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Most human protein-coding genes can be transcribed into multiple possible distinct mRNA isoforms. These alternative splicing patterns encourage molecular diversity and dysregulation of isoform expression plays an important role in disease…

Fragment-based shape signature techniques have proven to be powerful tools for computer-aided drug design. They allow scientists to search for target molecules with some similarity to a known active compound. They do not require reference…

Pathway enrichment analysis has become a key tool for biomedical researchers to gain insight into the underlying biology of differentially expressed genes, proteins and metabolites. It reduces complexity and provides a system-level view of…

The Longest Path Problem is a question of finding the maximum length between pairs of vertices of a graph. In the general case, the problem is NP-complete. However, there is a small collection of graph classes for which there exists an…

We present S-Path-RAG, a semantic-aware shortest-path Retrieval-Augmented Generation framework designed to improve multi-hop question answering over large knowledge graphs. S-Path-RAG departs from one-shot, text-heavy retrieval by…

The advancement of single-cell RNA-sequencing (scRNA-seq) technologies allow us to study the individual level cell-type-specific gene expression networks by direct inference of genes' conditional independence structures. scRNA-seq data…

We study the knapsack problem with graph theoretic constraints. That is, we assume that there exists a graph structure on the set of items of knapsack and the solution also needs to satisfy certain graph theoretic properties on top of…

Motivated by the surge of large language models, there has been a push to formally characterize the symbolic abilities intrinsic to the transformer architecture. A programming language, called RASP, has been proposed, which can be directly…

We propose a new deterministic methodology to predict RNA sequence and protein folding. Is stem enough for structure prediction? The main idea is to consider all possible stem formation in the given sequence. With the stem loop energy and…

Urothelial cell carcinoma (UCC) is the ninth most common cancer that accounts for 4.7% of all the new cancer cases globally. UCC development and progression are due to complex and stochastic genetic programmes. To study the cascades of…

RNA-Seq is a widely-used method for studying the behavior of genes under different biological conditions. An essential step in an RNA-Seq study is normalization, in which raw data are adjusted to account for factors that prevent direct…

Network quantification (NQ) is the problem of estimating the proportions of nodes belonging to each class in subsets of unlabelled graph nodes. When prior probability shift is at play, this task cannot be effectively addressed by first…

Graph neural networks (GNNs) have recently become the standard approach for learning with graph-structured data. Prior work has shed light into their potential, but also their limitations. Unfortunately, it was shown that standard GNNs are…

The NP-complete $k$-Path problem asks whether a given undirected graph has a (simple) path of length at least $k$. We prove that $k$-Path has polynomial-size Turing kernels when restricted to planar graphs, graphs of bounded degree,…

Estimating slide- and patch-level gene expression profiles from pathology images enables rapid and low-cost molecular analysis with broad clinical impact. Despite strong results, existing approaches treat gene expression as a mere slide- or…

Regular Path Queries (RPQs), which are essentially regular expressions to be matched against the labels of paths in labeled graphs, are at the core of graph database query languages like SPARQL. A way to solve RPQs is to translate them into…

Graph transformers extend global self-attention to graph-structured data, achieving notable success in graph learning. Recently, random walk structural encoding (RWSE) has been found to further enhance their predictive power by encoding…

The Shortest Path Reconfiguration problem has as input a graph G (with unit edge lengths) with vertices s and t, and two shortest st-paths P and Q. The question is whether there exists a sequence of shortest st-paths that starts with P and…

RNA sequencing (RNA-seq) is the conventional genome-scale approach used to capture the expression levels of all detectable genes in a biological sample. This is now regularly used for population-based studies designed to identify genetic…

Current computational methods for exon-intron structure prediction from a cluster of transcript (EST, mRNA) data do not exhibit the time and space efficiency necessary to process large clusters of over than 20,000 ESTs and genes longer than…