Related papers: Reconstructing Isoform Graphs from RNA-Seq data

Single-cell RNA sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity, enabling detailed analysis of complex biological systems at single-cell resolution. However, the high dimensionality and technical noise…

Recently, Retrieval-Augmented Generation (RAG) has achieved remarkable success in addressing the challenges of Large Language Models (LLMs) without necessitating retraining. By referencing an external knowledge base, RAG refines LLM…

Graph Neural Networks (GNNs) have recently been explored as surrogate models for numerical simulations. While their applications in computational fluid dynamics have been investigated, little attention has been given to structural problems,…

The renaissance of neural architecture search (NAS) has seen classical methods such as genetic algorithms (GA) and genetic programming (GP) being exploited for convolutional neural network (CNN) architectures. While recent work have…

Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society. This novel approach is a newbie and has critical advantages over the traditional Capillary…

Subgraph isomorphism is a well-known NP-hard problem which is widely used in many applications, such as social network analysis and knowledge graph query. Its performance is often limited by the inherent hardness. Several insightful works…

Double-strand DNA breaks (DSBs) are a form of DNA damage that can cause abnormal chromosomal rearrangements. Recent technologies based on high-throughput experiments have obvious high costs and technical challenges.Therefore, we design a…

We propose a novel two-stage Gene Set Gibbs Sampling (GSGS) framework, to reverse engineer signaling pathways from gene sets inferred from molecular profiling data. We hypothesize that signaling pathways are structurally an ensemble of…

Surgical instrument segmentation (SIS) on endoscopic images stands as a long-standing and essential task in the context of computer-assisted interventions for boosting minimally invasive surgery. Given the recent surge of deep learning…

Graphs are naturally used to describe the structures of various real-world systems in biology, society, computer science etc., where subgraphs or motifs as basic blocks play an important role in function expression and information…

This study aims to optimize the existing retrieval-augmented generation model (RAG) by introducing a graph structure to improve the performance of the model in dealing with complex knowledge reasoning tasks. The traditional RAG model has…

Biosciences have been revolutionized by next generation sequencing (NGS) technologies in last years, leading to new perspectives in medical, industrial and environmental applications. And although our motivation comes from biosciences, the…

This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…

Subgraph isomorphism counting is known as #P-complete and requires exponential time to find the accurate solution. Utilizing representation learning has been shown as a promising direction to represent substructures and approximate the…

In this paper we discuss reconstruction problems for graphs. We develop some new ideas like isomorphic extension of isomorphic graphs, partitioning of vertex sets into sets of equivalent points, subdeck property, etc. and develop an…

Subgraph counting aims to count the occurrences of a subgraph template T in a given network G. The basic problem of computing structural properties such as counting triangles and other subgraphs has found applications in diverse domains.…

We propose a method to reconstruct and cluster incomplete high-dimensional data lying in a union of low-dimensional subspaces. Exploring the sparse representation model, we jointly estimate the missing data while imposing the intrinsic…

Next-generation RNA sequencing (RNA-seq) technology has been widely used to assess full-length RNA isoform abundance in a high-throughput manner. RNA-seq data offer insight into gene expression levels and transcriptome structures, enabling…

Motivation: Data volumes generated by next-generation sequencing technolo- gies is now a major concern, both for storage and transmission. This triggered the need for more efficient methods than general purpose compression tools, such as…

Partitioning a graph into groups of vertices such that those within each group are more densely connected than vertices assigned to different groups, known as graph clustering, is often used to gain insight into the organisation of large…