Related papers: pHapCompass: Probabilistic Assembly and Uncertaint…
Medical imaging involves high-dimensional data, yet their acquisition is obtained for limited samples. Multivariate predictive models have become popular in the last decades to fit some external variables from imaging data, and standard…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
Epidemiologic and genetic studies in chronic obstructive pulmonary disease (COPD) and many complex diseases suggest subgroup disparities (e.g., by sex). We consider this problem from the standpoint of integrative analysis where we combine…
Despite exceptional predictive performance of Deep sequence models (DSMs), the main concern of their deployment centers around the lack of uncertainty awareness. In contrast, probabilistic models quantify the uncertainty associated with…
The AUTO-PCOS Classification Challenge seeks to advance the diagnostic capabilities of artificial intelligence (AI) in identifying Polycystic Ovary Syndrome (PCOS) through automated classification of healthy and unhealthy ultrasound frames.…
A looming question that must be solved before robotic plant phenotyping capabilities can have significant impact to crop improvement programs is scalability. High Throughput Phenotyping (HTP) uses robotic technologies to analyze crops in…
Background: Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substantial evaluation time…
Peptide compounds demonstrate considerable potential as therapeutic agents due to their high target affinity and low toxicity, yet their drug development is constrained by their low membrane permeability. Molecular weight and peptide length…
For the vast majority of genome wide association studies (GWAS) published so far, statistical analysis was performed by testing markers individually. In this article we present some elementary statistical considerations which clearly show…
Probabilistic graphical models (PGMs) are widely used to discover latent structure in data, but their success hinges on selecting an appropriate model design. In practice, model specification is difficult and often requires iterative…
Upcoming stage-IV surveys such as Euclid and Rubin will deliver vast amounts of high-precision data, opening new opportunities to constrain cosmological models with unprecedented accuracy. A key step in this process is the reconstruction 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…
A hypercomplex representation of DNA is proposed to facilitate comparison of DNA sequences with fuzzy composition. Using hypercomplex number representation, conventional sequence analysis method, such as, dot matrix analysis, dynamic…
The availability of multi-omics data has revolutionized the life sciences by creating avenues for integrated system-level approaches. Data integration links the information across datasets to better understand the underlying biological…
Organoids, sophisticated in vitro models of human tissues, are crucial for medical research due to their ability to simulate organ functions and assess drug responses accurately. Accurate organoid instance segmentation is critical for…
Multimodal approaches that integrate histology and genomics hold strong potential for precision oncology. However, phenotypic and genotypic heterogeneity limits the quality of intra-modal representations and hinders effective inter-modal…
One of the most significant obstacles in bearing fault diagnosis is a lack of labeled data for various fault types. Also, sensor-acquired data frequently lack labels and have a large amount of missing data. This paper tackles these issues…
How do we estimate the probability of an abundant objects' formation, with minimal context or assumption about is origin? To explore this we have previously introduced the concept of pathway assembly (as pathway complexity), in a graph…
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to…
While metagenomics has emerged as a technology of choice for analyzing bacterial populations, assembly of metagenomic data remains difficult thus stifling biological discoveries. metaSPAdes is a new assembler that addresses the challenge of…