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Graph classification has gained significant attention due to its applications in chemistry, social networks, and bioinformatics. While Graph Neural Networks (GNNs) effectively capture local structural patterns, they often overlook global…
Recent advances in biological research have seen the emergence of high-throughput technologies with numerous applications that allow the study of biological mechanisms at an unprecedented depth and scale. A large amount of genomic data is…
The connectional brain template (CBT) captures the shared traits across all individuals of a given population of brain connectomes, thereby acting as a fingerprint. Estimating a CBT from a population where brain graphs are derived from…
Graph Transformers have recently attracted attention for molecular property prediction by combining the inductive biases of graph neural networks (GNNs) with the global receptive field of Transformers. However, many existing hybrid…
In genome-scale constraint-based metabolic models, gene deletion strategies are essential for achieving growth-coupled production, where cell growth and target metabolite synthesis occur simultaneously. Despite the inherently networked…
Comparison of human and chimpanzee genomes has received much attention, because of paramount role for understanding evolutionary step distinguishing us from our closest living relative. In order to contribute to insight into Y chromosome…
We consider multivariate two-sample tests of means, where the location shift between the two populations is expected to be related to a known graph structure. An important application of such tests is the detection of differentially…
As they carry great potential for modeling complex interactions, graph neural network (GNN)-based methods have been widely used to predict quantum mechanical properties of molecules. Most of the existing methods treat molecules as molecular…
DNA methylation is a crucial epigenetic marker used in various clocks to predict epigenetic age. However, many existing clocks fail to account for crucial information about CpG sites and their interrelationships, such as co-methylation…
Multi-label chest X-ray (CXR) recognition involves simultaneously diagnosing and identifying multiple labels for different pathologies. Since pathological labels have rich information about their relationship to each other, modeling the…
Exchange type chromosome aberrations (ETCAs) are rearrangements of the genome that occur when chromosomes break and the resulting fragments rejoin with other fragments from other chromosomes. ETCAs are commonly observed in cancer cells and…
Graph-based models have emerged as a powerful paradigm for modeling multimodal urban data and learning region representations for various downstream tasks. However, existing approaches face two major limitations. (1) They typically employ…
It is generally assumed that all cells in models of the electrical behavior of cardiac tissue have the same properties. However, there are differences in cardiac cells that are not well characterized but cause spatial heterogeneity of the…
Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively…
This study presents a multi-faceted approach combining stereotactic biopsy with standard clinical open-craniotomy for sample collection, voxel-wise analysis of MR images, regression-based Generalized Additive Models (GAM), & whole-exome…
Precise prognostic stratification of colorectal cancer (CRC) remains a major clinical challenge due to its high heterogeneity. The conventional TNM staging system is inadequate for personalized medicine. We aimed to develop and validate a…
Continuous Hand Gesture Recognition (CHGR) has been extensively studied by researchers in the last few decades. Recently, one model has been presented to deal with the challenge of the boundary detection of isolated gestures in a continuous…
We examine the distribution of heterozygous sites in nine European and nine Yoruban individuals whose genomic sequences were made publicly available by Complete Genomics. We show that it is possible to obtain detailed information about…
Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system…
In medical imaging, chromosome straightening plays a significant role in the pathological study of chromosomes and in the development of cytogenetic maps. Whereas different approaches exist for the straightening task, typically geometric…