Related papers: Joint Overlap Analysis of Multiple Genomic Interva…

Joint Alignment (JA) of images aims to align a collection of images into a unified coordinate frame, such that semantically-similar features appear at corresponding spatial locations. Most existing approaches often require long training…

We consider the problem of including additional knowledge in estimating sparse Gaussian graphical models (sGGMs) from aggregated samples, arising often in bioinformatics and neuroimaging applications. Previous joint sGGM estimators either…

In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…

Various modifications of decision trees have been extensively used during the past years due to their high efficiency and interpretability. Tree node splitting based on relevant feature selection is a key step of decision tree learning, at…

Multi-Object Tracking (MOT) aims to detect and associate all targets of given classes across frames. Current dominant solutions, e.g. ByteTrack and StrongSORT++, follow the hybrid pipeline, which first accomplish most of the associations in…

Functional data analysis (FDA) and ensemble learning can be powerful tools for analyzing complex environmental time series. Recent literature has highlighted the key role of diversity in enhancing accuracy and reducing variance in ensemble…

Analyses of high-throughput genomic data often lead to ranked lists of genomic loci. How to characterize concordant signals between two rank lists is a common problem with many applications. One example is measuring the reproducibility…

We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…

In this paper, a new and novel data structure is proposed to dynamically insert and delete segments. Unlike the standard segment trees[3], the proposed data structure permits insertion of a segment with interval range beyond the interval…

Graph neural networks are increasingly becoming the framework of choice for graph-based machine learning. In this paper, we propose a new graph neural network architecture that substitutes classical message passing with an analysis of the…

Automatic source code summarization is the task of generating natural language descriptions for source code. Automatic code summarization is a rapidly expanding research area, especially as the community has taken greater advantage of…

Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use…

Gene-gene interactions have long been recognized to be fundamentally important to understand genetic causes of complex disease traits. At present, identifying gene-gene interactions from genome-wide case-control studies is computationally…

Dynamic techniques are a scalable and effective way to analyze concurrent programs. Instead of analyzing all behaviors of a program, these techniques detect errors by focusing on a single program execution. Often a crucial step in these…

Unsupervised domain adaptation (UDA) aims to enhance the generalization capability of a certain model from a source domain to a target domain. Present UDA models focus on alleviating the domain shift by minimizing the feature discrepancy…

Judge agents are fundamental to agentic AI frameworks: they provide automated evaluation, and enable iterative self-refinement of reasoning processes. We introduce JAF: Judge Agent Forest, a framework in which the judge agent conducts joint…

The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequencing is still a time-consuming and…

Spatial join processing techniques that identify intersections between complex geometries (e.g., polygons) commonly follow a two-step filter-and-refine pipeline. The filter step evaluates the query predicate on the minimum bounding…

Motivation: A major challenge in metabolomics is annotation: assigning molecular structures to mass spectral fragmentation patterns. Despite recent advances in molecule-to-spectra and in spectra-to-molecular fingerprint prediction (FP),…

A merge tree is a fundamental topological structure used to capture the sub-level set (and similarly, super-level set) topology in scalar data analysis. The interleaving distance is a theoretically sound, stable metric for comparing merge…