitative biological data. While deconvolution methods and other…
Effective data imputation demands rich latent ``structure" discovery capabilities from ``plain" tabular data. Recent advances in graph neural networks-based data imputation solutions show their strong structure learning potential by…
Graph neural networks (GNNs) have emerged as powerful tools for learning protein structures by capturing spatial relationships at the residue level. However, existing GNN-based methods often face challenges in learning multiscale…